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https://openalex.org/W4237426094
https://europepmc.org/articles/pmc3954389?pdf=render
English
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Explantation of aortic infrarenal stent graft
Annals of the Royal College of Surgeons of England
2,012
cc-by
603
A technique for optimal manipulation of rotation of the flexible ureterorenoscope G Ellis, S Pridgeon, S Graham Whipps Cross University Hospital NHS Trust, UK G Ellis, S Pridgeon, S Graham Whipps Cross University Hospital NHS Trust, UK CORRESPONDENCE TO Stuart Graham, E: stuart@stuartgraham.com Figure 1 A Foley catheter is inserted through the stent graft and placed in the suprarenal aorta, after which the balloon is inflated. TECHNICAL SECTION TECHNICAL SECTION Figure 2 A second Foley catheter is passed through a limb of the new graft. TECHNIQUE Pass a drill guide through the jig used for inserting proximal screws. Leave the drill guide in position against the limb. This can now be used to align the C-arm. Position the C-arm distally and adjust its position until it is parallel to the drill guide in its orbital and swivel axis. This will give near perfect alignment to the distal locking holes. Finer adjustments may be needed under image intensifier guidance to gain the final position. Once satisfactory alignment is achieved, insert the distal screws as usual. BACKGROUND Three different types of movement are required to perform flexible ureterorenoscopy: insertion/retraction, rotation and deflection of the tip. Many trainee urologists struggle to manipulate the rotation of the scope. We describe a technique for optimally controlling this rotation. end of the stent graft is extracted from the aorta. If another graft is used, proximal anastomosis is carried out with the balloon inflated. To complete the anastomosis a second Foley catheter is passed through a limb of the new graft (Fig 2). While the original catheter is deflated and removed, the second balloon is inflated in the suprarenal aorta (Fig 3) and the anastomosis completed. Explantation of aortic infrarenal stent graft J Krysa, PR Taylor Guy’s and St Thomas’ NHS Foundation Trust, UK J Krysa, PR Taylor Guy’s and St Thomas’ NHS Foundation Trust, UK This technique has helped us to achieve proximal control during stent graft explantation. A large Foley catheter is inserted through a discon- nected limb of stent graft and placed in the suprarenal aorta. Infla- tion of the balloon provides proximal control (Fig 1). The proximal Figure 3 The original catheter is deflated and removed, and the second balloon is inflated in the suprarenal aorta. Figure 3 The original catheter is deflated and removed, and the second balloon is inflated in the suprarenal aorta. Figure 1 A Foley catheter is inserted through the stent graft and placed in the suprarenal aorta, after which the balloon is inflated. ACKNOWLEDGEMENT We would like to thank James Clark for his help with the drawings. A technique for optimal manipulation of rotation of the flexible ureterorenoscope DISCUSSION This simple technique is effective, saves time and reduces radiation exposure to both the patient and surgeon. This technique is free as it uses standard equipment that comes with the nail. Figure 2 A second Foley catheter is passed through a limb of the new graft. Figure 2 A second Foley catheter is passed through a limb of the new graft. Figure 2 A second Foley catheter is passed through a limb of the new graft. Figure 3 The original catheter is deflated and removed, and the second balloon is inflated in the suprarenal aorta. TECHNIQUE When performing ureterorenoscopy, the scope is extended in a straight line (Fig 1) rather than held in a curved position (Fig 2). By applying When performing ureterorenoscopy, the scope is extended in a straight line (Fig 1) rather than held in a curved position (Fig 2). By applying 365 Ann R Coll Surg Engl 2012; 94: 359–372 365 Ann R Coll Surg Engl 2012; 94: 359–372
https://openalex.org/W4390674781
https://www.qeios.com/read/P3DQEZ/pdf
English
null
Review of: "Synthesis and Antibacterial Screening of Cefradine Schiff Bases and Their Metal Salts"
null
2,024
cc-by
582
Review of: "Synthesis and Antibacterial Screening of Cefradine Schiff Bases and Their Metal Salts" Jed Fisher1 1 University of Notre Dame Potential competing interests: No potential competing interests to declare. Ali et al. report the synthesis of the Schiff base condensation products of substituted benzaldehydes, acetophenone, and benzophenone. These products are formulated successively as their sodium, potassium, silver, calcium, and barium salts (with respect to the carboxylic acid of the cephem). The different salts were evaluated qualitatively for their antimicrobial activity by disk diffusion assay against S. aureus and E. coli. All are less active than the parent. Some are inactive. •One prior Schiff base derivative of cefradine, with a 2-[[(2-hydroxyphenyl)methylene] substitution [CAS 879281-13-7], is known in the literature. The bibliography cites correctly its first synthesis, but not a second manuscript reporting additional microbiological data: Anacona, Juan R.; Marquez, Victoria. Latin American Journal of Pharmacy (2013), 32(6), 887-891. This specific structure was not re-synthesized by Ali et al. for use as a positive control. This failure is unfortunate. •The failure of the authors’ Scheme 1 to depict the stereochemistry of cefradine is not acceptable. The stereochemistry of the imine was not determined for CAS 879281-13-7 from its synthesis by others. The imine stereochemistry of these new structures also is not addressed. •The compounds of this manuscript are characterized by IR and 1H NMR. The 1H NMR data are interpreted superficially (for example, the coupling constants of the coupled methine resonances of the beta-lactam are not given). The 1H NMR spectra are not given for assessment of the compound purity. It is remarkable, given the low electrophilicity of the benzophenone carbonyl, that imine formation is claimed for benzophenone, using the same reaction conditions (AcOH, MeOH) as is successful with benzaldehyde (1H NMR data correct for 8?). The successful reaction of acetophenone is also remarkable (albeit less so). More rigorous characterization of the ketone-derived imine structures would be highly desirable. •An important aspect of the chemistry which is not discussed is the aqueous solubility of the salts. For example, while monovalent (Na, K) salts are generally regarded as having aqueous solubility, divalent (Ba, Ca) salts are generally regarded as insoluble in water. Here, it is a pleasant surprise for one of the more active structures (the 2-[[(4- methoxyphenyl)methylene] imine) that its Ba and Ca salts (26, 27) are equally active to its sodium salt (23). Qeios, CC-BY 4.0 · Review, January 8, 2024 Qeios ID: P3DQEZ · https://doi.org/10.32388/P3DQEZ Review of: "Synthesis and Antibacterial Screening of Cefradine Schiff Bases and Their Metal Salts" The claimed complete inactivity of the potassium salt (24) is, however, inexplicable, especially since the Na and K salts of a different imine (18, 19) are equally active. Specific comment as to the possibility of aqueous solubility/insolubility as an influencing factor on the biological activity is desirable. •The terse conclusion statement—that the poorer microbiological activity of these imines reflects the unavailability of the Qeios ID: P3DQEZ · https://doi.org/10.32388/P3DQEZ 1/2 Qeios, CC-BY 4.0 · Review, January 8, 2024 (protonated) amine (presumably, for target recognition)—is unsatisfactory. Are these imines pro-drugs? The formation of imine derivatives from related compounds, such as cephalexin, is not well explored. However, such structures appear in the patent literature (for example, CAS 42286-22-6 & 67834-16-6) and are claimed as having antimicrobial activity. Does a broader examination of Schiff base derivatives, such as these latter two cephalexin-derived structures, support the assertion that the formation of these derivatives correlates strongly with the diminution of antimicrobial activity? Qeios ID: P3DQEZ · https://doi.org/10.32388/P3DQEZ 2/2
https://openalex.org/W4238982298
https://ejournal.up45.ac.id/index.php/maksipreneur/article/download/156/151
Indonesian
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Motivasi dan Perilaku Konsumen dalam Keputusan Pembelian Produk Kerajinan Kulit di Yogyakarta
Jurnal Maksipreneur/Jurnal maksipreneur: manajemen, koperasi, dan entrepreneurship
2,014
cc-by
3,873
MOTIVASI DAN PERILAKU KONSUMEN DALAM KEPUTUSAN PEMBELIAN PRODUK INDUSTRI KERAJINAN KULIT DI YOGYAKARTA Fakultas Ekonomi Universitas Proklamasi 45 Yogyakarta Abstract. Success in carrying out business activities can not be separated from the marketing concept of customer satisfaction or customer priority . Likewise, the leather industry in Yogyakarta . To achieve business success , must be able to understand what motivates consumers to buy their products , including also understand consumer behavior . The decision will purchase a product by the consumer is influenced by various factors , both internal and external factors . Factors include cultural factors , social factors , Personal factors , psychological factors which include motvasi , perception , knowledge and beliefs and attitudes pendirian.Determine the factors that are considered by consumers to buy the product , then the manufacturer will be able to determine the right strategy in improving business . Keywords : motivation - behavioral consumer - purchasing decisions Dalam rangka meningkatkan perekonomian masyarakat di wilayah Daerah Istimewa Yogyakarta dewasa ini telah terjadi perubahan tenaga kerja dari sektor pertanian ke sektor industri kecil. Industri kecil yang bertumpu pada tenaga kerja terlatih (train labour) akan mengalihkan tenaga kerja dari pekerjaan yang berupah tinggi dan membantu memecahkan masalah-masalah pengangguran dan kekurangan kesempatan kerja yang serius di sektor pertanian. Daerah Istimewa Yogyakarta merupakan kota budaya yang memiliki prospek cerah dalam meningkatkan produk non migas yaitu sektor industri kerajinan kulit yang merupakan komoditas khas budaya daerah. Adapun jenis kerajinan kulit yang dihasilkan antara lain berupa tas, sepatu, dompet, ikat pinggang dan sebagainya. Sedangkan industri yang bergerak di bidang perkulitan sangat beragam diantaranya, perusahaan barang-barang kulit, perusahaan kulit sungging atau hiasan dan perusahaan sepatu. Potensi pasar dari industri kerajinan kulit di Daerah Istimewa Yogyakarta cukup baik. Hal ini salah satunya disebabkan oleh Yogyakarta sebagai kota tujuan wisata, sehingga hasil dari industri kerajinan kulit ini menjadi alternatif buah tangan wisatawan. Dalam melakukan pembelian, konsumen dipengaruhi berbagai pertimbangan baik faktor internal maupun faktor eksternal. Faktor tersebut meliputi desain produk yang dihasilkan oleh pengrajin mengikuti modis atau tidak, harga yang ditawarkan sebanding atau tidak dengan barang yang dibeli konsumen, kwalitas produk yang ditawarkan memenuhi kwalitas yang diinginkan, awet dan kuat serta mudah pemeliharaan dan penggunaannya, dll. Dalam industri kulit , pemasaran merupakan salah satu kegiatan yang sangat penting , apalagi perusahaan tahu benar tentang perilaku konsumen yang akan membelanjakan uangnya untuk kerajinan kulit. Perusahaan harus memperhatikan faktor-faktor yang mempengaruhi perilaku konsumen, yang meliputi : faktor budaya, faktor sosial, faktor Pribadi, faktor Psikologis yang meliputi motvasi, persepsi, pengetahuan dan kepercayaan dan sikap pendirian. Dalam ilmu ekonomi dikenal ada 3 teori motivasi yang dominan yang ikut mempengaruhi pembentukan perilaku konsumen dalam keputusan pembelian suatu produk. Ketiga teori tersebut dikemukakan oleh Abraham Maslow, Sigmud Frued dan Frederick Herzbverg.(Philip Kotler , 2005 : 196) Abraham Maslow mengemukakan pada dasarnya setiap manusia dalam bertindak selalu didorong oleh kebutuhan tertentu dalam waktu yang tertentu pula. Menurut Maslow kebutuhan manusia tersusun dalam sebuah jenjang (hirarki) dari tingkatan yang paling mendesak hingga yang kurang mendesak. Tingkatan kebutuhan tersebut adalah kebutuhan fisiologis, kebutuhan akan rasa aman, kebutuhan sosial, kebutuhan akan harga diri, kebutuhan pernyataan diri. Setiap orang berusaha untuk memuaskan kebutuhannya yang paling mendasar, dan bila berhasil memenuhinya, maka hal itu bukan menjadi pendorong pada waktu itu. Tetapi orang yang bersangkutan akan didorong untuk memuaskan kebutuhan terpenting selanjutnya. Dari latar belakang tersebut permasalahanya adalah bagaimana motivasi dan perilaku konsumen ibu rumah tangga dan karyawati dalam pembelian produk kerajinan kulit di kota Yogyakarta serta adakah perbedaan motivasi diantara keduanya. Ada perbedaan motivasi antara konsumen ibu rumah tangga dan karyawati dalam pembelian produk industri kerajinan kulit. Sedangkan teori motivasi Freud menyatakan bahwa kekuatan psikologis yang sebenarnya membentuk perilaku pembeli yang sebagian besar berasal dari alam bawah sadar. Freud melihat bahwa seseoranga menekan berbagai keinginan dan dorongan kebagian bawah sadar dalam proses menjadi dewasa dan menerima aturan sosial yang ada disekitarnya. Semua keinginan atau dorongan tersebut tidak pernah terhapuskan atau terkendali secara sempurna. Di lain pihak, Frederick Herzberg dalam teori motivasinya mengembangkan apa yang dinamakan dengan ‘teori dua faktor’ yaitu motivasi yang membedakan antara faktor-faktor yang menyebabkan ketidakpuasan dengan factor-faktor yang menyebabkan kepuasan. Teori motivasi ini mengandung dua implikasi. Pertama, para penjual perlu berusaha untuk mencegah hal-hal yang tidak memuaskan konsumen. Kedua, produk perlu mengenal secara cermat faktor-faktor utama yang memuaskan atau mendorong konsumen untuk membeli produk dari produsen. Sedang perilaku konsumen dapat didefinisikan sebagai kegiatan- kegiatan individu yang secara langsung terlibat dalam mendapatkan dan mempergunakan barang-barang dan jasa-jasa. Termasuk di dalamnya proses penyembangan keputusan pada persiapan dan penentuan kegiatan tersebut ( Basu Swastha DH & T. Hani Handoko, 1993 : 9) Penelitian ini diharapkan akan memberikan manfaat sebagai informasi kepada para pengrajin industri kulit tentang hal – hal yang mempengaruhi konsumen dalam membeli kerajinan kulit, sehingga bisa dijadikan bahan pengrajin untuk menyusun strategi perusahaan. Seluruh aktifitas perusahaan pada akhirnya diarahkan pada pemikiran-pemikiran bagaimana suatu produk yang dihasilkan dapat dirasakan sebagai suatu kebutuhan oleh konsumen. Bilamana perusahaan membutuhkan produk dapat tercapai pada diri konsumen, maka secara teoritis dorongan dan motivasi konsumen akan tercipta, sehingga timbullah tingkah laku yang diarahkan untuk memenuhi kebutuhan- kebutuhan tersebut. Tujuan akhir dari aktifitas pemasaran tidak lain adalah untuk memperhitungkan kemungkinan-kemungkinan yang sangat diperlukan agar konsumen mau membeli hasil produksi perusahaan. Hal-hal yang perlu diperhatikan agar produk-produk yang dihasilkan mencapai sasaran adalah: a. Pasar Perusahaan harus memperhatikan segmen pasar manakah yang akan dituju, berapa kira-kira jumlah pembeli yang bisa dijangkau. Ini a. Pasar Perusahaan harus memperhatikan segmen pasar manakah yang akan dituju, berapa kira-kira jumlah pembeli yang bisa dijangkau. Ini a. Pasar Perilaku pembeliannya dipengaruhi pula oleh beberapa faktor antara lain faktor kebudayaan, sosial, pribadi dan psikologis.(Philip Kotler,2005 : 178) a. Pasar Perusahaan harus memperhatikan segmen pasar manakah yang akan dituju, berapa kira-kira jumlah pembeli yang bisa dijangkau. Ini penting sekali sebab menyangkut persoalan daya beli dan prestise pembeli. Jangan sampai konsumen merasa mempunyai prestise yang rendah. Oleh karena itu perlu ditimbulkan rasa bangga terhadap produk perusahaan. Dengan demikian produk tersebut tidak hanya merangsang tingkah laku pembeli dari kelas masyarakat tertentu, tetapi juga dari kelas sosial lainpun akan mencoba memakai produk tersebut guna mendapatkan prestise tertentu pula. b. Level pembeli yang mana yang akan dijangkau Dalam hal ini konsumen perlu dirinci kedalam faktor-faktor pendidikan, pekerjaan atau jabatan. Dengan merinci target dari konsumen tersebut maka promosi dari produk yang akan dipasarkan dapat diarahkan dengan pasti. Dalam hal ini pengaruh psikologis akan banyak berperan dibandingkan dengan pengaruh-pengaruh lainnya. Misalkan dengan ditonjolkannya dalam promosi bahwa produk tersebut digemari oleh masyarakat dari tingkat pendidikan tinggi, maka secara psikologis demi harga diri atau respon emosionalnya, tidak jarang pula orang yang mempunyai pendidikan yang lebih rendah akan mengkonsumsinya agar merasa diklasifikasikan sebagai orang yang berpendidikan tinggi. c. Kompetisi dengan produsen lain yang sejenis Produsen harus memperhatikan apa yang telah dilakukan oleh saingannya, misalnya di daerah mana saja pesaing mempunyai aktifitas promosi yang sangat kuat, di daerah mana pemasaran mereka dirasa akan melemah, keuntungan-keuntungan apa saja yang ditonjolkan oleh pesaing dalam memasarkan produknya tersebut d. Kondisi pasar Produsen perlu mengembangkan dan menyajikan produk-produk dalam bentuk yang efisien. Perkembangan produk merupakan suatu hal yang sangat penting, sebab apabila suatu produk tetap dalam keadaan statis, maka secara psikologis dapat membuat konsumen menjadi bosan. Bilamana suatu produk dirasa sudah membosankan, maka kebutuhan konsumen tidak lagi terpenuhi secara sempurna, sehingga berakibat kekecewaan. Hal ini secara tidak langsung akan mempengaruhi tingkah laku pembeli, dan konsumen akan berpindah membeli produk saingan yang sejenis. Dalam kaitannya dengan keputusan untuk membeli dan memakai produk atau jasa, maka pemahaman akan perilaku konsumen meliputi juga jawaban atas pertanyaan seperti; apa (what) yang dibeli, dimana (where) membelinya, bagaiman (how) kebiasaannya membeli, dan dalam keadaan apa barang-barang dan jasa dibeli. Sementara itu di lain pihak, dalam membuat keputusan konsumen tidak berada dalam suatu tempat yang terisolir dari lingkungan sekitarnya. Perilaku pembeliannya dipengaruhi pula oleh beberapa faktor antara lain faktor kebudayaan, sosial, pribadi dan psikologis.(Philip Kotler,2005 : 178) Sementara itu di lain pihak, dalam membuat keputusan konsumen tidak berada dalam suatu tempat yang terisolir dari lingkungan sekitarnya. Titik sentral dari riset tentang motivasi sebagai keputusan pembelian adalah pencarian jawaban atas pertanyaan mengapa tingkah laku manusia atau masyarakat tertentu dalam hal keputusan pembelian suatu produk. Setiap riset yang berkenaan dengan tingkah laku pembeli tersebut sangat penting dalam rangka membantu usaha mempengaruhi pembeli dalam rangka merebut pasaran potensial. Dari uraian tersebut dapat dikatakan bahwa mempelajari pemasaran pada dasarnya tidak lepas dari tingkah laku konsumennya. Sedangkan untuk mengetahui latar belakang tingkah laku konsumen tersebut, tidak lepas begitu saja tanpa mempelajari tentang motivasi. Motivasi itu sendiri diartikan sebagai suatu dorongan kebutuhan dan keinginan individu yang diarahkan pada tujuan untuk memperoleh kepuasan. Motivasi berhubungan erat dengan kebutuhan. Konsekuensi dari hubungan tersebut adalah bahwa keputusan harus dibangun atau dirangsang sebelum motif. Sebab bukan tidak mungkin orang mempunyai kebutuhan yang belum termunculkan dan kebutuhan seperti ini tidak cukup kuat mengaktifkan perilakunya. Demikian pula halnya dengan keputusan pembelian. Proses pembentukan keputusan dalam membeli selalu diawali dengan kebutuhan yang dirasakan. Suatu kebutuhan akan membangun motivasi seseorang dalam bertindak untuk mencapai pemenuhan kebutuhan tersebut. Perilaku konsumen sebagai suatu proses yang berupa pengambilan keputusan dan kegiatan yang bersifat fisik, pada akhirnya akan melibatkan individu dalam menilai, ia mendapatkan dan mempergunakan barang-barang dan jasa-jasa ekonomis. Secara garis besar, terdapat kekuatan besar yang mempengaruhi perilaku konsumen, yaitu kekuatan ekstern dan intern. Dalam penelitian ini industri kerajinan kulit dikategorikan sebagai kebutuhan sekunder dari konsumen, variabel yang muncul sebagai motivasi adalah harga,design dan kwalitas produk. Disamping motivasi tersebut, terdapat pula motivasi dari konsumen yang muncul dikarenakan adanya rasa ketertarikan terhadap design yang diciptakan oleh industri kerajinan kulit dan ketertarikan terhadap kualitas yang baik. Populasi dalam penelitian ini adalah wanita dewasa terdiri dari ibu- ibu rumah tangga dan karyawati yang menggunakan kerajinan kulit Yogyakarta yang berasal dari industri kerajinan kulit. Sedangkan metode pangambilan sampel yang digunakan adalah convenien sampling. Penentuan sampel dengan menggunakan rumus: (Samsubar Saleh, 1998 : 161) Dengan standar eror 17.5%. dan standar deviasi ditentukan sebesar satu, karena hal ini didasarkan pada tanggapan bahwa bila n menjadi semakin besar sampai tak terhingga, maka standar deviasi sampel (s) akan mendekati standar deviasi populasi (a) s=a, maka Data yang digunakan dalam penelitian ini meliputi data primer yaitu yang diperoleh langsung dari sumbernya, diamati dan dicatat untuk pertama kalinya.(Marzuki, 2002 : 54) dengan menggunakan interview dan kuesioner . Sedang data sekunder yang digunakan diperoleh dari pihak lain yang bukan diusahakan sendiri pengumpulannya oleh peneliti, misalnya dari majalah-majalah, keterangan-keterangan atau publikasi lainnya.(Marzuki, 2002 : 56) Analisis data yang digunakan dalam penelitian ini meliputi analisa kwalitatif dan kwantitatif. Analisis kwantitatif menggunakan 3 macam analisa secara statistik yaitu : a. Analisis rata-rata hitung atau mean (Sutrisno Hadi 1993 : 126) , digunakan untuk menjawab rumusan masalah yang pertama. a. Analisis rata-rata hitung atau mean (Sutrisno Hadi 1993 : 126) , digunakan untuk menjawab rumusan masalah yang pertama. Perhitungan bobot nilai digunakan dengan skala dengan ketentuan sebagai berikut: Data yang diberi bobot nilai tersebut kemudian dikelompokkan kedalam empat kelas interval,dengan kriteria : b. Analisis chi-kuadrat b. Analisis chi-kuadrat b. Analisis chi-kuadrat Hasil dari daftar pertanyaan responden, maka dapat dicari perilaku konsumen terhadap produk dengan menggunakan rumus statistik chi-kuadrat (Djarwanto PS, 1994 : 186) Keterangan: g nij = frekuensi pengamatan dari baris i dan kolom j g nij = frekuensi pengamatan dari baris i dan kolom j eij = frekuensi yang diharapkan dari baris i dan kolom j i = baris j = kolom Untuk mencari frekuensi yang diharapkan dari (eij) dihitung dengan formula : Keterangan: ni = jumlah baris i nij = jumlah baris j n = jumlah sampel Kurva chi square distribution bisa digambar sebagai berikut: Langkah didalam menguji hipotesa dalam penelitian ini adalah sebagai berikut: 1. Menentukan formulasi hipotesis nihil dan hipotesis alternatif: Ho : P1 = P2 = ...................................................... = pk (=P) H1 : P1 ≠P2 = ...................................................... ≠pk (≠P) Ho = Tidak ada perbedaan motivasi konsumen ibu rumah tangga dan karyawati dalam pembelian produk kerajinan kulit. H1 = Ada perbedaan motivasi konsumen ibu rumah tangga dan karyawati dalam pembelian produk kerajinan kulit. H1 = Ada perbedaan motivasi konsumen ibu rumah tangga dan karyawati dalam pembelian produk kerajinan kulit. 2. Dipilih level of significance tertentu 2. Dipilih level of significance tertentu 2. Dipilih level of significance tertentu 2. Dipilih level of significance tertentu 3. Kriteria pengujian Ho diterima apabila : 2 ≤2 [ ;(r-1)(k-1)] Ho ditolak apabila : 2 > 2 [ ;(r-1)(k-1)] 3. Kriteria pengujian Ho diterima apabila : 2 ≤2 [ ;(r-1)(k-1)] Ho ditolak apabila : 2 > 2 [ ;(r-1)(k-1)] 3. Kriteria pengujian Ho diterima apabila : 2 ≤2 [ ;(r-1)(k-1)] Ho ditolak apabila : 2 > 2 [ ;(r-1)(k-1)] 4. Dari sampel yang diambil atau dari hasil pengamatan yang dilakukan, kemudian dihitung nilai 2 dengan rumus : Keterangan: i = 1, 2 ………………… r j = 1, 2 ………………… k nij = Actual frequency/observed frekuency eij = Expected frekuency/teoritical frekuency nij = Actual frequency/observed frekuency j q y y eij = Expected frekuency/teoritical frekuency 5. Kesimpulan : Dengan membandingkan hasil perhitungan dalam langkah 4 dengan kriteria pengujian langkah 3, diambillah suatu kesimpulan, apakah Ho diterima atau ditolak. Dengan membandingkan hasil perhitungan dalam langkah 4 dengan kriteria pengujian langkah 3, diambillah suatu kesimpulan, apakah Ho diterima atau ditolak. Analisa ini digunakan untuk mengetahui ada tidaknya perbedaan yang nyata dari dua variabel, atau tidak mengetahui hubungan yang signifikan (meyakinkan) antara dua variabel. Atau untuk mengetahui hubungan yang signifikan (tidak meyakinkan) antara dua variabel. (Zaenal Mustafa, 1995 : 92) Dengan rumus sebagai berikut : Kemudian hasil perhitungan dibandingkan dengan dalam tabel statistik pada tingkat kebebasan tertentu. Bilamana harga hasil perhitungan penelitian ternyata lebih besar dari harga tabel, maka hal tersebut menyatakan bahwa Ho ditolak yang artinya terdapat perbedaan dalam taraf yang meyakinkan antara variabel yang satu dengan yang lain. Angket yang disebarkan pada responden semuanya berjumlah 175 eksemplar, dan yang kembali dalam keadaan utuh dan layak untuk diteliti adalah sebanyak 125 eksemplar. Tabel 1 Kriteria Responden Berdasarkan Usia Tabel 1 Kriteria Responden Berdasarkan Usia Tabel 1 Kriteria Responden Berdasarkan Usia Tabel 1 Dari tabel tersebut menunjukkan bahwa responden berdasarkan usia sebanyak 36 orang (28,8%) kelompok usia 18 – 23 tahun, sebanyak 28 orang ( 22,4%) kelompok usia 24 – 29 tahun dan 61 orang ( 48,8%) usia 30 tahun ke atas. Tabel 2. Kriteria Responden Berdasarkan Pekerjaan Tabel 2. Kriteria Responden Berdasarkan Pekerjaan Tabel 2. Berdasarkan tabel tersebut terlihat sebanyak 62 orang ( 49,6%) responden berasal dari karyawati, 63 orang (50,4%) responden berasal dari ibu rumah tanggaa. a. Yang Memberi Informasi Dalam Pembelian Dalam analisa ini yang dimaksud yaitu pihak yang memberikan informasi kepada responden untuk melakukan pembelian. Penulis mengelompokkan menjadi 4 (empat) macam yang memberikan informasi, yaitu : saudara, teman, iklan dan melihat di toko. Dari 125 responden disusun dalam suatu tabel sebagai berikut : Tabel 3. Pemberi informasi dalam pembelian Tabel 3. Pemberi informasi dalam pembelian Berdasar pada data tabel 3 bahwa 125 responden diketahui yang memberikan informasi pembelian yang dilakukan oleh responden karyawati dan ibu rumah tangga banyaknya sama yaitu 24% dari saudara ada pada urutan kedua, 52% dari teman ada pada urutan pertama, 16% dari iklan ada pada urutan ketiga, dan 8% dari melihat di toko ada pada urutan keempat. b. Yang Mempengaruhi Dalam Pembelian Mengenai siapa yang mempengaruhi respoden dalam melakukan pembelian penulis mengemukakan 4 (empat) faktor yang bisa memberikan pengaruh pada respoden dalam perilaku pembeliannya. Keempat faktor tersebut adalah : Saudara, teman, iklan dan lain-lain. Data lengkap mengenai hal yang mempengaruhi responden dalam pembelian ini dapat dilihat pada tabel 4 sebagai berikut : Tabel 4. Yang mempengaruhi dalam Pembelian Tabel 4. Dari data pada tabel 4 bahwa 125 responden yang mempengaruhi dalam pembelian kerajinan kulit untuk responden karyawati menunjukkan 56% dari teman ada pada urutan pertama, 19% dari iklan ada pada urutan kedua, 17% dari saudara ada pada urutan ketiga, 8% dari lain-lain urutan keempat. Untuk responden ibu rumah tangga 32% dari saudara ada pada urutan pertama, prosentase sama sebesar 32% dari teman ada pada urutan kedua, 24% dari iklan urutan ketiga dan 12% lain- lain. Untuk menganalisa bagaimana motivasi konsumen terhadap produk industri kerajinan kulit digunakan analisa rata-rata hitung dengan menggunakan rumus sebagai berikut : Dalam memberikan skor jawaban responden penulis menggunakan bobot nilai yang tertera sebagai berikut : Tabel : Skor Jawaban Responden Tabel : Skor Jawaban Responden Berikut ini penilaian terhadap faktor-faktor motivasi responden dalam pembelian produk industri kerajinan kulit. a. Motivasi Responden Membeli Kerajinan Kulit Berdasarkan Harga Dari hasil pengumpulan data yang telah dilakukan terhadap 62 orang responden karyawati dan 63 orang responden ibu rumah tangga yang bermotivasi membeli kerajinan kulit berdasarkan harga diperoleh data sebagai berikut : Tabel 5. Tabel 5. Tabel 5. Motivasi Responden Membeli Kerajinan Kulit Berdasarkan Harga Motivasi Responden Membeli Kerajinan Kulit Berdasarkan Harga Dari tabel 5 dapat diketahui bahwa responden karyawati dalam membeli produk kerajinan kulit mencapai nilai rata-rata 3,25 yang berarti sangat kuat karena berada pada kelas interval 3,25 < M ≤4. Sementara itu untuk responden ibu rumah tangga dalam membeli produk kerajinan kulit mencapai nilai rata-rata 3,53 yang berarti juga sangat kuat karena berada pada kelas interval 3,25 < M ≤4. Jadi dapat diperoleh jumlah responden karyawati dan ibu rumah tangga dalam membeli produk kerajinan kulit mencapai nilai rata-rata hitung 3,25 yang berarti sangat kuat. Dengan demikian terdapat hubungan yang sangat kuat antara motivasi dan kepuasan membeli produk kerajinan kulit, khususnya berdasarkan harga. b. Motivasi Responden Membeli Kerajinan Kulit Berdasarkan Design Dari hasil pengumpulan data yang telah dilakukan terhadap 62 orang responden karyawati dan 63 orang responden ibu rumah tangga yang bermotivasi membeli kerajinan kulit berdasarkan design diperoleh data sebagai berikut : Tabel 6. Motivasi Responden Membeli Kerajinan Kulit Berdasarkan Design Dari tabel diatas dapat diketahui bahwa responden karyawati dalam membeli produk kerajinan kulit mencapai nilai rata-rata hitung 2,84 dan untuk responden ibu rumah tangga dalam membeli produk kerajinan kulit mencapai rata-rata hitung 3,11. Jadi dapat diperoleh nilai rata-rata hitung untuk kedua responden 2,97. Keduanya berada pada kelas “Setuju” atau kuat karena berada pada kelas interval 2,50 < M ≤3,25. Dengan demikian menunjukkan bahwa ada hubungan yang kuat antara motivasi dan keputusan membeli produk kerajinan kulit, khususnya berdasarkan design. c. Motivasi Responden Membeli Kerajinan Kulit Berdasarkan Kualitas c. Dari hasil pengumpulan data yang telah dilakukan terhadap 62 orang responden karyawati dan 63 orang responden ibu rumah tangga yang bermotivasi membeli kerajinan kulit berdasarkan kualitas diperoleh data sebagai berikut : Tabel 7. Pengujian Hipotesis Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan kualitas c. Pengujian Hipotesis Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan kualitas Tabel 7. Motivasi Responden Membeli Kerajinan Kulit Berdasarkan Kualitas Motivasi Responden Membeli Kerajinan Kulit Berdasarkan Kualitas Dari tabel diatas dapat diketahui bahwa responden karyawati dalam membeli produk kerajinan kulit mencapai nilai rata-rata hitung 2,68 dan untuk responden ibu rumah tangga dalam membeli produk kerajinan kulit mencapai rata-rata hitung 2,82. Untuk nilai rata-rata hitung secara keseluruhan yaitu 2,75. Keduanya berada pada kelas interval 2,50 < M ≤ 3,25 yang berarti kuat. Dengan demikian terdapat hubungan yang kuat antara motivasi dan keputusan membeli produk kerajinan kulit, khususnya berdasarkan kualitas. a. Pengujian Hipotesis Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan Harga Tabel 8. Penilaian Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan Harga a. Pengujian Hipotesis Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan Harga Tabel 8. Penilaian Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan Harga Tabel 8. Tabel 8. Penilaian Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan Harga Berdasarkan pada tabel diatas dapat dicari atau diuji hipotesis perbedaan motivasi responden dalam pembelian produk kerajinan kulit. Menggunakan level of significance (a) 0,05, maka dapat diperoleh kai -kwadrat tabel sebesar 7,851, sedang kai-kwadrat hitung sebesar 1,084 . Karena kai-kuadrat hitung lebih kecil dari kai-kuadrat tabel, maka Ho diterima. Dengan demikian dapat disimpulkan bahwa tidak ada perbedaan motivasi dari sisi harga antara karyawati dan ibu rumah tangga dalam pembelian produk kerajinan kulit. b. Pengujian Hipotesis Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan Design Pengujian Hipotesis Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan Design Tabel 9 Penilaian Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan Design Tabel 9 Penilaian Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan Design Berdasarkan tabel diatas diuji hipotesis perbedaan motivasi responden dalam pembelian produk kerajinan kulit. Menggunakan level of significance (a) 0.05, diperoleh kai-kwadrat tabel sebesar 7.851, kai-kwadarat hitung sebesar 5,9682. Karena kai- kwadrat hitung lebih kecil dari kai-kwadrat tabel berarti HO diterima. Dengan demikian dapat disimpulkan bahwa tidak ada perbedaan motivasi dari sisi design antara karyawati dan ibu rumah tangga dalam pembelian produk kerajinan kulit. c. Pengujian Hipotesis Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan kualitas Tabel 10 Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan Design S b D t P i di l h c. Pengujian Hipotesis Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan kualitas Tabel 10 Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan Design Sumber : Data Primer yang diolah c. c. Pengujian Hipotesis Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan kualitas Tabel 10 Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan Design S b D P i di l h Tabel 10 Motivasi Responden Karyawati dan Ibu Rumah Tangga Berdasarkan Design Sumber : Data Primer yang diolah Berdasarkan tabel 10 dapat dicari atau diuji hipotesis perbedaan motivasi responden dalam pembelian produk kerajinan kulit. Menggunakan level of significance (a) 0.05, maka dapat diperoleh kai -kwadrat tabel sebesar 7.851, sedang kai-kwadrat hitung 6,519. Karena kai-kuadrat hitung lebih kecil dari kai-kuadrat tabel, maka HO diterima. Dengan demikian dapat disimpulkan bahwa tidak ada perbedaan motivasi dari sisi kualitas antara karyawati dan ibu rumah tangga dalam pembelian produk kerajinan kulit. 1. Dari analisa perilaku konsumen dapat disimpulkan bahwa yang memberikan informasi dalam pembelian kerajinan kulit Yogyakarta sebanyak 24% dari saudara, 52% dari teman, 16% dari iklan, dan 18% melihat ditoko. 2. Berdasarkan kelompok responden karyawati menunjukkan sebanyak 56% dari teman, 19% dari iklan, 17% dari saudara, dan 8% dari lain-lain. Sedangkan berdasarkan kelompok ibu rumah tangga menunjukkan 32% dari saudara, prosentase sama sebesar 32% dari teman, 24% dari iklan dan 12% dari lain-lain. 3. Motivasi konsumen berdasarkan harga ditunjukkan mean 3,53 yang berarti motivasi sangat kuat. 3. Motivasi konsumen berdasarkan harga ditunjukkan mean 3,53 yang berarti motivasi sangat kuat. 4. Motivasi konsumen berdasarkan design menunjukkan mean 2,97 yang berarti motivasi kuat. 5. Motivasi konsumen berdasarkan kualitas menunjukkan Mean yaitu 2,75 yang berarti kuat. 6. Tidak ada perbedaan motivasi antara karyawati dan ibu rumah tangga dalam membeli kerajinan kulit dari faktor harga, design dan kwalitas. 1. Motivasi konsumen dalam membeli produk kerajinan kulit Yogyakarta, faktor harga merupakan motivasi yang sangat kuat sehingga pengrajin perlu memperhatikan besarnya harga jual yang bisa terjangkau . 2. Motivasi konsumen dalam membeli produk kerajinan kulit Yogyakarta, berdasarkan design dan kwalitas merupakan motivasi yang kuat, hal ini menunjukan bahwa design produk dan kwalitas juga harus selalu menjadi perhatian perusahaan kulit. 3. Motivasi konsumen baik karyawati maupun ibu rumah tangga tidak ada perbedaan, berarti produk kerajinan kulit dengan segmen ini tidak perlu dibedakan baik dari sisi harga, design maupun kwalitas. Swasta Basu,DH & Handoko Hani,T, 1993, Manajemen Pemasaran, Analisis Perilaku Konsumen, Liberty, Yogyakarta. Subagiyo Pangestu & P.S.Jarwanto, 1994, Statistik Induktif, edisi ke-2, BPFE, Yogyakarta. Marzuki, 2002, Metodologi Riset, Bagian Penerbitan Fakultas Ekonomi UII, Yogyakarta, Edisi II Kotler Philip, 2005, Manajemen Pemasaran¸ 1995, Edisi Pertama, Cetakan Pertama BPFE UGM, Yogyakarta. Saleh Samsubar, 1996, Statistik Induktif, Unit Penerbit dan Percetakan AMP YKPN, Edisi I, Cetakan I. Hadi Sutrisno, 1993, Metodologi Research, jilid ke-3 Andi Offset, Yogyakarta. Mustafa Zaenal, 1995, Pengantar Statistik Terapan Untuk Ekonomi. Cetakan II, Bagian Penerbit Fakultas Ekonomi UII, Yogyakarta.
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Research on the Design of the General Hospital Wayfinding and Signage System based on the Universal Design Concept - A Case Study of the Second Affiliated Hospital of Nanchang University
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1 Introduction Universal design is produced on the basis of barrier-free design and is an extension of the human-oriented concept. It refers to the design of the environment, products and services that can be used by anyone without special design or adjustment[1]. It is not designed specifically for a certain kind of people, and it is not influenced by the economy, education, status, ability and other factors. It is a comprehensive design to truly realize the equality of all people. Children, adults, the elderly and people with disabilities can all benefit from it. Universal design has the characteristics of inclusiveness, convenience, comfort and flexibility. It is applicable to all fields and all people. It covers most groups and integrates individual differences. It is additive design, which can meet people’s more accurate and simple use requirements, and make visual, tactile, auditory and other effects better. Hospital is a place closely related to people. In recent years, the medical environment and service level in our country have gradually increased. For a general hospital, the flow of people is large, the action line is complex, and there are many medical procedures. In order to get treatment safely, quickly and effectively, the wayfinding and signage system must be clear, scientific and humanized. The earliest research on hospital wayfinding and signage system in China dates back to 2004 when the research was mainly about the aspects of humanistic care, interest and functionality. For example, Fu Tiantian, from Research on the Design of the General Hospital Wayfinding and Signage System based on the Universal Design Concept - A Case Study of the Second Affiliated Hospital of Nanchang University Xinbo Shen1,*, Min Li1 and Lei Yu1 1Art College, Jiangxi University of Finance and Economics, Nanchang City, Jiangxi Province, 330013, China 1Art College, Jiangxi University of Finance and Economics, Nanchang City, Jiangxi Province, 3 Abstract. With the continuous improvement of the medical level in China, the quality of hospital service and the environment have attracted people’s attention. The hospital is a place with relatively dense population, and the general hospital consists of a number of departments with complicated procedures and staggered routes. In order to improve the efficiency of medical treatment, stabilize the mood of patients, and respond to the call of establishing a human-oriented hospital, it is particularly important to design a reasonable and comprehensive hospital wayfinding and signage system. In this paper, the universal design concept and principles which are more suitable for everyone are applied to the hospital wayfinding and signage system. Through the field investigation of the Second Affiliated Hospital of Nanchang University, the author analyzes the problems and sums up the design criteria which are suitable for the hospital wayfinding and signage system. the Qilu University of Technology, put forward the method, principle and implementation of the design of hospital wayfinding and signage system based on human in Research on “Human-oriented” Design in Visual Wayfinding and Signage System of Hospital. Chen Le, from Anhui University of Engineering finished the Research on the Individualized Design of Modern Medical Environment Wayfinding and Signage System. In this paper, he explores the methods, processes and principles of hospital individualized design, and makes case analysis of municipal hospitals, which involves less universal design theory. Through field and literature research, together with analysis and induction, the author mainly analyzes the deficiencies of the wayfinding and signage system of the general hospital - the Second Affiliated Hospital of Nanchang University. The universal design is used to optimize its wayfinding and signage system, to improve the difficulty of people’s medical treatment caused by the lack and confusion of wayfinding and signage, to enable patients to arrive at the destination clearly, quickly and accurately, to improve the service quality and image of the hospital, and to provide reference for the design and application of the wayfinding and signage system of the general hospital. https://doi.org/10.1051/e3sconf/202017902058 https://doi.org/10.1051/e3sconf/202017902058 E3S Web of Conferences 179, 02058 (2020) EWRE 2020 © The Authors, published by EDP Sciences. This is an open access article distributed under the terms of the Creative Commons Attribution License 4.0 (http://creativecommons.org/licenses/by/4.0/). *Corresponding author e-mail: 870664319@qq.com 2.1. Concept of general hospital wayfinding and signage system more standardized, avoid the waste of resources, and make the division of labor in the design process clearer. The general hospital has a wide range of targeted patients which sets up a number of specialized projects composed of internal and external, traditional Chinese and western medical departments with its sections focusing on maternal and child, ear, nose and throat[2]. The wayfinding and signage system of the hospital is a wayfinding and signage system that uses the physical properties of materials and colors, as well as various text and graphic signs to guide the logistics and people flow within or around the hospital[3]. A good, standardized and human-oriented hospital wayfinding and signage system can guide patients and their families to find their way quickly and accurately. It can also guide patients to see a doctor in time with the improving working efficiency of medical staff, and stabilizing the working order of the hospital. It is an essential hardware facility of the hospital as well as a miniature of the image of the hospital. 2 The wayfinding and signage system of general hospital and its classification *Corresponding author e-mail: 870664319@qq.com *Corresponding author e-mail: 870664319@qq.com E3S Web of Conferences 179, 02058 (2020) EWRE 2020 https://doi.org/10.1051/e3sconf/202017902058 3 Problems in the wayfinding and signage system of the Second Affiliated Hospital of Nanchang University 3 The Second Affiliated Hospital of Nanchang University is a comprehensive 3A hospital in Jiangxi Province, which integrates medical treatment, scientific research and rehabilitation. It has more than 2000 beds and 51 departments. It is mainly divided into three main buildings: outpatient department complex building, inpatient department and physical examination building, as well as canteen and office building. Its large scale and complex distribution highlight the importance of a proper guide wayfinding and signage system. Based on the field investigation of the Second Affiliated Hospital, the author finds out the problems in the practical application of the wayfinding and signage system, which are summarized as follows: 3.1. The imperfect wayfinding and signage system and the lack of planning Accurate information classification is the key to the establishment of hospital wayfinding and signage system. In the document Code for Architectural Design of General Hospitals issued by China, it clearly points out that the hospital wayfinding and signage system is divided into four levels: (1) the first-level wayfinding and signage system: it is mainly the wayfinding and signage outside hospitals or on the building including building name, entrance and exit, together with general layout, road diversion, public service, and the overall image and other signs; (2) the second-level wayfinding and signage system: it mainly includes channel and floor sign, including index and plan of each floor, guidance of step elevator, expert column, visit form, entrance and exit, etc; (3) the third-level wayfinding and signage system: it mainly involves the sign of functional areas, including the sign of medical care, administrative logistics and other units; (4) the forth-level wayfinding and signage system: it mainly refers to room window and doorplate, including each ward, sickbed, department and other doorplate window plates. The classification of hospital wayfinding and signage system can make the system A complete, standardized and integrated wayfinding and signage system plays an important role in the complex hospital environment. If the system fails to perform the function, patients and their families are unable to get information signs and will be left in confusion. There is no standard wayfinding and signage system inside and outside the Second Affiliated Hospital, which is mainly reflected in the disordered and crowded wayfinding sign and its irregular placement. Some specific hints are not given. The signs of outpatient department, comprehensive building and inpatient department are blue, while the physical examination area of female guests in the physical examination building is red, and the radiotherapy area is green, ‘figure 1’; there is only a simple planar graph in the entrance of the hospital instead of index plan of the whole hospital. There is no any floor guidance in the physical examination building and the comprehensive building; some signs are placed on the ground or near stairway in disorder without standard size or forms, ‘figure 2’. Also, the warning sign is inadequate and fuzzy, which is not easy to find in walking. Figure 1. The wayfinding and signage system of female physical examination area and radiotherapy area in the physical examination building of the Second Affiliated Hospital of Nanchang University. 3.4. Lack of human-oriented awareness The aging of our country is gradually increasing with more and more people suffering from disability and color blindness. For the special group of people, the hospital wayfinding and signage system should be human-oriented and comprehensive. The Second Affiliated Hospital is a large-scale comprehensive hospital located in the center of the city, consisting of a large number of people who live in counties, districts and towns. Each of them has a different education level. However, the hospital does not provide illiterate signs for people with limited literacy; as a special group, most of the children are afraid when seeking medical treatment, but the design of the signs for pediatrics lacks interest and flexibility, which is not helpful for children to overcome anxiety in diagnosis and treatment. The tactile signs for disabled patients and some signs for wheelchair users are not offered in the hospital, such as the specific 3.1. The imperfect wayfinding and signage system and the lack of planning nding and signage system of female physical examination area and radiotherapy area in the physical examination building of the Second Affiliated Hospital of Nanchang University. Figure 1. The wayfinding and signage system of female physical examination area and radiotherapy area examination building of the Second Affiliated Hospital of Nanchang University. 2 2 E3S Web of Conferences 179, 02058 (2020) EWRE 2020 https://doi.org/10.1051/e3sconf/202017902058 Figure 2. The ground wayfinding and signage system of the inpatient department and multi-functional building of the Second Affiliated Hospital of Nanchang University. process of medical treatment is not considered in the setting of signs Figure 2. The ground wayfinding and signage system of the inpatient department and multi-functional building of the Second Affiliated Hospital of Nanchang University. process of medical treatment is not considered in the i f i Figure 2. The ground wayfinding and signage system of the inpatient department and multi-functional building of the Second Affiliated Hospital of Nanchang University. process of medical treatment is not considered in the setting of signs. process of medical treatment is not considered in the setting of signs. 3.3. Lack of aesthetics and design sense Unnecessary troubles can be prevented with appropriately located signs and clear directions when people seek medical treatment. The problems of the Second Affiliated Hospital appear are mainly reflected in the fact that patients are difficult in finding the designated area because of unclear signs. For example, when one go to pediatrics obeying the sign, he will get to surgery; besides, the location of some signs are too high, such as department wayfinding and signage, floor guidance at stairs and the guidance of inpatient department, whereas some outdoor wayfinding and signage are so lower to the ground that vehicle can easily block them, making these signs inconvenient to identify; in addition, there are no signs in the places where the flow of people is large and chaos is easy to cause, and the The hospital’s wayfinding and signage system should not only be intuitive and clear, but also pay attention to the combination of the three elements of graphics, color and text so as to show the aesthetic sense and significance of the wayfinding and signage. The problems of the Second Affiliated Hospital are mainly reflected on the facts that some fonts are too small to recognition, especially when the fonts are all in bold type without distinction; the wayfinding and signage on the graphics are often arrows, and the logo patterns are international style without unique graphic signs or creativity, ‘figure 3’; although most of the colors are blue, they are in different shades and some parts are even red and green, which are in disorder and lack aesthetics. p p g y Figure 3. The wayfinding and signage system of the outpatient departments of the Second Affiliated Hospital of Nanchang University. 4. Lack of human-oriented awareness height and proportion of corridors and elevators, making people difficult to get accurate information of the wayfinding and signage. Figure 3. The wayfinding and signage system of the outpatient departments of the Second Affiliated Hospital of Nanchang University. 4. Lack of human-oriented awareness height and proportion of corridors and elevators, making people difficult to get accurate information of the wayfinding and signage. 4 Universal design of the wayfinding and signage system of the Second Affiliated Hospital of Nanchang University Although the wayfinding and signage system of the Second Affiliated Hospital has played a guiding role in reality, there are still many problems to be improved. The design of wayfinding and signage system in hospital is complicated. It is not easy to adapt to different groups of people and to be used by all people. Therefore, it is necessary to apply the universal design theory to solve the problem of wayfinding and signage system, and fully consider the needs and psychology of all kinds of people. Based on the literature review and the analysis of the problems of the wayfinding and signage of the Second 3 https://doi.org/10.1051/e3sconf/202017902058 E3S Web of Conferences 179, 02058 (2020) E3S Web of Conferences 179, 02058 (2020) EWRE 2020 Affiliated Hospital, three principles for the design of the wayfinding and signage system of the hospital are summarized: Affiliated Hospital, three principles for the design of the wayfinding and signage system of the hospital are summarized: Considering the complexity of the hospital population, corresponding signs should be set up at home and abroad to meet different needs for old children, defective patients and family members, medical staff, etc. The book Design in Design written by Kenya Hara refers to the theory of “five senses” that integrates vision, touch, hearing, smell and taste into the design[5], which can transmit information in various ways, allowing people to look up information from different aspects, and add voice and Braille prompts to the literal wayfinding and signage. When using the wayfinding and signage, the adjustment of people’s actions should be reduced as much as possible, with more attention to the safety, and the appearance of sharp and fragile materials shall be avoided. Also, information in the dangerous area should be put noticeably and the risk coefficient should be reduced. Green design has gradually become the mainstream. Hospital wayfinding and signage can be made of environmental friendly materials instead of traditional materials, which are durable, recyclable, cost-effective, and easy to change. Moreover, they can transmit emotions through the selection and use of materials. For example, Meitian hospital, a Japanese specialized hospital for women and children breaks through the traditional concept of industrial materials and uses soft white pure cotton cloth to make signs in shape of everyday products. In this way, affinity is increased, fear eliminated, a clean, warm and comfortable image of the hospital displayed[6]. 5 Conclusion The service quality of the hospital has been a prior concern in the life of the public. A well-established hospital wayfinding and signage system helps to save more time in saving patients’ lives and provide convenience for medical treatment. The Second Affiliated Hospital of Nanchang University is a 3A comprehensive hospital with many departments, complex processes and transportation, and it also undertakes various duties like high-level medical treatment, scientific research, practical teaching and other tasks. This paper summarizes the existing problems of the Second Affiliated Hospital’s wayfinding and signage system, such as lack of planning and unreasonable setting. The paper applies the universal design theory to real problems and puts forward three principles for improvements which can promote practical problems such as humanization and systematization with the explanation of relevant concepts. The author hopes the paper serves as a reference for the design of similar hospitals’ wayfinding and signage systems. 4.1. Integration and rationalization The wayfinding and signage system of the hospital shall be complete and systematic, conform to the relevant national standards, and the wayfinding and signage of all regions and types shall be unified, and be consistent with the hospital's own culture and style, such as the font size, font, spacing and typesetting of the characters, and the color system, material, form, layout, size, location and graphic design of the signs at all levels shall be unified, concise and beautiful. Besides, the identification of special prompt shall be obvious. The setting of wayfinding and signage should be clearly divided into four levels, so that patients can be guided to each functional area according to the indoor and outdoor wayfinding and signage. On this basis, the scale of signs at all levels should also be reasonably set, taking into account the spatial relationship, floor height, visual comfort of people in different postures and body shapes. For example, Budapest Airport has set up a series of special reasonable signs beside the normal size signs to remind wheelchair users and children. 4 Universal design of the wayfinding and signage system of the Second Affiliated Hospital of Nanchang University Such signs are designed from the perspective of human care. 4.2. Easy to distinguish with accuracy The perfect layout of hospital wayfinding and signage shall be accurate. According to the flow of people, medical treatment process and building characteristics, the appropriate placement position, size and frequency shall be calculated to avoid the absence of signs and the occlusion caused by height. The ground, wall, ceiling and other forms shall be selected at the reasonable position to enhance the clarity. The medical wayfinding and signage system should be in consistency and relevance. It is necessary to set up corresponding bifurcated wayfinding and signage at the turning of the intersection and special areas[4], such as elevator stairs, entrances and exits, so as to prevent the delay of diagnosis and treatment due to route deviation, ensure the accuracy of orientation and information, and indicate the destination. Secondly, the information of logo should be well arranged according to importance. Also, when typesetting, important information should be highlighted, omitting unnecessary details. Chinese and English words should be used accurately. Graphics should be matched with words. The size, proportion, color and brightness of light should be compared. The visual background should be simple and intuitive, easy to understand and reduce confusion caused by ambiguous content. References The human-oriented medical service is improved constantly in which patients are regarded as the center of the hospital. The hospital wayfinding and signage system designed for people can optimize the service level and improve the diagnosis and treatment environment. 1. Zeng, L.X., Jiang, X. (2014) Concept analysis of universal design. CAD / CAM and Manufacturing Informatization, 7: 25-26. 4 E3S Web of Conferences 179, 02058 (2020) EWRE 2020 https://doi.org/10.1051/e3sconf/202017902058 2. Chu, L.F. (2005) Research on the design of wayfinding sign recognition system of general hospital. Jiangnan University, 8-9. g y 3. Wang, W.Z. (2013) Research and design of Z Hospital wayfinding and signage system . Hebei University of Technology, 12-13. y gy 4. Wang, L. (2007) Research on humanized design of medical wayfinding and signage system. Hefei University of Technology, 24-25. y gy 5. Kenya, H. (2006) Design in Design. Shandong People's Publishing House, Jinan. 6. Li, G., Li, W.Y. (2015) Analysis of emotional design in Meitian Hospital’s wayfinding and signage system. Design, 1: 92-93. 7. Li, M. (2015) Research on the design method of urban public environment wayfinding and signage system - Taking Matsushan City, Japan as an example. New arts, 5: 120-124. 8. Li, M. (2014) Research on the design of urban public environment wayfinding and signage system. New arts, 7: 109-110. 9. Li, M., Hu, Y. (2012) Research on the design method of urban wayfinding and signage system. New arts, 5: 68-72. 10. Wu, X.X. (2015) Design and research on passenger flow wayfinding and signage system of medical institutions. Donghua University, 45-47. 5 5
https://openalex.org/W4214579131
https://digital.csic.es/bitstream/10261/273176/1/ijms-23-02549.pdf
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Alternative Brain Slice-on-a-Chip for Organotypic Culture and Effective Fluorescence Injection Testing
International journal of molecular sciences
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    Citation: Herreros, P.; Tapia-González, S.; Sánchez-Olivares, L.; Laguna Heras, M.F.; Holgado, M. Alternative Brain Slice-on-a-Chip for Organotypic Culture and Effective Fluorescence Injection Testing. Int. J. Mol. Sci. 2022, 23, 2549. https://doi.org/10.3390/ ijms23052549 Academic Editors: Bruce Milthorpe, Loredana De Bartolo, Antonella Piscioneri and Seeram Ramakrishna Received: 21 December 2021 Accepted: 23 February 2022 Published: 25 February 2022 Keywords: microfluidics; organ-on-a-chip; brain slice; fluorescence imaging; cell labelling Article Alternative Brain Slice-on-a-Chip for Organotypic Culture and Effective Fluorescence Injection Testing Pedro Herreros 1,2 , Silvia Tapia-González 3,4,5 , Laura Sánchez-Olivares 1, María Fe Laguna Heras 1,2,6 and Miguel Holgado 1,2,6,* 1,2 , Silvia Tapia-González 3,4,5 , Laura Sánchez-Olivares 1, María Fe Laguna Heras 1,2,6 1 2 6 1 Group of Optics, Photonics and Biophotonics (GOFB), Center for Biomedical Technology, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcon, Spain; pedro.herreros@ctb.upm.es (P.H.); laura.sanchezo@estudiante.uam.es (L.S.-O.); mariafe.laguna@upm.es (M.F.L.H.) 1 Group of Optics, Photonics and Biophotonics (GOFB), Center for Biomedical Technology, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcon, Spain; pedro.herreros@ctb.upm.es (P.H.); laura.sanchezo@estudiante.uam.es (L.S.-O.); mariafe.laguna@upm.es (M.F.L.H.) 2 Group of Organ and Tissue on-a-Chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos, 28040 Madrid, Spain 3 Departamento de Neurobiología Funcional y de Sistemas, Instituto Cajal, CSIC, 28002 Madrid, Spain; silvia.tapia@ctb.upm.es 3 Departamento de Neurobiología Funcional y de Sistemas, Instituto Cajal, CSIC, 28002 Madrid, Spain; silvia.tapia@ctb.upm.es 4 Laboratorio Cajal de Circuitos Corticales (CTB), Universidad Politécnica de Madrid, 28223 Madrid, Spain 5 Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, 4 Laboratorio Cajal de Circuitos Corticales (CTB), Universidad Politécnica de Madrid, 28223 Madrid, Spain 5 Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED) ISCIII 4 Laboratorio Cajal de Circuitos Corticales (CTB), Universidad Politécnica de Madrid, 28223 Madrid, Spain 5 Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, 28031 Madrid, Spain 6 6 Department of Applied Physics and Materials Engineering, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, 28006 Madrid, Spain Abstract: Mouse brain slices are one of the most common models to study brain development and functioning, increasing the number of study models that integrate microfluidic systems for hippocam- pal slice cultures. This report presents an alternative brain slice-on-a-chip, integrating an injection system inside the chip to dispense a fluorescent dye for long-term monitoring. Hippocampal slices have been cultured inside these chips, observing fluorescence signals from living cells, maintaining the cytoarchitecture of the slices. Having fluorescence images of biological samples inside the chip demonstrates the effectiveness of the staining process using the injection method avoiding leaks or biological contamination. The technology developed in this study presents a significant improvement in the local administration of reagents within a brain slice-on-a-chip system, which could be a suitable option for organotypic cultures in a microfluidic chip acting as a highly effective bioreactor. International Journal of Molecular Sciences International Journal of Molecular Sciences International Journal of Molecular Sciences International Journal of Molecular Sciences 1. Introduction problems is interface culturing using porous membranes, where the brain slice is placed on a membrane insert in a multiwell plate, thus the tissue can simultaneously be exposed to culture medium and oxygen [12,13]. However, brain slice cultures have been a great challenge so far, mainly due to the metabolic disintegration that the tissue undergoes due to the limited supply of culture medium and oxygen, waste accumulation, and poor control over the culture environment [14]. Because of this, there was a need to develop new culture methods for brain slice studies. In recent years, microfluidics and microfabrication have become powerful tools for tis- sue engineering, allowing the recreation of miniaturized cell microenvironments with high control and precision [15,16]. The combination of both sciences has led to the concept of organ-on-a-chip, a culture model capable of reproducing tissue equivalents or miniaturized- scale organs [17]. Organ-on-a-chip systems have advantages over roll tube and interface culturing systems: the volumes of culture medium required are lower, prevent the ac- cumulation of depleted media, improve handling culture without risk of contamination, and enable higher control over cell environment. Apart from that, most organ-on-a-chip applications are conducted under flow conditions, leading to real-time screening of secreted molecules [18]. All the benefits of microfluidic systems have been applied to brain slice cultures. The use of continuous flow for brain slice cultures has made it possible to consider an alternative method: submerged culturing, in which the tissue is entirely covered by hy- peroxygenated medium [19,20]. This type of culture has better preservation of morphology, but oxygen exchange is less efficient than interface culturing [21,22]. Interphase culturing has been adapted to fluidic systems equally, converging the advantages of the interface culturing systems and microfluidic approaches [23]. Previous works based on fluidic devices for brain slice culture are focused on con- trolling brain slice microenvironment. There are two different approaches to accomplish this: microperfusion systems [24,25] and microfluidic devices, such as bioreactors [23,26]. This ability to regulate the microenvironment makes microfluidic systems handy tools in the study and development of drugs. Therefore, organ-on-a-chips have been developed to culture brain slices specifically for this bio-application [27,28]. These alternatives arise from certain limitations posed by most fluidic platforms. Specific reagents, such as pharma- cological agents or fluorescent dyes, can be dissolved in the reservoir fluid, either by not reaching their optimal concentration or by constantly exposing brain slices to these stimula- tions. 1. Introduction There are brain-on-a-chip devices [29–31] focused on localized drug application for brain-on-a-chip, but the alternatives for this application in brain slice-on-a-chip cultures are minimal [28,32]. For this reason, it is necessary to develop alternative methodologies for local delivery in fluidic chips for brain slice evaluation without depending on a flow. y p p g This scientific report presents a new alternative of brain slice-on-a-chip for organotypic culture, integrating an injection system inside the chip to dispense a fluorescent dye. This indicator is used to analyze the slice’s status by fluorescence imaging. The chip presents two interconnected chambers by a permeable membrane and an air bubble pre-chamber in the injection area. This work demonstrates that the injection methodology works correctly and is reproducible through the fluorescence images obtained from the brain slices cultured on the chips. 1. Introduction Brain slices preparation under in vitro conditions are a powerful approach that allows neuroscientists to have accurate control over experimental conditions and study neural networks, individual cells, processes, and synapses. For neuroscience research, several experimental 2D and 3D models have been used to study the complexity of brain functions. Although a large number of studies analyze networks of neurons cultured in vitro, 2D cultures cannot simulate brain complexity due to the isolation and lack of contact with other cells [1]. An emerging alternative for the recreation of complex interactions is the culture of human pluripotent stem cells for organoid development. However, high costs and cellular complexity prevent these 3D cultures from being postulated as viable study models [2]. Organotypic brain slice cultures have been widely used for their ability to preserve cytoarchitecture under ex vivo conditions [3], having a very relevant role in studies that have allowed us to know more in-depth processes, such as neurogenesis [4,5], synaptic transmission [6,7], protein expression [8], or responses to physical trauma [9]. Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). There are different approaches for organotypic culture of brain slices. A first approach for mouse hippocampal culture is creating a roll tube culturing system, where the tissue is periodically exposed to air and culture medium [10,11]. A second approach to avoid these https://www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2022, 23, 2549. https://doi.org/10.3390/ijms23052549 Int. J. Mol. Sci. 2022, 23, 2549 2 of 13 problems is interface culturing using porous membranes, where the brain slice is placed on a membrane insert in a multiwell plate, thus the tissue can simultaneously be exposed to culture medium and oxygen [12,13]. However, brain slice cultures have been a great challenge so far, mainly due to the metabolic disintegration that the tissue undergoes due to the limited supply of culture medium and oxygen, waste accumulation, and poor control over the culture environment [14]. Because of this, there was a need to develop new culture methods for brain slice studies. 2.1. Chip Development and Injection System Implementation (B) Picture of the final chip version employed for hippocampal slices culture. At the preliminary design stage, it was defined that OGB solution must be injected through the lower chamber. There were several reasons to make that decision: it allows a pre-chamber to inject solutions and act as a bubble-trap, maintain the PC membrane’s integrity, and after injection, OGB solution would be mixed with the perfused culture me- dium. Due to this, the flow could remove the fluorescence solution overload and decrease the background signal. I iti l t t f d b di tl t i th PDMS bl k i G25 At the preliminary design stage, it was defined that OGB solution must be injected through the lower chamber. There were several reasons to make that decision: it allows a pre-chamber to inject solutions and act as a bubble-trap, maintain the PC membrane’s integrity, and after injection, OGB solution would be mixed with the perfused culture medium. Due to this, the flow could remove the fluorescence solution overload and decrease the background signal. Initial tests were performed by directly puncturing the upper PDMS block using G25 gauge needles, observing two events: the microfluidic chamber’s cross-contamination and leaks through the PDMS layer. It was also noteworthy that the injection of microvolumes (50 µL) tended to produce bubbles within the fluidic chamber, negatively impacting the laminar flow and microscope observation. Af h i bl h fi l hi i l d d PTFE l i d i Initial tests were performed by directly puncturing the upper PDMS block using G25 gauge needles, observing two events: the microfluidic chamber’s cross-contamination and leaks through the PDMS layer. It was also noteworthy that the injection of microvolumes (50 µL) tended to produce bubbles within the fluidic chamber, negatively impacting the laminar flow and microscope observation. After these persistent problems, the final chip included a PTFE plug integrated into the PDMS block and pre-chamber in the lower microfluidic channel (Figure 2). The pre- chamber acted as a bubble trap for air bubbles both present in the flow and those gener- ated by injection. The PTFE plug was capable of self-sealing after being perforated by a needle, preserving the parallel flow inside the microfluidic chamber. During the develop- ment stage, the chips were punctured up to five perforations through the PTFE plug, showing no leaks or cross-contamination in any of the chips. 2.1. Chip Development and Injection System Implementation The developed engineered chip had two differentiated microfluidic chambers: a lower chamber with flow inlet and outlet, a constant renewal of the culture medium, and an upper chamber that was not subjected to flow (Figure 1). A permeable polycarbonate (PC) membrane delimits both compartments. This chip was subjected to a flow range between 0.1 and 250 µL/min without presenting leaks, keeping the upper chamber airtight, without the perfused flow filling the chamber volume. Additionally, the lower layout featured a pre- chamber to allow reagent injection to avoid bubbles in the chambers. In order to preserve the tightness of the chip, the injection was performed through a polytetrafluoroethylene Int. J. Mol. Sci. 2022, 23, 2549 3 of 13 order fl (PTFE) plug, avoiding potential leaks. The reagent administered through the injection system was a 50 µL of Oregon Green Bapta (OGB) solution (20 µM). injection system was a 50 µL of Oregon Green Bapta (OGB) solution (20 µM). (PTFE) plug, avoiding potential leaks. The reagent administered through the injection system was a 50 µL of Oregon Green Bapta (OGB) solution (20 µM). injection system was a 50 µL of Oregon Green Bapta (OGB) solution (20 µM). system was a 50 µL of Oregon Green Bapta (OGB) solution (20 µM). Figure 1. (A) 3D exploded view representation of the brain slice-on-a-chip, showing the microfluidic chamber the four layers that shape the chip: 1—polydimethylsiloxane (PDMS) block with two holes for inserting the tubing of the fluidic system, and with an integrated PTFE plug to allow needle puncture of the chip and maintain the chip’s tightness; 2—upper vinyl layer with polycarbonate membrane adhered to the underside; 3—lower vinyl layer through which the flow is perfused. Two compartments form this layout: a prechamber where the reagents are injected, acting as an air bub- ble trap, and the chamber which interacts with the tissue; 4—75 × 25 mm glass substrate. 2 and 3 present four holes in the corners for a correct overlapping between the vinyl sheets. (B) Picture of the final chip version employed for hippocampal slices culture. Figure 1. 2.1. Chip Development and Injection System Implementation (A) 3D exploded view representation of the brain slice-on-a-chip, showing the microfluidic chamber the four layers that shape the chip: 1—polydimethylsiloxane (PDMS) block with two holes for inserting the tubing of the fluidic system, and with an integrated PTFE plug to allow needle puncture of the chip and maintain the chip’s tightness; 2—upper vinyl layer with polycarbonate membrane adhered to the underside; 3—lower vinyl layer through which the flow is perfused. Two compartments form this layout: a prechamber where the reagents are injected, acting as an air bubble trap, and the chamber which interacts with the tissue; 4—75 × 25 mm glass substrate. 2 and 3 present four holes in the corners for a correct overlapping between the vinyl sheets. (B) Picture of the final chip version employed for hippocampal slices culture. Figure 1. (A) 3D exploded view representation of the brain slice-on-a-chip, showing the microfluidic chamber the four layers that shape the chip: 1—polydimethylsiloxane (PDMS) block with two holes for inserting the tubing of the fluidic system, and with an integrated PTFE plug to allow needle puncture of the chip and maintain the chip’s tightness; 2—upper vinyl layer with polycarbonate membrane adhered to the underside; 3—lower vinyl layer through which the flow is perfused. Two compartments form this layout: a prechamber where the reagents are injected, acting as an air bub- ble trap, and the chamber which interacts with the tissue; 4—75 × 25 mm glass substrate. 2 and 3 present four holes in the corners for a correct overlapping between the vinyl sheets. (B) Picture of the final chip version employed for hippocampal slices culture. Figure 1. (A) 3D exploded view representation of the brain slice-on-a-chip, showing the microfluidic chamber the four layers that shape the chip: 1—polydimethylsiloxane (PDMS) block with two holes for inserting the tubing of the fluidic system, and with an integrated PTFE plug to allow needle puncture of the chip and maintain the chip’s tightness; 2—upper vinyl layer with polycarbonate membrane adhered to the underside; 3—lower vinyl layer through which the flow is perfused. Two compartments form this layout: a prechamber where the reagents are injected, acting as an air bubble trap, and the chamber which interacts with the tissue; 4—75 × 25 mm glass substrate. 2 and 3 present four holes in the corners for a correct overlapping between the vinyl sheets. 2.2. Labeling of OGB in Hippoca 2.2. Labeling of OGB in Hippocampal Sections g f pp p In order to check the efficiency of the brain slice-on-a-chip device an method by injection system, four chips were manufactured to host two hippo per chip. An OGB labeling was performed to analyze possible effects along t ity and integrity of mouse hippocampal tissue inside the chip In order to check the efficiency of the brain slice-on-a-chip device and a staining method by injection system, four chips were manufactured to host two hippocampal slices per chip. An OGB labeling was performed to analyze possible effects along time in viability and integrity of mouse hippocampal tissue inside the chip. ity and integrity of mouse hippocampal tissue inside the chip. As shown in Figure 3, OGB fluorescent dye penetrated the tissue, demo membrane’s permeability and effectiveness of the injection system g y As shown in Figure 3, OGB fluorescent dye penetrated the tissue, demonstrating the membrane’s permeability and effectiveness of the injection system. membrane s permeability and effectiveness of the injection system. The viability of the hippocampal sections was observed each day for 10 (DIV) in chips and organotypic hippocampal slice culture (OHSC). Since s visualized using staining techniques are typically found from measuremen ment, even using sections from the same hippocampi, subtle changes are diff pret, as previously discussed in several works [33,34]. Thus, the objective of t to identify differences between large, obvious differences along time. There tern of fluorescence labeling of OGB was qualitatively analyzed as well as th the ti ue i the hi a d OHSC a o t ol (Fi u e 3 5) The viability of the hippocampal sections was observed each day for 10 days in vitro (DIV) in chips and organotypic hippocampal slice culture (OHSC). Since small changes vi- sualized using staining techniques are typically found from measurement to measurement, even using sections from the same hippocampi, subtle changes are difficult to interpret, as previously discussed in several works [33,34]. Thus, the objective of this work was to identify differences between large, obvious differences along time. Therefore, the pattern of fluorescence labeling of OGB was qualitatively analyzed as well as the integrity of the tissue in the chip and OHSC as control (Figures 3–5). the tissue in the chip and OHSC as control (Figures 3–5). 2.1. Chip Development and Injection System Implementation After these persistent problems, the final chip included a PTFE plug integrated into the PDMS block and pre-chamber in the lower microfluidic channel (Figure 2). The pre- chamber acted as a bubble trap for air bubbles both present in the flow and those generated by injection. The PTFE plug was capable of self-sealing after being perforated by a needle, preserving the parallel flow inside the microfluidic chamber. During the development stage, the chips were punctured up to five perforations through the PTFE plug, showing no leaks or cross-contamination in any of the chips. Int. J. Mol. Sci. 2022, 23, 2549 4 of 13 Figure 2. (A) Schematic diagram flow of the brain slice-on-a-chip. Hippocampal b over the PC membrane, whereas the culture medium and the OGB solution are perf lower compartment. (B) A real injection test replicates Figure 2A. Green fluid is p lower chamber, and the red fluid is injected through the PTFE plug in the pre-chamb Figure 2. (A) Schematic diagram flow of the brain slice-on-a-chip. Hippocampal brain-slices rest over the PC membrane, whereas the culture medium and the OGB solution are perfused across the lower compartment. (B) A real injection test replicates Figure 2A. Green fluid is perfused in the lower chamber, and the red fluid is injected through the PTFE plug in the pre-chamber. Figure 2. (A) Schematic diagram flow of the brain slice-on-a-chip. Hippocampal b over the PC membrane, whereas the culture medium and the OGB solution are perf lower compartment. (B) A real injection test replicates Figure 2A. Green fluid is p lower chamber, and the red fluid is injected through the PTFE plug in the pre-chamb Figure 2. (A) Schematic diagram flow of the brain slice-on-a-chip. Hippocampal brain-slices rest over the PC membrane, whereas the culture medium and the OGB solution are perfused across the lower compartment. (B) A real injection test replicates Figure 2A. Green fluid is perfused in the lower chamber, and the red fluid is injected through the PTFE plug in the pre-chamber. 2.2. Labeling of OGB in Hippoca 2.2. Labeling of OGB in Hippocampal Sections Septal sections of P7 mice hippocampal formation into brain slice-on-a-chi photographs from slices placed into Chip 1 (A,D,G,J,M), Chip 2 (B,E,H,K,N), and Chi at 1, 5, and 10 DIV. (A–F,J–L) showed a progressive change in transparency of the tiss age in section thickness from 1 DIV (A,B,C) to 5 DIV (D,E,F), that was more evident at (G–I,M–O), low-magnification photomicrographs demonstrated similar distribution of OGB marker in the hippocampus section at 5 DIV (G–I) and 10 DIV (M–O) in all c marker showed two types of labeling (see also Figure 4) in chip sections along tim shaped labeling (early-medium phase) (G,I), and a sharp decrease labeling with part of OGB labeled cells (late phase) (M–O) in some zones of the hippocampal subfie sented a better preservation of the hippocampal cytoarchitecture at 5 DIV compared to that in (N) there was a dramatic reduction of DG size. Solid-arrows display outgrowt Figure 3. Septal sections of P7 mice hippocampal formation into brain slice-on-a-chip. Low- power photographs from slices placed into Chip 1 (A,D,G,J,M), Chip 2 (B,E,H,K,N), and Chip 3 (C,F,I,L,O) at 1, 5, and 10 DIV. (A–F,J–L) showed a progressive change in transparency of the tissue and shrinkage in section thickness from 1 DIV (A–C) to 5 DIV (D–F), that was more evident at 10 DIV (J–L). (G–I,M–O), low-magnification photomicrographs demonstrated similar distribution and intensity of OGB marker in the hippocampus section at 5 DIV (G–I) and 10 DIV (M–O) in all chips. The OGB marker showed two types of labeling (see also Figure 4) in chip sections along time: a dense dot-shaped labeling (early-medium phase) (G,I), and a sharp decrease labeling with partial or total lack of OGB labeled cells (late phase) (M–O) in some zones of the hippocampal subfields. (D–I) presented a better preservation of the hippocampal cytoarchitecture at 5 DIV compared to Figure 3. Septal sections of P7 mice hippocampal formation into brain slice-on-a-chi photographs from slices placed into Chip 1 (A,D,G,J,M), Chip 2 (B,E,H,K,N), and Chi at 1, 5, and 10 DIV. 2.2. Labeling of OGB in Hippoca 2.2. Labeling of OGB in Hippocampal Sections OGB labeled all living cells virtually, which allowed the cytoarchitecton the different hippocampal subregions: cornu Ammonis subfield (CA); denta and hilus (h), and the limits between them to be distinguished, according tions of the atlas of the dorsal mouse hippocampus from Bregma −1.46 to −2 3G I M O d 4) OGB labeled all living cells virtually, which allowed the cytoarchitectonic features of the different hippocampal subregions: cornu Ammonis subfield (CA); dentate gyrus (DG) and hilus (h), and the limits between them to be distinguished, according to the indications of the atlas of the dorsal mouse hippocampus from Bregma −1.46 to −2.30 [35] (Figures 3G–I,M–O and 4). ures 3G–I,M–O and 4). Although no quantitative evaluation of living cells number or intensi cence labeling was performed, differences were found in the pattern of OGB pocampi sections between 5 DIV and 10 DIV. In general, OGB marker show of staining along time: In 1–5 DIV “early-medium phase”, a dense dot-shape which individual cells were distinguished and scattered through whole hipp mation was observed. In 5–10 DIV “late phase”, a worse defined labeling, w total lack of labeled cells in some zones of hippocampal subregions, and an in slice’s background was shown. As shown in Figures 3G–I,M–O, and 4, the gressive decrease in the labeling and a change in the distribution pattern marker mainly in the cornu Ammonis, dentate gyrus, and hilus from 5 DIV, t Although no quantitative evaluation of living cells number or intensity of fluorescence labeling was performed, differences were found in the pattern of OGB in chip hippocampi sections between 5 DIV and 10 DIV. In general, OGB marker showed two types of staining along time: In 1–5 DIV “early-medium phase”, a dense dot-shaped labeling, in which individual cells were distinguished and scattered through whole hippocampal formation was observed. In 5–10 DIV “late phase”, a worse defined labeling, with partial or total lack of labeled cells in some zones of hippocampal subregions, and an increase of the slice’s background was shown. As shown in Figures 3G–I,M–O and 4, there was a progressive decrease in the labeling and a change in the distribution pattern of the OGB marker mainly in the cornu Ammonis, dentate gyrus, and hilus from 5 DIV, that was more dramatically pronounced at 10 DIV (Figures 3G–I,M–O and 4). Int. J. Mol. Sci. 2022, 23, 2549 Int. J. Mol. S 5 of 13 Figure 3. 2.2. Labeling of OGB in Hippoca 2.2. Labeling of OGB in Hippocampal Sections Scale bar shown in O indicates 500 µm in (A–F,J–L) and 400 µm in (G–I,M–O). Figure 4. Photomicrographs of hippocampal slices from Chips 1, 2, and 3 illustrating in greater de- tail the different patterns of OGB marker in CA, DG, and h, at 5 DIV (A–C) and 10 DIV (D–F). Note the evident changes in the OGB labeling distribution between 5 and 10 DIV. A dense dot-shaped labeling, corresponding living cells (open arrows) was scattered through whole hippocampal for- mation, at 5 DIV (medium phase) (A–C). By contrast, at 10 DIV there was a sharp decrease labeling with partial or total lack of OGB labeled cells (white solid arrows) in some zones of CA, DG, and h (late phase) (D–F). CA, cornu Ammonis subfield; DG, dentate gyrus; DIV, days in vitro; h, hilus. Scale bar shown in F indicates 270 µm in (A–F). Figure 4. Photomicrographs of hippocampal slices from Chips 1, 2, and 3 illustrating in greater detail the different patterns of OGB marker in CA, DG, and h, at 5 DIV (A–C) and 10 DIV (D–F). Note the evident changes in the OGB labeling distribution between 5 and 10 DIV. A dense dot-shaped labeling, corresponding living cells (open arrows) was scattered through whole hippocampal formation, at 5 DIV (medium phase) (A–C). By contrast, at 10 DIV there was a sharp decrease labeling with partial or total lack of OGB labeled cells (white solid arrows) in some zones of CA, DG, and h (late phase) (D–F). CA, cornu Ammonis subfield; DG, dentate gyrus; DIV, days in vitro; h, hilus. Scale bar shown in F indicates 270 µm in (A–F). Figure 4. Photomicrographs of hippocampal slices from Chips 1, 2, and 3 illustrating in greater de- tail the different patterns of OGB marker in CA, DG, and h, at 5 DIV (A–C) and 10 DIV (D–F). Note the evident changes in the OGB labeling distribution between 5 and 10 DIV. A dense dot-shaped labeling, corresponding living cells (open arrows) was scattered through whole hippocampal for- mation, at 5 DIV (medium phase) (A–C). By contrast, at 10 DIV there was a sharp decrease labeling with partial or total lack of OGB labeled cells (white solid arrows) in some zones of CA, DG, and h (late phase) (D–F). CA, cornu Ammonis subfield; DG, dentate gyrus; DIV, days in vitro; h, hilus. Scale bar shown in F indicates 270 µm in (A–F). 2.2. Labeling of OGB in Hippoca 2.2. Labeling of OGB in Hippocampal Sections Figure 4. Photomicrographs of hippocampal slices from Chips 1, 2, and 3 illustrating in greater detail the different patterns of OGB marker in CA, DG, and h, at 5 DIV (A–C) and 10 DIV (D–F). Note the evident changes in the OGB labeling distribution between 5 and 10 DIV. A dense dot-shaped labeling, corresponding living cells (open arrows) was scattered through whole hippocampal formation, at 5 DIV (medium phase) (A–C). By contrast, at 10 DIV there was a sharp decrease labeling with partial or total lack of OGB labeled cells (white solid arrows) in some zones of CA, DG, and h (late phase) (D–F). CA, cornu Ammonis subfield; DG, dentate gyrus; DIV, days in vitro; h, hilus. Scale bar shown in F indicates 270 µm in (A–F). Besides, a slight and progressive shrinkage, especially section thickness, was detect- able at 5 DIV (Figure 3D–F) compared to 1 DIV (Figure 3A–C), which was stronger at 10 DIV (Figure 3J–O). Besides, a slight and progressive shrinkage, especially section thickness, was detectable at 5 DIV (Figure 3D–F) compared to 1 DIV (Figure 3A–C), which was stronger at 10 DIV (Figure 3J–O). Besides, a slight and progressive shrinkage, especially section thickness, was detect- able at 5 DIV (Figure 3D–F) compared to 1 DIV (Figure 3A–C), which was stronger at 10 DIV (Figure 3J–O). Besides, a slight and progressive shrinkage, especially section thickness, was detectable at 5 DIV (Figure 3D–F) compared to 1 DIV (Figure 3A–C), which was stronger at 10 DIV (Figure 3J–O). Two important criteria for evaluating whether the slices are well-cultured are a change in transparency and cellular spread [1]. As shown the Figure 3, the slices under- went a general change in color and transparency from brownish-opaque at 1 DIV to light brownish-transparent during the first week and outgrowth of cells from the edge chip Two important criteria for evaluating whether the slices are well-cultured are a change in transparency and cellular spread [1]. As shown the Figure 3, the slices underwent a general change in color and transparency from brownish-opaque at 1 DIV to light brownish- transparent during the first week and outgrowth of cells from the edge chip section. section. No changes in the general pattern of distribution of OGB labeling throughout the hippocampal subregions up to 10 DIV were observed in the OHSC compared to the chip (Figure 5). 2.2. Labeling of OGB in Hippoca 2.2. Labeling of OGB in Hippocampal Sections (A–F,J–L) showed a progressive change in transparency of the tissu age in section thickness from 1 DIV (A,B,C) to 5 DIV (D,E,F), that was more evident at (G–I,M–O), low-magnification photomicrographs demonstrated similar distribution of OGB marker in the hippocampus section at 5 DIV (G–I) and 10 DIV (M–O) in all ch marker showed two types of labeling (see also Figure 4) in chip sections along time shaped labeling (early-medium phase) (G,I), and a sharp decrease labeling with parti of OGB labeled cells (late phase) (M–O) in some zones of the hippocampal subfiel sented a better preservation of the hippocampal cytoarchitecture at 5 DIV compared to that in (N) there was a dramatic reduction of DG size. Solid-arrows display outgrowt Figure 3. Septal sections of P7 mice hippocampal formation into brain slice-on-a-chip. Low- power photographs from slices placed into Chip 1 (A,D,G,J,M), Chip 2 (B,E,H,K,N), and Chip 3 (C,F,I,L,O) at 1, 5, and 10 DIV. (A–F,J–L) showed a progressive change in transparency of the tissue and shrinkage in section thickness from 1 DIV (A–C) to 5 DIV (D–F), that was more evident at 10 DIV (J–L). (G–I,M–O), low-magnification photomicrographs demonstrated similar distribution and intensity of OGB marker in the hippocampus section at 5 DIV (G–I) and 10 DIV (M–O) in all chips. The OGB marker showed two types of labeling (see also Figure 4) in chip sections along time: a dense dot-shaped labeling (early-medium phase) (G,I), and a sharp decrease labeling with partial or total lack of OGB labeled cells (late phase) (M–O) in some zones of the hippocampal subfields. (D–I) presented a better preservation of the hippocampal cytoarchitecture at 5 DIV compared to Int. J. Mol. Sci. 2022, 23, 2549 Int. J. Mol. Sci. 2022, 23, x FOR P 6 of 13 of 13 10 DIV. Note, that in (N) there was a dramatic reduction of DG size. Solid-arrows display outgrowth of cells from the edge chip section (D,G). The area indicated by a rectangle in (G–I,M–O) was shown at a higher magnification in Figure 3. CA, cornu Ammonis subfield; DG, dentate gyrus; DIV, days in vitro; h, hilus. Scale bar shown in O indicates 500 µm in (A–F,J–L) and 400 µm in (G–I,M–O). the edge chip section (D,G). The area indicated by a rectangle in (G–I,M–O) was shown at a higher magnification in Figure 3. CA, cornu Ammonis subfield; DG, dentate gyrus; DIV, days in vitro; h, hilus. 2.2. Labeling of OGB in Hippoca 2.2. Labeling of OGB in Hippocampal Sections Furthermore, as shown in Figure 5, the progressive shrinkage of section thick- ness displayed was smaller than the chip slices (Figure 3). The hippocampal sections were fully attached to the PC membrane at 7 DIV whereas this happens from 14 DIV in the insert membrane, as previously mentioned by other authors [1,36]. However, a better preservation of the typical hippocampal cytoarchitecture in the chip was observed com- No changes in the general pattern of distribution of OGB labeling throughout the hippocampal subregions up to 10 DIV were observed in the OHSC compared to the chip (Figure 5). Furthermore, as shown in Figure 5, the progressive shrinkage of section thickness displayed was smaller than the chip slices (Figure 3). The hippocampal sections were fully attached to the PC membrane at 7 DIV whereas this happens from 14 DIV in the insert membrane, as previously mentioned by other authors [1,36]. However, a better preservation of the typical hippocampal cytoarchitecture in the chip was observed compared to OHSC at 5 DIV (Figures 3D–I and 5). Int. J. Mol. Sci. 2022, 23, 2549 nt. J. Mol. Sci. 2022, 23, x FOR P 7 of 13 of 13 Figure 5. A representative septal section of P7 mice hippocampal formation in OHSC. Low-power photographs from a slice placed onto cell culture insert at 1 (A), 5 (B,D), and 10 DIV (C,E). (A–C) displayed a progressive shrinkage of section thickness (black solid arrows) from 1 DIV (A) to 10 DIV (C) lower than chip slices (B) (see also Figure 3). (D,E) showed the same general pattern of distribu- tion of OGB labeling throughout the hippocampal subregions up to 10 DIV observed in the organ- on-a-chip. Note the changes in the OGB labeling distribution between 5 and 10 DIV. At 5 DIV (me- dium phase) a dense dot-shaped labeling was observed through whole hippocampal formation (open arrows) (D). By contrast, at 10 DIV there was a sharp decrease labeling with partial or total lack of OGB labeled cells (solid arrows) in some zones of hippocampal formation (late phase) (D– E). CA, cornu Ammonis subfield; DG, dentate gyrus; DIV, days in vitro; h, hilus. Scale bar shown in E indicates 510 µm in (A–C) and 480 µm in (D,E). 3 Di i Figure 5. A representative septal section of P7 mice hippocampal formation in OHSC. 2.2. Labeling of OGB in Hippoca 2.2. Labeling of OGB in Hippocampal Sections Low-power photographs from a slice placed onto cell culture insert at 1 (A), 5 (B,D), and 10 DIV (C,E). (A–C) dis played a progressive shrinkage of section thickness (black solid arrows) from 1 DIV (A) to 10 DIV (C) lower than chip slices (B) (see also Figure 3). (D,E) showed the same general pattern of dis tribution of OGB labeling throughout the hippocampal subregions up to 10 DIV observed in the organ-on-a-chip. Note the changes in the OGB labeling distribution between 5 and 10 DIV. At 5 DIV (medium phase) a dense dot-shaped labeling was observed through whole hippocampal formation (open arrows) (D). By contrast, at 10 DIV there was a sharp decrease labeling with partial or total lack of OGB labeled cells (solid arrows) in some zones of hippocampal formation (late phase) (D–E) CA, cornu Ammonis subfield; DG, dentate gyrus; DIV, days in vitro; h, hilus. Scale bar shown in E indicates 510 µm in (A–C) and 480 µm in (D,E). igure 5. A representative septal section of P7 mice hippocampal formation in OHSC. Low-power hotographs from a slice placed onto cell culture insert at 1 (A), 5 (B,D), and 10 DIV (C,E). (A–C) isplayed a progressive shrinkage of section thickness (black solid arrows) from 1 DIV (A) to 10 DIV C) lower than chip slices (B) (see also Figure 3). (D,E) showed the same general pattern of distribu- ion of OGB labeling throughout the hippocampal subregions up to 10 DIV observed in the organ- n-a-chip. Note the changes in the OGB labeling distribution between 5 and 10 DIV. At 5 DIV (me- ium phase) a dense dot-shaped labeling was observed through whole hippocampal formation open arrows) (D). By contrast, at 10 DIV there was a sharp decrease labeling with partial or total ack of OGB labeled cells (solid arrows) in some zones of hippocampal formation (late phase) (D– ). CA, cornu Ammonis subfield; DG, dentate gyrus; DIV, days in vitro; h, hilus. Scale bar shown n E indicates 510 µm in (A–C) and 480 µm in (D,E). Figure 5. A representative septal section of P7 mice hippocampal formation in OHSC. Low-power photographs from a slice placed onto cell culture insert at 1 (A), 5 (B,D), and 10 DIV (C,E). (A–C) dis- played a progressive shrinkage of section thickness (black solid arrows) from 1 DIV (A) to 10 DIV (C) lower than chip slices (B) (see also Figure 3). 2.2. Labeling of OGB in Hippoca 2.2. Labeling of OGB in Hippocampal Sections (D,E) showed the same general pattern of dis- tribution of OGB labeling throughout the hippocampal subregions up to 10 DIV observed in the organ-on-a-chip. Note the changes in the OGB labeling distribution between 5 and 10 DIV. At 5 DIV (medium phase) a dense dot-shaped labeling was observed through whole hippocampal formation (open arrows) (D). By contrast, at 10 DIV there was a sharp decrease labeling with partial or total lack of OGB labeled cells (solid arrows) in some zones of hippocampal formation (late phase) (D–E). CA, cornu Ammonis subfield; DG, dentate gyrus; DIV, days in vitro; h, hilus. Scale bar shown in E indicates 510 µm in (A–C) and 480 µm in (D,E). . Discussion The distinct 3. Discussion In the first instance, any potential reactive must be loaded into the inlet reservoir at its optimal concentration. Depending on the reservoir volume, the required amount to reach its optimal dose could significantly increase the study costs. A second drawback would be the exposure time of the stimuli; the biological sample would be subject to overexposure to any reagent found in the input reservoir until it is depleted or changed. Such overexposure could interact harmfully with the culture. Both hindrances are even more critical if the study requires frequent reagent dispensing and could induce a slowdown in the transition to microfluidic models. A new reagent injection system was implemented in this brain slice-on-a-chip to overcome the gap between microfluidic and traditional methods, such as roll tube culturing or membrane inserts methods. This methodology allows the local administration into the microfluidic chamber of the chip, interacting instantaneously with the culture avoiding extra microfluidic components to optimize the process. After chip fabrication, it was necessary to test two conditions. On the one hand, if the chip remains watertight, without causing biological contamination and alterations in the internal pressure of the chip after several injections, and on the other hand, if the administered reagent interacts with the sample on the membrane. The fluorescent marker OGB was dispensed through the injection system in every chip to verify those statements. The results obtained have demonstrated the methodology’s effectiveness for injecting reagents and the system’s reproducibility. There were no leaks in any of the chips tested through the perforated PTFE plug, and all hippocampi slices were efficiently labeled by fluorescent staining. This second fact confirmed the interaction between the flow of the lower microfluidic chamber and the brain slices through the PC membrane. Microscope imaging outcomes further highlight better preservation of the typical hippocampal cytoarchitecture in the chip at 5 DIV observed in the present study. This is in line with results obtained by Bakmand T. et al. [23] showing that a fluidic system maintained the characteristic cytoarchitecture seen in hippocampal slices far better than the tissue slices cultured by standard method of organotypic culture. Moreover, the huge presence of OGB living cells [37,38] combined with a change in color to light brownish- transparent of chip sections and outgrowth of cells from the edge chips slices during the first week [1], represent important criteria that show good viability of hippocampal slices inside brain slice-on-a-chips. . Discussion The distinct 3. Discussion The distinctive feature of an organ-on-a-chip system is the generation of a closed con- tinuous system, where any external reagent must be supplemented through the microflu- dic set-up. The advantages compared to roll tube culturing and membrane insert cultures are clear: accurate control over the flow and microenvironment, avoiding cross-contami- nation, and collecting the culture’s metabolic products. Hippocampal slices are fragile samples susceptible to damage in their cytoarchitec The distinctive feature of an organ-on-a-chip system is the generation of a closed con- tinuous system, where any external reagent must be supplemented through the microfluidic set-up. The advantages compared to roll tube culturing and membrane insert cultures are clear: accurate control over the flow and microenvironment, avoiding cross-contamination, and collecting the culture’s metabolic products. Hippocampal slices are fragile samples susceptible to damage in their cytoarchitec- ure; disturbances in their maintenance conditions must be avoided in order not to cause mechanical damage to the sample. Due to this, brain slice on-a-chip devices must preserve heir hermetic and tightness status to achieve an optimal flow and sterility conditions. These requirements present a disadvantage compared to standard cell culture methodol- ogy; traditional multiwell plates have better accessibility to the sample by removing their Hippocampal slices are fragile samples susceptible to damage in their cytoarchitecture; disturbances in their maintenance conditions must be avoided in order not to cause mechan- ical damage to the sample. Due to this, brain slice on-a-chip devices must preserve their hermetic and tightness status to achieve an optimal flow and sterility conditions. These requirements present a disadvantage compared to standard cell culture methodology; traditional multiwell plates have better accessibility to the sample by removing their lids. It Int. J. Mol. Sci. 2022, 23, 2549 8 of 13 8 of 13 is possible to administrate reagents, the most common one being fresh culture medium, but there are more attractive alternatives, such as drugs to analyze the behavior of the sample or fluorescence dyes. is possible to administrate reagents, the most common one being fresh culture medium, but there are more attractive alternatives, such as drugs to analyze the behavior of the sample or fluorescence dyes. y Most current microfluidic systems suitable for mouse hippocampal cultures do not have such accessibility for local tissue interaction because only a single flow is used to preserve the tissue. This limitation generates a series of drawbacks. 4 2 B i Sli Chi F b i ti 4.2. Brain Slice-on-a-Chip Fabrication 4 2 B i Sli Chi F b i ti 4.2. Brain Slice-on-a-Chip Fabrication 4.2. Brain Slice-on-a-Chip Fabrication The materials used in this article and their assembly process are based on a previous work [41], where an organ-on-a-chip composed of glass, vinyl, and PDMS was presented. In this article, these three materials were preserved, and two more components were added—a polycarbonate membrane and a circular PTFE plug (Merck KGaA, Darmstadt, Germany). The dimension of the glass substrate remained at 75 mm × 25 mm, and the vinyl layer was redesigned up to 70 × 25 mm. This area expansion allowed for the intro- duction of a pre-chamber and a larger main fluidic chamber. Two different vinyl layouts were used for the upper and lower chambers. The lower one was 600 µm wide, and the upper one was 750 µm wide. These chambers were delimited by a polycarbonate mem- brane (0.4 µm pores, 10 µm wide, Merck KGaA, Darmstadt, Germany). PDMS blocks were made using SYLGARD 184 in a 10:1.5 ratio (elastomer: curing agent) in a mold with the exact dimensions as the vinyl sheets. During the curing process, the PTFE plug was placed in the mold, and subsequently, the elastomer/curing agent mixture was poured into the The materials used in this article and their assembly process are based on a previous work [41], where an organ-on-a-chip composed of glass, vinyl, and PDMS was presented. In this article, these three materials were preserved, and two more components were added—a polycarbonate membrane and a circular PTFE plug (Merck KGaA, Darmstadt, Germany). The dimension of the glass substrate remained at 75 mm × 25 mm, and the vinyl layer was redesigned up to 70 × 25 mm. This area expansion allowed for the introduction of a pre-chamber and a larger main fluidic chamber. Two different vinyl layouts were used for the upper and lower chambers. The lower one was 600 µm wide, and the upper one was 750 µm wide. These chambers were delimited by a polycarbonate membrane (0.4 µm pores, 10 µm wide, Merck KGaA, Darmstadt, Germany). PDMS blocks were made using SYLGARD 184 in a 10:1.5 ratio (elastomer: curing agent) in a mold with the exact dimensions as the vinyl sheets. During the curing process, the PTFE plug was placed in the mold, and subsequently, the elastomer/curing agent mixture was poured into the mold. . Discussion The distinct 3. Discussion p The OGB marker enables real-time imaging evaluation of culture viability due to its permeable nature. Nevertheless, additional analysis would provide a more accurate evaluation of the slices. Permanent fluorescence markers can be applied to effectively demonstrate live/dead staining at the finalization of the culture period. In addition, chip material composition allows the extraction of the cultured slices by cutting the PDMS top block and the PC membrane. This feature permits staining protocols where the slice must be fixed as immunostaining, a standard practice for brain slice imaging [39,40]. For future studies, combining OGB real-time analysis and selective labeling of brain cell types by immunostaining as well as live/dead staining would allow a deeper evaluation of brain slice status. The results obtained from this study prove the effectiveness of this chip for the main- tenance of fragile organotypic and allow a local interaction with a fast and straightforward methodology without needing extra components making this chip easy to use. Int. J. Mol. Sci. 2022, 23, 2549 9 of 13 4.1. Design of the Brain Slice-on-a-Chip Device The device was a monolithic chip com 4.1. Design of the Brain Slice-on-a-Chip Device The device was a monolithic chip com The device was a monolithic chip composed of two interconnected microfluidic cham- bers delimited by a polycarbonate (PC) membrane (Figure 1). The upper chamber did not present any inlet or outlet connection, and it had a rectangular area exclusively to host the biological sample. The lower chamber presented two different compartments, a pre-chamber where the fluorescent dye was injected and acted as an air bubble trap, and the microfluidic chamber itself, which was in contact with the upper chamber through the PC membrane. The device included a PTFE plug above the pre-chamber to allow the injection of OGB dye inside the chip using a syringe and real-time microscopic monitoring (Figure 6). chambers delimited by a polycarbonate (PC) membrane (Figure 1). The upper chamber did not present any inlet or outlet connection, and it had a rectangular area exclusively to host the biological sample. The lower chamber presented two different compartments, a pre-chamber where the fluorescent dye was injected and acted as an air bubble trap, and the microfluidic chamber itself, which was in contact with the upper chamber through the PC membrane. The device included a PTFE plug above the pre-chamber to allow the in- jection of OGB dye inside the chip using a syringe and real-time microscopic monitoring (Figure 6). Figure 6. Flowchart showing the main procedures conducted for the brain slice culture and micro- scope monitoring. Figure 6. Flowchart showing the main procedures conducted for the brain slice culture and micro- scope monitoring. Figure 6. Flowchart showing the main procedures conducted for the brain slice culture and micro- scope monitoring. Figure 6. Flowchart showing the main procedures conducted for the brain slice culture and micro- scope monitoring. 4.6. Organotypic Hippocampal Slice Culture In order to test the effectiveness of the chip, a conventional method of organotypic hippocampal slice culture (OHSC) was used as control for each chip. Briefly, hippocampal sections (400 µm) described above were transferred onto cell culture inserts in P24 multiwell plates and cultivated for 10 days with the same nutrition medium used for the chip and kept in an incubator (37 ◦C, 5% CO2). The depleted medium was changed every third day due to the lack of a continuous flow supply. 4 2 B i Sli Chi F b i ti 4.2. Brain Slice-on-a-Chip Fabrication After the curing process, the plug remained embedded inside the PDMS block, creating a high adhesion between both polymeric materials. Two holes were drilled in the block with a 2 mm puncher to accommodate the microfluidic connections. On the top of the chip, a PDMS block was positioned to seal the device. In order to achieve strong bonding between Int. J. Mol. Sci. 2022, 23, 2549 10 of 13 10 of 13 the PDMS and the upper vinyl layer, the PDMS block had to undergo an oxygen plasma treatment (80 Watts, 120”). This surface activation treatment made possible an optimum vinyl-PDMS bonding [42]. 4.3. Hippocampal Slices MICE Male 7 day-old CD1 mice were obtained from our breeding colony (CTB), maintained under a controlled environment (12-h light/12-h dark cycle; 22 ± 1 ◦C; ad libitum access to food and water). All the biosafety procedures for handling and sacrificing animals were approved by the bioethics committee from the Research Ethics Committee at the Universidad Politécnica de Madrid and followed the European Commission guidelines for the welfare of experimental animals (2010/63/EU, 86/609/EEC). 4.4. Slice Preparation The hippocampal sections were prepared using a method described by Stoppini et al. [13] with slight modifications. Briefly, P7-CD1 pups were decapitated. The brain was rapidly removed and placed in ice-cold DMEM-high glucose medium. Both hippocampi were dissected under a dissecting microscope and cleaned of the choroid plexus and meninges and transversally cut into 400-µm-thick slices using a tissue chopper VWR. Intact slices from septal hippocampi were then transferred onto the pertinent culture substrate; two hip- pocampal slices were placed per chip PC membrane ( Merck KGaA, Darmstadt, Germany) and one hippocampal slice per insert membrane of the commercial transwell (Merck KGaA, Darmstadt, Germany). Darmstadt, Germany). 4.5. Procedure of the Brain Slice-on-a-Chip Set-Up Two hippocampal slices were placed over the membrane in each chip. For a proper chip sealing, the PDMS block underside was previously exposed to a plasma activation, and subsequently, it was attached to the upper vinyl layer. Immediately, the lower mi- crofluidic chamber was filled to have fresh medium using a micropipette to avoid the slice dehumidification, and in addition, inlet and outlet tubings were fitted into the PDMS perforations. Next, a 1 mL syringe (B. Braun, Melsungen, Germany) was charged with cell culture medium DMEM-high glucose, 20% Horse Serum heat-inactivated and 1% antibi- otic and antimycotic solution (Thermo Fisher Scientific, Madrid, Spain) and connected to the chip by the inlet tubing. This syringe was positioned into a perfusion pump with a 1 µL/min flow rate being this flow perfused only through the lower microfluidic chamber. A CO2 incubator (37 ◦C, 5% CO2) was employed to preserve the microfluidic platform in equal temperature, humidity, and CO2 atmosphere conditions for 10 days. 4.7. Dye Injection and Image Acquisition The evaluation of brain slice status has been performed by using the fluorescent dye Oregon Green Bapta 488 (06807 Thermo Fisher), a highly sensitive intracellular Ca2+ indicator, allowing the acquisition of real-time imaging of living cells. The loading of calcium indicator dye was performed as follows: stock solutions (5 mM) OGB were made using a solution of 20% (w/v) Pluronic F-127 in absolute dimethylsulphoxide (DMSO). The final volume employed was 50 µL of OGB solution (20 µM) per chip. After 4 DIV, it was injected with a 100 µL Hamilton syringe through the PTFE plug reaching the pre- chamber (Figure 2). An equal volume of OGB was administered for control slices cultured Int. J. Mol. Sci. 2022, 23, 2549 11 of 13 11 of 13 on transwells. Then, sections on the chip, as on the OHSC (control), were incubated for one hour in the culture incubator. After that, the OHSC transwell was transferred to a new well to decrease the fluorescence background signal. Moreover, for a proper penetration of the dye in the chip, a flow of 0.1 µL/min was set for the OGB incubation. In order to elute the excess of OGB, hippocampal slices were visualized one day after (5 DIV). At 9 DIV, this protocol was repeated to obtain images with an optimal fluorescence signal at 10 DIV. During the imaging process, the chip remained sealed, enabling the analysis of the slices inside the chips in real-time. Photographs were acquired with a direct fluorescence microscope Olympus BX51 (Olympus SE & Co. KG, Hamburg, Germany)and inverted fluorescence microscope Leica DMI3000 B (Leica Microsystems, Wetzlar, Germany). 5. Conclusions A current challenge in culturing mouse brain slices is to preserve the intact cytoarchi- tecture due to its structural fragility. In this article, a brain slice-on-a-chip device has been fabricated as an alternative culture method for mouse hippocampal slices to improve the culture conditions. This chip allows dispensing microvolumes within the chip indepen- dently from the microfluidic system. This attribute allows working with low complexity microfluidic platforms, reducing assay costs. The injection system has been successfully tested, obtaining fluorescence staining in hippocampal slices, proving better preservation of the cytoarchitecture of the brain slices on the chip versus traditional culture methods. Local delivery feature enables the injection of stimuli on the brain slices cultured inside the chip and simultaneously allows the analysis of the tissue’s behavior against these reagents by real-time imaging. The developed methodology opens a new opportunity to apply this organ-on-a-chip alternative for other organotypic cultures with an easy-to-use and disposable device. Author Contributions: Conceptualization, S.T.-G. and M.H.; methodology, P.H., S.T.-G., and L.S.-O.; software, P.H. and S.T.-G.; imaging analysis, S.T.-G.; investigation, P.H., S.T.-G., M.F.L.H., and M.H.; writing—original draft preparation, P.H.; writing—review and editing: P.H., S.T.-G., and M.F.L.H.; supervision, M.F.L.H., S.T.-G., and M.H.; funding acquisition, M.H. All authors have read and agreed to the published version of the manuscript. Funding: The research was funded by the Ministerio de Economía y Competitividad of Spain (grant TEC2017-84846-R); Comunidad de Madrid, grant (P2018/BAA-4480); Spanish “Ministerio de Ciencia e Innovación” (grant PGC2018-094307-B-I00); and Cajal Blue Brain Project (the Spanish partner of the Blue Brain Project initiative from EPFL (Switzerland)). Institutional Review Board Statement: The study was conducted according to the guidelines of the Declaration of Helsinki and approved by the Institutional Review Board (or Ethics Committee) of Universidad Politécnica de Madrid (PROEX number 312/16). Informed Consent Statement: Not applicable. Data Availability Statement: The authors have considered to exclude this statement. Data Availability Statement: The authors have considered to exclude this statemen Acknowledgments: We would like to thank Javier DeFelipe for his help during this research and support in personnel cost. Acknowledgments: We would like to thank Javier DeFelipe for his help during this research and support in personnel cost. Conflicts of Interest: The authors declare no conflict of interest. 12 of 13 Int. J. Mol. Sci. 2022, 23, 2549 12 of 13 References 1. Humpel, C. Neuroscience Forefront Review Organotypic Brain Slice Cultures: A Review. Neuroscience 2015, 305, 86–98. [CrossRef] [PubMed] [ ] 2. Pas, S.P. The Rise of Three-Dimensional Human Brain Cultures. Nature 2018, 553, 437–445. 3. Croft, C.L.; Futch, H.S.; Moore, B.D.; Golde, T.E. Organotypic Brain Slice Cultures to Model Neurodegenerative Proteinopathies. Mol. Neurodegener. 2019, 14, 1–11. [CrossRef] [PubMed] 4. Raineteau, O.; Rietschin, L.; Gradwohl, G.; Guillemot, F.; Gähwiler, B.H. Neurogenesis in Hippocampal Slice Cultures. Mol. Cell. Neurosci. 2004, 26, 241–250. [CrossRef] [PubMed] 5. Reshetnikov, V.; Ryabushkina, Y.; Kovner, A.; Lepeshko, A.; Bondar, N. Repeated and Single Maternal Separation Specifically Alter Microglial Morphology in the Prefrontal Cortex and Neurogenesis in the Hippocampus of 15-Day-Old Male Mice. NeuroReport 2020, 31, 1256–1264. [CrossRef] 6. Nikonenko, I.; Toni, N.; Moosmayer, M.; Shigeri, Y.; Muller, D.; Sargent Jones, L. Integrins Are Involved in Synaptogenesis, Cell Spreading, and Adhesion in the Postnatal Brain. Brain Res. Dev. Brain Res. 2003, 140, 185–194. [CrossRef] nenko, I.; Toni, N.; Moosmayer, M.; Shigeri, Y.; Muller, D.; Sargent Jones, L. Integrins Are Involved in Synap 6. Nikonenko, I.; Toni, N.; Moosmayer, M.; Shigeri, Y.; Muller, D.; Sargent Jones, L. Integrins Are Involved in Synaptogenesis, Cell Spreading, and Adhesion in the Postnatal Brain. Brain Res. Dev. Brain Res. 2003, 140, 185–194. [CrossRef] ding, and Adhesion in the Postnatal Brain. Brain Res. Dev. Brain Res. 2003, 140, 185–194. [CrossRef] 7. Lee, K.H.; Lee, H.; Yang, C.H.; Ko, J.S.; Park, C.H.; Woo, R.S.; Kim, J.Y.; Sun, W.; Kim, J.H.; Ho, W.K.; et al. Bidirectional Signaling of Neuregulin-2 Mediates Formation of GABAergic Synapses and Maturation of Glutamatergic Synapses in Newborn Granule Cells of Postnatal Hippocampus. J. Neurosci. 2015, 35, 16479–16493. [CrossRef] [PubMed] pp p J , , [ ] [ ] 8. Kim, J.; Byun, J.-W.; Choi, I.; Kim, B.; Jeong, H.-K.; Jou, I.; Joe, E. PINK1 Deficiency Enhances Inflammatory Cytokine Release from Acutely Prepared Brain Slices. Exp. Neurobiol. 2013, 22, 38–44. [CrossRef] pp p 8. Kim, J.; Byun, J.-W.; Choi, I.; Kim, B.; Jeong, H.-K.; Jou, I.; Joe, E. PINK1 Deficiency Enhances I from Acutely Prepared Brain Slices. Exp. Neurobiol. 2013, 22, 38–44. [CrossRef] 9. Pandamooz, S.; Salehi, M.S.; Zibaii, M.I.; Safari, A.; Nabiuni, M.; Ahmadiani, A.; Dargahi, L. Modeling Traumatic Injury in Organotypic Spinal Cord Slice Culture Obtained from Adult Rat. Tissue Cell 2019, 56, 90–97. [CrossRef] 10. Gähwiler, B.H. Organotypic Monolayer Cultures of Nervous Tissue. J. Neurosci. Methods 1981, 4, 329–342. References [CrossRef] 11. Victorov, I.V.; Lyjin, A.A.; Aleksandrova, O.P. A Modified Roller Method for Organotypic Brain Cultures: Free-Floating Slices of Postnatal Rat Hippocampus. Brain Res. Protoc. 2001, 7, 30–37. [CrossRef] , g yp y J , , 11. Victorov, I.V.; Lyjin, A.A.; Aleksandrova, O.P. A Modified Roller Method for Organotypic Brain Cultur Postnatal Rat Hippocampus. Brain Res. Protoc. 2001, 7, 30–37. [CrossRef] 12. de Simoni, A.; Yu, L.M.Y. Preparation of Organotypic Hippocampal Slice Cultures: Interface Method. Nat. Protoc. 2006, 1, 1439–1445. [CrossRef] 13. Stoppini, L.; Buchs, P.A.; Muller, D. A Simple Method for Organotypic Cultures of Nervous Tissue. J. Neurosci. Methods 1991, 37, 173–182. [CrossRef] ájos, N.; Ellender, T.J.; Zemankovics, R.; Mann, E.O.; Exley, R.; Cragg, S.J.; Freund, T.F.; Paulsen, O. Main ctivity in Submerged Hippocampal Slices: Importance of Oxygen Supply. Eur. J. Neurosci. 2009, 29, 319–327 15. Lu, R.X.Z.; Radisic, M. Organ-on-a-Chip Platforms for Evaluation of Environmental Nanoparticle Toxicity. Bioact. Mater. 2021, 6, 2801. [CrossRef] 16. Rothbauer, M.; Rosser, J.M.; Zirath, H.; Ertl, P. Tomorrow Today: Organ-on-a-Chip Advances towards Clinically Relevant Pharmaceutical and Medical in Vitro Models. Curr. Opin. Biotechnol. 2019, 55, 81–86. [CrossRef] 17. Tian, C.; Tu, Q.; Liu, W.; Wang, J. Recent Advances in Microfluidic Technologies for Organ-on-a-Chip. TrAC-Trends Anal. Chem. 2019, 117, 146–156. [CrossRef] 18. Yi, L.; Wang, X.; Dhumpa, R.; Schrell, A.M.; Mukhitov, N.; Roper, M.G. Integrated Perfusion and Separation Systems for Entrainment of Insulin Secretion from Islets of Langerhans. Lab Chip 2015, 15, 823–832. [CrossRef] 19. Shah, P.; Vedarethinam, I.; Kwasny, D.; Andresen, L.; Dimaki, M.; Skov, S.; Svendsen, W.E. Microfluidic Bioreactors for Culture of Non-Adherent Cells. Sens. Actuators B Chem. 2011, 156, 1002–1008. [CrossRef] 20. Vedarethinam, I.; Avaliani, N.; Tønnesen, J.; Hansen, J.; Sabourin, D.; Dimaki, M.; Kokaia, M.; Dufva, M.; Svendsen, W.E.; Emnéus, J.; et al. Long-Term Brain Slice Culturing in a Microfluidic Platform. In Proceedings of the 15th International Conference on Miniaturized Systems for Chemistry and Life Sciences, Seattle, WA, USA, 2–6 October 2011; pp. 1560–1563. y y , , , , ; pp 21. Hájos, N.; Mody, I. Establishing a Physiological Environment for Visualized in Vitro Brain Slice Reco Supply and Modifying ACSF Content. J. Neurosci. Methods 2009, 183, 107–113. [CrossRef] y y 21. Hájos, N.; Mody, I. Establishing a Physiological Environment for Visualized in Vitro Brain Slice Recordings by Increasing Oxygen Supply and Modifying ACSF Content. J. Neurosci. Methods 2009, 183, 107–113. [CrossRef] pp y y g 22. References Three-Dimensional Brain-on-a-Chip with an Interstitial Leve plication as an in Vitro Model of Alzheimer’s Disease Lab Chip 2015 15 141 150 [CrossRef] Lee, B.K.; Jeong, G.S.; Hyun, J.K.; Lee, C.J.; Lee, S.H. Three-Dimensional Brain-on-a-Chip with an Interstiti 31. Park, J.; Lee, B.K.; Jeong, G.S.; Hyun, J.K.; Lee, C.J.; Lee, S.H. Three-Dimensional Brain-on-a-Chip with an Interstitial Level of Flow and Its Application as an in Vitro Model of Alzheimer’s Disease. Lab Chip 2015, 15, 141–150. [CrossRef] rk, J.; Lee, B.K.; Jeong, G.S.; Hyun, J.K.; Lee, C.J.; Lee, S.H. Three-Dimensional Brain-on-a-Chip with an In ow and Its Application as an in Vitro Model of Alzheimer’s Disease. Lab Chip 2015, 15, 141–150. [CrossRef] g y p Its Application as an in Vitro Model of Alzheimer’s Disease. Lab Chip 2015, 15, 141–150. [CrossRef] 32. Hasan, M.N.; Radwan, A.N.; Kim, M.; Kucukal, E.; Maji, D.; Pashaei, V.; Chung, C.-Y.; Kakkar, A.; Gurkan, U.A. Emerging Micro and Nanotechnologies in Neuroscience: Devices, Fabrication Methods, and Implementation in Monitoring of Neural Activity and Drug Delivery. Technology 2019, 7, 57–83. [CrossRef] g y gy 33. Gonzalez-Riano, C.; Tapia-González, S.; García, A.; Muñoz, A.; DeFelipe, J.; Barbas, C. Metabolomics and Neuroanatomical Evaluation of Post-Mortem Changes in the Hippocampus. Brain Struct. Funct. 2017, 222, 2831–2853. [CrossRef] [PubMed] pia-González, S.; García, A.; Muñoz, A.; DeFelipe, J.; Barbas, C. Metabolomics and Neuroanatomical tem Changes in the Hippocampus. Brain Struct. Funct. 2017, 222, 2831–2853. [CrossRef] [PubMed] nzalez-Riano, C.; Tapia-González, S.; García, A.; Muñoz, A.; DeFelipe, J.; Barbas, C. Metabolomics and aluation of Post-Mortem Changes in the Hippocampus. Brain Struct. Funct. 2017, 222, 2831–2853. [CrossRe g pp p 34. Tapia-González, S.; Insausti, R.; DeFelipe, J. Differential Expression of Secretagogin Immunostaining in the Hippocampal Formation and the Entorhinal and Perirhinal Cortices of Humans, Rats, and Mice. J. Comp. Neurol. 2020, 528, 523–541. [CrossRef] [PubMed] 35. The Mouse Brain in Stereotaxic Coordinates, Compact-3rd Edition. Available online: https://www.elsevier.com/books/the- mouse-brain-in-stereotaxic-coordinates-compact/franklin/978-0-12-374244-5 (accessed on 23 October 2021). 36. Guy, Y.; Rupert, A.E.; Sandberg, M.; Weber, S.G. A Simple Method for Measuring Organotypic Tissue Slice Culture Thickness. J. Neurosci. Methods 2011, 199, 78–81. [CrossRef] 37. Thomas, D.; Tovey, S.C.; Collins, T.J.; Bootman, M.D.; Berridge, M.J.; Lipp, P. A Comparison of Fluorescent Ca2+ Indicator Properties and Their Use in Measuring Elementary and Global Ca2+ Signals. Cell Calcium 2000, 28, 213–223. [CrossRef] p g y g 38. Garaschuk, O.; Milos, R.I.; Konnerth, A. Targeted Bulk-Loading of Fluorescent Indicators for Two-Phot Nat. Protoc. References Huang, Y.; Williams, J.C.; Johnson, S.M. Brain Slice on a Chip: Opportunities and Challenges of Appl to Intact Tissues. Lab Chip 2012, 12, 2103–2117. [CrossRef] [PubMed] pp y y g 22. Huang, Y.; Williams, J.C.; Johnson, S.M. Brain Slice on a Chip: Opportunities and Challenges of Applying J.C.; Johnson, S.M. Brain Slice on a Chip: Opportunities and Challenges of Applying Microfluidic Technology b Chip 2012, 12, 2103–2117. [CrossRef] [PubMed] 22. Huang, Y.; Williams, J.C.; Johnson, S.M. Brain Slice on a Chip: Opportuni to Intact Tissues. Lab Chip 2012, 12, 2103–2117. [CrossRef] [PubMed] 23. Bakmand, T.; Troels-Smith, A.R.; Dimaki, M.; Nissen, J.D.; Andersen, K.B.; Sasso, L.; Waagepetersen, H.S.; Gramsbergen, J.B.; Svendsen, W.E. Fluidic System for Long-Term in Vitro Culturing and Monitoring of Organotypic Brain Slices. Biomed. Microdevices 2015, 17, 71. [CrossRef] [PubMed] 24. Queval, A.; Ghattamaneni, N.R.; Perrault, C.M.; Gill, R.; Mirzaei, M.; McKinney, R.A.; Juncker, D. Ch Probe for Microperfusion of Organotypic Brain Slices. Lab Chip 2010, 10, 326–334. [CrossRef] maneni, N.R.; Perrault, C.M.; Gill, R.; Mirzaei, M.; McKinney, R.A.; Juncker, D. Chamber and Microfluidic usion of Organotypic Brain Slices. Lab Chip 2010, 10, 326–334. [CrossRef] 25. Rambani, K.; Vukasinovic, J.; Glezer, A.; Potter, S.M. Culturing Thick Brain Slices: An Interstitial 3D Microperfusion System for Enhanced Viability. J. Neurosci. Methods 2009, 180, 243–254. [CrossRef] y 26. Blake, A.J.; Pearce, T.M.; Rao, N.S.; Johnson, S.M.; Williams, J.C. Multilayer PDMS Microfluidic Chamber for Controlling Brain Slice Microenvironment. Lab Chip 2007, 7, 842–849. [CrossRef] p 27. Liu, J.; Pan, L.; Cheng, X.; Berdichevsky, Y. Perfused Drop Microfluidic Device for Brain Slice Culture-Based Drug Discovery. Biomed. Microdevices 2016, 18, 1–10. [CrossRef] 28. Sun, M.; Kaplan, S.V.; Gehringer, R.C.; Limbocker, R.A.; Johnson, M.A. Localized Drug Application and Sub-Second Voltammetric Dopamine Release Measurements in a Brain Slice Perfusion Device. Anal. Chem. 2014, 86, 4151–4156. [CrossRef] 13 of 13 Int. J. Mol. Sci. 2022, 23, 2549 13 of 13 29. Wilhelm, I.; Krizbai, I.A. In Vitro Models of the Blood-Brain Barrier for the Study of Drug Delivery to the Brain. Mol. Pharm. 2014, 11, 1949–1963. [CrossRef] [ ] 30. Fan, Y.; Nguyen, D.T.; Akay, Y.; Xu, F.; Akay, M. Engineering a Brain Cancer Chip for High-Throughput Drug Screening. Sci. Rep. 2016, 6, 25062. [CrossRef] K.; Jeong, G.S.; Hyun, J.K.; Lee, C.J.; Lee, S.H. References 2006, 1, 380–386. [CrossRef] s, R.I.; Konnerth, A. Targeted Bulk-Loading of Fluorescent Indicators for Two-Photon Brain Imaging in Vivo 380–386. [CrossRef] 39. Yuan, F.; Xiong, G.; Cohen, N.A.; Cohen, A.S. Optimized Protocol of Methanol Treatment for Immunofluorescent Staining in Fixed Brain Slices. Appl. Immunohistochem. Mol. Morphol. 2017, 25, 221–224. [CrossRef] pp p [ ] 40. Dissing-Olesen, L.; MacVicar, B.A. Fixation and Immunolabeling of Brain Slices: SNAPSHOT Method. Curr. Protoc. Neurosci. 2015, 71, 1.23.1–1.23.12. [CrossRef] 41. Herreros, P.; Ballesteros-Esteban, L.M.; Laguna, M.F.; Leyva, I.; Sendiña-Nadal, I.; Holgado, M. Neuronal Circuits on a Chip for Biological Network Monitoring. Biotechnol. J. 2021, 16, 2000355. [CrossRef] [PubMed] 42. Kim, H.T.; Jeong, O.C. PDMS Surface Modification Using Atmospheric Pressure Plasma. Microelectron. Eng. 2011, 88, 2281–2285. [CrossRef]
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Mild poikilocapnic hypoxia increases very low frequency haemoglobin oxygenation oscillations in prefrontal cortex
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Mild Poikilocapnic Hypoxia Increases Very Low Frequency Haemoglobin Oxygenation Oscillations in Prefrontal Cortex in Prefrontal Cortex Agnieszka Gruszecka  Medical University of Gdansk: Gdanski Uniwersytet Medyczny Monika Waskow  Akademia Pomorska w Slupsku Marta A. Malkiewicz  Medical University of Gdansk: Gdanski Uniwersytet Medyczny J. Patrick Neary  University of Regina Jyotpal Singh  University of Regina Taylor Teckchandani  University of Regina Gregory P. Kratzig  University of Regina Magdalena Wszedybyl-Winklewska  Medical University of Gdansk: Gdanski Uniwersytet Medyczny Andrzej F. Frydrychowski  NIRTI SA, Wroclaw Jacek Rumiński  Gdańsk University of Technology: Politechnika Gdanska Natalia Głowacka  Gdansk University of Technology: Politechnika Gdanska Piotr Lass  Medical University of Gdansk: Gdanski Uniwersytet Medyczny Pawel J. Winklewski  Medical University of Gdansk: Gdanski Uniwersytet Medyczny Marcin Gruszecki  (  mgruszecki@gumed.edu.pl ) Medical University of Gdansk Center for Maritime and Tropical Med Medyczny Centrum Medycyny Morskiej i Tropikalnej https://orcid.o R h Research Research Keywords: hypoxia, wavelet transform, blood pressure, subarachnoid space width, near infrared spectroscopy Posted Date: June 29th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-645557/v1 DOI: https://doi.org/10.21203/rs.3.rs-645557/v1 License:   This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at Biological Research on December 1st, 2021. See the published version at https://doi.org/10.1186/s40659-021-00362-2. Key Words: hypoxia, wavelet transform, blood pressure, subarachnoid space width, near infrared spectroscopy Abstract The aim of the study was to investigate the effect of mild cerebral hypoxia on haemoglobin oxygenation (HbO2), cerebrospinal fluid dynamics and cardiovascular physiology. To achieve this goal, four signals were recorded simultaneously: blood pressure, ECG, HbO2 from right hemisphere and changes of SAS width from left hemisphere. Signals were registered from 30 healthy, young participants (2 females and 28 males, BMI = 24.5 ± 2.3 kg/m2, age 30.8 ± 13.4 years). We analysed the recorded signals using wavelet transform (WT). We demonstrated for the first time that in healthy subjects exposed to mild poikilokapnic hypoxia that there were increases in very low frequency HbO2 oscillations (< 0.052 Hz) in prefrontal cortex. Additionally, SAS fluctuation diminishes in the whole frequency range which could be explained by brain oedema. Consequently the study provides insight into mechanisms governing brain response to a mild hypoxic challenge. Our study supports the notion that HbO2 and SAS width monitoring might be beneficial for patients with acute lung disease, including SARS-CoV-2. Mild poikilocapnic hypoxia increases very low frequency haemoglobin oxygenation oscillations in prefrontal cortex Agnieszka Gruszecka1, Monika Waskow2, Marta A. Malkiewicz3,4, J. Patrick Neary5, Jyotpal Singh5, Taylor Teckchandani5, Gregory P. Kratzig6, Magdalena Wszedybyl- Winklewska7, Andrzej F. Frydrychowski8, Jacek Rumiński9, Natalia Głowacka9, Piotr Lass10, Pawel J. Winklewski7, Marcin Gruszecki*1,9 1Department of Radiology Informatics and Statistics, Faculty of Health Sciences, Medical University of Gdansk, Gdansk, Poland 2Institute of Health Sciences, Pomeranian University of Slupsk, Slupsk, Poland 3Applied Cognitive Neuroscience Lab, Department of Human Physiology, Medical University of Gdansk, Gdansk, Poland 4Department of Psychiatry, Medical University of Gdansk, Gdansk, Poland 5Faculty of Kinesiology and Health Studies, University of Regina, Regina, Canada 6Department of Psychology, University of Regina, Regina, SK, Canada 7Department of Human Physiology, Faculty of Health Sciences, Medical University of Gdansk, Gdansk, Poland 8NIRTI SA, Wroclaw, Poland 9Department of Biomedical Engineering, Faculty of Electronics, Telecommunications and Informatics, Gdansk University of Technology, Gdansk, Poland 10Department of Nuclear Medicine, Medical University of Gdansk, Gdansk, Poland *Corresponding author: Marcin Gruszecki, PhD, DSc Department of Radiology Informatics and Statistics, Medical University of Gdansk Tuwima Str. 15, 80-210 Gdansk, Poland E-mail: mgruszecki@gumed.edu.pl; Tel./Fax: +48 58 349-15-08 6Department of Psychology, University of Regina, Regina, SK, Canada *Corresponding author: Marcin Gruszecki, PhD, DSc Department of Radiology Informatics and Statistics, Medical University of Gdansk Tuwima Str. 15, 80-210 Gdansk, Poland E-mail: mgruszecki@gumed.edu.pl; Tel./Fax: +48 58 349-15-08 Introduction Hypoxia is frequently observed in a number of clinical situations such as lung disease, sleep apnoea, as well as cardiac and cerebrovascular dysfunction associated with aging. Mild hypoxia is also an eminent feature of the respiratory distress syndrome evoked by the coronavirus (SARS-CoV-2). A number of cognitive and neuropsychiatric manifestations of SARS-CoV-2 have been observed in a proportion of patients such as depressed mood, anxiety, post-traumatic stress disorder and cognitive decline. Although these are multifactorial, changes in cerebral oxygen supply and related pathophysiological consequences may play a role (Alonso-Lana et al. 2020). It is well-known that hypoxia leads to a decline in haemoglobin oxygenation (HbO2) in cerebral cortex (Hampson et al. 1990). Diminished oxygen supply to the brain results in several compensatory mechanisms, which in turn trigger substantial changes in various aspects of brain functioning. Augmented cerebral blood flow (Kety and Schmidt 1948) and cerebral blood volume (Dubowitz et al. 2009; DiPasquale et al. 2016) together with blood-brain barrier impairment (Halder and Milner 2020) lead to discrete brain oedema and increases in intracranial pressure (Dubowitz et al. 2009; DiPasquale et al. 2016). Furthermore, brain hypoxia results in a number of metabolic changes associated with an augmented cerebral metabolic rate of oxygen, lactate and glutamate concentrations accompanied by a diminished creatinine concentration. Taken together, these metabolic alterations suggest higher neural activity and increased oxidative metabolism (Vestergaard et al. 2016). The autoregulation dogma is constantly challenged with increasing emphasis on either local neural or metabolic mechanisms (Saleem et al. 2016; Marina et al. 2020). The role of intracranial pressure in the feedback loops regulating widely understood cerebral metabolic homeostasis is continuously highlighted (Winklewski et al. 2019; Marina et al. 2020). Consequently, in this study we aimed at assessing the effect of hypoxia on the oscillatory behaviour of blood pressure (BP), oxygenated haemoglobin (HbO2), electrocardiogram (ECG), and subarachnoid space (SAS) width using established non-invasive methods (Ferrari and Quaresima 2012, Gruszecki et al. 2018). The relative concentrations of the oxygenated and deoxygenated haemoglobin can be measured in the prefrontal area with near infrared spectroscopy (NIRS) (Ferrari and Quaresima 2012). Oscillatory changes in the SAS width, reflecting cerebrospinal fluid pulsatility (Gruszecki et al. 2018), can be instantly monitored with the method developed by our team, called near-infrared transillumination-backscattering sounding (NIR-T/BSS) (Frydrychowski et al. 2002; Frydrychowski et al 2011, Gruszecki et al. 2018). Both methods can be used simultaneously (Gruszecka et al. 2020). Introduction Wavelet transform analysis of biological signals can elegantly quantify and delineate the investigated interactions in both frequency and time domains (Stefanovska et al. 1999; Saleem et al. 2016). We hypothesized that mild hypoxia would increase the prominence of very low- frequency HbO2 local brain oscillations while maintaining or even decreasing the impact of central oscillatory components generated by the heart and lungs. We also expected SAS oscillations to diminish in the whole frequency range as a result of simulated altitude at approximately 2900 - 3000 m. impact of central oscillatory components generated by the heart and lungs. We also expected SAS oscillations to diminish in the whole frequency range as a result of simulated altitude at approximately 2900 - 3000 m. Results Four signals were continuously and simultaneously recorded from the volunteers: BP, ECG, HbO2 RIGHT and SASLEFT while breathing normal room air (19.8% O2), and during normobaric hypoxia (14.8% O2) in an environmental chamber to simulate altitude at 2900-3000m. The atmospheric pressure for whole time of experiment was kept at the same level 712 mmHg, while the level of oxygen during normobaric hypoxia was reduced to 14.8%. A gas mixture of 19.8% O2 was used as the normoxic condition as this is the native partial pressure of oxygen in Regina, Saskatchewan, Canada (577 meters above sea level) where the testing was performed. According to nonparametric Wilcoxon rank sum test (see Table 1) there was a statistically significant drop in amplitude of all measured signals during mild normobaric hypoxia. Gas mixture with 19.8% O2 Gas mixture with 14.8% O2 HR [beats/min] 61.2±3.6 66.6±3.4*** DBP [mmHg] 65.17±9.65 68.16±9.34* SBP [mmHg] 112.79±14.51 119.67±13.08*** MAP [mmHg] 81.04±10.88 85.32±10.06* SASLEFT [AU] 0.22±0.01 0.19±0.01* HbO2 RIGHT [%O2] 0.72±0.28 0.45±0.13*** tHb [µM] 12.03±0.43 15.27±0.51** SaO2 [%O2] 97.81±0.61 92.67±0.97*** EtCO2 [mmHg] 32.95±3.16 30.61±3.25*** EtO2 [mmHg] 128.74±3.29 93.66±3.67*** Table 1: Subject characteristics during breathing a gas mixture with 19.8% and 14.8% O2. Values shown are mean ± standard deviation. p-values were estimated between two stages of the experimental procedure. *p < 0.05; **p < 0.01; ***p < 0.001. Used abbreviation: HR – heart rate, DBP – diastolic blood pressure, SBP – systolic blood pressure, MAP – mean arterial pressure, SASLEFT – subarachnoid width, HbO2 RIGHT - relative changes in oxyhaemoglobin, tHb - relative changes in total haemoglobin SaO2 – oxyhaemoglobin saturation, EtCO2 – end-tidal CO2, EtO2 - end-tidal O2. Table 1: Subject characteristics during breathing a gas mixture with 19.8% and 14.8% O2. Values shown are mean ± standard deviation. p-values were estimated between two stages of the experimental procedure. *p < 0.05; **p < 0.01; ***p < 0.001. Used abbreviation: HR – heart rate, DBP – diastolic blood pressure, SBP – systolic blood pressure, MAP – mean arterial pressure, SASLEFT – subarachnoid width, HbO2 RIGHT - relative changes in oxyhaemoglobin, tHb - relative changes in total haemoglobin SaO2 – oxyhaemoglobin saturation, EtCO2 – end-tidal CO2, EtO2 - end-tidal O2. Table 1: Subject characteristics during breathing a gas mixture with 19.8% and 14.8% O2. Values shown are mean ± standard deviation. p-values were estimated between two stages of the experimental procedure. *p < 0.05; **p < 0.01; ***p < 0.001. Results Used abbreviation: HR – heart rate, DBP – diastolic blood pressure, SBP – systolic blood pressure, MAP – mean arterial pressure, SASLEFT – subarachnoid width, HbO2 RIGHT - relative changes in oxyhaemoglobin, tHb - relative changes in total haemoglobin SaO2 – oxyhaemoglobin saturation, EtCO2 – end-tidal CO2, EtO2 - end-tidal O2. Figure 1 shows the result of the amplitude of the wavelet transform (WT) for one representative volunteer. Left and right columns of Fig. 1 corresponds to breathing a gas mixture with 19.8% and 14.8% O2, respectively. We estimated WT for all four measured signals: BP (a, e), ECG (b, f), HbO2 RIGHT (c, g) and SASLEFT (d, h). Cardiac oscillations (~1 Hz) are clearly visible for the whole duration of all signals. Additionally, collected signals (excluding ECG) manifest over a wide frequency range, but SASLEFT and HbO2 RIGHT signals have more prominent low frequency components than BP signal (Gruszecka et al. 2020). To simplify the comparison between two stages of experimental procedure in terms of their frequency content, we plotted the median of the time-averaged amplitude of wavelet transforms (Figure 2). In this plot, we added six different frequency intervals which correspond to different physiological functions described previously by Stefanovska et al. 1999 and Gruszecki et al. 2018. Additionally, we estimated the p- value of the differences between the results for breathing a gas mixture with 19.8% and 14.8% O2 for all measured signals. We observed the highest differences (p<0.001) for WT amplitude for SASLEFT for all frequency intervals. For HbO2 RIGHT the differences between amplitude of wavelet transform were associated with respiration (II, 0.145– 0.6 Hz), neurogenic (IV, 0.021–0.052 Hz), endothelial nitric oxide (NO) dependent (V, 0.0095–0.021) and NO independent (VI, 0.005–0.0095 Hz). In turn, WT amplitude of the BP signal only has differences (p<0.05) in myogenic (III, 0.052–0.145 Hz) and neurogenic (IV) intervals. We did not observe any statistically significant differences for the ECG signal. Figure 1: Wavelet transform of recorded signals: BP (a and e), ECG (b and f), HbO2 RIGHT (c and g) and SASLEFT (d and h) for one of the volunteers. Left (right) columns of plots illustrate results for breathing a gas mixture with 19.8% (14.8%) O2. Figure 1: Wavelet transform of recorded signals: BP (a and e), ECG (b and f), HbO2 RIGHT (c and g) and SASLEFT (d and h) for one of the volunteers. Results Left (right) columns of plots illustrate results for breathing a gas mixture with 19.8% (14.8%) O2. Figure 3 illustrates the wavelet phase coherence (left column) and phase difference (right column) between pairs of all collected signals. The value of phase coherence was significant when the value of phase coherence was higher than 95th percentile of 435 (2-permutation of 30 subjects) inter-subject surrogate. When we observed statistically significant phase coherence at certain frequencies, we assumed the same for phase differences. For phase coherence we found statistically significant differences for BP-SASLEFT and BP-ECG only for the cardiac interval. We did not observe any statistically significant difference for phase difference for all considered pairs of signals. edian (thick lines) of the time-averaged wavelet transforms of signals recorded in all BP, (b) ECG, (c) HbO2 RIGHT and (d) SASLEFT obtained from the 30 minutes continuo haded areas indicate the inter-quartile range (25th, 75th percentiles). Red (blue) lines a correspond to breathing a gas mixture with 19.8% (14.8%) O2. *p < 0.05; **p < 0.01; ** Figure 2: Median (thick lines) of the time-averaged wavelet transforms of signals recorded in all 30 subjects: (a) BP, (b) ECG, (c) HbO2 RIGHT and (d) SASLEFT obtained from the 30 minutes continuous recordings. Shaded areas indicate the inter-quartile range (25th, 75th percentiles). Red (blue) lines and shade areas correspond to breathing a gas mixture with 19.8% (14.8%) O2. *p < 0.05; **p < 0.01; ***p < 0.001. e 3: Median (thick lines) of wavelet phase coherence (left column) and phase differen mn) between (a, g) BP vs SASLEFT, (b, h) BP vs HbO2, (c, i) BP vs ECG, (d, j) ECG vs SASLEFT, (e bO2 and (f, l) SASLEFT vs HbO2. Coloured shading indicates the interquartile range (25 entiles) for 30 subjects. Coherence below the 95th percentile of the surrogates (light grey ing) is not considered significant. Red (blue) lines and shade areas correspond to breathi ure with 19.8% (14.8%) O2. *p < 0.05; **p < 0.01; ***p < 0.001. Figure 3: Median (thick lines) of wavelet phase coherence (left column) and phase difference (right column) between (a, g) BP vs SASLEFT, (b, h) BP vs HbO2, (c, i) BP vs ECG, (d, j) ECG vs SASLEFT, (e, k) ECG vs HbO2 and (f, l) SASLEFT vs HbO2. Coloured shading indicates the interquartile range (25th, 75th percentiles) for 30 subjects. Results Coherence below the 95th percentile of the surrogates (light grey line and shading) is not considered significant. Red (blue) lines and shade areas correspond to breathing a gas mixture with 19.8% (14.8%) O2. *p < 0.05; **p < 0.01; ***p < 0.001. Discussion The novel findings of our study showed that mild poikilocapnic hypoxia increases the very low frequency HbO2 oscillations (< 0.052 Hz) in prefrontal cortex while diminishing SAS oscillations in the whole frequency range. In addition we confirmed that prefrontal cortex HbO2 and SAS width decline during exposure to lowered oxygen partial pressure. In recent years there has been an increased interest in cerebrovascular mechanisms related to normal and pathological physiology. As such, we have witnessed a substantial paradigm shift in our thinking in regard to brain perfusion control mechanisms. The increasing accumulation of evidence suggests that astrocytes act as physiological sensors reacting to changes in the brain parenchymal levels of metabolic substrates (such as oxygen), cerebral perfusion and intracranial pressure changes (Angelova et al. 2015, Marina et al. 2018, Turovsky et al. 2020, Marina et al. 2020). In particular, astrocytes might be responsible for local cellular signalling mechanisms adjusting cerebral perfusion to brain metabolic needs (Marina et al. 2020). Our study strongly supports the view that local brain mechanisms, rather than systemic control-level mechanisms are responsible for adaptation to mild poikilocapnic (normoxic) hypoxia. We observed decreases in respiratory contribution to HbO2 prefrontal cortex oscillations, while at the same time observing substantially increased very low frequency HbO2 oscillations (< 0.052 Hz). Very low frequency periodic dynamism is believed to reflect neural sympathetic and metabolic activity (Saleem et al. 2016, Chow et al. 2007), and is most likely linked to increased neural metabolism (Vestergaard et al. 2016). Prefrontal cortex HbO2 fluctuations at the 0.145 – 0.052 Hz frequency were reported to be linked to general BP oscillations (van Beek et al. 2012, Vermeij et al. 2014, Yunjie et al. 2010). In response to normobaric hypoxia, BP fluctuations did not change in the 0.145 – 0.052 frequency. We also did not observe any phase difference in the HbO2 and BP signals. Stabilisation of BP-brain signals oscillations at the 0.145 – 0.052 Hz frequency are most likely driven by increased sympathetic activity related to hypoxia and slightly increased intracranial pressure (Talbot et al. 2005, Dubowitz et al. 2009, DiPasquale et al. 2016). We have previously shown that high sympathetic drive strengthen the links between BP and SAS signal (Winklewski et al. 2019). Slightly increased intracranial pressure and discrete brain swelling previously reported in hypoxia could have resulted in a decline of SAS oscillations across the whole frequency range. Discussion Although we cannot confirm discrete brain swelling from our study, our findings extend previous results collected in our laboratory where healthy subjects were exposed to 5 minutes of poikilokapnic (normobaric) hypoxia, and we observed a trend towards a decline in SAS width and diminished BP-SAS amplitude coupling (Wszedybyl-Winklewska et al. 2017). In the current study, we observed diminished BP- SAS and ECG-BP phase coherences within the cardiac frequency band. Suppression of respiratory SAS oscillations were reported previously by our team as an early indicator of rising intracranial pressure in rabbit (Frydrychowski et al. 2011). A decline in the modulation of cerebral blood flow by even moderately increased intracranial pressure was also observed in humans (Haubrich et al. 2007). This study used poikilocapnic (normobaric) hypoxia to challenge whether EtCO2 fluctuations varied in response to reflexive hyperventilation. We preferred this over an isocapnic hypoxic challenge, defined by hypoxia in the presence of maintained CO2 within the bloodstream, as we believe our chosen methodology better mimicked clinical conditions. A gas mixture of 19.8% O2 was used as the normoxic condition as this is the native partial pressure of oxygen in Regina, Saskatchewan, Canada (577 meters above sea level) where the testing was performed. Our study demonstrates that clinical situations associated with even mild cerebral hypoxia may result in several pathophysiological adaptations including changes in brain metabolism and cerebrospinal fluid dynamics. Non-invasive modalities that enable continuous brain monitoring could provide several benefits to patients suffering from diseases associated with declined brain oxygenation, stroke or traumatic brain injury. Experimental design Two tests of breathing a gas mixture with 19.8% and 14.8% O2 were conducted in a quiet room and environmental chamber. Room and chamber were pre-set to a temperature of 18–20 °C. After all of the medical research equipment was attached to the volunteer participant (see Measurements below), they were instructed to lie supine on a bed with a pillow to support their head during breathing a gas mixture of normal room air (19.8% O2) and during normobaric hypoxia (14.8% O2). The first 30 minutes of experiment, subjects were asked to breath room air (19.8% O2), and then they moved to the environmental chamber with the aid of a research assistant (it took about 3-5 minutes). During the next 30 minutes, volunteer subjects breathed freely in the hypoxic chamber with reduced levels of oxygen (14.8%). The hypoxic oxygen condition mimiced the elevation of approximately 2900-3000 meters above sea level. Subjects A group of 30 healthy and not smoking volunteers (28 males and 2 females, age 30.8±13.4 years, BMI = 24.5±2.3 kg/m2) were involved in the experiments, which were carried out in accordance with the recommendations of Helsinki. The Ethics Committee of University of Regina (REB#2017-013) approved this study and the experimental protocol. All subjects were older than 18 years and signed a consent form to participate in the study. Participants were asked to avoid any alcohol at least 24 hours before the experiment, and tea, coffee, nicotine, cocoa and any food and beverages containing methylxanthine for at least 12 hours before the experiment. Intense exercise training was not allowed at least 6 hours prior to testing, and all subjects were asked to void their bladder within 30 minutes of testing. All procedures were preceded by 10 minutes of rest in the sitting position in a comfortable chair located in quiet room. Conclusions In subjects exposed to mild poikilokapnic hypoxia we have demonstrated for the first time that: 1) very low HbO2 oscillations (< 0.052 Hz) increase in prefrontal cortex, and 2) SAS fluctuation diminishes in the whole frequency range. Consequently the study provides insights into the physiological mechanisms governing brain response to a mild hypoxic challenge. Our study supports the notion that HbO2 and SAS width monitoring might be beneficial for patients with acute lung disease, including SARS-CoV-2. Measurements A Finometer (Finapres Medical Systems, Arnhem, The Netherlands) was used to measure heart rate (HR) and BP. Finger photoplethysmography BP was calibrated against brachial arterial pressure. The signal was collected from the left middle finger at all times during both normoxia (19.8% O2) and hypoxia (14.8% O2). Oxyhaemoglobin saturation (SaO2) was measured using a Nellcor PM10N Portable SpO2 Patient Monitoring System (Medtronic Canada, Vancouver, BC). During the experiment, the device was placed on the right index finger. Expired respiratory gas samples from the mouthpiece were constantly analysed using the side-stream technique for end-tidal CO2 (EtCO2) using AD Instruments ML206 gas analyser (Colorado Springs, USA). SAS signal was collected using an SAS Monitor (NIRTI SA, Wierzbice, Poland). A detailed description of the SAS Monitor has been provided previously (e.g. Gruszecki et al. 2018). The NIRS signal was collected by PortaLite system (Artinis Medical, The Netherlands). The sensor was positioned over pre-frontal cortex of the right hemisphere during the experiment. NIRS contains transmitters at 30, 35 and 40 mm from the receiver, which allows a penetration depth of approximately one-third to one- half of the distance between optodes (Cui et al. 1991). During the experiment, we collected the following NIRS signals: relative changes in oxy- (HbO2), deoxy- (HHb), total haemoglobin (tHb = HbO2 + HHb) and haemoglobin difference (Hbdiff = HbO2- HHb). To avoid admission of background light the NIRS sensor was secured with a black coloured tensor bandage. We decided to analyse a NIRS signal that penetrate the deepest regions of head to be sure that we truly analyse signals from brain vessels. Like many others, (Bernjak et al. 2012, Cui et al. 2014, Kim et al. 2020) we focused our analyses on the oxyhaemoglobin (HbO2) signal. Additionally, to avoid any interference between NIRS and SAS signals, we recorded only SASLEFT from left hemisphere. All parameters were recorded and saved simultaneously for further analysis. This was completed for both segments, with the first 30 minute normoxic condition completed first, followed by the subsequent 30 minute normobaric hypoxic second. To import and view collected signals, a PowerLab 8/32 amplifier was coupled with LabChart 7 Pro (AD Instruments, Colorado Springs, Colorado, USA). All signals before analysis were down sampled to 10 Hz, detrended using a moving average with a window size of 220 seconds, and normalized by subtraction of their mean and division by their standard deviation. Measurements Wavelet transform To detect and perform analysis of physiological processes that are responsible for generating oscillations in the cardiovascular system, we used wavelet analysis. The wavelet transform is a method that transforms a signal from the time domain to the time-frequency domain. The definition of the wavelet transform is: 𝑊(𝑠, 𝑡) = 1 √𝑠∫ 𝜑( 𝑢−𝑡 𝑠) +∞ −∞ 𝑔(𝑢)𝑑𝑢, where 𝑊(𝑠, 𝑡) is the wavelet coefficient, 𝑔(𝑢) is the time series and 𝜑 is the Morlet mother wavelet, scaled by factor 𝑠 and translated in time by 𝑡. The Morlet mother wavelet is defined by the equation: 𝜑(𝑢) = 1 √𝜋 4 exp⁡(−𝑖2𝜋𝑢)exp⁡(−0.5𝑢2), where 𝑖= √−1. The rationale for using the Morlet wavelet is that it affords good localization of events in time and frequency due to its Gaussian shape (Bernjak et al. 2012). The wavelet coefficients are complex numbers in the time-frequency plane when the Morlet wavelet is used: where 𝑖= √−1. The rationale for using the Morlet wavelet is that it affords good localization of events in time and frequency due to its Gaussian shape (Bernjak et al. 2012). The wavelet coefficients are complex numbers in the time-frequency plane when the Morlet wavelet is used: 𝑋(𝜔𝑘, 𝑡𝑛) = 𝑋𝑘,𝑛= 𝑎𝑘,𝑛+ 𝑖𝑏𝑘,𝑛. They define the instantaneous relative phase, 𝜃𝑘,𝑛= arctan⁡( 𝑏𝑘,𝑛 𝑎𝑘,𝑛), and the absolute amplitude, |𝑋𝑘,𝑛| = √𝑎𝑘,𝑛 2 + 𝑏𝑘,𝑛 2 , |𝑋𝑘,𝑛| = √𝑎𝑘,𝑛 2 + 𝑏𝑘,𝑛 2 , for each frequency and time. for each frequency and time. During the measurement, hypoxia may create phase modulations. A mathematical tool to find the relationship between the phases of two signals is the wavelet phase coherence (WPCO). WPCO enables us to determine whether the oscillations detected are significantly correlated over time. To estimate the WPCO we used the following expression (Lachaux et al. 2002): 𝐶𝜃(𝑓𝑘) = 1 𝑛|∑ exp⁡[𝑖(𝜃2𝑘,𝑛−𝜃1𝑘,𝑛)] 𝑛 𝑡=1 |, where 𝜃𝑘,𝑛= arctan⁡( 𝑏𝑘,𝑛 𝑎𝑘,𝑛) is an instantaneous measure of phases at each time tn and frequency 𝑓𝑘 for both signals. When two oscillations are unrelated (related), their phase difference continuously changes (remain constant) with time, thus their 𝐶𝜃(𝑓𝑘) approaches zero (one). Additionally, we can calculate the phase difference ∆𝜃𝑘, which provides information about the phase lag of one oscillator compared to the other: ∆𝜃𝑘= 𝑎𝑟𝑐𝑡𝑎𝑛( 1 𝑛∑ 𝑠𝑖𝑛(∆𝜃2𝑘,𝑛−∆𝜃1𝑘,𝑛) 𝑛 𝑡=1 1 𝑛∑ 𝑐𝑜𝑠(∆𝜃2𝑘,𝑛−∆𝜃1𝑘,𝑛) 𝑛 𝑡=1 ), where⁡∆𝜃𝑘∈(−180°, 180°). Statistical analysis To avoid the assumption of normality in the results, nonparametric statistical tests were used for all comparisons. The Wilcoxon rank sum test was used to compare whether the median of results for breathing a gas mixture with 19.8% O2 and 14.8% O2 was significantly different. The results of our calculations are found in Tables 1 and Figures 2, and 3. To test whether the estimated values of phase coherence are statistically significant, the surrogate data testing method was used (Lancaster et al. 2018). As we know there are naturally less cycles of oscillations the lower in frequency that we consider. This can cause artificially increased wavelet phase coherence at low frequencies, even in cases where there is none. The surrogate analysis helps us to find a significance level above which the phase coherence may be regarded as physically meaningful. To estimate significance level, we used intersubject surrogates (Sun et al. 2012), which assumes that the signals collected from different subjects must be independent, while having similar characteristic properties. The actual value of phase coherence obtained at each frequency can then be compared with the surrogate threshold. When the phase coherence is located above the threshold it is considered to be statistically significant. Authors’ contributions Conceived and designed the experiments: A.G., M.G., J.P.N., P.J.W. Performed the experiments: J.S., T.T., M.G. Analysed the data: A.G. M.G. Contributed reagents/materials/analysis tools: M.A.M., P.N., G.P.K., M.W.W., A.F., J.R., N.G., A.G., P.L., M.G. Co-wrote the paper: A.G., M.G., P.J.W. All authors reviewed the manuscript and agreed to publish the paper. Acknowledgements We would like to thank all of the volunteer participants that contributed their valuable time to these experiments. Funding Dr Marcin Gruszecki was supported by the NCN-grant number 2018/02/X/NZ4/00464. Competing interests Profs Andrzej F. Frydrychowski and Pawel J. Winklewski are stakeholders in NIRTI SA. The other authors declare no competing interests. Data Availability Statement The data presented in this study are available on request from the corresponding author. The data are not publicly available due to privacy. References Alonso-Lana, S., Marquié, M., Ruiz, A., Boada, M. Cognitive and Neuropsychiatric Manifestations of COVID-19 and Effects on Elderly Individuals With Dementia, Front. Aging Neurosci. 2020; 12, 588872 Hampson, N.B., Camporesi, E.M., Stolp, B.W., Moon, R.E., Shook, J.E., Griebel, J.A., and Piantadosi, C.A., Cerebral oxygen availability by NIR spectroscopy during transient hypoxia in humans J Appl Physiol. 1990; 69(3):907-13 Alonso-Lana, S., Marquié, M., Ruiz, A., Boada, M. Cognitive and Neuropsychiatric Manifestations of COVID-19 and Effects on Elderly Individuals With Dementia, Front. Aging Neurosci. 2020; 12, 588872 Hampson, N.B., Camporesi, E.M., Stolp, B.W., Moon, R.E., Shook, J.E., Griebel, J.A., and Piantadosi, C.A., Cerebral oxygen availability by NIR spectroscopy during transient hypoxia in humans J Appl Physiol. 1990; 69(3):907-13 Kety, S.S., Schmidt, C.F. The effects of altered arterial tensions of carbon dioxide and oxygen on cerebral blood flow and cerebral oxygen consumption of normal young men J. Clin. Invest. 1948; 27(4): 484-92 Dubowitz, D.J., Dyer, E.A.W., Theilmann, R.J., Buxton, R.B. and Hopkins, S.R. Early brain swelling in acute hypoxia, J Appl Physiol 2009; 107:244–252 Alonso-Lana, S., Marquié, M., Ruiz, A., Boada, M. Cognitive and Neuropsychiatric Manifestations of COVID-19 and Effects on Elderly Individuals With Dementia, Front. Aging Neurosci. 2020; 12, 588872 Front. Aging Neurosci. 2020; 12, 588872 Hampson, N.B., Camporesi, E.M., Stolp, B.W., Moon, R.E., Shook, J.E., Griebel, J.A., and Piantadosi, C.A., Cerebral oxygen availability by NIR spectroscopy during transient hypoxia in humans J Appl Physiol. 1990; 69(3):907-13 Hampson, N.B., Camporesi, E.M., Stolp, B.W., Moon, R.E., Shook, J.E., Griebel, J.A., and Piantadosi, C.A., Cerebral oxygen availability by NIR spectroscopy during transient hypoxia in humans J Appl Physiol. 1990; 69(3):907-13 Kety, S.S., Schmidt, C.F. The effects of altered arterial tensions of carbon dioxide and oxygen on cerebral blood flow and cerebral oxygen consumption of normal young men J. Clin. Invest. 1948; 27(4): 484-92 Kety, S.S., Schmidt, C.F. The effects of altered arterial tensions of carbon dioxide and oxygen on cerebral blood flow and cerebral oxygen consumption of normal young men J. Clin. Invest. 1948; 27(4): 484-92 Dubowitz, D.J., Dyer, E.A.W., Theilmann, R.J., Buxton, R.B. and Hopkins, S.R. Early brain swelling in acute hypoxia, J Appl Physiol 2009; 107:244–252 Dubowitz, D.J., Dyer, E.A.W., Theilmann, R.J., Buxton, R.B. and Hopkins, S.R. Early brain swelling in acute hypoxia, J Appl Physiol 2009; 107:244–252 Dubowitz, D.J., Dyer, E.A.W., Theilmann, R.J., Buxton, R.B. and Hopkins, S.R. References Early brain swelling in acute hypoxia, J Appl Physiol 2009; 107:244–252 DiPasquale, D.M., Muza, S.R., Gunn, A.M., Li, Z., Zhang, Q., Harris, N.S., Strangman, G.E. Evidence for cerebral edema, cerebral perfusion, andintracranial pressure elevations in acute mountain sickness 2016, Brain and Behavior; 6(3), e00437 Halder, S.K., Milner, R. Mild hypoxia triggers transient blood–brain barrier disruption: a fundamental protective role for microglia, Acta Neuropath. Communications 2020; 8:175 Vestergaard, M.B., Lindberg, U., Aachmann-Andersen, N.J., Lisbjerg, K., Christensen, S.J., Law, I., Rasmussen, P., Olsen, N.V., Larsson, H.B.V. Acute hypoxia increases the cerebral metabolic rate – a magnetic resonance imaging study 2016; 36(6):1046-58 Saleem, S., Teal, P.D., Kleijn W.B., Ainslie, P.N., Tzeng, Y.C. Identification of human sympathetic neurovascular control using multivariate wavelet decomposition analysis Am J Physiol Heart Circ Physiol. 2016 ;311(3):H837-48 Marina, N., Christie, I.N., Korsak, A., Doronin, M., Brazhe, A., Hosford, P.S., Wells, J.A., Sheikhbahaei, S., Humoud, I., Paton, J.F.R., Lythgoe, M.F., Semyanov, A., Kasparov S.,. Gourine, A.V. Astrocytes monitor cerebral perfusion and control systemic circulation to maintain brain blood flow 2020, Nature Communications, 11:131 Saleem, S., Teal, P.D., Kleijn W.B., Ainslie, P.N., Tzeng, Y.C. Identification of human sympathetic neurovascular control using multivariate wavelet decomposition analysis Am J Physiol Heart Circ Physiol. 2016 ;311(3):H837-48 Marina, N., Christie, I.N., Korsak, A., Doronin, M., Brazhe, A., Hosford, P.S., Wells, J.A., Sheikhbahaei, S., Humoud, I., Paton, J.F.R., Lythgoe, M.F., Semyanov, A., Kasparov S Gourine A V Astrocytes monitor cerebral perfusion and control Saleem, S., Teal, P.D., Kleijn W.B., Ainslie, P.N., Tzeng, Y.C. Identification of human sympathetic neurovascular control using multivariate wavelet decomposition analysis Am J Physiol Heart Circ Physiol. 2016 ;311(3):H837-48 Marina N Christie I N Korsak A Doronin M Brazhe A Hosford P S Wells Marina, N., Christie, I.N., Korsak, A., Doronin, M., Brazhe, A., Hosford, P.S., Wells, J.A., Sheikhbahaei, S., Humoud, I., Paton, J.F.R., Lythgoe, M.F., Semyanov, A., Kasparov S.,. Gourine, A.V. Astrocytes monitor cerebral perfusion and control systemic circulation to maintain brain blood flow 2020, Nature Communications, 11:131 Winklewski, P.J., Wolf, J., Gruszecki, M., Wszedybyl-Winklewska, M., Narkiewicz, K. Current understanding of the effects of inspiratory resistance on the interactions between systemic blood pressure, cerebral perfusion, intracranial pressure, and cerebrospinal fluid dynamics. J Appl Physiol 2019, 127: 1206–1214 Winklewski, P.J., Wolf, J., Gruszecki, M., Wszedybyl-Winklewska, M., Narkiewicz, K. Current understanding of the effects of inspiratory resistance on the interactions between systemic blood pressure, cerebral perfusion, intracranial pressure, and cerebrospinal fluid dynamics. References J Appl Physiol 2019, 127: 1206–1214 Ferrari, M., Quaresima, V. A brief review on the history of human functional near- infrared spectroscopy (fNIRS) development and fields of application Neuroimage, 2012; 63(2):921-35 Gruszecki, M., Nuckowska, M.K., Szarmach, A., Radkowski, M., Szalewska, D., Waskow, M., Szurowska, E., Frydrychowski, A.F., Demkow, U., Winklewski, P.J. Oscillations of Subarachnoid Space Width as a Potential Marker of Cerebrospinal Fluid Pulsatility Adv. Exp. Med. Biol. 2018; 1070:37-47 Oscillations of Subarachnoid Space Width as a Potential Marker of Cerebrospinal Fluid Pulsatility Adv. Exp. Med. Biol. 2018; 1070:37-47 Oscillations of Subarachnoid Space Width as a Potential Marker of Cerebrospinal Fluid Pulsatility Adv. Exp. Med. Biol. 2018; 1070:37-47 y y , , , , j , , , , , Technical foundations for noninvasive assessment of changes in the width of the subarachnoid space with near-infrared transillumination-backscattering sounding (NIR-TBSS). Ieee Transactions On Biomedical Engineering 2002; 49(8):887-904 Stefanovska, A., Bracic, M., Kvernmo, H.D. Wavelet analysis of oscillations in the peripheral blood circulation measured by laser Doppler technique IEEE Technical foundations for noninvasive assessment of changes in the width of the subarachnoid space with near-infrared transillumination-backscattering sounding (NIR-TBSS). Ieee Transactions On Biomedical Engineering 2002; 49(8):887-904 Stefanovska, A., Bracic, M., Kvernmo, H.D. Wavelet analysis of oscillations in the peripheral blood circulation measured by laser Doppler technique IEEE Transactions on Biomedical Engineering 1999; 46(10):1230-9 Finch CA, Lenfant C. Oxygen transport in man. N Engl J Med 1972; 286(8):407–415 Talbot NP, Balanos GM, Dorrington KL, Robbins PA. Two temporal components within the human pulmonary vascular response to approximately 2 h of isocapnic hypoxia. J Appl Physiol. 2005; 98, 1125 Dubowitz DJ, Dyer EA, Theilmann RJ, Buxton RB, Hopkins SR. Early brain swelling in acute hypoxia. J. Appl Physiol. 2009; 107: 244-52 Dubowitz DJ, Dyer EA, Theilmann RJ, Buxton RB, Hopkins SR. Early brain swelling in acute hypoxia. J. Appl Physiol. 2009; 107: 244-52 Greitz D, Franck A, Nordell B. On the pulsatile nature of intracranial and spinal CSF-circulation demonstrated by MR imaging. Acta Radiol. 1993; 34: 321 Linninger AA, Tsakiris C, Zhu DC, Xenos M, Roycewicz P, Danziger Z, et al. Pulsatile cerebrospinal fluid dynamics in the human brain. IEEE Trans Biomed Eng. 2005; 52: 557-565. Greitz D, Franck A, Nordell B. On the pulsatile nature of intracranial and spinal CSF-circulation demonstrated by MR imaging. Acta Radiol. 1993; 34: 321 Linninger AA, Tsakiris C, Zhu DC, Xenos M, Roycewicz P, Danziger Z, et al. Clin. Neurophysiol. 32, 157 (2002). Lancaster, G. et al. Surrogate data for hypothesis testing of physical systems. Physics Rep. 748, 1-60, (2018). Sun, J., Hong, X. & Tong, S. Phase synchronization analysis of EEG signals: an evaluation based on surrogate tests. IEEE Trans. Biomed. Eng. 59, 2254–2263 (2012). Stefanovska A, Bračič M, Kvernmo HD. Wavelet analysis of oscillations in the peripheral blood circulation measured by laser Doppler technique, IEEE Trans. Bio. Med. Eng., 1999;46:1230–1239. Stefanovska A, Bračič M, Kvernmo HD. Wavelet analysis of oscillations in the peripheral blood circulation measured by laser Doppler technique, IEEE Trans. Bio. Med. Eng., 1999;46:1230–1239. Med. Eng., 1999;46:1230–1239. Cui, W., Kumar, C. & Chance, B. Experimental study of migration depths for the photons measured at sample surface. SPIE 1431, 180–191 (1991) Bernjak, A., Stefanovska, A. & McClintock, P. V. E. Coherence between fluctuations in blood flow and oxygen saturation. Fluct. Noise Lett. 11, 1–12 (2012) Cui, R. et al. Wavelet coherence analysis of spontaneous oscillations in cerebral tissue oxyhaemoglobin concentrations and arterial blood pressure in elderly subjects. Microvasc Res. 93, 14–20 (2014). Kim, T. J. et al. Prognostication of neurological outcome after cardiac arrest using wavelet phase coherence analysis of cerebral oxygen Resuscitation 150 41–49 Cui, W., Kumar, C. & Chance, B. Experimental study of migration depths for the photons measured at sample surface. SPIE 1431, 180–191 (1991) Bernjak, A., Stefanovska, A. & McClintock, P. V. E. Coherence between fluctuations in blood flow and oxygen saturation. Fluct. Noise Lett. 11, 1–12 (2012) Cui, R. et al. Wavelet coherence analysis of spontaneous oscillations in cerebral ti h l bi t ti d t i l bl d i ld l bj t Kim, T. J. et al. Prognostication of neurological outcome after cardiac arrest using wavelet phase coherence analysis of cerebral oxygen. Resuscitation 150, 41–49 (2020) Kim, T. J. et al. Prognostication of neurological outcome after cardiac arrest using wavelet phase coherence analysis of cerebral oxygen. Resuscitation 150, 41–49 (2020) Wszedybyl-Winklewska, M., Wolf, J., Świerblewska, E., Kunicka, K., Gruszecka, A., Gruszecki, M., Kucharska, W., Winklewski, P.J., Zabulewicz, J., Gumiński, W., Pietrewicz, M., Frydrychowski, A.F., Bieniaszewski, L., Narkiewicz, K. Acute hypoxia diminishes the relationship between blood pressure and subarachnoid space width oscillations at the human cardiac frequency. 2017, Plos One, 12(2), 1-13 Baumann, R., Bauer, Ch., and Bartels, H., Sixth Intern. Berlin Symp. Structure and Function of Erythrocytes, August 19-22 (1970) Lenfant, C. T., Torrance, E., Englisch, E., Finch, C. References Pulsatile cerebrospinal fluid dynamics in the human brain. IEEE Trans Biomed Eng. 2005; 52: 557-565. Gruszecki, M. et al. Human subarachnoid space width oscillations in the resting state. Sci. Rep. 8, 3057 (2018) Gruszecki, M. et al. Human subarachnoid space width oscillations in the resting state. Sci. Rep. 8, 3057 (2018) Gruszecka A. et al. Comparison of near infrared spectroscopy (NIRS) and near- infrared transillumination-backscattering sounding (NIR-T/BSS) methods. Sci. Rep. 10(1), 18668 (2020) Bernjak, A. et al. Coherence between fluctuations in blood flow and oxygen saturation. Fluct. Noise Lett. 11, 1–12 (2012). Lachaux, J. P. et al. Estimating the time-course of coherence between single-trial brain signals: an introduction to wavelet coherence. Clin. Neurophysiol. 32, 157 (2002). A., Reynafafje, C., Ramos, J., and Faura, J., J. Clin. Invest., 47, 2652 (1968) Lenfant, C. T., Torrance, E., Englisch, E., Finch, C. A., Reynafafje, C., Ramos, J., and Faura, J., J. Clin. Invest., 47, 2652 (1968) Dubowitz DJ, Dyer EA, Theilmann RJ, Buxton RB, Hopkins SR. Early brain swelling in acute hypoxia. J. Appl Physiol. 2009; 107: 244 Dubowitz DJ, Dyer EA, Theilmann RJ, Buxton RB, Hopkins SR. Early brain swelling in acute hypoxia. J. Appl Physiol. 2009; 107: 244 DiPasquale DM, Muza SR, Gunn AM, Li Z, Zhang Q, Harris NS, et al. Evidence for cerebral edema, cerebral perfusion, and intracranial pressure elevations in acute mountain sickness. Brain Behav. 2016; 6: e00437 DiPasquale DM, Muza SR, Gunn AM, Li Z, Zhang Q, Harris NS, et al. Evidence for cerebral edema, cerebral perfusion, and intracranial pressure elevations in acute mountain sickness. Brain Behav. 2016; 6: e00437 Michiels, C., Arnould, T., Remacle, J., Endothelial cell responses to hypoxia: initiation of a cascade of cellular interactions, Biochimica et Biophysica Acta, 2000, 1497(1), 1- 10 Michiels, C., Arnould, T., Remacle, J., Endothelial cell responses to hypoxia: initiation of a cascade of cellular interactions, Biochimica et Biophysica Acta, 2000, 1497(1), 1- 10 10 10 Angelova, P.R., Kasymov, V., Christie, I., Sheikhbahaei, S., Turovsky, E., Marina, N., Korsak, A., Zwicker, J., Teschemacher, A.G., Ackland, G.L., Funk, G.D., Kasparov, S., Abramov A.Y., Gourine, A.V. Functional Oxygen Sensitivity of Astrocytes Journal of Neuroscience 2015; 35(29):10460-10473 Marina, N., Turovsky, E., Christie, I.N., Hosford, P.S., Hadjihambi, A., Korsak, A., Ang, R., Mastitskaya, S., Sheikhbahaei, S., Theparambil, S.M., Gourine, A.V. Brain metabolic sensing and metabolic signaling at the level of an astrocyte Glia 2018; 66(6):1185-1199 10 Angelova, P.R., Kasymov, V., Christie, I., Sheikhbahaei, S., Turovsky, E., Marina, N., Korsak, A., Zwicker, J., Teschemacher, A.G., Ackland, G.L., Funk, G.D., Kasparov, S., Abramov A.Y., Gourine, A.V. Functional Oxygen Sensitivity of Astrocytes Journal of Neuroscience 2015; 35(29):10460-10473 Marina, N., Turovsky, E., Christie, I.N., Hosford, P.S., Hadjihambi, A., Korsak, A., Ang, R., Mastitskaya, S., Sheikhbahaei, S., Theparambil, S.M., Gourine, A.V. Brain metabolic sensing and metabolic signaling at the level of an astrocyte Glia 2018; 66(6):1185-1199 Angelova, P.R., Kasymov, V., Christie, I., Sheikhbahaei, S., Turovsky, E., Marina, N., Korsak, A., Zwicker, J., Teschemacher, A.G., Ackland, G.L., Funk, G.D., Kasparov, S., Abramov A.Y., Gourine, A.V. Clin. Neurophysiol. 32, 157 (2002). Functional Oxygen Sensitivity of Astrocytes Journal of Neuroscience 2015; 35(29):10460-10473 Turovsky, E.A., Braga, A., Yu, Y., Esteras, N., Korsak, A., Theparambil, S.M., Hadjihambi, A., Hosford, P.S., Teschemacher, A.G., Marina, N., Lythgoe, M.F., Haydon P.G., Gourine, A.V. Mechanosensory Signaling in Astrocytes Journal of Neuroscience 2020; 40(49):9364-9371 Turovsky, E.A., Braga, A., Yu, Y., Esteras, N., Korsak, A., Theparambil, S.M., Hadjihambi, A., Hosford, P.S., Teschemacher, A.G., Marina, N., Lythgoe, M.F., Haydon P.G., Gourine, A.V. Mechanosensory Signaling in Astrocytes Journal o Neuroscience 2020; 40(49):9364-9371 Chow, N., Bell, R.D., Deane, R., Streb, J.W., Chen, J., Brooks, A., Nostrand, W.V., Miano, J.M., Zlokovic, B.V. Serum response factor and myocardin mediate arterial hypercontractility and cerebral blood flow dysregulation in Alzheimer's phenotype PNAS 2007; 104(3):823-828 van Beek, A.H.E.A., Lagro, J., Olde-Rikkert, M.G.M., Zhang, R., Claassen, J.A.H.R. Oscillations in cerebral blood flow and cortical oxygenation in Alzheimer's disease Neurobiol Aging 2012; 33(2):428.e21-31 van Beek, A.H.E.A., Lagro, J., Olde-Rikkert, M.G.M., Zhang, R., Claassen, J.A.H.R. Oscillations in cerebral blood flow and cortical oxygenation in Alzheimer's disease Neurobiol Aging 2012; 33(2):428.e21-31 Neurobiol Aging 2012; 33(2):428.e21-31 Vermeij, A., Meel-van den Abeelen, A.S.S., Kessels, R.P.C., van Beek, A.H.E.A., Claassen, J.A.H.R. Very-low-frequency oscillations of cerebral hemodynamics and blood pressure are affected by aging and cognitive load NeuroImage 2014; 85:608- 615 Yunjie, T., Blaise Deb, F. Time lag dependent multimodal processing of concurrent fMRI and near-infrared spectroscopy (NIRS) data suggests a global circulatory origin for low-frequency oscillation signals in human brain Neuroimage 2010; 53(2):553-64 Frydrychowski, A.F., Wszedybyl-Winklewska, M., Guminski, W., Przyborska, A., Kaczmarek, J., Winklewski, P.J. Use of Near Infrared Transillumination / Back Scattering Sounding (NIR-T/BSS) to assess effects of elevated intracranial pressure on width of subarachnoid space and cerebrovascular pulsation in animals Acta Neurobiol Exp. 2011; 71(3):313-21 Vermeij, A., Meel-van den Abeelen, A.S.S., Kessels, R.P.C., van Beek, A.H.E.A., Claassen, J.A.H.R. Very-low-frequency oscillations of cerebral hemodynamics and blood pressure are affected by aging and cognitive load NeuroImage 2014; 85:608- 615 Yunjie, T., Blaise Deb, F. Time lag dependent multimodal processing of concurrent fMRI and near-infrared spectroscopy (NIRS) data suggests a global circulatory origin for low-frequency oscillation signals in human brain Neuroimage 2010; 53(2):553-64 Frydrychowski, A.F., Wszedybyl-Winklewska, M., Guminski, W., Przyborska, A., Kaczmarek, J., Winklewski, P.J. Use of Near Infrared Transillumination / Back Scattering Sounding (NIR-T/BSS) to assess effects of elevated intracranial pressure on width of subarachnoid space and cerebrovascular pulsation in animals Acta Neurobiol Exp. 2011; 71(3):313-21 Haubrich, C., Czosnyka, Z., Lavinio, A., Smielewski, P., Diehl, R.R., Pickard, J.D., Czosnyka, M. Is there a direct link between cerebrovascular activity and cerebrospinal fluid pressure-volume compensation? Stroke, 2007; 38(10):2677-80 Haubrich, C., Czosnyka, Z., Lavinio, A., Smielewski, P., Diehl, R.R., Pickard, J.D., Czosnyka, M. Is there a direct link between cerebrovascular activity and cerebrospinal fluid pressure-volume compensation? Stroke, 2007; 38(10):2677-80 Haubrich, C., Czosnyka, Z., Lavinio, A., Smielewski, P., Diehl, R.R., Pickard, J.D., Czosnyka, M. Is there a direct link between cerebrovascular activity and cerebrospinal fluid pressure-volume compensation? Stroke, 2007; 38(10):2677-80
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https://link.springer.com/content/pdf/10.1007/s00347-021-01328-1.pdf
de
Visusverschlechterung nach intravitrealer Injektion von Dexamethason im vitrektomierten Auge
˜Derœ Ophthalmologe
2,021
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1,573
Der Ophthalmologe Bild und Fall Ophthalmologe 2021 · 118:1051–1053 https://doi.org/10.1007/s00347-021-01328-1 Eingegangen: 22. Dezember 2020 Überarbeitet: 17. Januar 2021 Angenommen: 19. Januar 2021 Online publiziert: 12. März 2021 © Der/die Autor(en) 2021 Victoria Reitmeier1 · Christoph Kern1 · Maria Poimenidou1 · Ines M. Lanzl2 Anamnese zeigten sich am rechten Auge im Bereich der Fovea intraretinale Zysten im Bereich der äußeren plexiformen Schicht im Sinne eines zystoiden Makulaödems bei einer Netzhautdicke von 350 μm (. Abb. 1). Ein 56-jähriger Patient stellte sich zur weiteren Behandlung eines postoperativ persistierenden zystoiden Makulaödems in unserer Praxis vor. Bei epiretinaler Gliose durch eine Uveitis unklarer Ursache wurden beide Augen vor 5 Jahren mit Membranpeeling plus Vitrektomie ophthalmochirurgisch versorgt. Binnen der letzten 3 Jahre erfolgte bereits mehrfach die intravitreale Gabe von VEGFInhibitoren durch einen niedergelassenen Kollegen. Hierdurch wurde am linken Auge ein stabiler, trockener Netzhautbefund mit einer bestkorrigierten Sehschärfe (BCVA) von 0,7 dezimal erreicht. Bei ausgeprägterem Befund und schwankender BCVA zwischen 0,3 und 0,5 am rechten Auge fand die letzte intravitreale Injektion mit Aflibercept 8 Wochen vor Erstvorstellung in unserer Praxis statt. Laut Übernahmebericht wurde im Behandlungsverlauf unter Aflibercept das beste therapeutische Ansprechen erreicht. 1 2 Chiemsee Augen Tagesklinik, Prien am Chiemsee, Deutschland Klinikum rechts der Isar der Technischen Universität München, München, Deutschland Visusverschlechterung nach intravitrealer Injektion von Dexamethason im vitrektomierten Auge Behandlungsverlauf Aufgrund der uveitischen Genese des Makulaödems und damit assoziierter entzündlicher Komponente entschieden wir uns initial für die probatorische Gabe von Nepafenac 3 mg/ml Augentropfen 2-mal täglich am rechten Auge und Verlaufskontrollen im Abstand von 6 Wochen. Dies entspricht nicht den Leitlinien der DOG zur Behandlung des Makulaödems bei Uveitis [1], jedoch wurde vom Patienten zunächst eine nichtinvasive Therapie gewünscht. Hierunter verschlechterte sich die BCVA auf 0,2 mit Zunahme der intraretinalen Flüssigkeit in der OCT. Bei schwankendem therapeutischem Ansprechen auf die Gabe von VEGF-Inhibitoren in der Vergangenheit entschieden wir uns deshalb für Dexamethason intravitreal (0,7 mg Dexamethason; Ozurdex, Pharm Allergan GmbH, Frankfurt/M., Deutschland). Die Injektion des Implantats verlief komplikationslos. Der Patient bemerkte jedoch sofort bei der Injektion eine plötzliche Visusverschlechterung, teilte dies der behandelnden Ärztin nicht mit, wie wir retrospektiv erfahren haben. Den Infektionsängsten zu Beginn der COVID-19Pandemie geschuldet, erschien er nicht zur vereinbarten postoperativen IVOMKontrolle in unserer Praxis. Bei Wiedervorstellung 8 Wochen später wurde eine BCVA von 1/25 Metervisus erreicht, der Augeninnendruck lag bei 31 mmHg. Fundoskopisch zeigten sich im papillomakulären Bereich intraretinale Blutungen und eine gelbliche scharf umschriebene Läsion parafoveal (. Abb. 2 und 3). Klinischer Befund Bei Erstuntersuchung präsentierte sich der Patient mit einer BCVA von 0,6 am rechten und 0,8 am linken Auge. Die vorderen Augenabschnitte waren reizfrei, der Patient pseudophak. Bis auf Pigmentepithelverschiebungen im Bereich der Makula und einem zystoiden Makulaödem war der fundoskopische Befund am rechten Auge unauffällig. In der optischen Kohärenztomographie (OCT) Abb. 1 8 OCT des rechten Auges bei Erstvorstellung in unserer Praxis. Es zeigt sich intraretinale Flüssigkeit mit Aufhebung der fovealen Kurvatur Der Ophthalmologe 10 · 2021 1051 Bild und Fall Abb. 2 8 Fundusfotografie des rechten Auges mit heller intra- und subretinaler Läsion und umgebenden intra- und subretinalen Blutungsresten im temporal oberen papillomakulären Bündel Abb. 3 8 OCT des rechten Auges im Bereich der fundoskopischen Läsion mit subretinaler solider Pigmentepithelabhebung D Wie lautet Ihre Diagnose? Das persistierende intraretinale zystoide Makulaödem nach vitreoretinaler Chi- rurgie konfrontiert behandelnde Ärzte oft mit ausbleibenden Visusverbesserungen, jedoch begrenzten therapeutischen Optionen. Bei intraretinalem zystoidem Ödem nachUveitis istdie Gabe vonOzurdex auch im vitrektomierten Auge eine therapeutische Option mit gutem Sicherheitsprofil und in der Regel komplikationsarmem Behandlungsverlauf [2, 3]. Bisher unauffällige Anti-VEGF-Injektionen und eine Bulbuslänge von 22,3 mm haben uns ex ante keinerlei Hinweise für ein erhöhtes Komplikationsrisiko gegeben. Gemäß den Herstellerangaben wurde der Applikator parallel zum Limbus eingebracht und für die Injektion senkrecht zum Zentrum des Auges Richtung hinterer Augenpol ausgerichtet [3]. Dies führte bei unserem Patienten zu einem traumatischen Netzhautschaden, welcher in der Literatur als eine äußerst seltene Komplikation sowohl bei vitrektomierten als auch in nicht ophthalmochirurgisch versorgten Augen bereits vorbeschrieben wurde [4–7]. Abb. 4 8 Fundusfotografie des rechten Auges 3 Monate nach traumatischem Netzhauschaden Abb. 5 8 OCT des rechten Auges mit Rückgang der fibrosierten Abhebung bei bestehendem Verlust der ellipsoiden Zone Therapieverlauf Zur Therapie verordneten wir am rechten Auge topisch Nepafenac 3 mg/ml Augentropfen 2-mal täglich und Dorzolamid 20 mg/ml /Timolol 5 mg/ml Augentropfen 2-mal täglich sowie oral 90 mg Celecoxib 1-mal täglich. Hierunter wurde im weiteren Behandlungsverlauf eine BCVA von 0,16 unter fundoskopischer Remission der Blutung und Resorption der Fibrinmassen erreicht (. Abb. 4). Bei Rückgang der subretinalen soliden Pigmentepithelabhebung blieb in der OCT ein Verlust der äußeren Netzhautschichten, vornehmlich der ellipsoiden Zone zurück (. Abb. 5). Das linke Auge zeigte im gesamten Behandlungszeitraum einen stabilen Befund klinisch und in der OCT. Diskussion 1052 Der Ophthalmologe 10 · 2021 Christensen et al. vermuteten in Konsequenz einen verstärkten Einfluss des veränderten Injektionsmediums nach Vitrektomie durch Fehlen kollagener Fasern, Hyaluronsäure und Opticin und stellten unterschiedliche Kräfte bei Injektion von Ozurdex in verschiedene Medien fest [4]. Vorausgegangene komplikationslose Injektionen von Ozurdex im vitrektomierten Auge bei Casati et al. relativieren diese Vermutung und lassen den traumatischen Netzhautschaden als eher schwer quantifizierbar einstufen [5]. Meyer et al. vermaßen die Mündungsgeschwindigkeit des Ozurdex-Implantates beim Verlassen des Injektors mit einer Hochgeschwindigkeitskamera in Glaskörper und Wasser [8]. Ihre Ergebnisse lassen darauf schließen, dass der direkte Impakt auf die Netzhaut in beiden Fällen keinen Schaden auslösen sollte. Die Autoren stellen auch klar, dass die Injektionsgeschwindigkeit des Implantates durch den Druck gesteuert werden kann, mit dem man auf den Abzugs- knopf drückt. Deshalb ist es gerade bei bereits vitrektomierten Augen wichtig, dass man den Auslöser langsam herunterdrückt. Darüber hinaus ist als Konsequenz aus unserem Fall der Injektionswinkel Richtung hinterer Pol, wie in der Gebrauchsanweisung beschrieben, im vitrektomierten Auge zu überdenken. Unserer Meinung nach sollte dieser nicht direkt auf den hinteren Pol, sondern leicht nach nasal ausgerichtet werden, um eine Läsion des papillomakulären Bündels, wie in unserem Fall, zu vermeiden. Eine Aufklärung über die Möglichkeit der traumatischen retinalen Läsion sollte immer und v. a. bei vitrektomierten Augen vor der Injektion erfolgen. Diagnose: traumatischer »Netzhautschaden nach Injektion eines DexamethasonImplantates In der OCT zeigte sich die fundoskopische Läsion als umschriebene fibrosierte Abhebung. Bei zentraler Netzhautdicke von 240 μm war nun eine Atrophie der vornehmlich äußeren Netzhautschichten mit komplettem Verlust der ellipsoiden Zone zu erkennen. In Zusammenschau der Befunde diagnostizierten wir deshalb einen durch das Dexamethason-Implantat hervorgerufenen traumatischen Netzhautschaden mit konsekutiver, vermutlich traumatisch und durch Blutabbauprodukte bedingter Atrophie im oberen Bereich des hinteren Pols in einem vitrektomierten Auge (. Abb. 5). Fazit für die Praxis 4 Injektionswinkel von Ozurdex im Korrespondenzadresse Ines M. Lanzl Klinikum rechts der Isar der Technischen Universität München München, Deutschland il@auge.bayern Funding. Open Access funding enabled and organized by Projekt DEAL. Einhaltung ethischer Richtlinien Interessenkonflikt. I.M. Lanzl weist auf folgende Beziehungen hin: Honoraria für Vorträge von Bayer, Santen und Thea Pharma. C. Kern weist auf folgende Beziehungen hin: Honoraria für Vorträge von Bayer. V. Reitmeier und M. Poimenidou geben an, dass kein Interessenkonflikt besteht. Für diesen Beitrag wurden vom Autor keine Studien an Menschen oder Tieren durchgeführt. Für die aufgeführten Studien gelten die jeweils dort angegebenen ethischen Richtlinien. Für Bildmaterial oder anderweitige Angaben innerhalb des Manuskripts, über die Patienten zu identifizieren sind, liegt von ihnen und/ oder ihren gesetzlichen Vertretern eine schriftliche Einwilligung vor. 3. Pelegrín L, de la Maza M, Molins B et al (2015) Longterm evaluation of dexamethasone intravitreal implant in vitrectomized and non-vitrectomized eyes with macular edema secondary to noninfectious uveitis. Eye 29:943–950. https://doi.org/ 10.1038/eye.2015.73 4. Christensen L, Sanders R, Olson J (2016) “Magic bullet”: eccentric macular hole as a complication from dexamethasone implant insertion. Case Rep Ophthalmol Med. https://doi.org/10.1155/2016/ 1706234 5. Casati S, Bruni E, Marchini G (2016) Retinal and vitreous hemorrhage after traumatic impact of dexamethasone implant in a vitrectomized eye. Eur J Ophthalmol 26(3):e55–e57. https://doi.org/ 10.5301/ejo.5000716 6. Lee SM, Jung JW, Park SW, Lee JE, Byon IS (2017) Retinal injury following intravitreal injection of a dexamethasone implant in a vitrectomized eye. Int J Ophthalmol 10(6):1019–1020. https://doi.org/ 10.18240/ijo.2017.06.31 7. Ekinci C, Kayıran A, Özdemir H (2019) Extramacular retinal hole following intravitreal dexamethasone implant: case report. Turk J Ophthalmol 49(3):175–177. https://doi.org/10.4274/ tjo.galenos.2019.98975 8. Meyer CH, Klein A, Alten F, Liu Z, Stanzel BV et al (2012) Release and velocity of micronized dexamethasone implants with an intravitreal drug delivery system. Retina 32:2133–2140 Open Access. Dieser Artikel wird unter der Creative Commons Namensnennung 4.0 International Lizenz veröffentlicht, welche die Nutzung, Vervielfältigung, Bearbeitung, Verbreitung und Wiedergabe in jeglichem Medium und Format erlaubt, sofern Sie den/die ursprünglichen Autor(en) und die Quelle ordnungsgemäß nennen, einen Link zur Creative Commons Lizenz beifügen und angeben, ob Änderungen vorgenommen wurden. Die in diesem Artikel enthaltenen Bilder und sonstiges Drittmaterial unterliegen ebenfalls der genannten Creative Commons Lizenz, sofern sich aus der Abbildungslegende nichts anderes ergibt. Sofern das betreffende Material nicht unter der genannten Creative Commons Lizenz steht und die betreffende Handlung nicht nach gesetzlichen Vorschriften erlaubt ist, ist für die oben aufgeführten Weiterverwendungen des Materials die Einwilligung des jeweiligen Rechteinhabers einzuholen. Weitere Details zur Lizenz entnehmen Sie bitte der Lizenzinformation auf http://creativecommons.org/ licenses/by/4.0/deed.de. vitrektomierten Auge überdenken. 4 Abzugsknopf von Ozurdex bei vitrek- Literatur tomierten Augen langsam durchdrücken. 4 Wichtigkeit von Anamnese und postoperativen Druckkontrollen nach IVOM. 4 Hinzunahme der Videosprechstunde als postoperative Nachsorge bei COVID-19-bedingten Präsenzeinschränkungen. 1. DOG, BVA, Retinologische Gesellschaft (2014) Stellungnahme der Deutschen Ophthalmologischen Gesellschaft, derRetinologischenGesellschaftund des Berufsverbandes der Augenärzte DeutschlandszurintravitrealenTherapiedesMakulaödems bei Uveitis. https://www.dog.org/?cat=7#9. Zugegriffen: 18.02.2021 2. Rajesh B, Zarranz-Ventura J, Fung AT et al (2020) Safety of 6000 intravitreal dexamethasone implants. Br J Ophthalmol 104(1):39–46. https:// doi.org/10.1136/bjophthalmol-2019-313991 Der Ophthalmologe 10 · 2021 1053
https://openalex.org/W2978399895
https://iris.unife.it/bitstream/11392/2415623/2/1-s2.0-S2213231719310602-main.pdf
English
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Altered inflammasome machinery as a key player in the perpetuation of Rett syndrome oxinflammation
Redox biology
2,020
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12,282
Altered inflammasome machinery as a key player in the perpetuation of Rett syndrome oxinflammation Alessandra Pecorellia,l, Valeria Cordonea,b,1, Nicolò Messanoa, Changqing Zhangc, Stefano Faloned, Fernanda Amicarellid, Joussef Hayeke, Giuseppe Valacchia,b,f,∗ a Plants for Human Health Institute, Dept. of Animal Science, NC Research Campus, NC State University, Kannapolis, 28081, NC, USA b Dept. of Biomedical and Specialist Surgical Sciences, University of Ferrara, 44121, Ferrara, Italy c Plants for Human Health Institute, Dept. of Plant and Microbial Biology, NC Research Campus, NC State University, Kannapolis, 28081, NC, USA d Dept. of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy e Child Neuropsychiatry Unit, University General Hospital, Azienda Ospedaliera Universitaria Senese, 53100, Siena, Italy f Dept. of Food and Nutrition, Kyung Hee University, 02447, Seoul, South Korea A B S T R A C T Keywords: NLRP3 ASC Inflammatory status Cytokines MeCP2 Rett syndrome (RTT) is a progressive neurodevelopmental disorder mainly caused by mutations in the X-linked MECP2 gene. RTT patients show multisystem disturbances associated with an oxinflammatory status. Inflammasomes are multi-protein complexes, responsible for host immune responses against pathogen infections and redox-related cellular stress. Assembly of NLRP3/ASC inflammasome triggers pro-caspase-1 activation, thus, resulting in IL-1β and IL-18 maturation. However, an aberrant activation of inflammasome system has been implicated in several human diseases. Our aim was to investigate the possible role of inflammasome in the chronic subclinical inflammatory condition typical of RTT, by analyzing this complex in basal and lipopoly- saccharide (LPS)+ATP-stimulated primary fibroblasts, as well as in serum from RTT patients and healthy vo- lunteers. RTT cells showed increased levels of nuclear p65 and ASC proteins, pro-IL-1β mRNA, and NLRP3/ASC interaction in basal condition, without any further response upon the LPS + ATP stimuli. Moreover, augmented levels of circulating ASC and IL-18 proteins were found in serum of RTT patients, which are likely able to amplify the inflammatory response. Taken together, our findings suggest that RTT patients exhibited a challenged in- flammasome machinery at cellular and systemic level, which may contribute to the subclinical inflammatory state feedback observed in this pathology. Keywords: NLRP3 ASC Inflammatory status Cytokines MeCP2 RTT symptoms are still not clear. Redox Biology 28 (2020) 101334 Redox Biology 28 (2020) 101334 https://doi.org/10.1016/j.redox.2019.101334 Received 4 September 2019; Received in revised form 23 September 2019; Accepted 26 September 2019 ∗Corresponding author. Dept. of Animal Science, North Carolina State University, Plants for Human Health Institute, NC Research Center, 28081, Kannapolis, NC, USA. E-mail address: gvalacc@ncsu.edu (G. Valacchi). 1 Authors contributed equally. Available online 06 October 2019 2213-2317/ © 2019 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecom m ons.org/licenses/BY/4.0/). 1. Introduction In the last decade, a growing body of evidence supported the idea that an OxInflammation condition, observed in brain and peripheral compartments of both RTT patients and animal models, could be in- volved in RTT pathophysiology [6]. This condition in RTT is due to the concomitant dysregulation of redox and immune homeostasis and characterized by a subclinical inflammatory status coupled with an increased production of oxidant species and a perturbed defense re- sponse [6–9]. Based on recent findings, cytosolic molecular complexes termed inflammasomes have emerged as central mediators in the crosstalk between redox imbalance and inflammation associated with a wide range of diseases [10]. The assembly of inflammasomes occurs following the recognition of multiple diverse endogenous and exo- genous signals such as “pathogen-associated” or “danger-associated Rett syndrome (RTT; OMIM identifier #312750), first described by the physician Andreas Rett [1], is a severe neurodevelopmental dis- order, predominantly affecting females (approx. 1 per 10,000 live births) [2]. In 90–95% of patients diagnosed with RTT, the disorder is due to de novo loss-of-function mutations in the X-linked MECP2 gene, which encodes methyl-CpG binding protein 2 [3]. After 6-18-months of apparently normal development [4], RTT leads to both developmental regression, involving loss of hand skills, motor skills and speech, and a number of co-morbidities, including breathing disturbances, seizures, gastro-intestinal complications, and scoliosis [5], allowing to define RTT as a ‘spectrum disorder’. Today, the complete pathogenic mechanisms linking MECP2 dysfunction to A. Pecorelli, et al. Redox Biology 28 (2020) 101334 approved by the Ethics Committee of Institutional Review Board of University Hospital, Azienda Ospedaliera Universitaria Senese (AOUS), Siena, Italy. A written form of the informed consents was signed from either the parents or the legal tutors of the participants. molecular patterns” (PAMPs or DAMPs) by a cytosolic subset of “pat- tern recognition receptors” (PRRs), named “nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins” [11]. The activation of these intracellular sensors such as NLRP3, the most widely studied member among them, triggers the oligomerization and the recruitment of the adaptor protein ASC, which in turn is able to recruit the effector protein pro-caspase 1 [12]. The proximity-induced pro-caspase 1 auto- cleavage leads to the generation of the catalytically active caspase 1 (CASP1), which prompts the downstream responses, consisting of the conversion of both pro-IL-1β and pro-IL-18 to their biologically active forms, and/or the proteolytic action of gasdermin D (GSDMD). 2.5. Western immunoblot analysis Fibroblasts were lysed in RIPA buffer (cat. J62524, Alfa Aesar, Tewksbury, MA, USA), supplemented with 1% (v/v) protease inhibitors and 1% (v/v) phosphatase inhibitors (cat. 78430 and cat. 1862495, respectively, Thermo Fisher Scientific, Waltham, MA, USA). After three freezing-thawing cycles, cell lysates were centrifuged at 17,000×g for 15 min at 4 °C, and supernatants were used for the evaluation of total protein concentration, by using the Quick Start™Bradford Protein Assay Kit (cat. 5000201, Bio-rad Laboratories) and bovine serum al- bumin (BSA) as standard. Samples were denatured and run in triplicates on 10–15% polyacrylamide gels, as previously reported [26]. Proteins were transferred from polyacrylamide gels onto polyvinylidene di- fluoride (PVDF) membranes by electrophoretic transfer. Non-specific binding sites were blocked at room temperature for 1 h with 5% (w/v) Blotting-Grade Blocker (cat. 170–6404, Bio-Rad Laboratories), in Tris- buffer saline containing 0.1% (v/v) Tween-20 (cat. P5927, Sigma–Al- drich) (TBS-T). Membranes were first incubated overnight with primary antibodies-containing TBS-T (see the antibodies section), and then with anti-rabbit or anti-mouse peroxidase-conjugated secondary antibodies diluted in TBS-T for 2 h at room temperature (see the antibodies sec- tion). The protein bands were detected by using Clarity™Western ECL Substrate Kit (cat. 1705060, Bio-Rad Laboratories) and ChemiDoc™MP Imaging System hardware and software (Bio-Rad Laboratories). Images of bands were analyzed by the Nonlinear Dynamics TotalLab software (TotalLab Ltd, Newcastle upon Tyne, UK). Data were normalized against HDAC1 or GAPDH, depending on nuclear or cytosolic/total proteins analyzed, and results were given as arbitrary units. 2.1. Antibodies Cell Signaling Technology, Inc. (Danvers, MA, USA) supplied the following antibodies: anti-nuclear factor κ-light-chain-enhancer of ac- tivated B cells (NF-κB) p65 subunit antibody (cat. 8242; dil. 1:1,000); anti-NACHT, LRR and PYD domains-containing protein 3 (NLRP3) an- tibody (cat. 13158; dil. for WB 1:500 and for IF 1:100); anti-caspase 1 (CASP1) antibody (cat. 2225; dil. 1:1,000), anti-cleaved-IL-1β (cat. 83186; dil. 1:100); anti-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (cat. 5174; dil. 1:5,000); anti-histone deacetylase 1 (HDAC1) antibody (cat. 8242; dil. 1:1,000), and peroxidase-conjugated anti- rabbit secondary antibody (cat. 7074; dil. 1:10,000). Santa Cruz Biotechnology, Inc. (Santa Cruz, CA) provided the anti-apoptosis-asso- ciated speck-like protein containing CARD (ASC) (cat. sc-271054; dil. for WB 1:800 and for IF 1:200) antibody. Both AlexaFluorTM 488 goat anti-rabbit IgG (H + L) (cat. A-11008; dil. 1:1,000) and AlexaFluorTM 568 goat anti-mouse IgG (H + L) (cat. A-11004; dil. 1:1,000) antibodies were provided by Thermo Fisher Scientific (Waltham, MA, USA). The peroxidase-conjugated anti-mouse secondary antibody (cat. 170–6515; dil. 1:10,000) was supplied by Bio-Rad Laboratories (Hercules, CA, USA). 2.4. Cell treatment with LPS and ATP Since the inflammasome pathway could contribute to the char- acteristic OxInflammatory status of RTT, this work was aimed at in- vestigating the activation state of the inflammasome in fibroblasts and serum samples from RTT patients. We revealed that a deregulated ac- tivation of inflammasome pathway occurs in RTT, as proved by the increased constitutive levels of inflammasome components in patient- derived serum and fibroblast cell lines and by the inability of RTT cells to activate properly this pathway after further pro-inflammatory chal- lenges. CTR and RTT fibroblasts were seeded (5,000 cells/cm2) in complete medium and after 48 h, cells were starved with 1% FBS-containing medium for 15 h to minimize cell proliferation. Cells were then in- cubated with or without 100 μg/ml lipopolysaccharide (LPS, dissolved in water), for 6 h in 1% FBS-supplemented medium and with 5 mM adenosine triphosphate (ATP, dissolved in water) for additional 30 min (cat. L2630 and cat. A6419, respectively, Sigma-Aldrich, St. Louis, MO, USA). The LPS concentration was calculated based on the evaluation of NLRP3 gene expression, in response to different concentrations (0, 10, 50, 100 and 200 μg/ml for 6 h), while the ATP treatment was estab- lished based on literature papers [24,25]. The chosen concentration of LPS (100 μg/ml) induced an inflammasome-related response and no cell death was observed (Supplementary Fig. S1). 2.3. Human fibroblasts culture Skin biopsies from healthy donors (CTR; N = 6) were taken during health checks or by donations, while skin biopsies from RTT patients (N = 6; age: 20 ± 3.8, expressed as mean ± SD) were obtained during the periodic clinical checks-up. Human skin fibroblasts were isolated by 3-mm skin punch biopsy, as previously described [23]. Before the experimental procedure, fibroblasts were stained for Vi- mentin and checked for mycoplasma contamination. Cells were cul- tured with DMEM medium, containing 10% (v/v) fetal bovine serum (cat. 10-014-CV and cat. 35-011-CV, respectively, Corning, New York, NY, USA), antibiotics (100 IU/ml penicillin, 100 mg/ml streptomycin) (cat. 30-002-CI; Corning) and incubated in humidified atmosphere (5% CO2) at 37 °C. All experiments were performed by using fibroblasts between the third and fifth passage in vitro. 1. Introduction This latter promotes the release of GSDMD N-terminal fragments that oli- gomerize into ring-shaped structures in membranes. GSDMD pores allow cells to release passively their cytoplasmic content in a size-de- pendent manner (i.e., cytokines like IL-1β) [13] or drive cells towards pyroptotic death [11]. Besides its involvement in innate immune re- sponses, NLRP3 inflammasome has been demonstrated to have a role in a wide range of inflammatory diseases, cancer, metabolic and auto- immune disorders, and aging [14–19]. The inflammasome pathway is implicated even in the neuroinflammation observed in neurodegen- erative disorders, like multiple sclerosis, Alzheimer's and Parkinson's disease [20,21] and in neurodevelopmental pathologies, like autistic spectrum disorders (ASDs) [22]. 2. Materials and methods 2.1. Antibodies 2.9. Serum sampling Serum samples were obtained from female patients with clinical diagnosis of typical RTT and MECP2 mutation (n = 42; median age: 15) and healthy controls (n = 16; median age: 16). As previously reported [31], fasting venous blood was collected at 8–10 a.m. following an overnight fast and all manipulations were carried out within 2 h. Blood was collected in tubes without anticoagulants and allowed to clot at RT. Following centrifugation at 1,500×g for 10 min, the sera were trans- ferred into clean tubes. Serum samples were stored at −80 °C for fur- ther immunoblot (ASC and CASP1) or ELISA (IL-18) analyses. 2.6. Subcellular protein fractionation Thornwood, NY, USA) and Zen 2008 Software (Carl Zeiss Microscopy GmbH, Jena, Germany). Digital images were analyzed by using an open source Java-based Fiji-ImageJ image processing package, and the coloc2 plug-in for colocalization. Results were given as Pearson coef- ficients [30]. Nuclear and cytoplasmic protein fractions were prepared by using the Nuclear Extraction Kit (cat. 2900, Merck Millipore, Burlington, MA, USA). Briefly, cells were washed with PBS and then were lysed with Cytoplasmic Lysis Buffer, containing 0.5 mM dithiothreitol (DTT) and 0.1% (v/v) protease inhibitor cocktail. After homogenization, the dis- rupted cell suspension was centrifuged at 8,000×g for 20 min at 4 °C, and the supernatant, containing the cytosolic portion, was recovered. The remaining pellet was then resuspended in Nuclear Extraction Buffer supplemented with 0.5 mM DTT and 0.1% (v/v) protease inhibitor cocktail and homogenized. The resulting nuclear suspension was cen- trifuged at 16,000×g for 5 min at 4 °C and the supernatant, containing the nuclear extract, was collected [27]. Total protein concentration was determined by Bradford analysis (Quick Start™Bradford Protein Assay Kit, cat. 5000201, Bio-rad Laboratories). 2.12. Statistics Statistical analyses were performed by using GraphPad Prism 6 and Statsoft Statistica10 softwares. One-way or factorial ANOVA, with post- hoc Tukey's tests were applied. The null hypothesis was rejected with P less than 0.05. All data were expressed as means ± standard deviations (SD). 2.10. ASC oligomerization assay As previously reported [28], total RNA was extracted from fibro- blasts by using Aurum Total RNA Mini Kit (cat.732–6820, Bio-Rad), removing genomic contamination by using DNase I, as recommended by the supplier. RNA (1 μg) was converted into complementary DNA by using iScript Reverse Transcription kit (cat. 1708841, Bio-Rad). The obtained cDNA (diluted 1:10) was used for the real time PCR step with SsoAdvanced Universal SYBR Green Supermix (cat. 172–5271, Bioline, London, UK) in a LightCycler® 480 Instrument (Roche, Indianapolis, IN, USA). Primers were synthetized by Sigma-Aldrich (St. Louis, MO, USA): NLRP3 (forward, 5′-CGGGGCCTCTTTTCAGTTCT-3′; reverse, 5′-CCCC AACCACAATCTCCGAA-3′) (Primer BLAST, accession number: NM_ 004895.4); CASP1 (forward, 5′-CCGTTCCATGGGTGAAGGTA-3′; re- verse, 5′-TGCCCCTTTCGGAATAACGG-3′) (Primer BLAST, accession number: NM_033292.4); IL-1β (forward, 5′-CACGATGCACCTGTACGA TCA-3'; reverse, 5′-GTTGCTCCATATCCTGTCCCT-3′) [58]; GAPDH (forward, 5′-TGACGCTGGGGCTGGCATTG-3′; reverse, 5′- GGCTGGTG GTCCAGGGGTCT-3′) [26]. For the ASC oligomerization assay, five μl of serum were suspended in 500 μL PBS and cross-linked with 2 mM disuccinimidyl suberate (DSS) for 30 min a room temperature. Cross-linked samples were cen- trifuged at 10,000×g for 15 min at 4 °C. The pellets containing ASC oligomers were boiled with 2x protein loading buffer for 5 min for Western blot analysis. 2.11. Enzyme-linked immunosorbent assay (ELISA) Serum concentrations of IL-18 were determined by ELISA using a commercial kit (RayBiotech Life, Peachtree Corners, GA, USA), ac- cording to the manufacturer's instructions. All samples were analyzed in duplicate. A calibration curve was performed using IL-18 as a standard. The optical absorbance was measured with a microplate reader at 450 nm, and results are expressed as pg/mL. The lower limit of detec- tion for IL-18 was 0.5 pg/mL. The PCR protocol was set as follows: polymerase activation and initial denaturation at 95 °C for 30 s, and 40 cycles of 95 °C for 15 s and 60 °C for 60 s. In order to check the presence of possible co-amplified undesired targets, melt-curve analysis was performed for all primer pairs (65 °C–95 °C, 0.5 °C increment, 2 s/step). Quantitative relative gene expression was calculated by using the 2−ΔΔCt method [29], using GAPDH as the reference mRNA and one of the controls as the internal calibrator. Each sample was processed by analyzing three replicates. 2.2. Study approval Female patients with classical RTT and healthy sex- and age-mat- ched controls were enrolled for the study. All patients were admitted to the Child Neuropsychiatry Unit of the University Hospital of Siena (Siena, Italy). Diagnosis and inclusion/exclusion criteria of RTT were set in agreement with revised RTT nomenclature consensus [4]. The study was conducted in accordance with the Code of Ethics of the World Medical Association (Declaration of Helsinki), and the protocol was 2 A. Pecorelli, et al. Redox Biology 28 (2020) 101334 2.8. Immunofluorescence analysis Fibroblasts were seeded (5,000 cells/cm2) and grown on coverslips in complete medium. CTR and RTT cells were starved and treated with LPS + ATP, as described in the “Cell treatment with LPS and ATP” sub- section. As previously reported [23], cells were washed twice with D- phosphate buffered saline (PBS), then fixed in 10% (w/v) neutral buf- fered formalin solution for 10 min, and permeabilized in PBS containing 0.25% (v/v) Triton X-100 for 10 min at 4 °C. Non-specific binding sites were blocked with 3% (w/v) BSA in PBS for 30 min. Cells were then incubated with primary antibodies that were diluted in PBS containing 0.5% (w/v) BSA at 4 °C overnight (see the “Antibodies” section for in- formation about dilutions). After three washes with PBS, cells were incubated with AlexaFluor 488 or AlexaFluor 568 antibodies-con- taining PBS at 4 °C for 1 h (see the “Antibodies” section for information about dilutions). After five washes with PBS, cells were incubated with a solution of 4′,6-diamidino-2-phenylindole (DAPI)-containing PBS for 1 min (dil. 1:20,000) and mounted with ProLong Diamond mounting medium (cat. D1306 and cat. P36965, respectively, Thermo Fisher Scientific). Cells were observed and photographed by confocal micro- scopy (objective 40×) by using a Zeiss LSM 710 microscope (Carl Zeiss, 3.1. Constitutive nuclear translocation of NF-κB p65 and increased levels of cleaved IL-1β in RTT fibroblasts 3.1. Constitutive nuclear translocation of NF-κB p65 and increased levels of cleaved IL-1β in RTT fibroblasts 3.1. Constitutive nuclear translocation of NF-κB p65 and increased levels of cleaved IL-1β in RTT fibroblasts Representative Western blots for NF-κB p65 in nuclear extracts from control and RTT fibroblasts stimulated with LPS 100 μg/ml for 2 and 6 h plus ATP 5 mM for 30 min. Quantification is showed in bottom panel. Data are given as means ± SD. Panel B. The mRNA levels of pro-IL-1β were analyzed by real-time RT-PCR. Data are expressed as 2−ΔΔCt, using GAPDH as the reference, and one of the controls as the internal calibrator. Data are given as means ± SD. Panel C. Immunofluorescence for cleaved IL-1β in control and RTT fibroblasts stimulated with LPS 100 μg/ml for 6 h and ATP 5 mM for 30 min. Nuclei are stained with DAPI. Bar = 15 μm. CTR, control; RTT, Rett syndrome; LPS, lipopolysaccharide; ATP, adenosine triphosphate. *P < 0.05; **P < 0.01. Results were analyzed by factorial ANOVA (with 2 × 2 × 3 design for panel A, and 2 × 2 design for panel B), with post-hoc Tukey's multiple comparisons test. Fig. 1. Constitutive nuclear translocation of NF-κB p65 and expression of cleaved IL-1β in RTT fibroblasts. Panel A. Representative Western blots for NF-κB p65 in nuclear extracts from control and RTT fibroblasts stimulated with LPS 100 μg/ml for 2 and 6 h plus ATP 5 mM for 30 min. Quantification is showed in bottom panel. Data are given as means ± SD. Panel B. The mRNA levels of pro-IL-1β were analyzed by real-time RT-PCR. Data are expressed as 2−ΔΔCt, using GAPDH as the reference, and one of the controls as the internal calibrator. Data are given as means ± SD. Panel C. Immunofluorescence for cleaved IL-1β in control and RTT fibroblasts stimulated with LPS 100 μg/ml for 6 h and ATP 5 mM for 30 min. Nuclei are stained with DAPI. Bar = 15 μm. CTR, control; RTT, Rett syndrome; LPS, lipopolysaccharide; ATP, adenosine triphosphate. *P < 0.05; **P < 0.01. Results were analyzed by factorial ANOVA (with 2 × 2 × 3 design for panel A, and 2 × 2 design for panel B), with post-hoc Tukey's multiple comparisons test. changes in pro-IL-1β levels were noticed in RTT fibroblasts after the pro-inflammatory stimulation (Fig. 1B). 3.2. 3.1. Constitutive nuclear translocation of NF-κB p65 and increased levels of cleaved IL-1β in RTT fibroblasts First critical step in inflammasome activation is the transcriptional up-regulation of inflammasome components via nuclear factor (NF)-κB signaling. As shown in Fig. 1A, RTT fibroblasts revealed highly aug- mented levels of nuclear NF-κB p65 subunit in basal condition (P < 0.01), as compared to unstimulated CTR. However, while CTR fibroblasts responded to LPS + ATP treatment by increasing p65 nu- clear translocation over time (after 2 and 6 h) (P < 0.05), p65 nuclear levels did not increase any further after LPS + ATP in RTT fibroblasts (Fig. 1A). NF-κB–activating stimulus induces elevated expression of pro-IL-1β, a key pro-inflammatory cytokine involved in the inflammasome pathway [32]. RTT fibroblasts displayed a robust constitutive pro-IL-1β mRNA expression in basal condition when compared to unstimulated CTR cells (P < 0.05) (Fig. 1B). As expected, increased transcriptional levels of pro-IL-1β have been detected in LPS + ATP-stimulated CTR cells (P < 0.05; as compared to untreated CTR); whereas no further 3 Redox Biology 28 (2020) 101334 A. Pecorelli, et al. n pro-IL-1β levels were noticed in RTT fibroblasts after the matory stimulation (Fig. 1B). with these results, immunofluorescence analysis for the 3.2. NLRP3 inflammasome components are constitutively expressed at high levels in RTT fibroblasts stitutive nuclear translocation of NF-κB p65 and expression of cleaved IL-1β in RTT fibroblasts. epresentative Western blots for NF-κB p65 in nuclear extracts from control and RTT fibroblasts stimulated with LPS 100 μg/ml for 2 and 6 h plus ATP 5 mM Quantification is showed in bottom panel. Data are given as means ± SD. Panel B. The mRNA levels of pro-IL-1β were analyzed by real-time RT-PCR. xpressed as 2−ΔΔCt, using GAPDH as the reference, and one of the controls as the internal calibrator. Data are given as means ± SD. Panel C. orescence for cleaved IL-1β in control and RTT fibroblasts stimulated with LPS 100 μg/ml for 6 h and ATP 5 mM for 30 min. Nuclei are stained with DAPI. m. CTR, control; RTT, Rett syndrome; LPS, lipopolysaccharide; ATP, adenosine triphosphate. *P < 0.05; **P < 0.01. Results were analyzed by factorial ith 2 × 2 × 3 design for panel A, and 2 × 2 design for panel B), with post-hoc Tukey's multiple comparisons test. gy Fig. 1. Constitutive nuclear translocation of NF-κB p65 and expression of cleaved IL-1β in RTT fibroblasts. Panel A. 3.1. Constitutive nuclear translocation of NF-κB p65 and increased levels of cleaved IL-1β in RTT fibroblasts After LPS + ATP stimulation, pro-CASP1 gene expression showed a trend in increase in CTR cells, while no significant changes were observed in RTT fibroblasts (Fig. 4B). 3 5 Increased release of inflammasome components in serum of RTT Fig. 2. Increased levels of NLRP3 and ASC in basal RTT fibroblasts. Panel A. Representative images and densitometric analysis of Western blotting for NLRP3 in control and RTT fibroblasts incubated without or with LPS 100 μg/ml for 6 h plus ATP 5 mM. Panel B. Representative images and densitometric analysis of Western blots for ASC in control and RTT fi- broblasts stimulated with LPS 100 μg/ml for 2 and 6 h plus ATP 5 mM. Data are given as means ± SD. CTR, control; RTT, Rett syndrome; LPS, lipopolysaccharide; ATP, adenosine tripho- sphate. *P < 0.05; **P < 0.01. Results were analyzed by Two-way ANOVA, with post-hoc Tukey's multiple comparisons test. A. Pecorelli, et al. Redox Biology 28 (2020) 101334 Fig. 2. Increased levels of NLRP3 and ASC in basal RTT fibroblasts. Panel A. Representative images and densitometric analysis of Western blotting for NLRP3 in control and RTT fibroblasts incubated without or with LPS 100 μg/ml for 6 h plus ATP 5 mM. Panel B. Representative images and densitometric analysis of Western blots for ASC in control and RTT fi- broblasts stimulated with LPS 100 μg/ml for 2 and 6 h plus ATP 5 mM. Data are given as means ± SD. CTR, control; RTT, Rett syndrome; LPS, lipopolysaccharide; ATP, adenosine tripho- sphate. *P < 0.05; **P < 0.01. Results were analyzed by Two-way ANOVA, with post-hoc Tukey's multiple comparisons test. (Fig. 4A). The basal levels of CASP1 p20 active form were similar be- tween CTR and RTT cells, while the treatment with LPS + ATP in- creased its levels in CTR cells (P < 0.05), no change was observed in RTT fibroblasts after the pro-inflammatory stimulus (Fig. 4A). To verify if regulation of pro-CASP1 protein expression occurs at the transcription level, we assessed its mRNA expression by real time PCR. As showed in Fig. 4B, in unstimulated conditions, RTT cells displayed a trend in reduction of pro-CASP1 mRNA levels compared to CTR fibro- blasts. After LPS + ATP stimulation, pro-CASP1 gene expression showed a trend in increase in CTR cells, while no significant changes were observed in RTT fibroblasts (Fig. 4B). 3.4. Altered levels of pro-CASP1 and active CASP1 form in RTT fibroblasts 3.4. Altered levels of pro-CASP1 and active CASP1 form in RTT fibroblasts The key outcome of NLRP3-ASC assembly is the self-cleavage and activation of pro-CASP1 that, then, leads to the processing and ma- turation of the pro-inflammatory cytokines IL-1β and IL-18 [12]. Given the higher levels of cleaved IL-1β and inflammasome assembly in RTT cells, we next evaluated the protein expression of the pro-form and active form of CASP1. 3.5. Increased release of inflammasome components in serum of RTT patients In CTR cells, the LPS + ATP treatment induced an increase of the NLRP3-related immunofluorescence signal into the cytoplasmic and perinuclear region (likely, endoplasmic reticulum), as well as an en- hanced ASC-related signal into the cytosol, as compared to un- stimulated CTR cells (Fig. 3A). Conversely, in RTT fibroblasts, basal signals of both NLRP3 and ASC are higher and localized in the cytosolic compartment, whereas LPS + ATP stimulation did not affect the cy- tosolic localization (Fig. 3A). A growing body of evidence supports a model whereby the cellular release of inflammasome proteins through extracellular vesicles such as exosomes delivers their cargo in vivo to amplify the inflammatory sig- naling in peripheral tissues [33,34]. Therefore, to further study in- flammasome activation in RTT, we evaluated the protein expression of the main inflammasome components in serum from RTT patients and control subjects. Consistent with the results obtained in fibroblasts, we found that ASC protein levels were higher in the serum of RTT patients than in the control group (Fig. 5A). Furthermore, immunoblot analysis of DSS-crosslinked ASC oligomers further confirmed a significant in- crease of catalytically active ASC oligomeric species in RTT serum samples (Fig. 5B). Next, as hallmark of inflammasome activation, we measured the serum levels of IL-18 by ELISA. As showed in Fig. 5C, serum IL-18 concentrations were significantly higher in RTT patients than in control subjects (p < 0.05). After co-localization analysis, we found that a significant NLRP3- ASC interaction was induced by LPS + ATP only in CTR fibroblasts (P < 0.05); while, RTT cells showed a significant increase of in- flammasome assembly already in basal condition (P < 0.05; as com- pared to untreated CTR), and were unable to respond to further chal- lenge with LPS + ATP (Fig. 3B). 3.1. Constitutive nuclear translocation of NF-κB p65 and increased levels of cleaved IL-1β in RTT fibroblasts NLRP3 inflammasome components are constitutively expressed at high levels in RTT fibroblasts In line with these results, immunofluorescence analysis for the cleaved IL-1β revealed an increase of green signal in cytoplasmic compartment of untreated RTT cells as compared to basal CTR fibro- blasts (Fig. 1C). No change in fluorescence intensity was observed in RTT fibroblasts upon LPS + ATP stimulation when compared to the unstimulated condition (Fig. 1C). On the other hand, an increased green fluorescence for the mature IL-1β was evident in CTR fibroblasts after LPS + ATP treatment (Fig. 1C). In addition to NF-κB p65, other key players in the inflammasome system were analyzed, including NLRP3 and ASC. Basal RTT fibroblasts showed higher NLRP3 protein levels compared to CTR (P < 0.05), without any evident change after pro-inflammatory stimulation (Fig. 2A). Instead, NLRP3 levels in CTR fibroblasts were increased significantly upon LPS + ATP treatment (P < 0.05; as compared to untreated CTR) (Fig. 2A). Similarly, an increase of ASC levels could be detected in basal RTT Similarly, an increase of ASC levels could be detected in 4 Redox Biology 28 (2020) 101334 A. Pecorelli, et al. fibroblasts as compared to untreated CTR (P < 0.01), but with no statistically significant variation in response to the pro-inflammatory stimuli (Fig. 2B). On the other hand, in CTR cells ASC levels were low in basal conditions, but significantly increased after LPS + ATP stimula- tion (P < 0.05) (Fig. 2B). 3.3. RTT fibroblasts show an increased colocalization between NLRP3 and ASC To determine if high constitutive levels of the inflammasome com- ponents in RTT cells paralleled with inflammasome assembly, we as- sessed the NLRP3-ASC interaction by evaluating their cellular locali- zation by immunofluorescence (Fig 3) (Fig. 4A). The basal levels of CASP1 p20 active form were similar be- tween CTR and RTT cells, while the treatment with LPS + ATP in- creased its levels in CTR cells (P < 0.05), no change was observed in RTT fibroblasts after the pro-inflammatory stimulus (Fig. 4A). To verify if regulation of pro-CASP1 protein expression occurs at the transcription level, we assessed its mRNA expression by real time PCR. As showed in Fig. 4B, in unstimulated conditions, RTT cells displayed a trend in reduction of pro-CASP1 mRNA levels compared to CTR fibro- blasts. 3.3. RTT fibroblasts show an increased colocalization between NLRP3 and ASC To determine if high constitutive levels of the inflammasome com- ponents in RTT cells paralleled with inflammasome assembly, we as- sessed the NLRP3-ASC interaction by evaluating their cellular locali- zation by immunofluorescence (Fig. 3). 3.1. Constitutive nuclear translocation of NF-κB p65 and increased levels of cleaved IL-1β in RTT fibroblasts fibroblasts as compared to untreated CTR (P < 0.01), but with no statistically significant variation in response to the pro-inflammatory stimuli (Fig. 2B). On the other hand, in CTR cells ASC levels were low in basal conditions, but significantly increased after LPS + ATP stimula- tion (P < 0.05) (Fig. 2B). (Fig. 4A). The basal levels of CASP1 p20 active form were similar be- tween CTR and RTT cells, while the treatment with LPS + ATP in- creased its levels in CTR cells (P < 0.05), no change was observed in RTT fibroblasts after the pro-inflammatory stimulus (Fig. 4A). To verify if regulation of pro-CASP1 protein expression occurs at the transcription level, we assessed its mRNA expression by real time PCR. As showed in Fig. 4B, in unstimulated conditions, RTT cells displayed a trend in reduction of pro-CASP1 mRNA levels compared to CTR fibro- blasts. After LPS + ATP stimulation, pro-CASP1 gene expression showed a trend in increase in CTR cells, while no significant changes were observed in RTT fibroblasts (Fig. 4B). 3.3. RTT fibroblasts show an increased colocalization between NLRP3 and ASC 4. Discussion The aim of our work was to elucidate the possible involvement of the inflammasome pathway as a key player in RTT subclinical in- flammation. Inflammasomes, cytoplasmic multi-protein complexes, provide host immune defense against a diverse range of pathogen in- fections and cellular stress signals [11]. As previously mentioned, In both basal and LPS + ATP stimulated conditions, RTT fibroblasts displayed low pro-CASP1 levels respect to the CTR cells (P < 0.05) 5 assembly of NLRP3/ASC inflammasome leads to subsequent recruit- ment and autocatalytic activation of CASP1 that, finally, promotes the maturation of IL-1β and IL-18 [11,35]. These key pro-inflammatory cytokines are able to promote a multitude of finely regulated immune responses useful for restoring the physiological conditions [11]. How- ever, it is also well known that an uncontrolled and prolonged in- flammasome activation with an excessive release of cytokines can participate in the onset and progression of chronic inflammatory states associated with a wide variety of human diseases [10,36,37]. Although RTT is primarily a genetic brain disorder with prominent neurological symptoms, a vast body of evidence supports a key role for the interplay between redox imbalance and a subclinical inflammatory status (oxinflammation phenomenon) in different systemic abnormal- ities observed in RTT patients (i.e., mitochondrial dysfunctions, meta- bolic alterations, immune dysregulation, gastrointestinal problems, breathing disturbances and recurrent infections) [6,38]. In this contest, the dysregulation of NLRP3 inflammasome pathway could be a new molecular mechanism able to contribute to RTT pathophysiology, in both brain and periphery. mainly driven by two different signals. Typically, ‘signal 1’ or ‘priming’ molecules (e.g., LPS) induce the expression of NLRP3, pro-IL-1β and pro-IL-18 via NF-κB activation [32,39]. Moreover, PAMPs or DAMPs (e.g., ATP, particulate matter, heme, pathogen-associated RNA, etc) activate the NLRP3 inflammasome assembly (‘signal 2’) [32]. The particular interest towards NLRP3 inflammasome lies in the broad range of molecular and cellular signaling events that are induced by its activators among which there are ionic flux (e.g., K+, Na+, chloride fluxes and Ca2+ signaling), ROS production, lysosomal destabilization, mitochondrial dysfunction and post-translational modifications of NLRP3 [40,41]. Of note, some of these stimuli are present in RTT pa- tients [42,43] and, therefore, could promote a dysregulated NLRP3 inflammasome function that, in turn, could contribute to the typical RTT subclinical inflammation [6,38,44]. In the present work, RTT cells showed an increased steady level of nuclear NF-κB p65 subunit, as compared to CTR cells. 4. Discussion Confocal images showing localization of NLRP3 (green fluorescence) and ASC (red fluor- escence) in control and RTT fibroblasts stimulated with LPS 100 μg/ml for 6 h and ATP 5 mM for 30 min. Overlay of the green and red channel shows that there is colocalization between NLRP3 and ASC. Nuclei are stained with DAPI. Bar = 15 μm. CTR, control; RTT, Rett syndrome; LPS, lipopolysaccharide; ATP, adenosine tripho- sphate. *P < 0.05. Panel B. Pearson's correlation coefficient values for colocalization of NLRP3 and ASC. Co-localization data were given as means ± SD. Results were analyzed by Two-way ANOVA, with post-hoc Tukey's multiple compar- isons test. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.) Panel A. Confocal images showing localization of NLRP3 (green fluorescence) and ASC (red fluor- escence) in control and RTT fibroblasts stimulated with LPS 100 μg/ml for 6 h and ATP 5 mM for 30 min. Overlay of the green and red channel shows that there is colocalization between NLRP3 and ASC. Nuclei are stained with DAPI. Bar = 15 μm. CTR, control; RTT, Rett syndrome; LPS, lipopolysaccharide; ATP, adenosine tripho- sphate. *P < 0.05. Panel B. Pearson's correlation coefficient values for colocalization of NLRP3 and ASC. Co-localization data were given as means ± SD. Results were analyzed by Two-way ANOVA, with post-hoc Tukey's multiple compar- isons test. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.) assembly of NLRP3/ASC inflammasome leads to subsequent recruit- ment and autocatalytic activation of CASP1 that, finally, promotes the maturation of IL-1β and IL-18 [11,35]. These key pro-inflammatory cytokines are able to promote a multitude of finely regulated immune responses useful for restoring the physiological conditions [11]. How- ever, it is also well known that an uncontrolled and prolonged in- flammasome activation with an excessive release of cytokines can participate in the onset and progression of chronic inflammatory states associated with a wide variety of human diseases [10,36,37]. assembly of NLRP3/ASC inflammasome leads to subsequent recruit- ment and autocatalytic activation of CASP1 that, finally, promotes the maturation of IL-1β and IL-18 [11,35]. These key pro-inflammatory cytokines are able to promote a multitude of finely regulated immune responses useful for restoring the physiological conditions [11]. 4. Discussion A significant increase of NF-κB p65 nuclear translocation was found in CTR cells after LPS + ATP treatment, whereas RTT fibroblasts did not undergo any significant change in the transcription factor nuclear levels in response Fig. 3. Increased formation of NLRP3/ASC in- flammasome complexes in RTT fibroblasts. Panel A. Confocal images showing localization of NLRP3 (green fluorescence) and ASC (red fluor- escence) in control and RTT fibroblasts stimulated with LPS 100 μg/ml for 6 h and ATP 5 mM for 30 min. Overlay of the green and red channel shows that there is colocalization between NLRP3 and ASC. Nuclei are stained with DAPI. Bar = 15 μm. CTR, control; RTT, Rett syndrome; LPS, lipopolysaccharide; ATP, adenosine tripho- sphate. *P < 0.05. Panel B. Pearson's correlation coefficient values for colocalization of NLRP3 and ASC. Co-localization data were given as means ± SD. Results were analyzed by Two-way ANOVA, with post-hoc Tukey's multiple compar- isons test. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.) A. Pecorelli, et al. Redox Biology 28 (2020) 101334 Redox Biology 28 (2020) 101334 A. Pecorelli, et al. A. Pecorelli, et al. Fig. 3. Increased formation of NLRP3/ASC in- flammasome complexes in RTT fibroblasts. Panel A. Confocal images showing localization of NLRP3 (green fluorescence) and ASC (red fluor- escence) in control and RTT fibroblasts stimulated with LPS 100 μg/ml for 6 h and ATP 5 mM for 30 min. Overlay of the green and red channel shows that there is colocalization between NLRP3 and ASC. Nuclei are stained with DAPI. Bar = 15 μm. CTR, control; RTT, Rett syndrome; LPS, lipopolysaccharide; ATP, adenosine tripho- sphate. *P < 0.05. Panel B. Pearson's correlation coefficient values for colocalization of NLRP3 and ASC. Co-localization data were given as means ± SD. Results were analyzed by Two-way ANOVA, with post-hoc Tukey's multiple compar- isons test. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.) A. Pecorelli, et al. Redox Biology 28 (2020) 101334 F fl P N e w 3 s a B L s c A m A i c t A. Pecorelli, et al. Panel A. Fig. 3. Increased formation of NLRP3/ASC in- flammasome complexes in RTT fibroblasts. Panel A. Confocal images showing localization of NLRP3 (green fluorescence) and ASC (red fluor- escence) in control and RTT fibroblasts stimulated with LPS 100 μg/ml for 6 h and ATP 5 mM for 30 min. Overlay of the green and red channel shows that there is colocalization between NLRP3 and ASC. Nuclei are stained with DAPI. Bar = 15 μm. CTR, control; RTT, Rett syndrome; LPS, lipopolysaccharide; ATP, adenosine tripho- sphate. *P < 0.05. Panel B. Pearson's correlation coefficient values for colocalization of NLRP3 and ASC. Co-localization data were given as means ± SD. Results were analyzed by Two-way ANOVA, with post-hoc Tukey's multiple compar- isons test. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.) 4. Discussion A study by Kishi and colleagues [52] on the cortex of Mecp2-null mice demonstrated an abnormal upregu- lation of NF-κB signaling, which reduction ameliorated the dendritic complexity of callosal projection neurons and prolonged their normal lifespan. Similarly, a marked decrease in inflammation markers was observed in the cerebellar area of Mecp2-knockout mice after treatment with a specific glycogen synthase kinase-3b (Gsk3b) inhibitor that at- tenuated the nuclear NF-κB activity [53]. Together, these evidence and our results suggest the hypothesis that NF-κB pathway dysregulation could play a significant role in RTT pathophysiology, as already proven in rheumatoid arthritis, inflammatory bowel disease, multiple sclerosis, atherosclerosis, systemic lupus erythematosus, type I diabetes, chronic obstructive pulmonary disease and asthma [54]. In addition to regulate multiple aspects of the immune and in- flammatory functions, NF-κB also has a role in regulating the activation of inflammasomes by inducing the transcriptional expression of NLRP3, pro-IL-1β and pro-IL-18 [32,39]. Therefore, based on the evidence of a constitutive activation of NF-κB p65 in RTT fibroblasts, we continued our study by analyzing the main components of NLRP3 signaling pathway. In order to achieve an effective inflammasome-mediated re- sponse, the presence of the adaptor protein ASC is crucial, since it can recruit the pro-caspase-1 through a “caspase activation and recruitment domain” (CARD), facilitating caspase-1 dimerization and activation, thus ensuring the formation of a fully functional inflammasome [55]. About ASC, as expected, LPS + ATP increased markedly the levels of ASC in CTR cells, whereas, although exhibiting significantly higher basal levels of ASC, as compared to CTR fibroblasts, RTT cells did not undergo any change upon LPS/ATP treatment. Several papers showed that ASC gene is under the control of a methylation-sensitive promoter [56,57]. In addition, Webb and colleagues [58], by using an IRIDESC- ENT algorithm analysis, revealed that ASC is sensitive to MECP2 ac- tivity and, moreover, transcriptional silencing of ASC gene, associated with the complete methylation of its promoter region, was observed in prostate cancer [59]. Therefore, we hypothesize that the loss of the transcriptional repression activity by a deficient MECP2 could be a mechanism able to explain the increase of ASC levels in RTT fibroblasts [60]. Furthermore, the increased basal levels of ASC in RTT fibroblasts could also be another hypothetic molecular mechanism able to explain the constitutive NF-κB p65 hyperactivation. Indeed, there is evidence that identified ASC as an upstream regulator of NF-κB signaling [61]. 4. Discussion How- ever, it is also well known that an uncontrolled and prolonged in- flammasome activation with an excessive release of cytokines can participate in the onset and progression of chronic inflammatory states associated with a wide variety of human diseases [10,36,37]. mainly driven by two different signals. Typically, ‘signal 1’ or ‘priming’ molecules (e.g., LPS) induce the expression of NLRP3, pro-IL-1β and pro-IL-18 via NF-κB activation [32,39]. Moreover, PAMPs or DAMPs (e.g., ATP, particulate matter, heme, pathogen-associated RNA, etc) activate the NLRP3 inflammasome assembly (‘signal 2’) [32]. The particular interest towards NLRP3 inflammasome lies in the broad range of molecular and cellular signaling events that are induced by its activators among which there are ionic flux (e.g., K+, Na+, chloride fluxes and Ca2+ signaling), ROS production, lysosomal destabilization, mitochondrial dysfunction and post-translational modifications of NLRP3 [40,41]. Of note, some of these stimuli are present in RTT pa- tients [42,43] and, therefore, could promote a dysregulated NLRP3 inflammasome function that, in turn, could contribute to the typical RTT subclinical inflammation [6,38,44]. Although RTT is primarily a genetic brain disorder with prominent neurological symptoms, a vast body of evidence supports a key role for the interplay between redox imbalance and a subclinical inflammatory status (oxinflammation phenomenon) in different systemic abnormal- ities observed in RTT patients (i.e., mitochondrial dysfunctions, meta- bolic alterations, immune dysregulation, gastrointestinal problems, breathing disturbances and recurrent infections) [6,38]. In this contest, the dysregulation of NLRP3 inflammasome pathway could be a new molecular mechanism able to contribute to RTT pathophysiology, in both brain and periphery. In the present work, RTT cells showed an increased steady level of nuclear NF-κB p65 subunit, as compared to CTR cells. A significant increase of NF-κB p65 nuclear translocation was found in CTR cells after LPS + ATP treatment, whereas RTT fibroblasts did not undergo any significant change in the transcription factor nuclear levels in response to the inflammatory stimuli. These peculiar results suggest that, in basal conditions, RTT fibroblasts exhibit a marked NF-κB p65 activation In general, although still under debate [39], it is accepted that the molecular mechanisms leading to the inflammasome activation are 6 Redox Biology 28 (2020) 101334 A. Pecorelli, et al. Fig. 4. Altered protein and mRNA levels of caspase 1 in RTT fibroblasts. Panel A. 4. Discussion Representative Western blots images for pro-CASP1 and active CA p20 in control and RTT fibroblasts stimulated with LPS 100 μg/ml for 6 h ATP 5 mM for 30 min. Quantification is showed in bottom panel. Data w given as means ± SD. CTR, control; RTT, Rett syndrome; LPS, lipop saccharide; ATP, adenosine triphosphate. *P < 0.05. Results were analyze Two-way ANOVA, with post-hoc Tukey's multiple comparisons test. Pane The mRNA levels of pro-CASP1 were analyzed by real-time RT-PCR. Data expressed as 2−ΔΔCt, using GAPDH as the reference, and one of the contro the internal calibrator. Data are given as means ± SD. CTR, control; RTT, syndrome; LPS, lipopolysaccharide; ATP, adenosine triphosphate. *P < 0 Results were analyzed by Two-way ANOVA, with post-hoc Tukey's mul comparisons test. morphology of peripheral blood mononuclear cells (PBMCs) [6]. Moreover, we recently demonstrated an increased gene expression of arachidonate 15-lipoxygenase (ALOX15) in RTT PBMC [44]. This en- zyme is able to oxidize polyunsaturated fatty acids such as linoleic acid, producing 13- and 9- hydroxyoctadecadienoic acid (13-HODE and 9- HODE, respectively); levels of these two compounds were found also increased in RTT serum [44]. High HODEs levels are able to exert pro- inflammatory effects such as the induction of cytokines and cell adhe- sion molecules expression, the modulation of immune cells chemotaxis and monocyte adhesion to vascular endothelial cells and the activation of transcription factors including NF-κB [46]. In addition, beyond the subclinical inflammation, also the redox imbalance, widely observed in RTT, could be another plausible mechanism able to induce the up- regulation of redox-sensitive transcriptional factors such as NF-κB [47]. Of note, an aberrant NF-κB signaling has been already reported in RTT and related to MECP2 deficiency, in both patients and animal models. Alterations of the NF-kB pathway were first revealed in a transcrip- tional profiling study on the whole blood of RTT patients [48]. Then, the possible involvement of MECP2 in immune function regulation was suggested by the enhanced NF-κB signaling coupled with an increased expression of inflammatory cytokines (i.e., TNFα, IL-6, and IL-3) found in MECP2-deficient human PBMCs and in the human monocyte line THP1 [49,50]. In line with these works, microglia and macrophages from Mecp2-deficient mice displayed a deregulated inflammatory re- sponse with an abnormal transcriptional expression of inflammatory genes after TNFα stimulation [51]. 4. Discussion Since NLRP3 protein expression in RTT fibroblasts was found to be Fig. 4. Altered protein and mRNA levels of caspase 1 in RTT fibroblasts. g p p Panel A. Representative Western blots images for pro-CASP1 and active CASP1 p20 in control and RTT fibroblasts stimulated with LPS 100 μg/ml for 6 h and ATP 5 mM for 30 min. Quantification is showed in bottom panel. Data were given as means ± SD. CTR, control; RTT, Rett syndrome; LPS, lipopoly- saccharide; ATP, adenosine triphosphate. *P < 0.05. Results were analyzed by Two-way ANOVA, with post-hoc Tukey's multiple comparisons test. Panel B. The mRNA levels of pro-CASP1 were analyzed by real-time RT-PCR. Data are expressed as 2−ΔΔCt, using GAPDH as the reference, and one of the controls as the internal calibrator. Data are given as means ± SD. CTR, control; RTT, Rett syndrome; LPS, lipopolysaccharide; ATP, adenosine triphosphate. *P < 0.05. Results were analyzed by Two-way ANOVA, with post-hoc Tukey's multiple comparisons test. Panel A. Representative Western blots images for pro-CASP1 and active CASP1 p20 in control and RTT fibroblasts stimulated with LPS 100 μg/ml for 6 h and ATP 5 mM for 30 min. Quantification is showed in bottom panel. Data were given as means ± SD. CTR, control; RTT, Rett syndrome; LPS, lipopoly- saccharide; ATP, adenosine triphosphate. *P < 0.05. Results were analyzed by Two-way ANOVA, with post-hoc Tukey's multiple comparisons test. Panel B. The mRNA levels of pro-CASP1 were analyzed by real-time RT-PCR. Data are expressed as 2−ΔΔCt, using GAPDH as the reference, and one of the controls as the internal calibrator. Data are given as means ± SD. CTR, control; RTT, Rett syndrome; LPS, lipopolysaccharide; ATP, adenosine triphosphate. *P < 0.05. Results were analyzed by Two-way ANOVA, with post-hoc Tukey's multiple comparisons test. which amplitude cannot be achieved by control cells even upon pro- inflammatory stimulation. This indicates the occurrence of an already activated inflammatory response in RTT fibroblasts that, on the other hand, seem unable to respond to further pro-inflammatory challenges. Our results on the constitutively activated status of NF-κB p65 sig- naling with the subsequent increased levels of IL-1β; production of which is induced only in response to inflammatory stimuli [45], may be likely related to the oxinflammation condition typical of RTT [6,38]. 4. Discussion Interestingly, recent findings also revealed a role for HODEs, that we found increased in RTT serum [44], as positive modulators of NLRP3 inflammasome assembly and caspase-1 activation [65]. Based on the evidence of the extracellular release of inflammasome components and a recent report that showed increased concentrations of caspase-1, IL-1β and IL-18 in serum samples from ASD patients [22] (clinically similar to RTT), we decided to confirm our in vitro results on RTT fibroblasts also in the serum from RTT patients. The increased serum levels of ASC oligomers and IL-18 corroborated our cellular findings on the occurrence of a deregulated inflammasome pathway in RTT. Indeed, there is evidence that ASC oligomers remain catalytically active in circulation and, after phagocytosis by adjacent cells, can propagate inflammasome activation, thereby augmenting the pro-in- flammatory cascade [67]. In addition, the LPS + ATP treatment enhanced the levels of the cleaved form of caspase-1 (p20) in CTR cells, in coherence with the increased co-localization of the sensor NLRP3 and the adaptor ASC proteins within the cytoplasm, thus confirming that the LPS + ATP promoted the functional assembly of inflammasome in fibroblasts from healthy individuals. In basal condition, RTT cells were found to have unchanged levels of CASP1 p20. However, the basal activation state of the CASP1 seemed to be higher in RTT fibroblasts than in CTR cells, as shown by the markedly lower pro-CASP1 protein levels found in fi- broblasts from RTT patients. This idea was confirmed by the fact that RTT cells did not undergo any statistically significant change of CASP1 p20 protein level upon pro-inflammatory stimulus. In addition, since images on cleaved IL-1β showed an increased green signal in un-treated RTT fibroblasts, similar to the fluorescence intensity of LPS plus ATP stimulated CTR fibroblasts, we can suppose that CASP1 is able to properly work in the cleavage and maturation of IL-1β. While this Therefore, taken together our data suggest that de-regulated in- flammasome activation may have a role in the occurrence of a sub- clinical inflammatory status in RTT. Several findings demonstrated that a low-grade inflammatory response, avoiding a negative feedback reg- ulation, together with the presence of ROS during the inflammatory processes play a key role in several pathologies: genetic diseases [11,69], diabetes [70], cardiovascular disease [71], cancer [72], and neurodegenerative disorders, such as Alzheimer's and Parkinson's dis- ease [73]. 4. Discussion CTR, control; RTT, Rett syndrome; *P < 0.05. Results were analyzed by t-test for independent groups (CTR N = 17; RTT N = 41). Fig. 5. Increased release of inflammasome components in serum of RTT patients. Panel A. Representative Western blots images for ASC in serum samples from control subjects and RTT patients. Quantification is showed in right panel. Panel B. Representative images and densitometric analysis of Western blotting for ASC oligomers in serum samples from control subjects and RTT patients. Quantification is showed in bottom panel. Panel C. Serum levels of IL-18 in control subjects and RTT patients were quantified by ELISA. For all the panels, the results are presented as means ± SD. CTR, control; RTT, Rett syndrome; *P < 0.05. Results were analyzed by t-test for independent groups (CTR N = 17; RTT N = 41). finding requires further investigations, a plausible explanation for the levels of CASP1 (pro-form and mature form) observed in RTT could be found in an enhanced extracellular release trough extracellular vesicles like exosomes [33,34]. Indeed, in addition to NLRP3 and ASC specks [66,67], also caspase-1 is found in extracellular vesicles. Moreover, recent papers revealed that pro-caspase-1 could be also activated in extracellular compartments, leading to the subsequent cleavage of its substrates in exocytotic secretory pathways, such as exosomes, to dis- seminate the inflammatory signals to adjacent cells and tissues [68]. substantially unchanged after LPS + ATP treatment, we performed a multiple immunofluorescence-based analysis of NLRP3 and ASC, in order to estimate the interaction between these proteins to determine the inflammasome assembly process [20]. Our results provided evi- dence of an increased interaction between NLRP3 and ASC in un- stimulated RTT cells. Furthermore, as expected, control fibroblasts showed increased NLRP3/ASC co-distribution, following the pro-in- flammatory challenge, whereas RTT cells were unable to display a si- milar behavior. Such results are consistent with the data related to NF- κB p65 signaling and cytosolic ASC levels discussed above. The pre- activated status of NLRP3/ASC inflammasome could be also linked to the redox imbalance and the mitochondrial dysfunction, aspects re- peatedly described in RTT [42]. Indeed, mitochondrial events have been associated with NLRP3 activation in several different pathological conditions [62]. By acting upstream of the NLRP3 activation, mi- tochondria can provide ROS to induce NLRP3 oligomerization and be a platform for inflammasome assembly [63,64]. 4. Discussion Indeed, multiple elements support the implication of a chronic, low- grade inflammation in RTT, including high levels of inflammatory markers and deregulation of acute phase response (APR) proteins, an unbalanced plasma cytokines profile coupled with an abnormal which amplitude cannot be achieved by control cells even upon pro- inflammatory stimulation. This indicates the occurrence of an already activated inflammatory response in RTT fibroblasts that, on the other hand, seem unable to respond to further pro-inflammatory challenges. Our results on the constitutively activated status of NF-κB p65 sig- naling with the subsequent increased levels of IL-1β; production of which is induced only in response to inflammatory stimuli [45], may be likely related to the oxinflammation condition typical of RTT [6,38]. Indeed, multiple elements support the implication of a chronic, low- grade inflammation in RTT, including high levels of inflammatory markers and deregulation of acute phase response (APR) proteins, an unbalanced plasma cytokines profile coupled with an abnormal 7 Redox Biology 28 (2020) 101334 A. Pecorelli, et al. Fig. 5. Increased release of inflammasome components in serum of RTT patients. Panel A. Representative Western blots images for ASC in serum samples from control subjects and RTT patients. Quantification is showed in right panel. Panel B. Representative images and densitometric analysis of Western blotting for ASC oligomers in serum samples from control subjects and RTT patients. Quantification is showed in bottom panel. Panel C. Serum levels of IL-18 in control subjects and RTT patients were quantified by ELISA. For all the panels, the results are presented as means ± SD. CTR, control; RTT, Rett syndrome; *P < 0.05. Results were analyzed by t-test for independent groups (CTR N = 17; RTT N = 41). A. Pecorelli, et al. Redox Biology 28 (2020) 101334 Fig. 5. Increased release of inflammasome components in serum of RTT patients. Fig. 5. Increased release of inflammasome components in serum of RTT patients. Panel A. Representative Western blots images for ASC in serum samples from control subjects and RTT patients. Quantification is showed in right panel. Panel B. Representative images and densitometric analysis of Western blotting for ASC oligomers in serum samples from control subjects and RTT patients. Quantification is showed in bottom panel. Panel C. Serum levels of IL-18 in control subjects and RTT patients were quantified by ELISA. For all the panels, the results are presented as means ± SD. 4. Discussion Some of these pathologies have been associated to in- flammasome de-regulated activation [21,32]. In addition, several authors demonstrated that ROS production, via the NAD(P)H-oxidase (NOX) activity, induces the formation and acti- vation of NLRP3 inflammasome in different in vitro and in vivo models [74,75]. Cervellati and co-workers [7] demonstrated that RTT fibro- blasts exhibited high NOX enzymatic activity, together with increased levels of superoxide anion and hydrogen peroxide. Hence, the reported 8 Redox Biology 28 (2020) 101334 A. Pecorelli, et al. A. Pecorelli, et al. Scheme 1. Proposed mechanisms of inflamma- some involvement in RTT OxInflammation. The scheme summarizes the basal and LPS + ATP- stimulated status of the inflammasome pathway by comparing the responses of CTR and RTT fibro- blasts. As showed in the right panels, RTT fibro- blasts were unable to further activate an in- flammasome-dependent response to the pro- inflammatory stimulus with LPS and ATP (bottom panel). Indeed, already in basal conditions (upper panel), they exhibited a pre-activated state of the inflammasome machinery, consisting in increased NLRP3/ASC interaction, CASP1 activation and cleaved IL-1β expression, coupled with an en- hanced nuclear translocation of NF-κB p65 sub- unit. In addition, the deregulation of inflamma- some pathway was associated with increased levels of inflammasome components in patient- derived serum. In conclusion, a state of con- stitutive inflammasome activation could play a key role in RTT oxinflammation by fueling and per- petuating the subclinical inflammatory condition observed in this syndrome. A. Pecorelli, et al. Redox Biology 28 (2020) 101334 S s T s c b b fl i p p i N c h u s l d s r p o A. Pecorelli, et al. Scheme 1. Proposed mechanisms of inflamma- some involvement in RTT OxInflammation. Scheme 1. Proposed mechanisms of inflamma- some involvement in RTT OxInflammation. The scheme summarizes the basal and LPS + ATP- stimulated status of the inflammasome pathway by comparing the responses of CTR and RTT fibro- blasts. As showed in the right panels, RTT fibro- blasts were unable to further activate an in- flammasome-dependent response to the pro- inflammatory stimulus with LPS and ATP (bottom panel). Indeed, already in basal conditions (upper panel), they exhibited a pre-activated state of the inflammasome machinery, consisting in increased NLRP3/ASC interaction, CASP1 activation and cleaved IL-1β expression, coupled with an en- hanced nuclear translocation of NF-κB p65 sub- unit. Declaration of competing interest The authors declare no conflict of interests. The authors declare no conflict of interests. 4. Discussion In addition, the deregulation of inflamma- some pathway was associated with increased levels of inflammasome components in patient- derived serum. In conclusion, a state of con- stitutive inflammasome activation could play a key role in RTT oxinflammation by fueling and per- petuating the subclinical inflammatory condition observed in this syndrome. perpetuate the subclinical inflammatory condition observed in this disease. inflammasome activation in RTT may be likely due also to a NOX-de- pendent response. Our experiments show that RTT fibroblasts were unable to activate an inflammasome-dependent response to pro-inflammatory stimuli, since they exhibited an already altered machinery, thus suggesting a role of inflammasome in the subclinical inflammatory status, char- acterizing the pathology (Scheme 1) [6,38]. It is known that stimulation of the immune system in response to sterile insults can lead to chronic debilitating conditions. Hence, for insulted cells it is crucial to co- ordinate the recognition, initiation, and elaboration of signals inducing inflammasome response, in order to promote the resolution. Whereas a dysregulation of this system can result in disease [14]. Appendix A. Supplementary data Supplementary data to this article can be found online at https:// doi.org/10.1016/j.redox.2019.101334. Supplementary data to this article can be found online at https:// doi.org/10.1016/j.redox.2019.101334. [2] T. Bienvenu, C. Philippe, N. De Roux, M. Raynaud, J.P. Bonnefond, L. Pasquier, G. Lesca, J. Mancini, P. Jonveaux, A. Moncla, J. Feingold, J. Chelly, L. Villard, The incidence of Rett syndrome in France, Pediatr. Neurol. 34 (2006) 372–375. [1] A. Rett, Über ein zerebral-atrophisches Syndrom bei Hyperammonämie, Hollinek, Wien, 1966. [2] T. Bienvenu, C. Philippe, N. De Roux, M. Raynaud, J.P. Bonnefond, L. Pasquier, G. Lesca, J. Mancini, P. Jonveaux, A. Moncla, J. Feingold, J. Chelly, L. Villard, The incidence of Rett syndrome in France, Pediatr. Neurol. 34 (2006) 372–375. [1] A. Rett, Über ein zerebral-atrophisches Syndrom bei Hyperammonämie, Hollinek, Wien, 1966. 5. Conclusions Harris, S. Jung, V. Litvak, J. Kipnis, Methyl-CpG binding protein 2 regulates microglia and macrophage gene expression in response to inflammatory stimuli, Immunity 42 (2015) 679–691. [23] C. Sticozzi, G. Belmonte, A. Pecorelli, F. Cervellati, S. Leoncini, C. Signorini, L. Ciccoli, C. De Felice, J. Hayek, G. Valacchi, Scavenger receptor B1 post-transla- tional modifications in Rett syndrome, FEBS Lett. 587 (2013) 2199–2204. [52] N. Kishi, J.L. MacDonald, J. Ye, B.J. Molyneaux, E. Azim, J.D. Macklis, Reduction of aberrant NF-κB signalling ameliorates Rett syndrome phenotypes in Mecp2-null mice, Nat. Commun. 7 (2016) 10520. [24] H. Li, X. Zhang, M. Chen, J. Chen, T. Gao, S. Yao, Dexmedetomidine inhibits in- flammation in microglia cells under stimulation of LPS and ATP by c-Fos/NLRP3/ caspase-1 cascades, EXCLI J 17 (2018) 302–311. [25] A. Zhang, P. Wang, X. Ma, X. Yin, J. Li, H. Wang, W. Jiang, Q. Jia, L. Ni, Mechanisms that lead to the regulation of NLRP3 inflammasome expression and activation in human dental pulp fibroblasts, Mol. Immunol. 66 (2015) 253–262. [53] O.C. Jorge-Torres, K. Szczesna, L. Roa, C. Casal, L. Gonzalez-Somermeyer, M. Soler, C.D. Velasco, P. Martínez-San Segundo, P. Petazzi, M.A. Sáez, R. Delgado-Morales, S. Fourcade, A. Pujol, D. Huertas, A. Llobet, S. Guil, M. Esteller, Inhibition of Gsk3b reduces Nfkb1 signaling and rescues synaptic activity to improve the Rett syndrome phenotype in Mecp2-knockout mice, Cell Rep. 23 (2018) 1665–1677. activation in human dental pulp fibroblasts, Mol. Immunol. 66 (2015) 253–262. [26] A. Pecorelli, C. Cervellati, A. Cortelazzo, F. Cervellati, C. Sticozzi, C. Mirasole, p p , ( ) [26] A. Pecorelli, C. Cervellati, A. Cortelazzo, F. Cervellati, C. Sticozzi, C. Mirasole, R. Guerranti, A. Trentini, L. Zolla, V. Savelli, J. Hayek, G. Valacchi, Proteomic analysis of 4-hydroxynonenal and nitrotyrosine modified proteins in RTT fibro- blasts, Int. J. Biochem. Cell Biol. 81 (2016) 236–245. phenotype in Mecp2-knockout mice, Cell Rep. 23 (2018) 1665–16 [54] S. Pai, R. Thomas, Immune deficiency or hyperactivity-Nf-kappab illuminates au- toimmunity, J. Autoimmun. 31 (2008) 245–251. [27] A. Pecorelli, G. Belmonte, I. Meloni, F. Cervellati, C. Gardi, C. Sticozzi, C. De Felice, C. Signorini, A. Cortelazzo, S. Leoncini, L. Ciccoli, A. Renieri, H. Jay Forman, J. Hayek, G. Valacchi, Alteration of serum lipid profile, SRB1 loss, and impaired Nrf2 activation in CDKL5 disorder, Free Radic. Biol. Med. 86 (2015) 156–165. d ll d l k ll [55] D. Boucher, M. Monteleone, R.C. Coll, K.W. Chen, C.M. Ross, J.L. 5. Conclusions [46] J R li A A M h hi I li i f h ki h ki d [16] M. Moossavi, N. Parsamanesh, A. Bahrami, S.L. Atkin, A. Sahebkar, Role of the NLRP3 inflammasome in cancer, Mol. Cancer 17 (2018) 158. [46] J. Rolin, A.A. Maghazachi, Implications of chemokines, chemokine receptors, and inflammatory lipids in atherosclerosis, J. Leukoc. Biol. 95 (2014) 575–585. [17] P.J. Shaw, M.F. McDermott, T.D. Kanneganti, Inflammasomes and autoimmunity, Trends Mol. Med. 17 (2011) 57–64. [47] Y. Kabe, K. Ando, S. Hirao, M. Yoshida, H. Handa, Redox regulation of NF-kappaB activation: distinct redox regulation between the cytoplasm and the nucleus, Antioxidants Redox Signal. 7 (2005) 395–403. [18] Y.S. Yi, Role of inflammasomes in inflammatory autoimmune rheumatic diseases, KOREAN J. PHYSIOL. PHARMACOL. 22 (2018) 1–15. [48] D. Colak, H. Al-Dhalaan, M. Nester, A. Albakheet, B. Al-Younes, Z. Al-Hassnan, M. Al-Dosari, A. Chedrawi, M. Al-Owain, N. Abudheim, L. Al-Alwan, A. Al-Odaib, P. Ozand, M.S. Inan, N. Kaya, Genomic and transcriptomic analyses distinguish classic Rett and Rett-like syndrome and reveals shared altered pathways, Genomics 97 (2011) 19–28. [19] R. Zhou, A. Tardivel, B. Thorens, I. Choi, J. Tschopp, Thioredoxin-interacting protein links oxidative stress to inflammasome activation, Nat. Immunol. 11 (2010) 136–140. [20] M. Saresella, F. La Rosa, F. Piancone, M. Zoppis, I. Marventano, E. Calabrese, V. Rainone, R. Nemni, R. Mancuso, M. Clerici, The NLRP3 and NLRP1 inflamma- somes are activated in Alzheimer's disease, Mol. Neurodegener. 11 (2016) 23. [49] C. O'Driscoll, W.E. Kaufmann, J. Bressler, Relationship between Mecp2 and NFκb signaling during neural differentiation of P19 cells, Brain Res. 1490 (2013) 35–42. , g ( ) [21] L. Song, L. Pei, S. Yao, Y. Wu, Y. Shang, NLRP3 inflammasome in neurological diseases, from functions to therapies, Front. Cell. Neurosci. 11 (2017) 63. [50] C.M. O'Driscoll, M.P. Lima, W.E. Kaufmann, J.P. Bressler, Methyl CpG binding protein 2 deficiency enhances expression of inflammatory cytokines by sustaining NF-κB signaling in myeloid derived cells, J. Neuroimmunol. 283 (2015) 23–29. [22] M. Saresella, F. Piancone, I. Marventano, M. Zoppis, A. Hernis, M. Zanette, D. Trabattoni, M. Chiappedi, A. Ghezzo, M.P. Canevini, F. la Rosa, S. Esposito, M. Clerici, Multiple inflammasome complexes are activated in autistic spectrum disorders, Brain Behav. Immun. 57 (2016) 125–133. [51] J.C. Cronk, N.C. Derecki, E. Ji, Y. Xu, A.E. Lampano, I. Smirnov, W. Baker, G.T. Norris, I. Marin, N. Coddington, Y. Wolf, S.D. Turner, A. Aderem, A.L. Klibanov, T.H. 5. Conclusions In conclusion, we report that, along with oxidative stress and mi- tochondrial dysfunction, a state of constitutive activation of the in- flammasome system occurs in RTT, which, in turn, may feed and 9 A. Pecorelli, et al. Redox Biology 28 (2020) 101334 disease, and therapeutics, Nat. Med. 21 (2015) 677–687. [3] R.E. Amir, I.B. Van den Veyver, M. Wan, C.Q. Tran, U. Francke, H.Y. Zoghbi, Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2, Nat. Genet. 23 (1999) 185–188. [33] E.A. Albornoz, T.M. Woodruff, R. Gordon, Inflammasomes in CNS diseases, Exp. Suppl. 108 (2018) 41–60. [4] J.L. Neul, W.E. Kaufmann, D.G. Glaze, J. Christodoulou, A.J. Clarke, N. Bahi- Buisson, H. Leonard, M.E.S. Bailey, N.C. Schanen, M. Zappella, A. Renieri, P. Huppke, A.K. Percy, RettSearch Consortium, Rett syndrome: revised diagnostic criteria and nomenclature, Ann. Neurol. 68 (2010) 944–950. [34] N. Kerr, M. García-Contreras, S. Abbassi, N.H. Mejias, B.R. Desousa, C. Ricordi, W.D. Dietrich, R.W. Keane, J.P. de Rivero Vaccari, Inflammasome proteins in serum and serum-derived extracellular vesicles as biomarkers of stroke, Front. Mol. Neurosci. 11 (2018) 309. P. Huppke, A.K. Percy, RettSearch Consortium, Rett syndrome: revised diagnostic criteria and nomenclature, Ann. Neurol. 68 (2010) 944–950. [5] C. Einspieler, M. Freilinger, P.B. Marschik, Behavioural biomarkers of typical Rett syndrome: moving towards early identification, Wien. Med. Wochenschr. 166 (2016) 333–337. [35] M. Monteleone, A.C. Stanley, K.W. Chen, D.L. Brown, J.S. Bezbradica, J.B. von Pein, C.L. Holley, D. Boucher, M.R. Shakespear, R. Kapetanovic, V. Rolfes, M.J. Sweet, J.L. Stow, K. Schroder, Interleukin-1ß maturation triggers its relocation to the plasma membrane for gasdermin-D-dependent and -independent secretion, Cell Rep. 24 (2018) 1425–1433. [6] A. Pecorelli, C. Cervellati, J. Hayek, G. Valacchi, OxInflammation in Rett syndrome, Int. J. Biochem. Cell Biol. 81 (2016) 246–253. [36] E. Latz, P. Duewell, NLRP3 inflammasome activation in inflammaging, Semin. Immunol. 40 (2018) 61–73. [7] C. Cervellati, C. Sticozzi, A. Romani, G. Belmonte, D. De Rasmo, A. Signorile, F. Cervellati, C. Milanese, P.G. Mastroberardino, A. Pecorelli, V. Savelli, H.J. Forman, J. Hayek, G. Valacchi, Impaired enzymatic defensive activity, mi- tochondrial dysfunction and proteasome activation are involved in RTT cell oxi- dative damage, Biochim. Biophys. Acta 1852 (2015) 2066–2074. [37] F.S. Sutterwala, S. Haasken, S.L. Cassel, Mechanism of NLRP3 inflammasome ac- tivation, Ann. N. Y. Acad. Sci. 1319 (2014) 82–95. [38] G. Valacchi, A. Pecorelli, C. Cervellati, J. 5. Conclusions Hayek, 4-hydroxynonenal protein adducts: key mediator in Rett syndrome oxinflammation, Free Radic. Biol. Med. 111 (2017) 270–280. [8] A. Pecorelli, L. Ciccoli, C. Signorini, S. Leoncini, A. Giardini, M. D'Esposito, S. Filosa, J. Hayek, C. De Felice, G. Valacchi, Increased levels of 4HNE-protein plasma adducts in Rett syndrome, Clin. Biochem. 44 (2011) 368–371. [39] D.E. Place, T.D. Kanneganti, Recent advances in inflammasome biology, Curr. Opin. Immunol. 50 (2018) 32–38. [9] G. Valacchi, F. Virgili, C. Cervellati, A. Pecorelli, OxInflammation: from subclinical condition to pathological biomarker, Front. Physiol. 9 (2018) 858. [40] N. Kelley, D. Jeltema, Y. Duan, Y. He, The NLRP3 inflammasome: an overview of mechanisms of activation and regulation, Int. J. Mol. Sci. 20 (2019). [10] A. Abderrazak, T. Syrovets, D. Couchie, K. El Hadri, B. Friguet, T. Simmet, M. Rouis, NLRP3 inflammasome: from a danger signal sensor to a regulatory node of oxidative stress and inflammatory diseases, Redox Biol 4 (2015) 296–307. [41] Y. Yang, H. Wang, M. Kouadir, H. Song, F. Shi, Recent advances in the mechanisms of NLRP3 inflammasome activation and its inhibitors, Cell Death Dis. 10 (2019) 128. [11] P. Broz, V.M. Dixit, Inflammasomes: mechanism of assembly, regulation and sig- nalling, Nat. Rev. Immunol. 16 (2016) 407–420. [42] S. Filosa, A. Pecorelli, M. D'Esposito, G. Valacchi, J. Hajek, Exploring the possible link between MeCP2 and oxidative stress in Rett syndrome, Free Radic. Biol. Med. 88 (2015) 81–90. [12] V.A.K. Rathinam, K.A. Fitzgerald, Inflammasome complexes: emerging mechanisms and effector functions, Cell 165 (2016) 792–800. [43] M. Müller, Disturbed redox homeostasis and oxidative stress: potential players in the developmental regression in Rett syndrome, Neurosci. Biobehav. Rev. 98 (2019) 154–163. [13] C.L. Evavold, J. Ruan, Y. Tan, S. Xia, H. Wu, J.C. Kagan, The pore-forming protein gasdermin D regulates interleukin-1 secretion from living macrophages, Immunity 48 (2018) 35–44 e6. [44] A. Pecorelli, C. Cervellati, V. Cordone, F. Amicarelli, J. Hayek, G. Valacchi, 13- HODE, 9-HODE and ALOX15 as potential players in Rett syndrome oxInflammation, Free Radic. Biol. Med. 134 (2019) 598–603. [14] B.K. Davis, H. Wen, J.P.Y. Ting, The inflammasome NLRs in immunity, inflamma- tion, and associated diseases, Annu. Rev. Immunol. 29 (2011) 707–735. [15] Q. He, Y. Fu, D. Tian, W. Yan, The contrasting roles of inflammasomes in cancer, Am J Cancer Res 8 (2018) 566–583. [45] Q. Zhu, T.D. Kanneganti, Cutting edge: distinct regulatory mechanisms control proinflammatory cytokines IL-18 and IL-1β, J. Immunol. 198 (2017) 4210–4215. 5. Conclusions Oncol. 9 (2016) 122. [60] B. Kinde, H.W. Gabel, C.S. Gilbert, E.C. Griffith, M.E. Greenberg, Reading the un- ique DNA methylation landscape of the brain: non-CpG methylation, hydro- xymethylation, and MeCP2, Proc. Natl. Acad. Sci. U.S.A. 112 (2015) 6800–6806. [61] G.A. Manji, L. Wang, B.J. Geddes, M. Brown, S. Merriam, A. Al-Garawi, S. Mak, J.M. Lora, M. Briskin, M. Jurman, J. Cao, P.S. DiStefano, J. Bertin, PYPAF1, a PYRIN-containing Apaf1-like protein that assembles with ASC and regulates acti- vation of NF-kappa B, J. Biol. Chem. 277 (2002) 11570–11575. [69] M. Perluigi, D.A. Butterfield, Oxidative stress and Down syndrome: a route toward Alzheimer-like dementia, Curr Gerontol Geriatr Res 2012 (2012) 724904. [ ] k i i i k k k [70] H. Kaneto, N. Katakami, D. Kawamori, T. Miyatsuka, K. Sakamoto, T.A. Matsuoka, M. Matsuhisa, Y. Yamasaki, Involvement of oxidative stress in the pathogenesis of diabetes, Antioxidants Redox Signal. 9 (2007) 355–366. [62] M. Yabal, D.J. Calleja, D.S. Simpson, K.E. Lawlor, Stressing out the mitochondria: mechanistic insights into NLRP3 inflammasome activation, J. Leukoc. Biol. 105 (2019) 377–399. [71] P. Wenzel, S. Kossmann, T. Münzel, A. Daiber, Redox regulation of cardiovascular inflammation - immunomodulatory function of mitochondrial and Nox-derived reactive oxygen and nitrogen species, Free Radic. Biol. Med. 109 (2017) 48–60. [63] E.I. Elliott, A.N. Miller, B. Banoth, S.S. Iyer, A. Stotland, J.P. Weiss, R.A. Gottlieb, F.S. Sutterwala, S.L. Cassel, Cutting edge: mitochondrial assembly of the NLRP3 inflammasome complex is initiated at priming, J. Immunol. 200 (2018) 3047–3052. [72] J.A. Dias, G.N. Fredrikson, U. Ericson, B. Gullberg, B. Hedblad, G. Engström, S. Borgquist, J. Nilsson, E. Wirfält, Low-grade inflammation, oxidative stress and risk of invasive post-menopausal breast cancer - a nested case-control study from the malmö diet and cancer cohort, PLoS One 11 (2016) e0158959. [64] R. Zhou, A.S. Yazdi, P. Menu, J. Tschopp, A role for mitochondria in NLRP3 in- flammasome activation, Nature 469 (2011) 221–225. [65] S. Schuster, C.D. Johnson, M. Hennebelle, T. Holtmann, A.Y. Taha, I.A. Kirpich, A. Eguchi, C.E. Ramsden, B.G. Papouchado, C.J. McClain, A.E. Feldstein, Oxidized linoleic acid metabolites induce liver mitochondrial dysfunction, apoptosis, and NLRP3 activation in mice, J. Lipid Res. 59 (2018) 1597–1609. [73] M.T. Heneka, M.J. Carson, J. El Khoury, G.E. Landreth, F. Brosseron, D.L. Feinstein, A.H. Jacobs, T. Wyss-Coray, J. Vitorica, R.M. Ransohoff, K. Herrup, S.A. Frautschy, B. Finsen, G.C. Brown, A. Verkhratsky, K. Yamanaka, J. Koistinaho, E. Latz, A. Halle, G.C. 5. Conclusions Teo, G.A. Gomez, C.L. Holley, D. Bierschenk, K.J. Stacey, A.S. Yap, J.S. Bezbradica, K. Schroder, Caspase-1 self-cleavage is an intrinsic mechanism to terminate inflammasome ac- tivity, J. Exp. Med. 215 (2018) 827–840. [56] B. Butts, J. Butler, S.B. Dunbar, E.J. Corwin, R.A. Gary, ASC Methylation and in- terleukin-1β are associated with aerobic capacity in heart failure, Med. Sci. Sport. Exerc. 49 (2017) 1072–1078. [28] V. Cordone, A. Pecorelli, M. Benedusi, S. Santini, S. Falone, J. Hayek, F. Amicarelli, G. Valacchi, Antiglycative activity and RAGE expression in Rett syndrome, Cells 8 (2019). [57] R.L. Collard, N.S. Harya, F.A. Monzon, C.E. Maier, D.S. O'Keefe, Methylation of the ASC gene promoter is associated with aggressive prostate cancer, The Prostate 66 (2006) 687–695. [29] K.J. Livak, T.D. Schmittgen, Analysis of relative gene expression data using real- time quantitative PCR and the 2(-Delta Delta C(T)) Method, Methods 25 (2001) 402–408. [30] B. Moser, B. Hochreiter, R. Herbst, J.A. Schmid, Fluorescence colocalization mi- croscopy analysis can be improved by combining object-recognition with pixel-in- tensity-correlation, Biotechnol. J. 12 (2017). [58] R. Webb, J.D. Wren, M. Jeffries, J.A. Kelly, K.M. Kaufman, Y. Tang, M.B. Frank, J. Merrill, R.P. Kimberly, J.C. Edberg, R. Ramsey-Goldman, M. Petri, J.D. Reveille, G.S. Alarcón, L.M. Vilá, M.E. Alarcón-Riquelme, J.A. James, T.J. Vyse, K.L. Moser, P.M. Gaffney, G.S. Gilkeson, J.B. Harley, A.H. Sawalha, Variants within MECP2, a key transcription regulator, are associated with increased susceptibility to lupus and differential gene expression in patients with systemic lupus erythematosus, Arthritis Rheum. 60 (2009) 1076–1084. [31] J. Hayek, C. Cervellati, I. Crivellari, A. Pecorelli, G. Valacchi, Lactonase activity and lipoprotein-phospholipase A(2) as possible novel serum biomarkers for the differ- ential diagnosis of autism spectrum disorders and Rett syndrome: results from a pilot study, Oxid Med Cell Longev 2017 (2017) 5694058, , https://doi.org/10. 1155/2017/5694058. [59] P.M. Das, K. Ramachandran, J. Vanwert, L. Ferdinand, G. Gopisetty, I.M. Reis, R. Singal, Methylation mediated silencing of TMS1/ASC gene in prostate cancer, [32] H. Guo, J.B. Callaway, J.P.Y. Ting, Inflammasomes: mechanism of action, role in 10 A. Pecorelli, et al. Redox Biology 28 (2020) 101334 [68] L. Wang, H. Fu, G. Nanayakkara, Y. Li, Y. Shao, C. Johnson, J. Cheng, W.Y. Yang, F. Yang, M. Lavallee, Y. Xu, X. Cheng, H. Xi, J. Yi, J. Yu, E.T. Choi, H. Wang, X. Yang, Novel extracellular and nuclear caspase-1 and inflammasomes propagate inflammation and regulate gene expression: a comprehensive database mining study, J. Hematol. 5. Conclusions Petzold, T. Town, D. Morgan, M.L. Shinohara, V.H. Perry, C. Holmes, N.G. Bazan, D.J. Brooks, S. Hunot, B. Joseph, N. Deigendesch, O. Garaschuk, E. Boddeke, C.A. Dinarello, J.C. Breitner, G.M. Cole, D.T. Golenbock, M.P. Kummer, Neuroinflammation in Alzheimer's disease, Lancet Neurol. 14 (2015) 388–405. [66] W. Cypryk, T.A. Nyman, S. Matikainen, From inflammasome to exosome-does ex- tracellular vesicle secretion constitute an inflammasome-dependent immune re- sponse? Front. Immunol. 9 (2018) 2188. [67] B.S. Franklin, L. Bossaller, D. De Nardo, J.M. Ratter, A. Stutz, G. Engels, C. Brenker, M. Nordhoff, S.R. Mirandola, A. Al-Amoudi, M.S. Mangan, S. Zimmer, B.G. Monks, M. Fricke, R.E. Schmidt, T. Espevik, B. Jones, A.G. Jarnicki, P.M. Hansbro, P. Busto, A. Marshak-Rothstein, S. Hornemann, A. Aguzzi, W. Kastenmüller, E. Latz, The adaptor ASC has extracellular and “prionoid” activities that propagate inflamma- tion, Nat. Immunol. 15 (2014) 727–737. [74] M.W. Ma, J. Wang, K.M. Dhandapani, D.W. Brann, NADPH oxidase 2 regulates NLRP3 inflammasome activation in the brain after traumatic brain injury, Oxid Med Cell Longev 2017 (2017) 6057609. [75] D.C. Thomas, How the phagocyte NADPH oxidase regulates innate immunity, Free Radic. Biol. Med. 125 (2018) 44–52. 11 11
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Affinity-Based Methods for the Separation of Parasite Proteins
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Affinity-Based Methods for the Separation of Parasite Proteins C.R. Alves, F.S. Silva, F.O. Oliveira Jr, B.A.S. Pereira, F.A. Pires and M.C.S. Pereira Instituto Oswaldo Cruz – Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil ves, F.S. Silva, F.O. Oliveira Jr, B.A.S. Pereira, F.A. Pires and M.C.S. Pereira Instituto Oswaldo Cruz – Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil Selection of our books indexed in the Book Citation Index in Web of Science™ Core Collection (BKCI) Interested in publishing with us? Contact book.department@intechopen.com Numbers displayed above are based on latest data collected. For more information visit www.intechopen.com Open access books available Countries delivered to Contributors from top 500 universities International authors and editors Our authors are among the most cited scientists Downloads We are IntechOpen, the world’s leading publisher of Open Access books Built by scientists, for scientists 14% 191,000 210M TOP 1% 154 7,200 16 www.intechopen.com 1. Introduction Certain glycoconjugates are important for the parasite life cycle, and lectin affinity chromatography can help to reveal their roles (Guha-Niyogi et al., 2001). specifically to certain oligosaccharide structures on glycoconjugates isolated from parasites. Parasite proteins are processed through a multi-lectin affinity column, and they bind to the immobilized lectins through their sugar chains. Certain glycoconjugates are important for the parasite life cycle, and lectin affinity chromatography can help to reveal their roles (Guha-Niyogi et al., 2001). The use of protease inhibitors in affinity chromatography is another important approach for assessing parasite proteins. Proteases hydrolyze peptide bonds and can therefore degrade proteins and peptides that influence a broad range of biological functions, including the process of parasite infection (Mackeron et al., 2006). The specificity of the protease inhibitor used is an important aspect of this methodology; L- trans-epoxy-succinylleucylamido-(4- guanidino) butane (specific to cysteine-protease), pepstatin A (to aspartyl-protease) and aprotinin (to serine-protease) are frequently immobilized on a solid matrix for this technique. Glycosaminoglycan (GAG) affinity is the only affinity chromatography method that is based on the sugar chains of lectin-like proteins. Some of these molecules (such as heparin sulfate, heparan sulfate, dermatan sulfate, keratan sulfate and chondroitin sulfate) contain complex oligosaccharide structures, which may be displayed on cell surfaces, incorporated into the extracellular matrix or attached to secreted glycoproteins, suggesting that they play structural roles (Dreyfuss et al., 2010). GAGs have been reported as potential candidates for therapeutic intervention against parasitic infections, such as leishmaniasis and Chagas diseases (Azevedo-Pereira et al., 2007; Oliveira-Jr et al., 2008). According to the general principle of affinity chromatography (Fig. 1), a protein of interest is recovered based on its capacity to bind a specific functional group (ligand) that is immobilized on a bead material (matrix) that has been packed into a solid support (column). Although many ligands (enzymatic substrates, inhibitors of an enzyme, lectin, sugar residues, vitamins, enzyme cofactors, monoclonal antibodies) have been used to isolate proteins based on affinity, only lectin, an enzyme inhibitor and glycosaminoglycans have been used to obtain parasite proteins. The most commonly used matrix materials for the attachment of the ligand are polysaccharide derivatives (cellulose, dextran and agarose) and polyacrylamide. Fig. 1. The principle of affinity chromatography. The ligand is covalently bound to a matrix (A). The functionalized matrix is then able to bind to a target protein aided by a binding buffer (B). 1. Introduction Affinity chromatography-based techniques have been developed to purify parasite proteins and improve our understanding of the parasite life cycle. These advances can be translated into concrete proposals for new drugs, diagnostic methods and vaccines for parasite diseases and help to reduce social inequality. Affinity chromatography has been demonstrated to be a powerful tool for the isolation and purification of parasite proteins and has potential applications for diagnosis and therapy. Many studies have focused on parasite proteins that modulate host cell defense, as gp63, a glycoprotein from Leishmania spp., that is involved in the cleavage of the complement factor C3b to iC3b, which promotes adhesion of promastigotes to macrophages via complement receptor 3 (Brittgham et al., 1995). This route of internalization does not lead to production of oxygen radicals or NO and favors parasite subsistence within the host cell. Another example is the cysteine protease B (CPB), an important virulence factor of the Leishmania (L.) mexicana complex, that inhibits lymphocytes Th1 and/or promotes the Th2 response either through proteolytic activity or through epitopes derived from its COOH-terminal extension (Pereira et al., 2011). Due to the important role of these molecules, many researchers seek to develop specific and potent inhibitors for therapeutic strategies. Aspartic protease, a potential target for antiparasitic therapies, has been isolated from Trypanosoma cruzi by affinity chromatography using a specific inhibitor of this enzyme (Pinho et al., 2009); this enzyme is target for treatment of infections caused by HIV (Wlodawer & Vondrasek, 1998) and Candida (Hoegl et al., 1999). This enzyme has also been reported in Plasmodium spp. and Schistosoma mansoni, where it plays an important role in host hemoglobin degradation (Klemba & Goldberg, 2002). Additionally, specific inhibitors of plasmepsins and renin are viable drugs for the treatment of patients with malaria and high blood pressure. These parasite proteins, along with others, have been tested as new targets for chemo- and immunotherapies for parasite diseases. They have been assessed by lectins or protease inhibitor affinity chromatography. The separation of sugars based on lectin affinity is one of main procedure that has been used. This technique is based on the ability of lectins to bind www.intechopen.com 334 Affinity Chromatography specifically to certain oligosaccharide structures on glycoconjugates isolated from parasites. Parasite proteins are processed through a multi-lectin affinity column, and they bind to the immobilized lectins through their sugar chains. 1. Introduction Afterwards, the bound proteins are eluted with a different buffer (C). Fig. 1. The principle of affinity chromatography. The ligand is covalently bound to a matrix (A). The functionalized matrix is then able to bind to a target protein aided by a binding buffer (B). Afterwards, the bound proteins are eluted with a different buffer (C). www.intechopen.com 335 Affinity-Based Methods for the Separation of Parasite Proteins In these procedures, the soluble proteins are prepared from crude parasite lysates (or sub- cellular fractions) and loaded onto a column under chemical (buffer) and physical (temperature and pressure) conditions that promote the specific binding of the protein to the immobilized ligand (affinity) in what is known as the binding phase. Proteins that do not bind to the immobilized ligand under these conditions are removed from the solid phase by application of a constant liquid phase, which is referred to as the wash phase. Then, the bound protein can be recovered by changing the buffer conditions to favor desorption during the elution phase. In this chapter, we describe the use of affinity chromatography to assess parasite proteins and the importance of these methods for public health. Several affinity chromatography protocols are considered. Additionally, we discuss our experience using affinity chromatography to obtain parasite proteins, and we include some unpublished results related to Dermatobia hominis third (L3) instar larvae proteases. 2. The use of affinity chromatography in parasite protein studies 2.1 Lectin affinity-based separation of parasite proteins There are relatively few studies available in the current literature describing the use of lectins to affinity-purify glycosylated proteins from parasites. However, the reports on this subject demonstrate that this technique is useful for the retrieval of putative virulence factors or potential protective immunogens from a large array of parasites, including apicomplexan, trypanosomatids and nematodes (e.g., Fauquenoy et al., 2008, Gardiner et al., 1996, Smith et al., 2000). In addition to its utility in the isolation of parasite factors, lectin- based affinity chromatography is also a valuable resource for characterization of the structure of carbohydrates bound to proteins from these organisms due to the distinct specificities of the lectins that are available for this type of analysis. Lectins are proteins that specifically bind to sugars, and they have been used for many types of studies, ranging from blood typing to immune regulation analysis (Rüdiger & Gabius, 2001). These proteins are generally isolated from plants (mostly legume seeds), where they can be found in abundance. Their usage is determined by the particular sugar structures that they are able to bind (Rüdiger & Gabius, 2001). The surveyed literature the use of six plant lectins [concanavalin A (Con A), ricin, jacalin, peanut agglutinin (PNA), wheat germ agglutinin (WGA) and Wisteria floribunda agglutinin (WFA)] in studies of parasites glycoproteins. Furthermore, one report described the use of Biomphalaria alexandrina lectin (BaSII), which in contrast to the others is a lectin obtained from an animal. Con A is a lectin that can be extracted from jack beans of the species Canavalia ensiformis (family Fabaceae). It binds to mannose or glucose residues and is thus characterized as a mannose-binding lectin. This lectin presents a high affinity for the oligosaccharide GlcNAcǃ2Manǂ6(GlcNAcǃ2Manǂ3)-Manǃ4GlcNAc. It is also known to be a potent mitogen (Beckert & Sharkey, 1970; Rüdiger & Gabius, 2001). Ricin, along with jacalin and PNA, is a lectin that binds to galactose. Specifically, it binds with high affinity to the motif Galǃ4GlcNAcǃ2Manǂ6 (Galǃ4-GlcNAcǃ2Manǂ3) Manǃ4GlcNAc. Ricin is highly toxic because it can impair ribosome activity through cleavage of the nucleobases of ribosomal RNA, and it has potential to be used as a biological www.intechopen.com 336 Affinity Chromatography weapon. This lectin is extracted from Ricinus communis (Family Euphorbiaceae) (Rüdiger & Gabius, 2001; Lord et al., 2003). weapon. This lectin is extracted from Ricinus communis (Family Euphorbiaceae) (Rüdiger & Gabius, 2001; Lord et al., 2003). 2. The use of affinity chromatography in parasite protein studies 2.1 Lectin affinity-based separation of parasite proteins Jacalin binds to galactose and N-acetylgalactosamine, and presents a high affinity for the motif Galǃ3GalNAcǂ. It is obtained from Artocarpus integrifolia (Family Moraceae). It is commonly used to isolate IgA from human plasma (Kabir, 1998, André et al., 2007). Like Con A, PNA is a legume lectin and is isolated from plants that belong to the family Fabaceae. It is extracted from Arachis hypogea and binds specifically to the monosaccharide galactose and to the motif Galǃ3GalNAcǂ, similarly to the binding motif of jacalin. PNA is used as a marker of T-cell subpopulations and to differentiate between the stages of the Leishmania parasites life cycle (Dumont & Nardelli, 1979, Wilson & Pearson, 1984, Rüdiger & Gabius, 2001). WGA is obtained from the species Triticum vulgare. It presents a low affinity for N- acetylgalactosamine, but it binds to the sialic acid N-acetylneuraminic and to the motif GlcNAcǃ4GlcNAcǃ4GlcNAcǃ4-GlcNAcǃ4GlcNAc. This lectin has been shown to bind more avidly to activated human T lymphocytes (Hellström et al., 1976, Rüdiger & Gabius, 2001). WFA is isolated from Wisteria floribunda, a woody liana of the family Fabaceae. Although some uncertainty regarding its binding specificity remains, it seems that this agglutinin binds preferentially to the monosaccharide N-acetylgalactosamine and to the motif GalNAcǂ6GalNAc. WFA is used to fractionate lymphocyte populations, and although it is not mitogenic like Con A, it can induce lymphokine production in murine splenocytes (Jacobs & Poretz, 1980; Rüdiger & Gabius, 2001). BaSII is a lectin that can be isolated from the snail B. alexandrina, an intermediate host of the trematoda parasite Schistosoma mansoni, the causative agent of schistosomiasis. It specifically binds to the motif Fucǂ1,2Galǃ1,4Glc (Mansour, 1996). 2.1.1 General procedures for the isolation of parasite proteins by lectin affinity The rational for lectin-based affinity chromatography is the same as for other types of affinity-based fractionation: a sample is exposed to a solid phase that has been coupled to an affinity separation molecule (a lectin, in this case) under conditions that are adequate for binding (Fig. 2A). The unbound material from the sample is washed away (generally using the same buffer applied to equilibrate the solid-phase), and in the final step, the affinity- bound fraction is recovered by altering the equilibrium conditions of the solid phase (by changing the system pH or salt concentration) or by adding a molecules that competes for the binding site of the ligand. To provide several practical examples, a collection of lectin affinity-based methodologies used to isolate and/or characterize glycoproteins from distinct parasites is listed in the Table 1. It is important to note that some techniques, such as metabolic radioactive labeling (by [3H]- myristic acid or [3H]-glucosamine, for example) and cell disruption (by Triton X-100, dioxane or hypotonic solution), must be applied prior to lectin chromatography to allow for the identification of molecules eluted from the column or the preparation of suitable samples for the chromatography column, respectively. www.intechopen.com Affinity-Based Methods for the Separation of Parasite Proteins 337 ble 1. Lectin affinity-based www.intechopen.com 338 Affinity Chromatography ble 1. (continued) 339 Affinity-Based Methods for the Separation of Parasite Proteins During the affinity chromatography procedure, other methods, such as isoelectric focusing, may be used instead of the application of competing carbohydrates to elude the column- bound material. Furthermore, distinct affinity columns can be used in sequence to purify fractions with specific characteristics from a single sample. As for the handling of the material that is eluted from an affinity column, many options for further purification are available, depending on the analysis method chosen for the study. Some of these options include: anion exchange chromatography, size exclusion chromatography and dialysis. The combination of these accessible approaches allows for a vast array of study possibilities. Several examples of the results obtained by applying lectin-affinity chromatography in association with other techniques are described in the following paragraphs. www.intechopen.com 2.1.2 Parasite proteins isolated by lectin affinity chromatography Additionally, ISG100 is encoded by a single gene, whereas the trypanosomal plasma membrane proteins are commonly encoded by tandemly repeated genes that are part of a multigene family. Nolan et al., (1997) identified a new invariant surface glycoprotein that is heavily N- glycosylated in the bloodstream forms of Trypanosoma brucei and designated it as ISG100. This glycoprotein presents a large internal domain composed of a serine-rich repetitive motif, which was previously undescribed, and N-glycosylation sites on the N-terminal domain. Additionally, ISG100 is encoded by a single gene, whereas the trypanosomal plasma membrane proteins are commonly encoded by tandemly repeated genes that are part of a multigene family. Potentially protective glycoprotein fractions from Haemonchus contortus, a parasitic nematode in ruminants, were also obtained by lectin chromatography (Smith et al., 2000). The findings from that study confirmed the potential of the H. contortus PNA-binding glycoprotein fraction as an efficacious antigen against this parasite infection in sheep. Furthermore, this study identified another highly protective fraction that binds to jacalin. This second protective fraction presents sialyted versions of the same oligosaccharides that bound to the PNA column. Another study on the protective properties of the glycoproteins of H. contortus was performed by the same group (Smith et al., 2003). The results showed that the four purified glycosylated zinc metalloproteinases from this parasite were such an efficacious antigen that, to an extent, they could account for most of the protection conferred by the urea- dissociated whole glycoproteins fraction. However, the role for the glycan moieties of these enzymes in the protection process was not clear. The capacity of glycoproteins from Caenorhabditis elegans, a free living nematode, to induce protection from a challenge with H. contortus in sheep was assayed by Redmond et al. (2004). The lectin affinity methodology was able to identify glycoproteins with molecular masses between 25 and 200 kDa in extracts prepared from C. elegans, but the fractionated glycoproteins were not able to confer protection against an H. contortus challenge. These findings suggest that the conserved glycan moieties between these two species of worm are not solely responsible for the protections levels observed when native H. contortus antigens are used. Trypanosoma brucei glycoproteins were shown to present distinctive structural features, such as the presence of giant poly-N-acetyllactosamine carbohydrate chains (Atrih et al., 2005). The recovered affinity-bound molecules were predominantly, but not exclusively, from the flagellar pocket. 2.1.2 Parasite proteins isolated by lectin affinity chromatography The structure of an N-linked oligosaccharide from a surface glycoprotein of Trypanosoma cruzi, an important human parasite that causes Chagas disease, was defined in a study using lectin chromatography (Couto et al., 1990). It was determined that the structure of this oligosaccharide is comprised of complex carbohydrate chains that possess a terminal sialic acid, ǂ-L-fucose and a galactosyl(ǂ1,3)galactose unit. The cellular localization of glycoproteins of Trypanosoma brucei rodhesiense, a subspecies of the parasite responsible for the African sleeping sickness, was analyzed using ricin-based chromatrography (Brickman & Balber, 1993). It was observed that the ricin-binding proteins were primarily located in the vesicles of the lysosomal /endosomal system. Gardiner et al., (1996) characterized small glycoproteins isolated from the surface of Trypanosoma vivax, which causes bovine trypanosomiasis. That study was the first to detail the characteristics of a T. vivax Variable Surface Glycoprotein (VSG). The isolated protein, designated ILDat 2.1 VSG, presented a molecular mass of 40 kDa and contained mannose (or a derivative sugar) in small quantities, and it was poorly retained by the lectin affinity column. It is possible that carbohydrates comprise only the C-terminal anchoring structure of this protein. The characteristics of a fucosyllactose determinant of a S. mansoni glycoprotein were identified using affinity chromatography based on a lectin that was isolated from a host of this parasite, B. alexandrina. This determinant is expressed in the outer chain of a single unit of complex type N-linked oligosaccharides (Mansour, 1996). Additionally, the VSG glycosyl-phosphatidylinositol membrane anchors of Trypanosoma congolense, another trypanosomatide species that causes bovine trypanosomiasis, were studied by lectin affinity (Gerold et al., 1996) using a modification of the technique in which the bound proteins are electrophoretically desorbed (Reinwald et al., 1981). This analysis allowed for description of the VSG GPI-anchor in this parasite: it contains a ǃ1,6-linked galactose as the terminal hexose of the branch and an N-acetyl-glucosamine residue. Also, it was observed that T. congolense synthesizes two potential GPI-anchor precursors, one of which is insensitive to phospholipase C activity. www.intechopen.com 340 Affinity Chromatography Nolan et al., (1997) identified a new invariant surface glycoprotein that is heavily N- glycosylated in the bloodstream forms of Trypanosoma brucei and designated it as ISG100. This glycoprotein presents a large internal domain composed of a serine-rich repetitive motif, which was previously undescribed, and N-glycosylation sites on the N-terminal domain. 2.1.3 Remarks on the isolation of proteins by lectin affinity chromatography These reports provide examples of the uses of lectin affinity chromatography to identify potentially antigenic fractions of parasites that could be used for vaccine development. Also, they point to the potential of this method to characterize glyconjugates, such as the glycoproteins that are present on the parasite surface or secreted by these organisms. However, apart from these purely structural or clinically oriented applications, this method may also be relevant in other investigations, including studies of host-parasite interactions. This hypothesis is reinforced by reports indicating that lectin-glycan binding is important for the infection and virulence processes of some parasites, e.g. Acanthamoeba castellanii (Garate et al., 2006), H. contortus (Turner et al., 2008), L. (V.) braziliensis (Rebello et al., 2009) and T. gondii (Fauquenoy et al., 2008) Fig. 2. Illustration of the affinity chromatography methodologies. The target molecules are bound to their ligands immobilized on a solid phase matrix. (A) Lectin affinity chromatography, (B) Protease inhibitor affinity chromatography and (C) Glycosaminoglycan affinity chromatography. Proteins = blue circle; carbohydrates = red pentagon and hexagon; protease inhibitors = green drop-like form; ions =yellow circles; and solid phase matrix beads = gray circle. Fig. 2. Illustration of the affinity chromatography methodologies. The target molecules are bound to their ligands immobilized on a solid phase matrix. (A) Lectin affinity chromatography, (B) Protease inhibitor affinity chromatography and (C) Fig. 2. Illustration of the affinity chromatography methodologies. The target molecules are bound to their ligands immobilized on a solid phase matrix. (A) Lectin affinity chromatography, (B) Protease inhibitor affinity chromatography and (C) Glycosaminoglycan affinity chromatography. Proteins = blue circle; carbohydrates = red pentagon and hexagon; protease inhibitors = green drop-like form; ions =yellow circles; and solid phase matrix beads = gray circle. g p y, ( ) y g p y ( ) Glycosaminoglycan affinity chromatography. Proteins = blue circle; carbohydrates = red pentagon and hexagon; protease inhibitors = green drop-like form; ions =yellow circles; and solid phase matrix beads = gray circle. 2.1.2 Parasite proteins isolated by lectin affinity chromatography These glycoproteins carry massive glycans, representing the largest poly- LacNAc structures reported to that date, and they may produce a gel-like matrix in the lumen of the flagellar pocket and/or the endosomal/lysosomal system. Despite their remarkable size, these glycans present a very simple neutral structure, containing only mannose, galactose and N-acetylglycosamine. Important glycoproteins from the apicomplexan parasite Toxoplasma gondii have also been analyzed by lectin affinity methods. It was shown that these components are pivotal factors for host invasion and intracellular development of parasites (Fauquenoy et al., 2008). Cysteine proteinases from promastigostes of Leishmania (Viannia) braziliensis were shown to be anchored to the membrane by glysoylphosphatidylinositol structures in an analysis of the hydrophobic fraction of promastigote forms. These enzymes are suggested to play a role in the process of parasite survival inside its hosts (Rebello et al., 2009). www.intechopen.com 341 Affinity-Based Methods for the Separation of Parasite Proteins www.intechopen.com www.intechopen.com 2.2 Protease inhibitors affinity-based separation of parasite proteins Methodologies for the purification of parasite proteases have been applied in studies investigating the biological roles of these enzymes in parasite, including their participation in the infection process and in the survival of the parasites inside their hosts (McKerrow et al, 2006). Inhibitor affinity chromatography consists of the fractionation of parasite samples based on the reversible interactions between proteases and their specific inhibitors while the latter are covalently attached to a matrix (Fig. 2B). This technique can also be performed using irreversible inhibitors under particular conditions that will be described further in this section. It is also interesting to note that, based on the specificity of the inhibitor used in the affinity chromatography, it is possible to suggest the enzyme class of the isolated protein. However, complementary analyses, such as characterization of the proteolytic activity, are often necessary to confirm these findings. Nevertheless, this purification strategy presents an initial advantage when compared to other methodologies. In this section, fractionation approaches for serine-, aspartic acid- and cysteine proteases in specific parasites will be described. These approaches must take the class of the studied enzyme into consideration, as well as the inhibitor to be used and the characteristics of the mobile phase used for chromatography. www.intechopen.com 342 Affinity Chromatography le 2. Protease Inhibitors affinity-based Table 2. Protease Inhibitors affinity-based www.intechopen.com Affinity-Based Methods for the Separation of Parasite Proteins 343 able 2. (continued) www.intechopen.com 344 Affinity Chromatography Aprotinin and pepstatin A are examples of inhibitors that are frequently used in the isolation of serine- and aspartic acid proteases, respectively, from many parasite species (Bond & Beynon). Other inhibitors that have been previously described in the isolation of serine proteases include soybean trypsin inhibitor (SBTI) and chloromethylketone (CMK). As for the purification of cysteine proteases, the use of three other inhibitors has been reported: L-transepoxysuccinyl-leucylamido-[4-guanidino]butane (E-64), bacitracin and glycyl-phenylalanyl-glycyl-semicarbazone (Table 2). It must be emphasized that these inhibitors cannot be used to isolate all of the proteases classes from parasites, as they present distinct affinities for members of different groups and families within these enzyme classes. Therefore, investigation of the possible variations present in the active site of these enzymes may prove useful. The features of the buffer (temperature, pH and ionic strength) to be used may vary according to the ligand’s physicochemical characteristics, the chemical environment of the parasite enzyme and the analyzed species of parasite. 2.2 Protease inhibitors affinity-based separation of parasite proteins For example, distinct buffers were used for the purification of serine proteases from S. mansoni and Trichinella spiralis using benzamidine. It is also noteworthy that for each organism, a different matrix was used to immobilize the inhibitor, sepharose for S. mansoni and celite for T. spiralis. The use of distinct buffers in studies that are based on the same inhibitor is also noted in reports of SBTI, E-64, bacitracin and glycyl-phenyalanyl-glycyl-semicarbazone, all of which are cysteine protease inhibitors. Affinity chromatography with an irreversible inhibitor has also been described previously; the cysteine-protease inhibitor is an example of this strong binding. In the interaction between E-64 and cysteine-protease, a covalent bond is established (Matsumoto, 1989). Therefore, a reaction between the epoxy groups of the inhibitor and the thiopropyl group of the sepharose matrix is necessary to bind E-64 to a solid support. This reaction prevents the reaction of E-64 with the cysteine residue at the protease catalytic center. However, this does not affect the bond between the inhibitor and cysteine-protease; instead, it only results in inhibition of the proteolytic activity (Govrin, 1999). 2.2.1 Parasite proteins isolated by cysteine-protease inhibitors affinity chromatography There is only one published example of the use of E-64 affinity chromatography to assess cysteine-protease isolated from a parasite, and this study was conducted with the T. cruzi epimastigote. In this study, chromatography was useful for assessing the effects of ǃ- Lapachone naphthoquinones on a 60 kDa cysteine-protease activity present in T. cruzi. The results demonstrated the potential of this protease inhibitor as a new antichagasic compound (Bourguignon et al., 2011). Another example of a cysteine-protease isolated by inhibitor affinity chromatography in parasites was described for Plasmodium falciparum. In this case, a glycyl- phenyalanyl-glycyl-semicarbazone-based column was used to isolate a protease with a molecular weight of 27 kDa, as determined by SDS-PAGE (Shenai et al, 2000). 2.2.2 Parasite proteins isolated by serine-protease inhibitors affinity chromatography Aprotinin affinity-based chromatography was useful for the isolation of a serine-protease of 115 kDa (Silva-Lopez et al., 2005), a 68 kDa (Morgado- Diaz et al., 2004; Silva-Lopez et al., 2004) and a 56kDa (Silva-Lopez et al., 2004) from L.(L.) amazonensis compared to other www.intechopen.com 345 Affinity-Based Methods for the Separation of Parasite Proteins purification procedures that were used to isolate parasite serine peptidase enzymes (Kong et al., 2000; Ribeiro de Andrade et al., 1998). In Leishmania (V) braziliensis promastigotes, 60 kDa and 45 kDa enzymes were purified using the aprotinin affinity-based and activity esterase assessed against N-alpha-benzoyl-L-arginine ethyl ester hydrochloride and Nalpha-p-tosyl- L-arginine methyl ester hydrochloride (Guedes et al., 2007). Furthermore, three protein profiles were isolated from Leishmania chagasi promastigotes, including LCSI (58 and 60 kDa), LCSII (60, 66, 105 and kDa) and LCSIII (68 and 76 kDa), which were characterized as serine-protease enzymes based on their activity toward ǂ-N-ρ-tosyl-L-arginine methyl ester substrate (Silva-Lopez et al., 2010). Furthermore, serine proteases with molecular weights of 75 kDa (Silva-Lopez et al., 2008) and 115 kDa (Choudhury et al., 2009) were identified as excretory products of T. cruzi and components of the sub-cellular environment in Leishmania donovani, respectively, although the chromatography step was not able to produce a homogeneous fraction. Furthermore, a intracellular serine protease of 58 kDa was were purified from Leishmania donovani (Choudhury et al., 2010). In addition, the aprotinin affinity-based chromatography was useful for the isolation of serine-proteases of 35 kDa and 26 kDa from Anisakis simpZex (Morris et al, 1994), 43 kDa from Candida albicans (Morrison et al, 1993), 15 kDa from Schistosoma mansoni (Salter et al, 2000), 42 kDa from Rhipicephalus (B.) microplus (Cruz et al, 2010), 60 kDa and 30 kDa from Trichomonas vaginalis (Sommer et al; 2005) and 35 to 52 from Caenorhabditis elegans (Geier et al; 1999). Benzamidine-celite was applied in the isolation of serine proteases among the excreted or secreted proteins of T. spirali. The recovered proteases were not purified to homogeneity, and they showed molecular masses of 18 kDa, 40 kDa and 50 kDa (Todorova & Stoyanov). A similar finding was reported for the serine-proteases of Chrysomya bezziana larvae by using an SBTI-based column to purify four proteins with molecular masses of 13 kDa, 16 kDa, 26 kDa and 28 kDa (Muharsini et al., 2000). www.intechopen.com 2.2.2 Parasite proteins isolated by serine-protease inhibitors affinity chromatography Because it is possible to isolate heterogeneous products using inhibitors for affinity-based chromatography, we assessed a serine-protease from the third (L3) instar larvae of D. hominis. This ectoparasite causes dermatobiose in vertebrates, including humans, and it is particularly relevant in cattle, where it can cause a drop in production of meat and milk, leather as well depreciation (Maia & Guimarães, 1985). Due to the association of DEAE-Sephacel with aprotinin agarose, it was possible to assess a serine protease from L3 larvae (Fig. 3). The fractions obtained by ion change chromatography containing estearasic activity were pooled and then fractionated on an aprotinin-agarose column. This fraction showed a profile with multiple bands by SDS-PAGE and silver staining, and only one band of enzyme activity (50 kDa) was detected by gelatin- SDS-PAGE at pH 7.5 (Fig. 3). Interestingly, this band of 50 kDa was not initially detected in the extracts from L3 by gelatin-SDS-PAGE. The expression of this enzyme is likely low in these larvae, and it can only be detected after concentration by chromatographic methods. The proposed strategy to isolate a serine protease allowed for the detection of a band of 50 kDa in extracts of L3 larvae, and this band had not been previously detected in the direct analysis of the total extract by gelatin-SDS-PAGE. Additionally, this fraction was found to have esterase activity (data not shown). www.intechopen.com 346 Affinity Chromatography Fig. 3. Electrophoresis of proteins from L3 instar larvae of Dermatobia hominis eluted from a column of aprotinin-agarose. A total of 20 μg of protein from each fraction was resolved by SDS-PAGE (A) and gelatin-SDS-PAGE (B) and the bands were detected by silver staining and negative coloration, respectively. The arrow indicates a serine protease of 50 kDa. The molecular mass markers are indicated (kDa). These results are representative of two independent assays Fig. 3. Electrophoresis of proteins from L3 instar larvae of Dermatobia hominis eluted from a column of aprotinin-agarose. A total of 20 μg of protein from each fraction was resolved by SDS-PAGE (A) and gelatin-SDS-PAGE (B) and the bands were detected by silver staining and negative coloration, respectively. The arrow indicates a serine protease of 50 kDa. The molecular mass markers are indicated (kDa). These results are representative of two independent assays 2.2.3 Parasite proteins isolated by aspartyl-protease inhibitors affinity chromatography Affinity-based chromatography based on pepstatine A was used to isolate a 52 kDa aspartyl protease from Neospora caninum tachyzoites (Naguleswaran et al., 2005) and a 45 kDa enzyme from S.mansoni (Valdivieso et al., 2003). In Trypanosoma cruzi epimastigotes, two aspartyl proteases were isolated (cruzipsin-I and cruzipsin-II). The molecular mass was estimated to be 120kDa by high performance liquid chromatography gel filtration, and the activities of these enzymes were detected in a doublet of bands (56 kDa and 48 kDa). These findings demonstrate that both proteases are novel T. cruzi acidic proteases. The physiological function of these enzymes in T. cruzi is not completely defined (Pinho et al., 2009). www.intechopen.com 347 Affinity-Based Methods for the Separation of Parasite Proteins An aspartyl protease with molecular mass of 37 kDa (plasmepsin) was isolated from the surface of Plasmodium ookinete, and its sequence was determined by mass spectrometry (Li et al., 2010). This protease was purified by using a benzamidine affinity-based column, which is typically used for the isolation of serine proteases. Structural similarity between the active site residues of the serine- and aspartyl proteases is possible, as some hydrogen-bonded residues can are arranged without any strain, such as in the formation of an oxyanion hole, in a manner that resembles the active site of a serine protease (Andreeva et al., 2004) 2.2.4 Remarks on the isolation of proteins by protease inhibitors affinity chromatography Although the studies that have been conducted to isolate parasite proteases are of great medical interest, no parasiticide drug has been proposed thus far. In general, the chromatography methods involving inhibitor-based affinity-capture have been useful only to describe these enzymes in parasites and to establish their biochemical properties, their functions and their application in drugs tests. Furthermore, the heterogeneous material obtained from affinity-based chromatography may require additional procedures for purification of the enzyme. Thus, other techniques must be applied to obtain proteases with greater purity, including molecular exclusion and ion exchange chromatography. 2.3 Glycosaminoglycans affinity-based separation of parasite proteins Microbes have developed different strategies to gain access into mammalian cells (Bermúdez et al., 2010; Caradonna & Burleigh 2011; Soong et al., 2011). The first step involves the recognition of molecules at the surface of the target cell, which triggers the activation of signaling pathways that are implicated in the parasite internalization (Abban & Meneses 2010; Epting et al., 2011). Host cell surface sulfated proteoglycans have been implicated as key molecules at the host cell-parasite interface, mediating the adhesion and invasion of numerous parasitic microorganisms (Jacquet et al., 2001; Kobayashi et al., 2010; O'Donnell & Shukla 2010). 2.3.2 Role of heparin-binding proteins in pathogen-host cell Many pathogens express surface proteins that interact with GAGs in different stages of their life cycle. Although some parasites can bind to multiple GAGs (Coppi et al., 2007; Fallgren et al., 2001), heparan sulfate proteoglycan (HSPG) has been implicated in the recognition and/or invasion process of a wide range of pathogens, including viruses, bacteria and protozoan parasites (Bambino-Medeiros et al., 2011; Dalrymple & Mackow 2011; Yan et al., 2006;). Despite the role of heparin-binding proteins in many physiological and pathological processes, the basis of the heparin-protein interaction at the molecular level is still unclear. Thus, efforts have been concentrated to enhance methods for the isolation and characterization of heparin-binding proteins, and, in parallel, to determine the role of this GAG in pathogen-host cell interaction. Currently, heparin affinity chromatography has been applied to the purification of GAG-binding proteins from different pathogens (Table 3). In these chromatography assays, the heparin is covalently coupled to agarose or sepharose beads and its sulfates and carboxylates chains are able to bind many proteins by basic amino acids (Fig. 2C). This technique has been used to isolate heparin-binding proteins without loss of their biological activity, leading to a better understanding of the mechanism involved in the parasite invasion process. For example, chlamydial outer membrane complex (OmcB), a 60 kDa cysteine-rich protein, displays a protein motif (50-70OmcB peptide) that acts as an acceptor molecule to bind heparan sulfate (HS) and promote Chlamydia invasion in eukaryotic cells (Stephens et al., 2001). Attachment of Helicobacter pylori to gastric epithelial cells also involves HS recognition. Two major proteins, one with a molecular mass of 71.5 kDa and pI 5.0 (HSBP50) and the other with a molecular mass of 66.2 kDa and pI 5.4 (HSBP54), have been identified on the surface of bacterial cells that are able to bind HS. The amino acid sequences of these proteins (HSBP50 – VPERAVRAHT; HSBP54 - VHLPADKTNV) are not homologous with bacterial adhesins or other HS-binding proteins (Ruzi-Bustos et al., 2001). Other proteins with the ability to bind heparin (66 and 60 kDa) have been identified in Staphylococcus aureus. The partial characterization of the amino acid sequences, which consist of DWTGWLAAA for the 66 kDa protein and MLVT for the 60 kDa protein, revealed no identity with HBPs from Chlamydia or Helicobacter pylori. HBPs from S. 2.3.1 Structure of glycosaminoglycans Proteoglycans (PGs) are composed of core proteins that are covalently linked to glycosaminoglycan (GAG) chains. As components of the extracellular matrix, the structural diversity of PGs depends on the identity of the core protein and the GAG composition. GAGs are linear polysaccharides comprised of disaccharide repeats containing uronic acid and hexosamine. GAGs vary in the type of hexosamine, hexose or hexuronic acid unit. The sulfated GAGs are classified as heparin [2-O-sulfo-ǃ-D-glucuronic acid (GlcUA-2S) or 2-O- sulfo-ǂ-L-iduronic acid (IdoUA-2S) and N-acetylglucosamine (GlcNAc) or N- sulfoglucosamine (GlcNS)], heparan sulfate [GlcUA, IdoUA or IdoUA-2S and GlcNAc or GlcNS], chondroitin sulfate [GlcUA and N-acetylgalactosamine (GalNAc)], dermatan sulfate [GlcUA or IdoUA and GalNAc] and keratan sulfate [galactose (Gal) and GlcNAc]. In fact, the structural diversity of PGs may provide sites of affinity for different ligands and, therefore, function as co-receptors or receptors for GAG-binding proteins (Dreyfuss et al., 2009; Ly et al., 2010). Although heparin is not found on the cell surface, this GAG has being www.intechopen.com 348 Affinity Chromatography commonly used as tool for pathogen-host cell interaction assays. Heparins are negativally charged structures and native heparin presents molecular weights in the range of 5 to 30 KDa, whereas commercial heparin preparations are in the range of 12 kDa to 15 kDa. 2.3.2 Role of heparin-binding proteins in pathogen-host cell aureus have been demonstrated to be sensitive to heat and proteases, such as pronase E, proteinase K, pepsin and chymotrypsin (Liang et al., 1992). Interestingly, a 17- kDa heparin-binding protein with pI 4.6 has also been isolated from S. epidermis and S. haemolyticus, but the amino acid sequence similarity is low between these two organisms (MXTAHSYTXKYNGYTAN and MATQTKGYYYSYNGYV, respectively) and other bacterial HBPs (Fallgren et al., 2001). Trypanosomatidaes also exploit HS for successful parasite attachment to and/or invasion of the mammalian and vector hosts. The adhesion of Leishmania amastigotes to macrophages is mediated by HS, but not other sulfated polysaccharides (Love et al., 1993). Two heparin- www.intechopen.com 349 Affinity-Based Methods for the Separation of Parasite Proteins binding proteins, (65 and 54.5 kDa) from L. (V.) braziliensis promastigotes (HBP-Lb) recognize several molecules in the gut of Lutzomyia intermedia and Lutzomyia whitmani (Azevedo-Pereira et al., 2007). The biochemical characterization of these proteins revealed that only the 65-kDa HBP-Lb has metallo-proteinase activity, and this protein is primarily localized at the flagellar domain of the promastigotes. Surface plasmon resonance (spr) also demonstrated high-affinity binding at the flagellar domain, which forms a stable binding complex (Côrtes et al., 2011). In T. cruzi, HBPs also mediate parasite adhesion by recognition of PGHS on the surface of the target cells (Bambino-Medeiros et al., 2011; Calvet et al., 2003; Oliveira-Jr et al., 2008; Ortega-Barria & Pereira, 1991). Currently, three HBPs have been described in this parasite: a 60-kDa protein named penetrin (Ortega-Barria & Pereira, 1991) and two other proteins of 65.8 and 59 kDa that bind heparin, HS and chondroitin sulfate (CS). These proteins have been identified in both trypomastigotes and amastigotes (Oliveira- Jr et al., 2008). Interestingly, the HBP-HS binding is related to a specific region of the HS chain, the N-acetylated/N-sulfated HS domain, which promotes parasite attachment and invasion (Oliveira-Jr et al., 2008). Although only HS binding triggers T. cruzi invasion of mammalian cells (Ortega-Barria & Pereira, 1991; Calvet et al., 2003; Oliveira-Jr et al., 2008; Bambino-Medeiros et al., 2003), the multiple GAG recognition may provide an efficient association with other GAGs within the parasite life cycle. Recently, it has been demonstrated that sulfated proteoglycans are involved in the adhesion of epimastigotes to the luminal midgut epithelial cells of Rhodnius prolixus (Gonzalez et al., 2011). www.intechopen.com 2.3.3 Remarks on the isolation of proteins by glycosaminoglycans affinity chromatography While the application of affinity chromatography has provided advances in our understanding of heparin-binding proteins, a large number of studies have focused on the parasite-host cell interface to improve our comprehension of the mechanisms that are activated by the receptor-ligand interaction (reviewed by Chen et al., 2008). The binding of Dengue virus to HS, for example, seems to result in the accumulation of virions at the surface of the human hepatoma cell line HuH-7 and elicit clathrin-dependent endocytosis (Hilgard & Stockert 2000). In addition to promote attachment and parasite invasion, HSPG also seems to be involved in the tropism of pathogen to specific tissues. The degree of HSPG sulfation guides the migration of Plasmodium sporozoites and the invasion of hepatocytes. Highly sulfated heparan sulfate at the surface of hepatocytes seems to regulate the proteolytic activity of the calcium-dependent protein kinase-6 on the CSP, which triggers the invasion of the parasite (Coppi et al., 2007). Another interesting phenomenon is the release of syndecan-1, a transmembrane PGHS, as a mechanism of host defense inhibition. Pseudomonas aeruginosa induces syndecan-1 shedding through the enzymatic activity of LasA, leading to an enhancement of bacterial virulence (Park et al., 2001). A similar mechanism has been described for Staphylococcus aureus in which ǃ-toxin, a secreted virulence factor, also induces syndecan-1 shedding by activating a metallo-proteinase involved in the host cell shedding mechanism, leading to enhancement of bacterial virulence due to the recruitment of inflammatory cells (Hayashida et al., 2009). Because heparan sulfate has been shown to be a receptor for a variety of pathogens, HS- binding polypeptides have been the subject of intense research and provide possibilities for drug intervention. www.intechopen.com 350 Affinity Chromatography Table 3. Heparin affinity-based www.intechopen.com 351 Affinity-Based Methods for the Separation of Parasite Proteins 3. Conclusion The chromatographic procedures described here maintain the minimal amount of native folding necessary for proteins to retain their biological and biochemical activities. Thus, the materials used as supports for packed affinity columns, including agarose, sepharose and celite (from diatomaceous earth), to immobilize ligands, such as lectins, protease inhibitors and glycosaminoglycans, do not interfere with the functional properties of these proteins. Furthermore, proteins obtained by affinity-based procedure have been useful in understanding the biological processes related to the life cycles of parasites and in the interaction with hosts. These studies are essential to developing strategies, such as the use of vaccines and drugs, to control the parasite diseases. 4. Acknowledgements We acknowledge the financial support Brazilian funding agencies, including CAPES, CNPq, FAPERJ and PAPES (CNPq/Fiocruz). Dr. Carlos Roberto Alves and Dr. Mirian Claudia de Souza Pereira are research fellows of CNPq We acknowledge the financial support Brazilian funding agencies, including CAPES, CNPq, FAPERJ and PAPES (CNPq/Fiocruz). Dr. Carlos Roberto Alves and Dr. Mirian Claudia de Souza Pereira are research fellows of CNPq 5. References Abban CY, & Meneses PI. 2010. Usage of heparan sulfate, integrins, and FAK in HPV16 infection. Virology. 403(1):1-16. André S, Sanchez-Ruderisch H, Nakagawa H, Buchholz M, Kopitz J, Forberich P, Kemmner W, Böck C, Deguchi K, Detjen KM, Wiedenmann B, von Knebel Doeberitz M, Gress TM, Nishimura S, Rosewicz S, & Gabius HJ. 2007. Tumor suppressor p16INK4a-- modulator of glycomic profile and galectin-1 expression to increase susceptibility to carbohydrate-dependent induction of anoikis in pancreatic carcinoma cells. FEBS J. 274(13):3233-56. Andreeva N, Bogdanovich P, Kashparov I, Popov M, & Stengach M. 2004. Is Histoaspartic Protease A Serine Protease With A Pepsin-Like Fold? Proteins. 55(3):705-10. Atrih A, Richardson JM, Prescott AR, & Ferguson MA. 2005. Trypanosoma brucei glycoproteins contain novel giant poly-N-acetyllactosamine carbohydrate chains. J Biol Chem. 280(2):865-71. Azevedo-Pereira RL, Pereira MC, Oliveria-Junior FO, Brazil RP, Côrtes LM, Madeira MF, Santos AL, Toma L, & Alves CR. Vet Parasitol. 2007. Heparin binding proteins from Leishmania (Viannia) braziliensis promastigotes. 145(3-4):234-9. Bambino-Medeiros R, Oliveira FO, Calvet CM, Vicente D, Toma L, Krieger MA, Meirelles MN, & Pereira MC. 2011. Involvement of host cell heparan sulfate proteoglycan in Trypanosoma cruzi amastigote attachment and invasion. Parasitology. 138(5):593-601. Beckert WH, & Sharkey MM. 1970. Mitogenic activity of the jack bean (Canavalia ensiformis) with rabbit peripheral blood lymphocytes. Int Arch Allergy Appl Immunol. (4):337- 41. Bermúdez A, Alba MP, Vanegas M, & Patarroyo ME. 2010. 3D structure determination of STARP peptides implicated in P. falciparum invasion of hepatic cells. Vaccine. 28(31):4989-96. Bond JS, & Beynon RJ., eds. 1989. Proteolytic enzymes: A practical approach. IRL Press/Oxford University Press, Oxford, United Kingdom www.intechopen.com 352 Affinity Chromatography Bourguignon SC, Cavalcanti DF, de Souza AM, Castro HC, Rodrigues CR, Albuquerque MG, Santos DO, da Silva GG, da Silva FC, Ferreira VF, de Pinho RT, & Alves CR. 2011. Trypanosoma cruzi: insights into naphthoquinone effects on growth and protease activity. Exp Parasitol. 127(1):160-6. Brickman MJ, & Balber AE. 1993. Trypanosoma brucei rhodesiense: membrane glycoproteins localized primarily in endosomes and lysosomes of bloodstream forms. Exp Parasitol. 76(4):329-44. Brittingham, A, Morrison, CJ, McMaster, WR, McGwire, BS, Chang, KP, & Mosser, DM. (1995). Role of the Leishmania surface protease gp63 in complement fixation, cell adhesion, and resistance to complement-mediated lysis. J of Immunol 155 (6) :3102-11. Calvet CM, Toma L, Souza FR, Meirelles MNL, & Pereira, MCP. 2003. Heparan Sulfate Proteoglycans mediate the invasion of cardiomyocytes by Trypanosoma cruzi. J Eukariot Microbiol. 50: 97-103. 5. References Caradonna KL, & Burleigh BA. 2011. Mechanisms of Host Cell Invasion by Trypanosoma cruzi. Adv Parasitol. 76:33-61. Chen Y, Götte M, Liu J, & Park PW. 2008. Microbial subversion of heparan sulfate proteoglycans. Mol Cells. 26(5):415-26. p g y ( ) Choudhury R, Bhaumik Sk, De T, Chakraborti, T. 2009. Identification, Purification & Characterization of a secretory serine protease in an indian strain of Leishmania donovani. Mol Cell Biochem. 320(1-2):1-14 Choudhury R, Das P, De T, Chakraborti T. 2010. Immunolocalization and characterization of two novel proteases in Leishmania donovani: putative roles in host invasion and parasite development. Biochimie. 92(10):1274-86. Coppi A, Tewari R, Bishop JR, Bennett BL, Lawrence R, Esko JD, Billker O, & Sinnis P. 2007. Heparan sulfate proteoglycans provide a signal to Plasmodium sporozoites to stop migrating and productively invade host cells. Cell Host Microbe. 2(5):316-27. g g y Côrtes LMC, Pereira MCS, Olivera-Jr FOR, Suzana Corte-Real, Silva FS, Pereira BAS, Madeira MF, Moraes MTB, Brazil RP, & Alves RA. 2011. Leishmania (Viannia) braziliensis: insights on subcellular distribution and biochemical properties of heparin-binding proteins. Parasitology. 7: 1-8. Couto AS, Gonçalves MF, Colli W, & de Lederkremer RM. 1990. The N-linked carbohydrate chain of the 85-kilodalton glycoprotein from Trypanosoma cruzi trypomastigotes contains sialyl, fucosyl and galactosyl (alpha 1-3)galactose units. Mol Biochem Parasitol. 39(1):101-7. Dalrymple N, & Mackow ER. 2011. Productive dengue virus infection of human endothelial cells is directed by heparan sulfate-containing proteoglycan receptors. J Virol. 85(18):9478-85. Ribeiro de Andrade AS, Santoro MM, De Melo MN, & Mares-Guia M. 1998. Leishmania (Leishmania) amazonensis: purification and enzymatic characterization of a soluble serine oligopeptidase from promastigotes. Exp Parasitol. 89(2):153-60. Dreyfuss JL, Regatieri CV, Jarrouge TR, Cavalheiro RP, Sampaio LO, & Nader HB. 2009. Heparan sulfate proteoglycans: structure, protein interactions and cell signaling. An Acad Bras Cienc. 81(3):409-29. Dreyfuss JL, Veiga SS, Coulson-Thomas VJ, Santos IA, Toma L, Coletta RD, & Nader HB. 2010. Differences in the expression of glycosaminoglycans in human fibroblasts www.intechopen.com www.intechopen.com 353 Affinity-Based Methods for the Separation of Parasite Proteins derived from gingival overgrowths is related to TGF-beta up-regulation. Growth Factors. 28(1):24-33. derived from gingival overgrowths is related to TGF-beta up-regulation. Growth Factors. 28(1):24-33. ( ) Dumont F, & Nardelli J. 1979. Peanut agglutinin (PNA)-binding properties of murine thymocyte subpopulation. Immunology. 37(1):217-24. Epting CL, Coates BM, & Engman DM. 2011. Molecular mechanisms of host cell invasion by Trypanosoma cruzi. Exp Parasitol. 127(2):607. 5. References Fallgren C, Utt M, & Ljungh A. 2001. Isolation and characterisation of a 17-kDa staphylococcal heparin-binding protein with broad specificity. J Med Microbiol. 50(6):547-57. Fauquenoy S, Morelle W, Hovasse A, Bednarczyk A, Slomianny C, Schaeffer C, Van Dorsselaer A, & Tomavo S. 2008. Proteomics and glycomics analyses of N- glycosylated structures involved in Toxoplasma gondii-host cell interactions. Mol Cell Proteomics. 7(5):891-910. Garate M, Marchant J, Cubillos I, Cao Z, Khan NA, & Panjwani N. 2006. In vitro pathogenicity of Acanthamoeba is associated with the expression of the mannose- binding protein. Invest Ophthalmol Vis Sci. 47(3):1056-62. g p p ( ) Gardiner PR, Nene V, Barry MM, Thatthi R, Burleigh B, & Clarke MW. 1996. Characterization of a small variable surface glycoprotein from Trypanosoma vivax. Mol Biochem Parasitol. 82(1):1-11. Geier G, Banaj HJ, Heid H, Bini L, Pallini V, & Zwilling R. 1999. Aspartyl proteases in Caenorhabditis elegans. Isolation, identification and characterization by a combined use of affinity chromatography, two-dimensional gel electrophoresis, microsequencing and databank analysis. Eur J Biochem. 264(3):872-9. Gerold P, Striepen B, Reitter B, Geyer H, Geyer R, Reinwald E, Risse HJ, & Schwarz RT. 1996. Glycosyl-phosphatidylinositols of Trypanosoma congolense: two common precursors but a new protein-anchor. J Mol Biol. 261(2):181-94. Gonzalez MS, Silva LC, Albuquerque-Cunha JM, Nogueira NF, Mattos DP, Castro DP, Azambuja P, & Garcia ES. 2011. Involvement of sulfated glycosaminoglycans on the development and attachment of Trypanosoma cruzi to the luminal midgut surface in the vector, Rhodnius prolixus. Parasitology. 9:1-8. Govrin E, & Levine A. 1999. Purification of active cysteine proteases by affinity chromatography with attached E-64 inhibitor. Protein Expr Purif. 15(3):247-50. Guedes HL, Rezende JM, Fonseca MA, Salles CM, Rossi-Bergmann B, & De-Simone SG. 2007. Identification of serine proteases from Leishmania braziliensis. Z Naturforsch C. 62(5-6):373-81. ( ) Guha-Niyogi A, Sullivan DR, &Turco SJ. 2001. Glycoconjugate structures of parasitic protozoa. Glycobiology. 11: 45R-59R. p y gy Hayashida A, Bartlett AH, Foster TJ, & Park PW. 2009. Staphylococcus aureus beta-toxin induces lung injury through syndecan-1. Am J Pathol. 174(2):509-18. Hellström U, Dillner ML, Hammarström S, & Perlmann P. 1976. Fractionation of human T lymphocytes on wheat germ agglutinin-sepharose. J Exp Med. 144(5):1381-5. Hilgard P, & Stockert R. 2000. Heparan sulfate proteoglycans initiate dengue virus infection of hepatocytes. Hepatology. 32(5):1069-77. p y p gy ( ) Hoegl L, Korting HC, & Klebe G. 1999. Inhibitors of aspartic proteases in human diseases: molecular modeling comes of age. Pharmazie. 5. References 54(5):319-29. www.intechopen.com 354 Affinity Chromatography Jacobs DB, & Poretz RD. 1980. Lectin induction of lymphokines in cultured murine leukocytes. Cell Immunol. 51(2):424-9. Jacquet A, Coulon L, De Nève J, Daminet V, Haumont M, Garcia L, Bollen A, Jurado M, & Biemans R. 2001. The surface antigen SAG3 mediates the attachment of Toxoplasma gondii to cell-surface proteoglycans. Mol Biochem Parasitol. 116(1):35-4 Kabir S. 1998. Jacalin: a jackfruit (Artocarpus heterophyllus) seed-derived lectin of versatile applications in immunobiological research. J Immunol Methods. 212(2):193-211. pp g ( ) Klemba M, & Goldberg DE. 2002. Biological roles of proteases in parasitic protozoa. Annu Rev Biochem. 71:275-305 Kobayashi K, Kato K, Sugi T, Takemae H, Pandey K , Gong H, Tohya Y, & Akashi H. 2010. Plasmodium falciparum BAEBL Binds to Heparan Sulfate Proteoglycans on the Human Erythrocyte Surface. J Biol Chem. 285(3): 1716–1725. y y ( ) Kong, H H, Kim, T H & Chung, D-Ii. 2000. Purification And Characterization of A Secretory serine protease of Acanthamoeba Healyi isolated from gae. Journal of Parasitology. 86, 12–17. Li F, Patra KP, Yowell CA, Dame JB, Chin K, & Vinetz JM. 2010. Apical surface expression of aspartic protease plasmepsin 4, A Potential. J Biol Chem. 285(11):8076-83. Liang OD, Ascencio F, Fransson LA, & Wadström T. 1992. Binding of heparan sulfate to Staphylococcus aureus. Infect Immun. 60(3):899-906. Lord MJ, Jolliffe NA, Marsden CJ, Pateman CS, Smith DC, Spooner RA, Watson PD, & Roberts LM. 2003. Ricin. Mechanisms of cytotoxicity. Toxicol Rev. 22(1):53-64. y y Love DC, Esko JD, & Mosser DM. 1993. A heparin-binding activity on Leishmania amastigotes which mediates adhesion to cellular proteoglycans. J Cell Biol. 123(3):759-66. Ly M, Laremore TN, & Linhardt RJ. 2010. Proteoglycomics: recent progress and future challenges. OMICS. 14(4):389-99. Maia, A.A.M. & Guimarães, M.P. Distribuição Sazonal De Larvas De Dermatobia Hominis (Linnaeus Jr., 1781) (Diptera: Cuterebridae) Em Bovinos De Corte Da Região De Governador Valadares - Minas Gerais. Arquivo Brasileiro De Medicina Veterinária E Zootecnia, Brasil. , 1985. V. 37, N. 5, P. 469-475. Mansour MH. 1996. Purification and characterization of SM 37: a fucosyllactose determinant-bearing glycoprotein probed by a Biomphalaria alexandrina lectin on adult male shistosomes. J Parasitol. 82(4):586-93. Matsumoto K, Yamamoto D, Ohishi H, Tomoo K, Ishida T, Inoue M, Sadatome T, Kitamura K, & Mizuno H. 1989. Mode of binding of E-64-c, a potent thiol protease inhibitor, to papain as determined by X-ray crystal analysis of the complex. FEBS. 5. References Lett 245, 177–180. McKerrow JH, Caffrey C, Kelly B, Loke P, & Sajid M. 2006. Proteases in parasitic diseases. Annu Rev Pathol. 1:497-536. Morgado-Díaz JA, Silva-Lopez RE, Alves CR, Soares MJ, Corte-Real S, & De Simone SG. 2005. An intracellular serine protease of 68 kDa in Leishmania (Leishmania) amazonensis promastigotes. Mem Inst Oswaldo Cruz. 100(4):377-83 Morris SR, & Sakanari JA. 1994. Characterization of The serine protease and serine protease inhibitor from the tissue-penetrating nematode Anisakis Simplex. J Biol Chem. 269(44):27650-6. www.intechopen.com www.intechopen.com 355 Affinity-Based Methods for the Separation of Parasite Proteins Morrison CJ, Hurst SF, Bragg SL, Kuykendall RJ, Diaz H, McLaughlin DW, & Reiss E. 1993. Purification and characterization of the extracellular aspartyl proteinase of Candida albicans: removal of extraneous proteins and cell wall mannoprotein and evidence for lack of glycosylation. J Gen Microbiol. 139 Pt 6:1177-86. Muharsini S, Sukarsih, Riding G, Partoutomo S, Hamilton S, Willadsen P, & Wijffels G. 2000. Identification and characterisation of the excreted/secreted serine proteases of larvae of the old world screwworm fly, Chrysomya Bezziana. Int J Parasitol. 30(6):705-14. Naguleswaran A, Alaeddine F, Guionaud C, Vonlaufen N, Sonda S, Jenoe P, Mevissen M, & Hemphill A. 2005. Neospora caninum protein disulfide isomerase is involved in tachyzoite-host cell interaction. Int J Parasitol. 35(13):1459-72. Nolan DP, Jackson DG, Windle HJ, Pays A, Geuskens M, Michel A, Voorheis HP, & Pays E. 1997. Characterization of a novel, stage-specific, invariant surface protein in Trypanosoma brucei containing an internal, serine-rich, repetitive motif. J Biol Chem. 272(46):29212-21. O'Donnell CD, & Shukla D. 2008. The importance of separan sulfate in herpesvirus infection. Virol Sin. 23(6):383-393. Oliveira FO Jr, Alves CR, Calvet CM, Toma L, Bouças RI, Nader HB, Côrtes LMC, Krieger MA, Meirelles MN, & Souza Pereira MC. 2008. Trypanosoma cruzi heparin-binding proteins and the nature of the host cell heparan sulfate-binding domain. Microb Pathog. 44(4):329-38 g Ortega-Barria E, & Pereira EA. 1991. A novel T. cruzi heparin-binding protein promotes fibroblast adhesion and penetration of engineered bacteria and trypanosomes into mammalian cells. Cell. 67: 411-421. Park PW, Pier GB, Hinkes MT, & Bernfield M. 2001. Exploitation of syndecan-1 shedding by Pseudomonas aeruginosa enhances virulence. Nature. 411(6833):98-102. Á Pereira BA, Silva FS, Rebello KM, Marín-Villa M, Traub-Cseko YM, Andrade TC, Bertho ÁL, Caffarena ER, & Alves CR. 2011. In silico predicted epitopes from the COOH- terminal extension of cysteine proteinase B inducing distinct immune responses during Leishmania (Leishmania) amazonensis experimental murine infection. 5. References BMC Immunol. 2011,12: 44. Pinho RT, Beltramini LM, Alves CR, & De-Simone SG. 2009. Trypanosoma cruzi: isolation and characterization of aspartyl proteases. Exp Parasitol. 122(2):128-33. Rebello KM, Côrtes LM, Pereira BA, Pascarelli BM, Côrte-Real S, Finkelstein LC, Pinho RT, d'Avila-Levy CM, & Alves CR. 2009. Cysteine proteases from promastigotes of Leishmania (Viannia) braziliensis. Parasitol Res. 106(1):95-104. ( ) Redmond DL, Geldhof P, & Knox DP. 2004. Evaluation of Caenorhabditis elegans glycoproteins as protective immunogens against Haemonchus contortus challenge in sheep. Int J Parasitol. 34(12):1347-53. Reinwald E, Rautenberg P, & Risse HJ. 1981. Purification of the variant antigens of Trypanosoma congolense: a new approach to the isolation of glycoproteins. Biochim Biophys Acta. 668(1):119-31. p y ( ) Rüdiger H, & Gabius HJ. 2001. Plant lectins: occurrence, biochemistry, functions and applications. Glycoconj J.18(8):589-613. www.intechopen.com www.intechopen.com 356 Affinity Chromatography Ruiz-Bustos E, Ochoa JL, Wadström T, & Ascencio F. 2001. Isolation and characterisation of putative adhesins from Helicobacter pylori with affinity for heparan sulphate proteoglycan. J Med Microbiol. 50(3):215-22. Shenai BR, Sijwali PS, Singh A, & Rosenthal PJ. 2000 Characterization of native and recombinant falcipain-2, a principal trophozoite cysteine protease and essential hemoglobinase of Plasmodium falciparum. J Biol Chem. 275(37):29000-10. Silva-Lopez RE, & Giovanni-De-Simone S. 2004. Leishmania (Leishmania) amazonensis: Purification and characterization of a promastigote serine protease. Exp Parasitol. 107(3-4):173-82. Silva-Lopez RE, Coelho MG, & De Simone SG. 2005. Characterization of an extracellular serine protease of Leishmania (Leishmania) amazonensis. Parasitology. 131(Pt 1):85-96. Silva-López RE, Dos Santos TR, Morgado-Díaz JA, Tanaka MN, & De Simone SG. 2010. Serine protease activities in Leishmania (Leishmania) chagasi promastigotes. Parasitol Res. 107(5):1151-62 Silva-Lopez RE, Morgado-Díaz JA, Alves CR, Côrte-Real S, & Giovanni-De-Simone S. 2004. Subcellular localization if an extracellular serine protease in Leishmania Leishmania) amazonensis. Parasitol Res. 93(4):328-31 ( ) Silva-Lopez RE, Morgado-Díaz JA, Dos Santos PT, & Giovanni-De-Simone S. 2008. Purification and subcellular localization of a secreted 75 KDa Trypanosoma cruzi serine oligopeptidase. Acta Trop. 07(2):159-67. Smith WD, Newlands GF, Smith SK, Pettit D, & Skuce PJ. 2003. Metalloendopeptidases from the intestinal brush border of Haemonchus contortus as protective antigens for sheep. Parasite Immunol. 25(6):313-23. ( ) Smith WD, Smith SK, Pettit D, Newlands GF, & Skuce PJ. 2000. Relative protective properties of three membrane glycoprotein fractions from Haemonchus contortus. Parasite Immunol. 22(2):63-71. Soong G, Martin FJ, Chun J, Cohen TS, Ahn DS, & Prince A. 2011. 5. References Staphylococcus aureus Protein A mediates invasion across airway epithelial Cells through activation of RhoA GTPase signaling and proteolytic activity. J Biol Chem. 286(41):35891-8. Stephens RS, Koshiyama K, Lewis E, & Kubo A. 2001. Heparin-binding outer membrane protein of chlamydiae. Mol Microbiol. 40(3):691-9. Todorova VK, & Stoyanov DI. 2000. Partial Characterization of Serine proteinases secreted By Adult Trichinella Spiralis. Parasitol Res. 86(8):684-7. y Turner DG, Wildblood LA, Inglis NF, & Jones DG. 2008. Characterization of a galectin-like activity from the parasitic nematode, Haemonchus contortus, which modulates ovine eosinophil migration in vitro. Vet Immunol Immunopathol. 122(1-2):138-45. Valdivieso E, Bermudez H, Hoebeke J, Noya O, & Cesari IM. 2003. Immunological similarity between Schistosoma and bovine cathepsin D. Immunol Lett. 89(1):81-8. Wlodawer A, & Vondrasek J. 1998. Inhibitors of HIV-1 protease: a major success of structure-assisted drug design. Annu Rev Biophys Biomol Struct.27:249-84. Wilson ME, & Pearson RD. 1984. Infect Immun. Stage-specific variations in lectin binding to Leishmania donovani. 46(1):128-34. Yan Y, Silvennoinen-Kassinen S, Leinonen M, & Saikku P. 2006. Inhibitory effect of heparin 41 sulfate-like glycosaminoglycans on the infectivity of Chlamydia pneumoniae in HL 42 cells varies between strains. Microbes Infect. 8:866-872 www.intechopen.com www.intechopen.com Affinity Chromatography Edited by Dr. Sameh Magdeldin ISBN 978-953-51-0325-7 Hard cover, 368 pages Publisher InTech Published online 21, March, 2012 Published in print edition March, 2012 Most will agree that one major achievement in the bio-separation techniques is affinity chromatography. This coined terminology covers a myriad of separation approaches that relies mainly on reversible adsorption of biomolecules through biospecific interactions on the ligand. Within this book, the authors tried to deliver for you simplified fundamentals of affinity chromatography together with exemplarily applications of this versatile technique. We have always been endeavor to keep the contents of the book crisp and easily comprehensive, hoping that this book will receive an overwhelming interest, deliver benefits and valuable information to the readers. Affinity Chromatography Edited by Dr. Sameh Magdeldin Affinity Chromatography Edited by Dr. Sameh Magdeldin Affinity Chromatography Edited by Dr. Sameh Magdeldin Affinity Chromatography ISBN 978-953-51-0325-7 Hard cover, 368 pages Publisher InTech Published online 21, March, 2012 Published in print edition March, 2012 Most will agree that one major achievement in the bio-separation techniques is affinity chromatography. This coined terminology covers a myriad of separation approaches that relies mainly on reversible adsorption of biomolecules through biospecific interactions on the ligand. 5. References Within this book, the authors tried to deliver for you simplified fundamentals of affinity chromatography together with exemplarily applications of this versatile technique. We have always been endeavor to keep the contents of the book crisp and easily comprehensive, hoping that this book will receive an overwhelming interest, deliver benefits and valuable information to the readers. How to reference In order to correctly reference this scholarly work, feel free to copy and paste the following: C.R. Alves, F.S. Silva, F.O. Oliveira Jr, B.A.S. Pereira, F.A. Pires and M.C.S. Pereira (2012). Affinity-Based Methods for the Separation of Parasite Proteins, Affinity Chromatography, Dr. Sameh Magdeldin (Ed.), ISBN: 978-953-51-0325-7, InTech, Available from: http://www.intechopen.com/books/affinity-chromatography/affinity- based-methods-in-separation-of-parasites-proteins InTech Europe University Campus STeP Ri Slavka Krautzeka 83/A 51000 Rijeka, Croatia Phone: +385 (51) 770 447 Fax: +385 (51) 686 166 www.intechopen.com InTech China Unit 405, Office Block, Hotel Equatorial Shanghai No.65, Yan An Road (West), Shanghai, 200040, China Phone: +86-21-62489820 Fax: +86-21-62489821 InTech China Unit 405, Office Block, Hotel Equatorial Shanghai No.65, Yan An Road (West), Shanghai, 200040, China Phone: +86-21-62489820 Fax: +86-21-62489821 InTech China Unit 405, Office Block, Hotel Equatorial Shanghai No.65, Yan An Road (West), Shanghai, 200040, China Phone: +86-21-62489820 Fax: +86-21-62489821 InTech Europe University Campus STeP Ri Slavka Krautzeka 83/A 51000 Rijeka, Croatia Phone: +385 (51) 770 447 Fax: +385 (51) 686 166 www.intechopen.com © 2012 The Author(s). Licensee IntechOpen. This is an open access artic stributed under the terms of the Creative Commons Attribution 3.0 cense, which permits unrestricted use, distribution, and reproduction in ny medium, provided the original work is properly cited. © 2012 The Author(s). Licensee IntechOpen. This is an open access article distributed under the terms of the Creative Commons Attribution 3.0 License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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The influence of moisture content on popping traits in popcorn
Journal on processing and energy in agriculture
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cc-by
4,884
Biblid: 1821-4487 (2018) 22; 4; p 184-187 UDK: 633.15 Biblid: 1821-4487 (2018) 22; 4; p 184-187 UDK: 633.15 Biblid: 1821-4487 (2018) 22; 4; p 184-187 5 Original Scientific Paper Originalni naučni rad Original Scientific Paper Originalni naučni rad Jelena SRDIĆ*, Vesna PERIĆ*, Ljubiša KOLARIĆ**,Natalija KRAVIĆ*,Vojka BABIĆ*, Milena SIMIĆ* *Maize Research Institute „Zemun Polje“, Slobodana Bajića 1, Zemun **Faculty of Agriculture, University of Belgrade, Nemanjina 6, Zemun e-mail: jsrdic@mrizp.rs Jelena SRDIĆ*, Vesna PERIĆ*, Ljubiša KOLARIĆ**,Natalija KRAVIĆ*,Vojka BABIĆ*, Mile *Maize Research Institute „Zemun Polje“, Slobodana Bajića 1, Zemun **Faculty of Agriculture, University of Belgrade, Nemanjina 6, Zemun e-mail: jsrdic@mrizp.rs ABSTRACT The influence of grain moisture content at harvest and at the moment of popping on popping volume and percentage of unpopped kernels was analysed. Four popcorn hybrids were studied. Hybrids were harvested when grain moisture content was: above 25%, between 20 – 25%, and below 18%. Each sample was popped at 20%, 18%, 16%, 14%, 12%, and 10% of grain moisture. All examined factors and their interactions significantly influenced both popping volume and percentage of unpopped kernels. The highest popping volume and the lowest percentage of unpopped kernels were observed at 14% grain moisture content. Hybrid ZP 608k had the highest popping volume and the lowest percentage of unpopped kernels at all treatments and overall. The lowest popping volume and the highest percentage of unpopped kernels were noticed for ZP 501k. The lowest percentage of unpopped kernels was observed in the last harvest term when grain moisture content was below 18%. g Key words: popcorn, grain moisture content, popping volume, percentage of unpopped kernels. REZIME If the moisture content is lower, there is not enough pressure to produce expansion of the grain. On the other hand if the moisture content is higher it softens the pericarp, which also reduces popping volume (Hosney et al., 1983). Popping volume is also significantly influenced by genotype (Srdić et al., 2015; Srdić et al., 2017), popping method (Gökmen, 2004), and kernel size (Pajić and Babić, 1991; Song and Eckhoff, 1994). Differences among genotypes are significant and important, because mostly higher yielding hybrids produce lower popping volumes (Srdić and Pajić, 2011; Pajić et al., 2012, Cabaral et al., 2016). The way to overcome this problem when moisture content is below 20%. Hosney et al. (1983) also stated that the best results of popping volume could be reached when grain moisture at harvest is between 15 – 18%. Biotic and abiotic stress factor during production, harvest and processing could lead to the decrease of the popping volume and also increase the percentage of unpopped kernels. Among those drought, frost, pests, diseases, mechanical kernel damaging are the most significant. Nevertheless, the most important factor influencing popping volume is the moisture content at the moment of popping. Researchers agree that the maximum of popping volume is produced at grain moisture ranging from 11.0% - 15.5% (Allerd-Coyle et al., 2000; Shimoni et al., 2002; Pajić et al., 2006). Moreover, grain moisture content of 14% is optimal, and produces highest popping volumes (Gökmen, 2004; Srdić et al., 2015). If the moisture content is lower, there is not enough pressure to produce expansion of the grain. On the other hand if the moisture content is higher it softens the pericarp, which also reduces popping volume (Hosney et al., 1983). Popping volume is also significantly influenced by genotype (Srdić et al., 2015; Srdić et al., 2017), popping method (Gökmen, 2004), and kernel size (Pajić and Babić, 1991; Song and Eckhoff, 1994). Differences among genotypes are significant and important, because mostly higher yielding hybrids produce lower popping volumes (Srdić and Pajić, 2011; Pajić et al., 2012, Cabaral et al., 2016). The way to overcome this problem REZIME Zapremina kokičavosti je pored potencijala rodnosti najvažnija osobina hibrida kokičara. Više faktora utiče na nju: genotip, uslovi proizvodnje, dorade i čuvanja zrna, kao i metode kokanja. Maksimalan potencijal zapremine kokičavosti postiže se samo ako je hibrid dostigao punu zrelost. Ipak, najvažniji je uticaj sadržaja vlage u trenutku kokanja. Sadržaj vlage od oko 14% je optimalan i pri njemu se ostvaruju najviše zapremine kokičavosti. U radu je ispitivan uticaj sadržaja vlage u zrnu prilikom berbe i u trenutku kokanja na osobine kokičavosti: zapremina kokičavosti i procenat neiskokanog zrna. Ove osobine proučavane su na na četiri hibrida kukuruza kokičara. Hibridi su brani u tri termina pri sadržaju vlage: preko 25%, između 20 – 25%, i nižoj od 18%. Zatim je svaki od uzoraka kokan pri sadržaju vlage od 20%, 18%, 16%, 14%, 12%, i 10%. Analiza varijanse ukazala je na značajan uticaj genotipa, sadržaja vlage prilikom berbe, kao i interakcija na zapreminu kokičavosti i procenat neiskokanog zrna. Najviša zapremina kokičavosti ostvarena je pri sadržaju vlage od 14%, a takođe pri ovom sadržaju vlage najmanji je bio i procenat neiskokanog zrna. Hibrid ZP 608k je imao najvišu zapreminu kokičavosti i najmanji procenat neiskokanog zrna, kako u proseku svih tretmana, tako i po proučavanim tretmanima, dok je najamnju zapreminu kokičavosti i najveći procenat neiskokanog zrna imao hibrid ZP 501k. Najmanji procenat neiskokanog zrna utvrđen je u zadnjem terminu berbe, kada je sadržaj vlage u zrnu bio ispod 18%. Ključne reči: kukuruz kokičar, sadržaj vlage u zrnu, zapremina kokičavosti, procenat neiskokanog zrna. when moisture content is below 20%. Hosney et al. (1983) also stated that the best results of popping volume could be reached when grain moisture at harvest is between 15 – 18%. Biotic and abiotic stress factor during production, harvest and processing could lead to the decrease of the popping volume and also increase the percentage of unpopped kernels. Among those drought, frost, pests, diseases, mechanical kernel damaging are the most significant. Nevertheless, the most important factor influencing popping volume is the moisture content at the moment of popping. Researchers agree that the maximum of popping volume is produced at grain moisture ranging from 11.0% - 15.5% (Allerd-Coyle et al., 2000; Shimoni et al., 2002; Pajić et al., 2006). Moreover, grain moisture content of 14% is optimal, and produces highest popping volumes (Gökmen, 2004; Srdić et al., 2015). MATERIAL AND METHOD Table 2. ANOVA and mean squares for popping volume, and % of unpopped kernels of four ZP maize hybrids Sources of variance Degrees of freedom Mean Square Popping volume percentage of unpopped kernels Replication 2 5.16 2.44 Genotype (A) 3 429.27** 1060.16** Moisture content at harvest (B) 2 298.74** 727.65** A x B 6 89.42** 53.81** Moisture content at popping (C) 5 3370.24** 2661.60** A x C 15 31.46** 164.43** B x C 10 45.534** 319.58** A x B x C 30 25.60** 72.79** Error 142 5.10 4.70 ** significant at the 0.01 probability level Table 2. ANOVA and mean squares for popping volume, and % of unpopped kernels of four ZP maize hybrids For this study four popcorn hybrids developed at Maize Research Institute Zemun Polje were selected: ZP 611k, ZP 616k, ZP 501k, and ZP 608k. Three hybrids are single cross hybrids, and only ZP 501k is a three way cross hybrid. Trial was set at the nursery field in Zemun Polje in 2015. Sowing was performed on 27th of April, and emergence was noticed on 6th of May. Each hybrid was sown in plots of 75 m2, i.e. 20 rows with inter row distance of 0.75 m, with 20 plant per row, with the final stand of 57,142 plants/ha. Two rows were border rows. Standard cropping practices were applied during growing season. Inner rows were harvested manually in three terms, six rows for each. The first term was when grain moisture was above 25%, the second when moisture content was 25 – 20%, and the last when the moisture dropped below 18%. Moisture content was measured with small samples by Dickey-john GAK II moisture meter. Meteorological conditions in 2015 had significant impact on grain maturation, so all harvest terms were performed until the fourth week of September (Table 1). Shelling of samples was performed manually in order to avoid damaging the pericarp, which could increase the percentage of unpopped kernels and lower the popping volume. Hybrid with the highest average popping volume was ZP 608k (22.32 cm3/g), while the lowest popping volume produced hybrid ZP 501k (15.67 cm3/g). Among each of the tested hybrids significant differences were found (Table 3). Hybrid ZP 608k had very high popping volume in all treatments. At the optimal grain moisture of 14% its popping volume was up to 41.33 cm3/g. MATERIAL AND METHOD Even at less favourable grain moistures this hybrid mostly had higher popping volumes than other three. On the other hand ZP 501k had lowest popping volumes at all grain moistures. Even at 14% moisture content its popping volume was below 28.00 cm3/g which is also considered very low and unsatisfactory popping volume. Average popping volume according to the grain moisture at harvest ranged from 17.65 cm3/g when grain moisture was 20 – 25%, up to 21.48 cm3/g when harvest was performed with the grain moisture below 18%. Previous studies also found significant differences among genotypes concerning popping volume (Srdić et al., 2015), and dependence of popping volume on the percentage of grain moisture (Srdić et al., 2017; Gökmen, 2004). In the study of Shimoni et al. (2002), it was found that popping volume ranged from 15.8 ml/g up to 47.9 ml/g depending on the moisture content at popping time, which ranged from 6.69 to 16.52%. Table 1. Meteorological conditions in 2015 and ten year average 2005 - 2014 Table 1. Meteorological conditions in 2015 and ten year average 2005 - 2014 Month 2015 2005-2014 Temperature (0C) Precipitation (mm) Temperature (0C) Precipitation (mm) April 12.9 19.7 14.2 39.4 May 19.1 97.8 18.3 69.1 June 22.1 31.1 21.9 83.4 July 26.4 7.2 23.6 55.6 August 25.7 56.0 23.6 54.6 September 20.2 73.6 18.9 44.6 Each sample of the four hybrids, from three harvests was tested at six moisture contents (10%, 12%, 14%, 16%, 18%, and 20%). Initial moisture content was between 16.5 – 28%, depending on the harvest term. Samples that had moisture content above desired were dried by natural convection at room temperature, until the correct moisture content was obtained. Samples with lower moisture content than wanted were rewetted with distilled water using sprayer. They were kept in the refrigerator at 5 0C in closed fabric bags, inverted and shaken daily in order to distribute moisture evenly throughout the sample. The moisture was checked daily. All four hybrids significantly differed concerning the trait percentage of unpopped kernels. Significant differences among another set of hybrids was also found in previous study (Srdić et al., 2017). Hybrid ZP 608k also showed best performances, i.e. 3.30% of unpopped kernels on average. INTRODUCTION Production and consumption of popcorn is constantly increasing due to the fact that popcorn is profitable crop both concerning producers and merchants (Silva et al., 2011; Moterele et al., 2012). Its nutritive properties on the other hand are very attractive to consumers, which makes it very popular and nutritious snack food with excellent functional properties. Popcorn grain is a good source of fibre, calcium, iron, phosphorus, niacin, and it is low in calories when popped without oil (Park et al., 2000; Paraginski et al., 2016). g Popping volume is beside the yielding potential the most important trait of popcorn hybrids. Beside popping volume, the number of unpopped kernels is the most studied quality parameter of popcorn (Ziegler, 2001). High popping volume is correlated with desirable consumer attributes (Ceylan and Karabab, 2002), while unpopped kernels are an undesirable nuisance to consumers and unrealized profit to producers (Sweley et al., 2012). Several factors influence popping volume and the percentage of unpopped kernels, such as: moisture content, genotype, production and harvesting conditions, as well as the condition of processing and grain storage, and popping methods (Gökmen, 2004; Allerd-Coyle et al., 2000; Karabab, 2006; Song et al., 1991). Maximum of the popping volume could be achieved when the hybrid is harvested at full maturity, Journal on Processing and Energy in Agriculture 22 (2018) 4 184 urnal on Processing and Energy in Agriculture 22 (2018 Srdić, Jelena et al./ The Influence of Moisture Content on Popping Traits in Popcorn in breeding high yielding and hybrids that produce high popping volume is found in the research of Amaral et al., (2016), where they introduced trait – expanded popcorn volume per ha PV, that could provide simultaneous gains in both traits. Regarding kernel size it is found that larger kernels produce lower popping volume because they contain a higher percentage of soft endosperm, which is not favourable for expansion (Pajić and Babić, 1991). The aim of this study was to observe the influence of grain moisture at harvest and grain moisture at the moment of popping in order to analyse their influences on popping volume and on the percentage of unpopped kernels. The study will also show weather there are differences among selected genotypes. Interaction of observed factors will also provide interesting information about how the grain moisture at harvest and at popping time influences popping volume and percentage of unpopped kernels. INTRODUCTION Tester, Creators which performs popping of kernels with oil. Popping volume is presented by the volume of popped kernel (cm3) per weight of the unpopped - fresh kernel (g). A standard sample was 250g and it was popped in three replications to obtain results of popping volume. Unpopped kernel weight was measured and it was turned into percentage of unpopped kernels. Data were analysed by three-way analysis of variance (ANOVA) and the treatment means were compared using Fisher’s least significant test – LSD (p<0.05). RESULTS AND DISCUSSION Popping volume and percentage of unpopped kernels were significantly influenced by the genotype, what was also found by others (Soylu and Tekkanat, 2007; Srdić et al., 2017). Other two factors (moisture content at harvest and moisture content at popping), as well as all interactions had also significant influence on these two traits (Table 2). Journal on Processing and Energy in Agriculture 22 (2018) 4 MATERIAL AND METHOD 1 Average estimates of popping volume and percentage of unpopped kernels depending on the moisture content at popping time 8,57 11,01 19,25 33,56 27,36 15,28 21,79 15,07 5,91 0,62 1,13 3,17 0,00 5,00 10,00 15,00 20,00 25,00 30,00 35,00 40,00 20 18 16 14 12 10 PV % of unpopped 5.92% of unpopped kernels. Table 4. Average estimates and LSD for % of unpopped kernels of four ZP maize hybrids (%) percentage of moisture at harvest percentage of moisture at popping ZP 611k ZP 616k ZP 501k ZP 608k > 25% 20 31.15 20.11 40.76 17.09 18 19.95 39.10 21.87 6.72 16 11.60 4.27 15.93 2.69 14 0.73 0.28 0.81 1.03 12 0.96 0.24 3.28 0.47 10 2.92 0.93 10.21 0.42 average 11.22 10.82 15.48 4.74 10.56 a 20-25% 20 35.00 26.47 48.60 11.27 18 8.35 14.20 23.37 6.18 16 6.44 3.65 9.94 2.58 14 0.33 0.16 1.21 0.29 12 0.63 0.20 3.07 0.27 10 0.65 0.24 9.30 0.58 average 8.57 7.49 15.91 3.53 8.87 b < 18% 20 14.74 0.69 11.46 4.17 18 13.49 0.42 25.53 1.70 16 2.84 0.32 8.16 2.53 14 0.58 0.14 1.34 0.51 12 0.58 0.22 3.20 0.45 10 1.41 0.87 10.15 0.36 average 5.61 0.44 9.97 1.62 4.41 c average 8.46 b 6.25 c 13.79 a 3.30 d Means followed by the same letter are not significantly different according to LSD0.05 Fig. 1 Average estimates of popping volume and percentage of unpopped kernels depending on the moisture content at popping time 8,57 11,01 19,25 33,56 27,36 15,28 21,79 15,07 5,91 0,62 1,13 3,17 0,00 5,00 10,00 15,00 20,00 25,00 30,00 35,00 40,00 20 18 16 14 12 10 PV % of unpopped Table 4. MATERIAL AND METHOD Average estimates and LSD for % of unpopped kernels of four ZP maize hybrids (%) percentage of moisture at harvest percentage of moisture at popping ZP 611k ZP 616k ZP 501k ZP 608k > 25% 20 31.15 20.11 40.76 17.09 18 19.95 39.10 21.87 6.72 16 11.60 4.27 15.93 2.69 14 0.73 0.28 0.81 1.03 12 0.96 0.24 3.28 0.47 10 2.92 0.93 10.21 0.42 average 11.22 10.82 15.48 4.74 10.56 a 20-25% 20 35.00 26.47 48.60 11.27 18 8.35 14.20 23.37 6.18 16 6.44 3.65 9.94 2.58 14 0.33 0.16 1.21 0.29 12 0.63 0.20 3.07 0.27 10 0.65 0.24 9.30 0.58 average 8.57 7.49 15.91 3.53 8.87 b < 18% 20 14.74 0.69 11.46 4.17 18 13.49 0.42 25.53 1.70 16 2.84 0.32 8.16 2.53 14 0.58 0.14 1.34 0.51 12 0.58 0.22 3.20 0.45 10 1.41 0.87 10.15 0.36 average 5.61 0.44 9.97 1.62 4.41 c average 8.46 b 6.25 c 13.79 a 3.30 d M f ll d b h l i ifi l Table 4. Average estimates and LSD for % of unpopped kernels of four ZP maize hybrids (%) Hybrid ZP 501k likewise in the popping volume had poorest results. Its percentage of unpopped kernels was the highest of all hybrids in this research (13.79% on average). This hybrid is therefore indicated as the least favourable concerning quality parameters. Mostly all hybrids had lowest percentage of unpopped kernels at 14% moisture content at popping, while some exceptions to this is found in hybrid ZP 608k which had even lower percentage at lower moisture contents at popping (12% and 10%). In the study of Sweley et al., (2012), percentage of unpopped kernels ranged from 10.1 – 12.5% depending on the genotype, which they indicated as consumers acceptable (Quinn et al., 2005). Our research is also in accordance with Gökmen, 2004, who investigate percentage of unpoped kernel (PUK) in dependence of moisture content at popping time, ranging from 8 -20%. Lowest PUK in their research was also found at 14% moisture content and highest at 20%. MATERIAL AND METHOD Percentage of unpopped kernels for this hybrid dropped with the lowering of moisture Popping volume (PV) was analysed by the standard procedure (MWVT- Metric Weight Volume Test), using the apparatus Cretors 2300w – Official Metric Wight Volume Journal on Processing and Energy in Agriculture 22 (2018) 4 185 Srdić, Jelena et al./ The Influence of Moisture Content on Popping Traits in Popcorn lowest percentage of unpopped kernels was, only 0.62%. This percentage slowly increased with the decrease of moisture content to 12 and 10% (1.13 and 3.17%, respectively), while this was more pronounced when the moisture content increased to 16, 18 and 20% (5.91, 15.07 and 21.79, respectively). This leads to the conclusion that higher moisture content at popping is less favourable for the quality of popcorn, than to the same extent less moisture content of kernels at popping. When popped at 12% moisture content average popping volume was 27.36 cm3/g, with only 0.62% of unpopped kernels, while at 16% moisture content average popping volume dropped to 19.25 cm3/g, with 5.92% of unpopped kernels. content at harvest. It was the highest at first harvest term (4.74%), while at the last harvest term it was only 1.62%. Beside this hybrid, ZP 616k at harvest moisture content below 18% had even lower percentage of unpopped kernels of 0.44% (Table 4). Table 3. Average estimates and LSD for popping volume of four ZP maize hybrids (cm3/g) percentage of moisture at harvest percentage of moisture at popping ZP 611k ZP 616k ZP 501k ZP 608k > 25% 20 5.83 4.50 6.00 7.17 18 10.83 4.17 6.67 13.33 16 18.3 19.00 12.83 22.83 14 35.17 35.67 27.33 41.33 12 28.00 30.67 22.33 31.17 10 13.17 14.33 12.67 17.67 average 18.55 18.06 14.64 22.25 18.38 b 20-25% 20 13.83 4.17 5.50 5.67 18 11.33 7.33 9.67 11.00 16 13.33 15.67 15.17 18.67 14 29.67 29.33 27.83 38.33 12 26.33 26.67 22.00 30.33 10 15.33 16.17 11.67 18.67 average 18.30 16.56 15.31 20.44 17.65 b < 18% 20 6.00 18.33 13.83 12.00 18 8.00 24.83 8.33 16.67 16 21.67 30.00 19.33 24.17 14 34.17 37.83 26.00 40.00 12 26.33 28.83 21.83 33.83 10 15.00 16.67 13.00 19.00 average 18.53 26.08 17.05 24.28 21.48 a average 18.46c 20.23b 15.67d 22.32 Means followed by the same letter are not significantly different according to LSD0.05 Table 3. MATERIAL AND METHOD Average estimates and LSD for popping volume of four ZP maize hybrids (cm3/g) Table 3. Average estimates and LSD for popping volume of four ZP maize hybrids (cm3/g) percentage of moisture at harvest percentage of moisture at popping ZP 611k ZP 616k ZP 501k ZP 608k > 25% 20 5.83 4.50 6.00 7.17 18 10.83 4.17 6.67 13.33 16 18.3 19.00 12.83 22.83 14 35.17 35.67 27.33 41.33 12 28.00 30.67 22.33 31.17 10 13.17 14.33 12.67 17.67 average 18.55 18.06 14.64 22.25 18.38 b 20-25% 20 13.83 4.17 5.50 5.67 18 11.33 7.33 9.67 11.00 16 13.33 15.67 15.17 18.67 14 29.67 29.33 27.83 38.33 12 26.33 26.67 22.00 30.33 10 15.33 16.17 11.67 18.67 average 18.30 16.56 15.31 20.44 17.65 b < 18% 20 6.00 18.33 13.83 12.00 18 8.00 24.83 8.33 16.67 16 21.67 30.00 19.33 24.17 14 34.17 37.83 26.00 40.00 12 26.33 28.83 21.83 33.83 10 15.00 16.67 13.00 19.00 average 18.53 26.08 17.05 24.28 21.48 a average 18.46c 20.23b 15.67d 22.32 Means followed by the same letter are not significantly different according to LSD0.05 J l P i d E i A i lt 22 (2018) 4 5.92% of unpopped kernels. Table 4. Average estimates and LSD for % of unpopped kernels of four ZP maize hybrids (%) percentage of moisture at harvest percentage of moisture at popping ZP 611k ZP 616k ZP 501k ZP 608k > 25% 20 31.15 20.11 40.76 17.09 18 19.95 39.10 21.87 6.72 16 11.60 4.27 15.93 2.69 14 0.73 0.28 0.81 1.03 12 0.96 0.24 3.28 0.47 10 2.92 0.93 10.21 0.42 average 11.22 10.82 15.48 4.74 10.56 a 20-25% 20 35.00 26.47 48.60 11.27 18 8.35 14.20 23.37 6.18 16 6.44 3.65 9.94 2.58 14 0.33 0.16 1.21 0.29 12 0.63 0.20 3.07 0.27 10 0.65 0.24 9.30 0.58 average 8.57 7.49 15.91 3.53 8.87 b < 18% 20 14.74 0.69 11.46 4.17 18 13.49 0.42 25.53 1.70 16 2.84 0.32 8.16 2.53 14 0.58 0.14 1.34 0.51 12 0.58 0.22 3.20 0.45 10 1.41 0.87 10.15 0.36 average 5.61 0.44 9.97 1.62 4.41 c average 8.46 b 6.25 c 13.79 a 3.30 d Means followed by the same letter are not significantly different according to LSD0.05 Fig. CONCLUSION ACKNOWLEDGMENT: This paper is a result of the research within the project TR31037, supported by the Ministry of Education, Science and Technological Development, Republic of Serbia. Silva, V.Q.R., A.T. Amaral Junior, L.S.A. Gonçalves, S.P. Freitas Junior, R.M. Ribeiro (2011). Heterotic parameterizations of crosses between tropical and temperate lines of popcorn. Acta Scientarium Agronomy, 33:243-249. Song, A., S.R. Eckhoff, M. Paulsen, J.B. Litchfield (1991). Effects of kernel size and genotype on popcorn popping volume and number of unpoppedn kernels. Cereal Chemistry, 68, 464-467. MATERIAL AND METHOD Means followed by the same letter are not significantly different according to LSD0.05 Means followed by the same letter are not significantly different according to LSD0.05 Fi 1 A i f i l d 8,57 11,01 19,25 33,56 27,36 15,28 21,79 15,07 5,91 0,62 1,13 3,17 0,00 5,00 10,00 15,00 20,00 25,00 30,00 35,00 40,00 20 18 16 14 12 10 PV % of unpopped As shown on the Figure 1. the best popping performances are produced at 14 % moisture content at popping. Average popping volume was highest at that moment (33.56 cm3/g), while it dropped with the increase or decrease of the moisture content at popping. The lowest average popping volume of all four hybrids was at 20 % moisture content (8.57 cm3/g). Nevertheless all other average popping volumes with the exception at 14 % moisture content are considered unsatisfactory from the commercial point of view, because popcorn is also sold by the popping volume (Shimoni et al., 2002). The other analysed trait the % of unpopped kernels is in reverse proportion to the popping volume (Figure 1). The more kernels succeed to develop into flake, the more commercial value of the final product is. So this is very important parameter of popcorn hybrids. At optimal moisture content of 14%, the Fig. 1 Average estimates of popping volume and percentage of unpopped kernels depending on the moisture content at popping time Journal on Processing and Energy in Agriculture 22 (2018) 4 186 Srdić, Jelena et al./ The Influence of Moisture Content on Popping Traits in Popcorn Quinn, Sr P.V., Hong, D.C., Both, J.A. (2005). Increasing the size of a piece of popcorn. Physica A 353, 637-648. Journal on Processing and Energy in Agriculture 22 (2018) 4 CONCLUSION Popping volume and percentage of unpopped kernels are very important traits which determine the quality of popcorn. Commercial value of popcorn increases with the higher popping volume, and the lower percentage of unpopped kernels. Therefore it is confirmed in this research that moisture content of 14% at popping is the best moment for popping. At this moisture content all hybrids produced highest popping volumes and lowest percentage of unpopped kernels, which on average were 33.56 cm3/g and 0.62% of unpopped kernels. With the increase or decrease of moisture content popping volume dropped and percentage of unpopped kernels increased. Among analysed hybrids significant differences were found both concerning popping volume and percentage of unpopped kernels. Best performances were noticed for ZP 608k, while the poorest results presented ZP 501k. Concerning the moment of harvest i.e. moisture content at harvest, best results were obtained at last harvest term when moisture content was below 18%. Average popping volume was highest at that point (21.48 cm3/g), and average percentage of unpopped kernels was lowest (4.41%). Therefore, for the best quality results of popcorn final product – the flake, its harvest should be performed when the moisture content drops below 18%. Pajić, Z., Babić, M. (1991). Interrelation of popping volume and some agronomic characteristics in popcorn hybrids. Genetika, 23, 137-144. Pajić, Z., Srdić J., Filipović, M. (2006). Odnos rodnosti i zapremine kokičavosti hibrida kukuruza kokičara (Zea mays L. everta).Selekcija i semenarstvo, 12, 81-83. Pajić, Z., Srdić, J., Todorović, G., Babić, M., Radosavljević, M. (2012). Odnosprinosazrna i drugihvažnih osobina kukuruza kokičara (Zea mazs L. everta). Selekcija i semenarstvo, 18, 27- 32. Paraginski, R.T., Ziegler, V., Ferreira, D.C., Coussi, R., Gutoski, L.C., da Rosa Zavareze, E., Elias, M.C. (2016). Properties of popcorn starch expanded in microwave, with and without the presence of vegetable oil. Journal of Food Processing and Preservation, doi:10.1111/jfpp.13142, in press. Park, D., Allen, K.G.D., Stermitz, F.R., Maga, J.A., (2000). Chemical composition and physical characteristics of unpopped popcorn hybrids. J. Food Compos. Anal., 13, 921- 934. Shimoni, E., E.M. Dirks, T.P. Labuza (2002). The relationship between final popped volume of popcorn and thermal-physical parameters.Lebensmittel-Wissenschaft und Technolgie, 35,93- 98. ACKNOWLEDGMENT: This paper is a result of the research within the project TR31037, supported by the Ministry of Education, Science and Technological Development, Republic of Serbia. Received: 15. 08. 2018. Accepted: 30. 10. 2018. Received: 15. 08. 2018. REFERENCES Allerd-Coyle,T.A., Toma, R.B., Reiboldt, W., Thaku, M. (2000). Effects of moisture content, hybrid variety, kernel size and microwave wattage on the expansion volume of microwave popcorn. International Journal of Food Sciences and Nutrition, 51, 389-394. Song, A., S.R. Eckhoff (1994). Optimum popping moisture content for popcorn kernels of different sizes. Cereal Chemistry, 71, 458-460. Soylu, S. and Tekkanat, A. (2007). Interaction amongst kernel properties and expansion volume in various popcorn genotypes. Journal of Food Engineering, 8, 336-341. Amaral, A.T., dos Santos, A., Gerhardt, I.F.S., Kurosawa, R.N.F., Moreira, N.F., Pereira, M.G., Gravina G. de A., de L. Silva F.H. (2016). Proposal of super trait for the optimum selection of popcorn progenies based on path analysis. Genetics and Molecular Research, 15 (4), gmr15049309, 1-9, DOI http://dx.doi.org/10.4238/gmr15049309. Srdić, J., Pajić, Z. (2011). Variability of yield and kernel quality parameters of pocorn hybrids (Zea mays L. everta). Journal on Processing and Energy in Agriculture 15, 84-86. g gy g Srdić, J., Z. Pajić, M. Filipović, M. Sečanski (2015). The influence of moisture content of grain on popping volume of popcorn hybrids. Journal on Processing and Energy in Agriculture, 19 (1): 24-26. Cabaral, P.D.S., Amaral Junior, A.T., Freitas, I.L.J, Ribeiro, R.M. (2016). Cause and effect of quantitative characteristics on grain expansion capacity in popcorn.Rev. Ciênc. Agron., 47 (1), 108-117. http://dx.doi.org/10.5935/1806-6690.20160013. Srdić, J., M. Milašinović-Šeremešić, M. Radosavljević, N. Kravić, V. Babić (2017). Evaluation of agronomic and sensory characteristics of popcorn kernel. Journal on Processing and Energy in Agriculture, 21 (4): 185-187. Ceylan, M., Karabab E. (2002). Comparison of sensory properties of popcorn from various types and sizes of kernel. Journal of the Science of Food and Agriculture, 82,127-133. Gökmen, S. (2004). Effects of moisture content and popping method on popping characteristics of popcorn. Journal of Food Engineering, 65, 357-362. Sweley, J.C., Rose, D.J., Jackson, D.S., (2012). Hybrid and environment effect on popcorn kernel physiochemical properties and their relationship to microwave popping performance. J. Cereal Sci., 55, 188-194. Hosney, R.C., Zeleznak, K., Abdelrahman, A. (1983). Mechanism of popcorn popping. J. Cereal Sci. 1, 43-52. http://dx.doi.org/10.1016/j.jcs.2011.11.006 Karabab, E. (2006). Physical properties of popcorn kernels. Journal of Food Engineering, 72, 100-107. Ziegler, K.E., 2001. Popcorn. In: Hallauer, A. (Ed.), Specialty Corn. CRC Press, Boca Raton, FL, pp. 199-234. Moterele, L.M., A.L. Braccini, C.A. Scapim, R.J.B. Pinto, L.S.A. Gonçalves, R. Rodrigues (2012): Combining ability of popcorn lines for seed quality and agronomic traits. Euphytica, 185: 337-347. Accepted: 30. 10. 2018. REFERENCES Accepted: 30. 10. 2018. Received: 15. 08. 2018. 187 Journal on Processing and Energy in Agriculture 22 (2018) 4
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The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing
Frontiers in microbiology
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ORIGINAL RESEARCH published: 17 June 2016 doi: 10.3389/fmicb.2016.00919 ORIGINAL RESEARCH Vera Thiel 1*†, Jason M. Wood 2, Millie T. Olsen 2, Marcus Tank 1 †, Christian G. Klatt 2, 3, David M. Ward 2 and Donald A. Bryant 1, 4* Vera Thiel 1*†, Jason M. Wood 2, Millie T. Olsen 2, Marcus Tank 1 †, Christian G. Klatt 2, 3, David M. Ward 2 and Donald A. Bryant 1, 4* Vera Thiel 1*†, Jason M. Wood 2, Millie T. Olsen 2, Marcus Tank 1 †, Christian G. Klatt 2, 3, David M. Ward 2 and Donald A. Bryant 1, 4* Keywords: hot spring, microbial community, microbial diversity, extreme environments, phototrophic bacteria Edited by: Anna-Louise Reysenbach, Portland State University, USA †Present Address: Vera Thiel and Marcus Tank, Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan †Present Address: Vera Thiel and Marcus Tank, Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan Specialty section: This article was submitted to Extreme Microbiology, a section of the journal Frontiers in Microbiology Specialty section: This article was submitted to Extreme Microbiology, a section of the journal Frontiers in Microbiology Received: 07 March 2016 Accepted: 27 May 2016 Published: 17 June 2016 Edited by: Anna-Louise Reysenbach, Portland State University, USA 1 Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA, 2 Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA, 3 Agricultural Research Service, United States Department of Agriculture, University of Minnesota, Saint Paul, MN, USA, 4 Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA Reviewed by: Charles K. Lee, University of Waikato, New Zealand Anirban Chakraborty, University of Calgary, Canada Wesley Douglas Swingley, Northern Illinois University, USA Microbial-mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin at Yellowstone National Park have been studied for nearly 50 years. The emphasis has mostly focused on the chlorophototrophic bacterial organisms of the phyla Cyanobacteria and Chloroflexi. In contrast, the diversity and metabolic functions of the heterotrophic community in the microoxic/anoxic region of the mat are not well understood. In this study we analyzed the orange-colored undermat of the microbial community of Mushroom Spring using metagenomic and rRNA-amplicon (iTag) analyses. Our analyses disclosed a highly diverse community exhibiting a high degree of unevenness, strongly dominated by a single taxon, the filamentous anoxygenic phototroph, Roseiflexus spp. The second most abundant organisms belonged to the Thermotogae, which have been hypothesized to be a major source of H2 from fermentation that could enable photomixotrophic metabolism by Chloroflexus and Roseiflexus spp. Other abundant organisms include two members of the Armatimonadetes (OP10); Thermocrinis sp.; and phototrophic and heterotrophic members of the Chloroflexi. Further, an Atribacteria (OP9/JS1) member; a sulfate-reducing Thermodesulfovibrio sp.; a Planctomycetes member; a member of the EM3 group tentatively affiliated with the Thermotogae, as well as a putative member of the Arminicenantes (OP8) represented ≥1% of the reads. Archaea were not abundant in the iTag analysis, and no metagenomic bin representing an archaeon was identified. A high microdiversity of 16S rRNA gene sequences was identified for the dominant taxon, Roseiflexus spp. Previous studies demonstrated that highly similar Synechococcus variants in the upper layer of the mats represent ecological species populations with specific ecological adaptations. This study suggests that similar putative ecotypes specifically adapted to different niches occur within the undermat community, particularly for Roseiflexus spp. Edited by: Anna-Louise Reysenbach, Portland State University, USA Edited by: Anna-Louise Reysenbach, Portland State University, USA INTRODUCTION have been suggested to perform inorganic carbon fixation (van der Meer et al., 2003, 2005, 2007, 2010; Klatt et al., 2007, 2013b). Synechococcus spp. fix CO2 and synthesize and excrete metabolites that are then consumed by (photo)heterotrophic members of the community, including several members of the Chloroflexi, and presumably Roseiflexus spp. (Anderson et al., 1987; Bateson and Ward, 1988; Kim et al., 2015). Collectively, cyanobacteria and Roseiflexus spp. account for the majority of the biomass of the upper 0–2 mm portion of the mat community. Two additional members of the phylum Chloroflexi, Chloroflexus sp. and an apparently phototrophic, “Anaerolineae-like” organism (“Ca. Roseilinea gracile”; Tank et al., in press), as well as two recently discovered aerobic/microaerophilic, anoxygenic photoheterotrophs, Cab. thermophilum (Bryant et al., 2007; Garcia Costas et al., 2012a,b; Tank and Bryant, 2015a,b) and “Ca. Tcb. aerophilum” (Liu et al., 2012), also occur in the upper photic layer of the mat. Early studies on the processes and organisms involved in aerobic and anaerobic decomposition of the mat have been discussed in a review by Ward et al. (1992; and earlier papers cited therein). Since the discovery of the aerobic heterotroph Thermus aquaticus (Brock and Freeze, 1969) many aerobic (e.g., Thermomicrobium roseum; Jackson et al., 1973) and anaerobic fermentative and sulfate-reducing bacteria were cultivated from these mats (e.g., Bacillus stearothermophilis, Thermoanaerobium brockii, Thermoanaerobacter ethanolicus, Thermodesulfotobacterium commune; see Ward et al., 1992 for primary references). Many of the latter were sought with the hope that thermophiles would be useful for biofuel production. However, critical review indicated that most of these isolates had not been cultivated from highly diluted mat samples, and thus their importance to the community remained unknown (see Ward et al., 1998). Indeed, with one exception, Thermomicrobium roseum (Wu et al., 2009), the genomes of these organisms did not recruit reads with high identity values from metagenomic analysis of the upper mat layer (Klatt et al., 2011). Only two low-abundance, unidentified heterotrophic bacteria lacking the genes needed to synthesize chlorophyll (Chl) were detected in the upper mat community represented by metagenomic bins (Klatt et al., 2011). Nevertheless, heterotrophs, together with the photoheterotrophic and photomixotrophic community members, can be considered potential consumers of metabolites produced by cyanobacteria and possibly other mat inhabitants. In more recent years, the activity and diversity of sulfate-reducing bacteria of the microbial mats have been more intensively studied. Dillon et al. INTRODUCTION FIGURE 1 | Sampling site at Mushroom Spring, Yellowstone National Park, and microbial mat core (adapted from Kim et al., 2015). Microbial mat communities inhabiting the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin at Yellowstone National Park (YNP) have been studied for nearly 50 years (Brock, 1967; Ward et al., 2012). In these studies, the chlorophototrophic bacterial populations, i.e., chlorophyll- based phototrophs including members of the Cyanobacteria, Chloroflexi and the newly discovered Chloracidobacterium (Cab.) thermophilum and “Candidatus Thermochlorobacter (Tcb.) aerophilum,” have generally been the main focus (Bauld and Brock, 1973; Nold and Ward, 1996; Bryant et al., 2007; van der Meer et al., 2007; Steunou et al., 2008; Becraft et al., 2011; Klatt et al., 2011, 2013b; Liu et al., 2011, 2012; Tank and Bryant, 2015a,b). In contrast, the diversity and metabolic functions of the heterotrophic community in the microoxic/anoxic region of the mat are not well understood. FIGURE 1 | Sampling site at Mushroom Spring, Yellowstone National Park, and microbial mat core (adapted from Kim et al., 2015). Using cultivation-based methods, early studies focused on the dominant Cyanobacteria and phototrophic Chloroflexi (Bauld and Brock, 1973; Bateson and Ward, 1988). Over time, these studies were extended by a variety of molecular methods with increasing molecular resolution. A pioneering molecular study targeting 16S rRNA gene sequences directly indicated a greater diversity of uncultivated bacteria in the mat than previously realized (Ward et al., 1990). However, only recently have metagenomic (Klatt et al., 2011), metatranscriptomic (Liu et al., 2011, 2012; Klatt et al., 2013b) and metametabolomic (Kim et al., 2015) analyses led to a holistic overview, in terms of the organisms present and their functional potentials, of the major taxa inhabiting the upper 2 mm of the 60–65◦C regions of the Mushroom Spring microbial mats (Figure 1). The microbial community of the upper green mat layer contains eight dominant bacterial populations, of which six are chlorophototrophs (Klatt et al., 2011). Oxygenic cyanobacteria from the genus Synechococcus have been shown to be the predominant primary producers in these communities by in situ studies of bicarbonate fixation and nitrogen fixation (Steunou et al., 2008) using stable and radioactive isotopes (Bateson and Ward, 1988; Nübel et al., 2002; van der Meer et al., 2007). In addition, anoxygenic photoheterotrophic members of the Roseiflexus spp. Citation: Thiel V, Wood JM, Olsen MT, Tank M, Klatt CG, Ward DM and Bryant DA (2016) The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing. Front. Microbiol. 7:919. doi: 10.3389/fmicb.2016.00919 June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 1 Composition of the Mushroom Spring Undermat Community Thiel et al. Frontiers in Microbiology | www.frontiersin.org MATERIALS AND METHODS The samples were collected on August 10th, 2011 from a chlorophototrophic microbial mat in an effluent channel of the siliceous and slightly alkaline Mushroom Spring in YNP, WY (USA). The samples were collected using a #4 cork borer at a site where the water above the mat was 60◦C (Figure 1). The microbial mat is made up of an upper green layer (1–2 mm thick), which mainly consists of different chlorophototrophic bacteria, and an orange-colored undermat layer (Figure 1). Genomic DNA was extracted from the orange-colored undermat layer (∼3–5 mm depth; DNA from below this level was too degraded to analyze). The metagenome as well as 16S rRNA gene PCR amplicons were sequenced at the DOE Joint Genome Institute (JGI) using HiSeq and MiSeq Illumina technologies. The iTtag sequences were analyzed at two different identity levels. All reads were clustered into operational taxonomic units (OTUs) with 97% sequence identity cutoffby using USEARCH, but they were also analyzed after dereplication (i.e., clustered by 100% nt identity, see Supplementary Materials). RDP Classifier (Wang et al., 2007; Cole et al., 2009), BLAST searches (Altschul et al., 1990) and phylogenetic analyses (Ludwig et al., 2004) were used to identify sequences. Microdiversity was assessed using the number of highly abundant dereplicated sequences, and the “oligotyping pipeline” (http://merenlab.org/projects/ oligotyping/). HiSeq metagenomic reads were assembled and then clustered into bins by oligonucleotide frequency pattern analyses using ESOM (Dick et al., 2009). Metagenomic bins were treated as partial genomes of single taxa and were taxonomically affiliated using Amphoranet (http://pitgroup.org/ amphoranet/, Kerepesi et al., 2014) to assess the phylogenetic marker genes present in each bin. Detailed descriptions of the methods for DNA extraction, library construction, sequencing, and data analyses are found in the Supplementary Materials. “Red-layer” communities, which may often be “orange” in color as is the case for the mats of Mushroom Spring, have been shown to contain novel chlorophototrophs (Boomer et al., 2000, 2002), whose pigments exhibit unusual in vivo absorption spectra (Boomer et al., 2000), but these communities have not yet been studied in detail. As part of a comparative study of YNP hot spring microbial mat communities, a 45-Mbp metagenome based on Sanger sequencing revealed some initial insights into the composition of the undermat microbial community of Mushroom Spring (Klatt et al., 2013a). INTRODUCTION (2007) showed that an active sulfur cycle occurs in the mat community despite very low sulfate concentrations. The highest rates of sulfate respiration were reportedly associated with Thermodesulfovibrio- like organisms and were measured close to the surface of the mat late in the day when photosynthetic oxygen production had ceased. Additionally, methane production has been detected in numerous alkaline siliceous hot spring microbial mats in YNP June 2016 | Volume 7 | Article 919 June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 2 Composition of the Mushroom Spring Undermat Community Thiel et al. to facilitate an active integration of these mostly heterotrophic members into models of the mat community. This paper describes the composition and diversity of the Mushroom Spring undermat community based on rRNA-amplicon (iTag) and deep metagenomic sequencing analyses, with an initial focus on the identity and taxonomic diversity of the community members. A description of the metabolic potential and putative interactions, including a metabolic description of the entire microbial mat community, will be published separately. (Ward, 1978; Sandbeck and Ward, 1981, 1982). Methanogenic archaea (∼107 to 108 ml−1) have been enumerated in small cores of Octopus Spring mats, which in combination with the detection of low levels of archaeal lipids, suggests that methanogenesis occurred in situ in those mats (Ward, 1978; Sandbeck and Ward, 1981; Ward et al., 1985). The relative rarity of these organisms compared to Synechococcus (on the order of 1% or less) suggests that these terminal anaerobes receive little of the energy recycled during decomposition of the mat (Ward et al., 1989). g p The first revolution of molecular microbial ecology enabled the study of uncultured bacterial diversity through amplification, sequencing and phylogenetic analysis of ribosomal RNA genes (Olsen et al., 1986; Ward et al., 1990; Amann et al., 1995; Hugenholtz and Pace, 1996; Hugenholtz et al., 1998a; Pace, 2009). Through such studies, our perspective on microbial diversity has increased enormously over the past three decades, and the impact of culture-independent studies on the emerging view of bacterial diversity cannot be overstated (Hugenholtz et al., 1998a). Ward and coworkers reported the presence of a number of uncultured bacterial lineages in their first molecular microbial diversity study of the mat community of Octopus Spring (Ward et al., 1990). INTRODUCTION Over the course of the past 25 years, several of those initially unidentified ribosomal RNA sequences have been associated with chlorophototrophic mat members (OS-A and B with Synechococcus spp., OS-C with Roseiflexus sp., OS-D with Cab. thermophilum, and OS-E with “Ca. Tcb. aerophilum”), whereas many others (OS-F, OS-G, OS-H, OS-K, OS-L, OS-M, OS-N, OS-R) still have not been identified and were not detected in the metagenome of the upper green layer (Klatt et al., 2011). Frontiers in Microbiology | www.frontiersin.org MATERIALS AND METHODS Compared to the upper green layer, fewer Synechococcus spp., a greater number of Roseiflexus spp., and several presumed anaerobic or fermentative organisms within the Bacteroidetes and Thermodesulfobacteria were identified. The undermat community contained a Thermotoga-like population as well as several low G+C organisms that could not be characterized (Klatt et al., 2013a). Low coverage and a small number of long scaffolds above the threshold used in most clustering analyses (>10 kb) limited the application of metagenomic binning approaches (Klatt et al., 2013a) and indicated that additional studies with much deeper sequencing would be needed to define the undermat community. RESULTS We used deep sequencing of rRNA gene amplicons (iTags) and total environmental DNA to study the subsurface community of the chlorophototrophic microbial mat at Mushroom Spring. We describe the diversity and community composition on both levels, based on “OTUs” (Figures 2A, 3A, Table 1 and Table S1) and based on “dereplicated iTag” sequences (Figures 2B, 3B, Table 2) in Section “16S rRNA Gene Amplicons (iTags),” as well as on metagenomic bins obtained based on The overall goal of this research is to investigate the complete microbial mat community at Mushroom Spring and to develop a comprehensive understanding of the microbial ecology of the microbial mats of this hot spring. The specific objectives of this study were to analyze the orange-colored undermat community, to identify those organisms that are present, and June 2016 | Volume 7 | Article 919 3 Composition of the Mushroom Spring Undermat Community Thiel et al. FIGURE 2 | Relative abundance of (A) the 15 most abundant 97% OTUs, and (B) the 17 most abundant dereplicated iTag sequences in the Mushroom Spring undermat 16S rRNA gene amplicon (iTag) analysis. All less abundant OTUs (<1,000 reads each) are shown combined as “Others.” FIGURE 2 | Relative abundance of (A) the 15 most abundant 97% OTUs, and (B) the 17 most abundant dereplicated iTag sequences in the Mushroom Spring undermat 16S rRNA gene amplicon (iTag) analysis. All less abundant OTUs (<1,000 reads each) are shown combined as “Others.” undermat community in both read abundance and diversity (Tables 1, 2, and Table S1, Figures 2A,B). Thirteen out of seventeen members of the microbial mat detected in previous 16S rRNA gene sequence cloning and DGGE studies (OS types, Table 4; Ward et al., 1990, 1992; Weller et al., 1992; Ferris et al., 1996b, 1997; Ferris and Ward, 1997), as well as relatives of ribosomal sequence types derived from a previous undermat study (Klatt et al., 2013a, Figure 5 and Figure S1) were detected in this study and thus confirmed as members of a compositionally and temporally stable microbial community. oligonucleotide frequency patterns in Section “Metagenome Sequencing” (Figure 4, Table 3). Frontiers in Microbiology | www.frontiersin.org Diversity Based on OTUs The 16S rRNA gene amplicon reads clustered into 317 OTUs of ≥97% nt identity, with abundances between 1 and 68,369 reads per OTU (Table S1). The community was characterized by a low degree of evenness (Figure 3A). The majority of the OTUs were present in low abundance; only 15 OTUs (5% of the taxa) were represented by 1,000 or more reads (Figure 3B). Due to the high number of singleton sequences, the estimated richness based on Chao1 (Schao1 = Sobs+ (no. of singletons2)/(2∗no. of doubletons) (Chao, 1984) was rather high, Chao1 = 369.74; a lower value of Chao1 = 220.9 was obtained in a previous study (Klatt et al., 2013a). In contrast, the Simpson’s Reciprocal Index (D = P n(n−1) N(N−1) ) obtained in this study is considerably lower than in previous studies (3.85 in this study vs. 37.5; Klatt et al., 2013a), reflecting the low evenness and strong dominance of only a few OTUs in the amplicon study. While an identity cut-offof 97% for rRNA gene sequences is often used to demarcate species (Stackebrandt and Goebel, 1994; Schloss and Handelsman, 2005; Koeppel and Wu, 2013), this is an arbitrary value that does 16S rRNA Gene Amplicons (iTags) 16S rRNA Gene Amplicons (iTags) 16S rRNA Gene Amplicons (iTags) Sequencing of partial 16S rRNA genes resulted in 139,326 total and 30,861 dereplicated (i.e., unique) reads after quality control. Abundance values of dereplicated reads varied between 1 and 30,285, with an average of 5.4 reads per sequence. Most Abundant Taxa Based on OTUs Most Abundant Taxa Based on OTUs When considering OTU sequences based on 97% nt sequence identity, 15 OTUs were identified with >1,000 reads each, varying in abundance between 1,008 and 68,369 reads (Table 1). These are considered to represent highly abundant taxa and thus are likely to represent key members of the Mushroom Spring undermat community. However, the threshold of 1,000 reads was arbitrarily chosen and does not necessarily correlate with activity or ecological importance. We will focus the discussion on the “very abundant” taxa listed in Table 1, but will also include selected “abundant” and “less abundant” OTUs with read abundances of ≥100 and less, respectively (Table S1). p y The 16S rRNA gene amplicons of the microbial undermat community were dominated by sequences derived from Roseiflexus spp. (Figure 2A, OTU-1, 49%) with the second most abundant sequences belonging to a Pseudothermotoga sp. (OTU-2, 10%). An unidentified Armatimonadetes (formerly known as OP10) bacterium (OTU-3), a member of the Aquificae (OTU-4), as well as the sequences derived from member of the Cyanobacteria each represented ∼4% of the sequences (Table 1). On the basis of psaA sequences the cyanobacterial sequences can be classified as belonging to ecotype populations of Synechococcus detected in the upper green layer of the mat and are considered likely to arise from buried surface populations that are not expected to represent metabolically active constituents of the undermat community. The sixth most abundant OTU was identified as a phototrophic member of the phylum Chloroflexi, which had previously been detected in the upper green layer using metagenome analysis and identified as the first phototrophic “Anaerolineae-like” Chloroflexi; it has provisionally been named “Ca. Roseilinea gracile” (Klatt et al., 2011, 2013b; Tank et al., in press). Additional abundant OTUs were affiliated with the Atribacteria (OP9) Nitrospirae, Planctomycetes and several phototrophic and non-phototrophic members of the phylum Chloroflexi (Table 1). Three of the fifteen most abundant OTU sequences from the undermat amplicon study represented sequences obtained from the mats of Octopus Spring in previous 16S rRNA gene surveys (OS-B: Synechococcus sp. Type B; OS-C: Roseiflexus sp. RS-1; and OS-L: Armatimonadetes member OTU-3) (Table 4, Ward et al., 1990, 1992; Ferris et al., 1996a; van der Meer et al., 2010). Frontiers in Microbiology | www.frontiersin.org Most Abundant Taxa Based on OTUs FIGURE 3 | Rank abundance curve of the 15 very abundant OTUs (>1,000 reads) obtained from the undermat 16S rRNA gene amplicon study (relative read counts) (A), and Log abundance plot of the all 317 OTUs obtained from the undermat 16S rRNA gene amplicon study (B). 15 OTUs (=5%) were detected more than 1,000 times. FIGURE 3 | Rank abundance curve of the 15 very abundant OTUs (>1,000 reads) obtained from the undermat 16S rRNA gene amplicon study (relative read counts) (A), and Log abundance plot of the all 317 OTUs obtained from the undermat 16S rRNA gene amplicon study (B). 15 OTUs (=5%) were detected more than 1,000 times. RESULTS An overview of the most important taxa detected in each phylum will be presented in Section “Overview of Phyla and Taxa Detected in the Mushroom Spring Undermat.” Each iTag OTU was found to represent a variable number of dereplicated iTtag sequences, which is interpreted as representing different degrees of microdiversity within a taxon (Figure 2B, Table 1). Members of 20 different phyla were identified (Figure 5 and Figure S1, Table S1). Organisms of the phylum Chloroflexi dominated the microbial June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 4 Composition of the Mushroom Spring Undermat Community Thiel et al. Thiel et al. FIGURE 3 | Rank abundance curve of the 15 very abundant OTUs (>1,000 reads) obtained from the undermat 16S rRNA gene amplicon study (relative read counts) (A), and Log abundance plot of the all 317 OTUs obtained from the undermat 16S rRNA gene amplicon study (B). 15 OTUs (=5%) were detected more than 1,000 times. not necessarily correlate with any species definition. Here, we refer to OTUs as “taxa,” use the term “populations” mainly for dereplicated iTag sequences, and discuss our understanding of the bacterial species concept in Section “Discussion.” Most Abundant Populations Based on Dereplicated iTag Sequences Seventeen dereplicated iTag sequences, representing members of the nine most abundant OTUs, were each detected more than 1,000 times, and in total represent more than half of all iTag reads recovered in this study (Table 2, Figure 2B). These sequences probably correspond to the most abundant “populations” (in contrast to “taxa” for OTUs). Five of these very abundant dereplicated iTag sequences belong to a single OTU representing the most abundant taxon, Roseiflexus spp. (Figure 2B, Table 2 June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 5 Composition of the Mushroom Spring Undermat Community Thiel et al. TABLE 1 | Most abundant OTUs (97% nt identity), number of reads and relative abundance, microdiversity in terms of represented dereplicated iTag sequences, corresponding metagenome sequences and next relatives determined by BLAST search. OTU-name Reads Rel. abundance (%) No. of derep. iTags Metagenome 16S rRNA Relevant Blast hits Acc. No. Ident (%) Total >100 Scaffold ID Avg. coverage Length (bp) OTU-01 68,369 49 6,193 24 101,6681 2,842 1,357 Roseiflexus sp. RS-1 NR_074197 100 OTU-02 14,480 10 1,664 3 1,000,336 458 1,426 Thermotoga hypogea NBRC 106472 (T) AP014508 98 OTU-03 6,203 4 2,082 9 1,062,246 951 710 Unc. bacterium clone SM2D03 AF445720 100 Eubacterium sp. (OS type L) L04707 98 OTU-04 6,160 4 899 3 1,002,657 262 1,434 clone YNP_SBC_BP2A_B2 HM448202 99 Thermocrinis ruber strain DSM 23557(T) CP007028 97 OTU-05 5,046 4 1,289 7 1,008,881 105 1,002 Synechococcus sp. JA-2-3B’a(2-13) CP000240 100 OTU-06 3,580 3 675 1 1,001,696 423 1,364 clone YNP_SBC_BP4_B2 HM448255 98 Thermanaerothrix daxensis GNS-1 (T) HM596746 87 OTU-07 3,350 2 564 1 1,014,288 189 1,444 OP9 bacterium clone TP29 EF205555 98 Ammonifex thiophilus strain SR(T) EF554597 83 OTU-08 3,283 2 705 2 1,000,748 135 1,413 clone SMD-B01 AB477993 99 Thermodesulfovibrio yellowstonii DSM11347(T) NR_074345 96 OTU-09 1,981 1 449 2 1,000,273 129 1,389 clone NY-30 KC290430 94 Thermanaerothrix daxensis GNS-1 (T) HM596746 91 OTU-10 1,715 1 510 6 1,001,962 67 1,406 EM3 clone OPB88 AF027006 99 Rhodothermus marinus SG0.5JP17-172 (T) CP003029 82 OTU-11 1,594 1 521 3 1,030,146 83 1,309 Chloroflexus sp. Most Abundant Populations Based on Dereplicated iTag Sequences MS-G KR230107 99 Chloroflexus aurantiacus J-10-fl (T) CP000909 95 OTU-12 1,569 1 477 3 1,003,586 802 1,415 OP10 clone OPB80 AF027089 94 Fimbriimonas ginsengisoli Gsoil 348 (T) CP007139 81 OTU-13 1,392 1 306 2 1,015,572 36 1,497 clone bac67 HM184963 95 Thermoanaerobaculum aquaticum MP-01 (T) NR_109681 88 OTU-14 1,260 1 322 3 1,003,293 60 1,420 clone TP5 EF205581 99 Thermogutta terrifontis R1 (T) KC867694 90 OTU-15 1,008 1 391 3 1,021,867 132 1,299 clone OB17 EF429491 98 Chloroflexus aurantiacus J-10-fl(T) CP000909 90 OTU-1, MSunder_iTags-1, 2, 4, 9, and 15). The third most abundant sequence (MSunder_iTag-3), as well as two additional abundant, dereplicated sequences (MSunder_iTags-12 and 14), were representatives of Pseudothermotoga spp. (OTU-2), the second most abundant taxon. The Armatimonadetes (OTU-3) and a member of the phylum Aquificae (OTU-4) contained two slightly different, highly abundant dereplicated iTag sequences each, whereas the other OTUs (OTUs 5–9) had only one very abundant dereplicated iTag sequence. With regard to the single dereplicated iTag sequences, cyanobacteria derived from the green upper layer of the mat community are represented by the eleventh most abundant iTag sequence, and thus the ten most abundant dereplicated iTag sequences (representing eight OTUs) are considered to represent the most abundant populations in the undermat community (MSunder_iTag-1 through MSunder_iTag-10; Table 2). Frontiers in Microbiology | www.frontiersin.org Microdiversity We used different methods to assess the degree of sequence heterogeneity and microdiversity within the microbial undermat community. Based on the number of different dereplicated iTag sequences within one 97% OTU, a high degree of diversity was Frontiers in Microbiology | www.frontiersin.org June 2016 | Volume 7 | Article 919 6 Composition of the Mushroom Spring Undermat Community Thiel et al. TABLE 2 | Most abundant dereplicated iTag sequences (100% nucleotide identity) detected in the Mushroom Spring undermat. MSunder_iTag (dereplicated iTag) Reads Relative abundance (%) Phylum Genus OTU MSunder_iTag-1 30,285 21.70 Chloroflexi Roseiflexus 1 MSunder_iTag-2 11,586 8.30 Chloroflexi Roseiflexus 1 MSunder_iTag-3 8,257 5.90 Thermotogae Pseudothermotoga 2 MSunder_iTag-4 4,712 3.40 Chloroflexi Roseiflexus 1 MSunder_iTag-5 3,760 2.70 Aquificae Thermocrinis 4 MSunder_iTag-6 2,551 1.80 Chloroflexi Ca. Roseilinea 6 MSunder_iTag-7 2,436 1.70 Atribacteria 7 MSunder_iTag-8 2,229 1.60 Armatimonadetes 3 MSunder_iTag-9 1,881 1.40 Chloroflexi Roseiflexus 1 MSunder_iTag-10 1,721 1.20 Nitrospirae Thermodesulfovibrio 8 MSunder_iTag-11 1,716 1.20 Cyanobacteria Synechococcus 5 MSunder_iTag-12 1,695 1.20 Thermotogae Pseudothermotoga 2 MSunder_iTag-13 1,542 1.10 Armatimonadetes 3 MSunder_iTag-14 1,370 1.00 Thermotogae Pseudothermotoga 2 MSunder_iTag-15 1,220 0.90 Chloroflexi Roseiflexus 1 MSunder_iTag-16 1,161 0.80 Chloroflexi 9 MSunder_iTag-17 1,027 0.70 Aquificae Thermocrinis 4 Read numbers, relative abundance, taxonomic affiliation and OTU affiliation are provided. TABLE 2 | Most abundant dereplicated iTag sequences (100% nucleotide identity) detected in the Mushroom Spring undermat. ost abundant dereplicated iTag sequences (100% nucleotide identity) detected in the Mushroom Spring undermat. otide identity) detected in the Mushroom Spring undermat. OTU FIGURE 4 | ESOM binning of Mushroom Spring assembled undermat metagenome sequences >5 kb. In order to show complete bins, the map is shown in tiled mode, displaying four connected partial copies of the grid with some redundancy of data points. Repeating colors imply repeating bins. Complete bins are labeled with numbers (number code and details of the bins is found in Table 3). Additional partial copies of the bins due to the tiled display are not labeled. The color gradient code on the right visualizes relative height values; the largest height normalized to 1. FIGURE 4 | ESOM binning of Mushroom Spring assembled undermat metagenome sequences >5 kb. In order to show complete bins, the map is shown in tiled mode, displaying four connected partial copies of the grid with some redundancy of data points. Repeating colors imply repeating bins. Complete bins are labeled with numbers (number code and details of the bins is found in Table 3). Microdiversity Additional partial copies of the bins due to the tiled display are not labeled. The color gradient code on the right visualizes relative height values; the largest height normalized to 1. of ∼39,000 upper green layer reads and 75,000 undermat reads). The total “purity scores” of 0.95 and 0.86 for >100 and >10 reads, respectively, indicates a good separation for the highly abundant oligotypes, but also implies further low abundance oligotypes in the samples. Differences in diversity and abundance of oligotypes between the upper green layer and the undermat were detected, e.g., for the most abundant Roseiflexus- oligotypes (Table S2, Figure S2). In general the undermat is more diverse. The upper green layer for example contains a lower number of highly abundant oligotypes (six oligotypes >1% of indicated, especially for the most abundant OTU, Roseiflexus spp. We detected 6,193 total dereplicated iTag sequences, 24 of which had >100 reads (Table 1). A similar microdiversity was identified by the oligotyping approach, and was also suggested by a high number of very similar but non-identical clone sequences obtained in a previous study (Klatt et al., 2013a; Figure 5A, and Figure S2, Table S2). Based on ten distinct nucleotide positions, 246 different oligotypes were identified, of which 55 were represented by >10 reads, 23 by >100 reads and nine by > 1,000 reads in the combined dataset (which consisted June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 7 Composition of the Mushroom Spring Undermat Community Thiel et al. Thiel et al. TABLE 3 | Metagenome bins recovered based on tetranucleotide frequencies. Bin* OTU Identity 16S rRNA Contigs Size [Mb] Marker genes 1 OTU-01 Roseiflexus sp. No 18 0.20 None 2 OTU-02 Thermotoga sp. Yes, scaffold00336 142 1.85 30 3$ OTU-03 Armatimonadetes (OP10) Yes 81 2.9 32 4 OTU-04 Aquificae / Thermocrinis sp. Yes, scaffold02657 44 0.22 5 5 OTU-05 Synechococcus sp. B’ No 68 0.43 13 6 OTU-06 “Ca. Roseilinea gracile” No 188 1.71 25 7 OTU-07 Atribacteria (OP9) No 136 1.45 26 8 OTU-08 Thermodesulfovibrio sp. Yes, scaffold00748 119 1.59 17 9 OTU-09 Chloroflexi, Anerolineae Yes, scaffold00273 220 2.62 26 10 OTU-10 Thermotogae-EM3/OPS-2 Yes, scaffold01962 157 1.38 18 11 OTU-11 Chloroflexus sp. MS-G No 336 3.1 21 12 OTU-12 Armatimonadetes_Gp6 (OP10) Yes, scaffold03586 200 1.72 24 13 OTU-13 Aminicenantes (OP8) No 94 2.54 30 14 OTU-14 Planctomycetes Yes, scaffold03293 258 1.90 19 15 OTU-15 “Ca. Frontiers in Microbiology | www.frontiersin.org Microdiversity Chloranaerofilum corporosum” No 299 2.26 19 16 OTU-17 Chloracidobacterium thermophilum No 220 2.07 21 17 OTU-18 Armatimonadetes_Gp 2 Yes, scaffold00584 207 2.64 31 18 OTU-21 Meiothermus sp. No 155 1.31 8 19 OTU-24 Chlorobi-lineage 5: OPB56 Yes, scaffold02638 137 1.17 18 20 OTU-36 Acidobacterium, OPB3 Yes, scaffold01343 253 2.60 6 21 OTU-38 “Ca. Thermochlorobacter aerophilum” No 198 2.09 27 22 OTU-46 Elioraea sp. No 229 2.02 26 23 Planctomycetes No 385 3.8 29 24 Ignavibacteriaceae No 75 2.50 31 25 OTU-31 Chloroflexi, Bellilinea sp. No 237 2.46 24 26 Unidentified No 130 1.78 28 27 Unidentified No 96 0.85 2 28 Unidentified No 110 0.84 3 29 Unidentified No 98 0.66 5 30 Unidentified No 22 0.27 None 31 Unidentified No 38 0.26 2 32 OTU-26 Thermodesulfobacteria No 27 0.18 12 33 Unidentified No 23 0.17 none 34 Unidentified No 23 0.17 none 35 Unidentified No 17 0.11 8 36 Unidentified No 12 0.09 none 37 Chloroflexi, Dehalocoocoides-like No 8 0.06 none *Numbers refer to ESOM bins shown in Figure 4. $ Bin 3 was obtained from an enrichment culture, not from the undermat metagenome. TABLE 3 | Metagenome bins recovered based on tetranucleotide frequencies. *Numbers refer to ESOM bins shown in Figure 4. $ Bin 3 was obtained from an enrichment culture, not from the undermat metagenom upper layer, namely “CCCCGCGTGC” (2.13% in undermat, 0.19% in upper layer) and “CCCCGCGGGC” (1.02 vs. 0.21%) (Table S2). upper layer, namely “CCCCGCGTGC” (2.13% in undermat, 0.19% in upper layer) and “CCCCGCGGGC” (1.02 vs. 0.21%) (Table S2). all Roseiflexus sequences), whereas the undermat is more diverse with nine oligotypes >1% (Table S2, Figure S2). Notably, the most abundant oligotypes are present in both samples in similar abundances. One oligotype dominates both datasets (48% in the upper layer vs. 54% in the undermat). The second most abundant oligotype “CTCTACGGGC” is more abundant in the upper layer (32 vs. 20% of the reads), whereas the third is more abundant in the undermat (9 vs. 6%, Table S2). In general the undermat is more diverse and some oligotypes show distinct differences. For example, the difference in the entropy figures from upper green layer and undermat after separate analyses (considerably lower entropy at pos. 104 and 109 in upper layer; Figures S2B,C) are indicative of a lower abundance of two oligotypes in the all Roseiflexus sequences), whereas the undermat is more diverse with nine oligotypes >1% (Table S2, Figure S2). Notably, the most abundant oligotypes are present in both samples in similar abundances. One oligotype dominates both datasets (48% in the upper layer vs. 54% in the undermat). The second most abundant oligotype “CTCTACGGGC” is more abundant in the upper layer (32 vs. 20% of the reads), whereas the third is more abundant in the undermat (9 vs. 6%, Table S2). In general the undermat is more diverse and some oligotypes show distinct differences. For example, the difference in the entropy figures from upper green layer and undermat after separate analyses (considerably lower entropy at pos. 104 and 109 in upper layer; Figures S2B,C) are indicative of a lower abundance of two oligotypes in the A high degree of microdiversity was also indicated for other OTUs obtained in this study, e.g., OTU-3 (Armatimonadetes member, OS type L) and OTU-5 (Synechococcus spp.) Overall, the twelve most abundant OTUs also exhibited the highest number of unique amplicon sequences, indicating a correlation between microdiversity and sequencing depth (Table 1). However, the number of abundant dereplicated sequences, i.e., putative ecotypes did not show the self-correlation with sequencing depth, but correlated with the metagenome assembly quality; a high microdiversity was suggested to be interfering with the sequence June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 8 Composition of the Mushroom Spring Undermat Community Thiel et al. Metagenome Bins Binning of the metagenome contigs based on tetranucleotide frequency patterns resulted in 36 clusters (Table 3, Figure 4). An additional bin, representing OTU-3 from the iTag study of the undermat, was obtained from an cyanobacterial enrichment culture metagenome (Olsen et al., 2015). Thus, 37 partial genomes, 26 of which contained ≥1 Mb of sequence information, were found by this method (Table 3). Twenty-six of the bins were identified taxonomically, and 22 could be affiliated with abundant OTUs. A specific cut-offwith regard to taxonomic levels or sequence threshold cannot be given for the represented populations. However, previous studies, as well as joint binning of the sequences from the presented study with reference genomes, suggest that genomes derived from bacterial populations with 16S rRNA gene sequences identities of ≥96% do upper layer, namely “CCCCGCGTGC” (2.13% in undermat, 0.19% in upper layer) and “CCCCGCGGGC” (1.02 vs. 0.21%) (Table S2). The occurrence of several metagenomic bins affiliated with the Chloroflexi as well as the separate clustering of the included Chloroflexi reference genomes, provides an estimate of the ability of this approach to discriminate and resolve among different members of the same phylum. Based on these observations, as well as 16S rRNA OTU similarities found in this study displaying values of either <95% or >96.8% nt identity, we expect genomes of populations sharing <95% 16S rRNA sequence identity to be represented by distinct metagenomic bins, whereas OTUs of >96.8% similarity would probably be represented by a single partial genome (i.e., metagenomic bin). upper layer, namely “CCCCGCGTGC” (2.13% in undermat, 0.19% in upper layer) and “CCCCGCGGGC” (1.02 vs. 0.21%) (Table S2). TABLE 4 | OS-type sequences from previous studies (Ward et al., 1990, 1992; Weller et al., 1992; Ferris et al., 1996b, 1997; Ferris and Ward, 1997) and the corresponding sequences obtained in this study. OS type Acc. Nos. Phylum Identity OTU Metagenome sequences [JGI24185J35167_] A X52544 Cyanobacteria Synechococcus sp. A OTU-22 10825551 (280 bp) 10154254 (272 bp) 10858251 (546 bp) B M62776 X52545 Cyanobacteria Synechococcus sp. B’ OTU-5 12370211 (272 bp) C X52546 U42421 U90433 Chloroflexi Roseiflexus sp. RS-1 OTU-1 10166812 (1357 bp) D X52547 Acidobacteria Chloracidobacterium thermophilum OTU-17 10032584 (1383 bp) E X52548 U42419 U42420 Chlorobi Ca. Thermochlorobacter aerophilum OTU-38 10007615 (1379 bp) F X52549 Chlorobi OPB56-like Chlorobi OTU-262 No scaffold G X52550 Betaproteobacteria Hydrogenophilus sp. OTU-101 No scaffold H X52551 Sprichoaetes Spirochaeta sp. OTU-41 No scaffold I L04709 Cyanobacteria Leptolyngbya sp. no OTU No scaffold J L04710 Cyanobacteria Synechococcus sp. no OTU 1045912 (920 bp) K L04711 Acidobacteria Thermoanaerobaculum sp. OTU-61 10096124 (954 bp) 10037885 (587 bp) L L04707 Armatimonadetes Uncultured Armatimonadetes (OP10) OTU-3 11621781 (295 bp) 10622461 (710 bp) 12054061 (298 bp) M L04708 Chlorobi Unidentified Ignavibacteriaceae OTU-34 1068906 (652 bp) 1010292 (1038 bp) N L05931 L05930 Betaproteobacteria Tepidimonas sp. No OTU No scaffold O L04706 Alphaproteobacteria Elioraea sp. OTU-46 10309321 (1157 bp) 10459122 (309 bp) Q U42422 Chloroflexi Candidatus Chlorothrix halophila No OTU No scaffold R U46750 Betaproteobacteria Uncultured Beta-Proteobacterium OTU-172 No scaffold TABLE 4 | OS-type sequences from previous studies (Ward et al., 1990, 1992; Weller et al., 1992; Ferris et al., 1996b, 1997; Ferris and Ward, 1997) and the corresponding sequences obtained in this study. assembly. Very few contigs with >5 kb length were assembled for the OTUs with the highest microdiversity (OTU-1 and OTU-3). not separate into distinct bins (data not shown; Klatt et al., 2011). In this study, the cyanobacterial genomes of Synechococcus Types A and B’ (97% 16S rRNA nt identity), and within the Chloroflexi, Roseiflexus castenholzii and Roseiflexus sp. RS-1 (95.6% 16S rRNA nt identity) as well as Chloroflexus aurantiacus J-10-fland Chloroflexus sp. MS-G (95.7% 16S rRNA nt identity) genomes clustered in single bins containing sequences of both genomes, respectively. All other included Chloroflexi reference genomes (<94% 16S rRNA nt identity) clustered in separate but sometimes adjacent bins. Frontiers in Microbiology | www.frontiersin.org Metagenome Sequencing One full lane of Illumina HiSeq sequencing led to 176,741,874 quality-passed reads. 169,595,919 (96%) of these reads were assembled into a 232-Mb metagenome comprising 315,154 total contigs with a maximum scaffold length of 158 kb and a N/L50 value of 32,529/1.24 kb, which defines the number of fragments at or above the Length50 cutoff. There were 13,766 contigs >2.5 kb, 5,362 contigs >5 kb, and 1,665 >10 kb. Contigs >50 kb (n = 38) accounted for 1.14% of all assembled sequence data. Overview of phyla and Taxa Detected in the Mushroom Spring Undermat In the following paragraphs we will describe selected taxa from each phylum detected in the undermat community based on combined information of iTag and metagenomic sequence data. The phyla and members thereof are presented in the order of abundance, starting with the most abundant phylum and the Frontiers in Microbiology | www.frontiersin.org June 2016 | Volume 7 | Article 919 9 Composition of the Mushroom Spring Undermat Community Thiel et al. Thiel et al. FIGURE 5 | Continued FIGURE 5 | Continued FIGURE 5 | Continued June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 10 Composition of the Mushroom Spring Undermat Community Thiel et al. Thiel et al. FIGURE 5 | Phylogenetic tree based on 16S rRNA gene sequences showing the phylogenetic relationship between members of the phylum Chloroflexi (A) and Bacteroidetes-Chlorobi (B) phyla and sequences obtained from the Mushroom Spring microbial undermat community. The tree was generated based on the Maximum Likelihood method using the phyML software included in the ARB package. Percentage numbers on nodes refer to 100 bootstrap pseudoreplicates conducted. Only values >50% are shown. Bold sequences were obtained from Mushroom or Octopus Spring in this or previous studies. Red bold labels indicate sequences obtained in this study. Blue bold labels indicate “OS type” sequences from previous studies. OTU numbers shown refer to the most abundant OTU represented by the sequence. Only sequences with length >1,000 bp were used for phylogenetic calculations. Sequence length <1,000 bp are given FIGURE 5 | Phylogenetic tree based on 16S rRNA gene sequences showing the phylogenetic relationship between members of the phylum Chloroflexi (A) and Bacteroidetes-Chlorobi (B) phyla and sequences obtained from the Mushroom Spring microbial undermat community. The tree was generated based on the Maximum Likelihood method using the phyML software included in the ARB package. Percentage numbers on nodes refer to 100 bootstrap pseudoreplicates conducted. Only values >50% are shown. Bold sequences were obtained from Mushroom or Octopus Spring in this or previous studies. Red bold labels indicate sequences obtained in this study. Blue bold labels indicate “OS type” sequences from previous studies. OTU numbers shown refer to the most abundant OTU represented by the sequence. Only sequences with length >1,000 bp were used for phylogenetic calculations. Overview of phyla and Taxa Detected in the Mushroom Spring Undermat Sequence length <1,000 bp are given in (gray) in the labels and corresponding sequences were added using the Parsimony method without changing tree topology | Phylogenetic tree based on 16S rRNA gene sequences showing the phylogenetic relationship between members of th acteroidetes-Chlorobi (B) phyla and sequences obtained from the Mushroom Spring microbial undermat community. Th ed on 16S rRNA gene sequences showing the phylogenetic relationship between members of the phylum Chloroflexi ) phyla and sequences obtained from the Mushroom Spring microbial undermat community. The tree was generated ( ) ( ) p y q p g y g based on the Maximum Likelihood method using the phyML software included in the ARB package. Percentage numbers on nodes refer to 100 bootstrap pseudoreplicates conducted. Only values >50% are shown. Bold sequences were obtained from Mushroom or Octopus Spring in this or previous studies. Red bold labels indicate sequences obtained in this study. Blue bold labels indicate “OS type” sequences from previous studies. OTU numbers shown refer to the most abundant OTU represented by the sequence. Only sequences with length >1,000 bp were used for phylogenetic calculations. Sequence length <1,000 bp are given in (gray) in the labels and corresponding sequences were added using the Parsimony method without changing tree topology. June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 11 Composition of the Mushroom Spring Undermat Community Thiel et al. A 1,364-bp partial 16S rRNA sequence identified OTU- 6 as a member of the Chloroflexi, which is most closely related to uncultured members in streamer biofilm-producing communities in YNP hot springs (Table 3; Meyer-Dombard et al., 2011). It represents an uncultured chlorophototrophic Anaerolineae-like organism, which was also identified in the upper green layer of the Mushroom Spring microbial mat in a previous metagenomic analysis (Klatt et al., 2011). Despite the absence of a 16S rRNA gene, Bin-6 was identified to represent OTU-6 based on 93 ± 5.6% average nt identity to Cluster 6 from the upper layer metagenome (Klatt et al., 2011), which did contain a ribosomal RNA sequence with 98% identity to OTU- 6, as well as 99% sequence identity to a 16S rRNA sequence detected in the metagenome of this study. When first reported by Klatt et al. (2011), this uncultured organism was identified as “Anaerolineae-like,” with Anaerolinea thermophila strain UNI-1 being its closest cultivated and described relative (85% nt identity, Sekiguchi et al., 2003). Chloroflexi b f h Members of the phylum Chloroflexi were the most diverse group of organisms present in the microbial undermat community. Overall, 41 OTUs were affiliated with the phylum Chloroflexi (Table S1), and twelve Chloroflexi sequences were identified phylogenetically (Figure 5A). Five of the fifteen most abundant OTUs (>1,000 reads), as well as four abundant OTUs with ≥100 reads, were identified as members of the Chloroflexi (Table S1, Figure 5A). Based on the metagenomic information for these taxa, four out of five very abundant Chloroflexi are chlorophototrophic members of this phylum (OTUs-1, 6, 11, and 15; see Figure 5A), while one is a putative chemoheterotroph (OTU-9). Three additional abundant OTUs also are associated with putatively chemoheterotrophic members of this phylum (OTUs 23, 31, and 39). Thirty-two less abundant OTUs were also affiliated with the phylum Chloroflexi (Table S1, Figure 5A). Binning of the assembled metagenomic data yielded only a very small partial genome for Roseiflexus spp., the most abundant and most diverse OTU in the undermat (Bin- 1; Figures 2, 3, 5, Tables 1–3 and Table S1). Bin-1 did not contain any phylogenetic marker genes but was identified by high nucleotide sequence identities (92 ± 5%; range 79– 100%) to the Roseiflexus sp. RS-1 genome (CP000686, 5.8 Mb, van der Meer et al., 2010). The Roseiflexus sp. RS- 1 genome recruited 23,534 contigs from the metagenome (≥85% nt identity and ≥75 coverage), of which 13,329 contigs showed sequence identity of ≥95%. Only 12 of those contigs were >5 kb in length, sharing a minimum of 94.52% nt identity with the Roseiflexus sp. RS-1 genome sequence. Roseiflexus sp. RS-1 is a filamentous anoxygenic phototroph that synthesizes bacteriochlorophyll (BChl) a but not BChl c. It was previously isolated from Mushroom Spring and was affiliated with OS Type C sequences obtained in early molecular studies (Ward et al., 1990; Ferris et al., 1996b, 1997; Ferris and Ward, 1997). In addition to BChl a- containing photosynthetic reaction centers, the genome of this organism encodes xanthorhodopsin, which was also detected in the undermat metagenome (RoseRS_2966, GenBank Acc. no. ABQ91330.1; JGI24185J3567_10248071), and indicates a possible additional use of light energy (Choi et al., 2014). The small number of long contigs affiliated with this OTU, in combination with the broad coverage range from 31× to 1,557×, reflects a high microdiversity as well as the high abundance of the core genome sequences. Overview of phyla and Taxa Detected in the Mushroom Spring Undermat At the time of this writing [February 2016], a BLAST search identified Thermanaerothrix daxensis strain GNS-1T (Grégoire et al., 2011) and Thermomarinilinea lacunofontalis strain SW7 (Nunoura et al., 2013) as the closest isolated relatives with a 16S rRNA sequence identity value of 87% (Table 1). Phylogenetic analysis based on the full-length 16S rRNA sequences supports a phylogenetic affiliation to the Anaerolineales as well as a more distant relationship to known chlorophototrophic Chloroflexi (Figure 5A). Genes annotated within this metagenomic bin suggest that, like Roseiflexus spp., this anoxygenic chlorophototroph has the potential to produce BChl a but probably doesn’t contain BChl c or chlorosomes, although it does possess a putative xanthorhodopsin-like gene (Klatt et al., 2011). Thin short filaments possibly representing this Anaerolineae-like phototrophic Chloroflexi, tentatively named “Ca. Roseilinea gracile” (Tank et al., in press), have been observed in fresh mat samples and enrichment cultures. They exhibit BChl a but not BChl c autofluorescence. most abundant member, respectively. Taxonomic identification was always based on the longest 16S rRNA sequence available, in conjunction with phylogenetic marker genes. Information on additional taxa and phyla can be found in the phylogenetic trees and the Supplemental Materials (Figure 5, and Figure S1, Table S1). Phylogenetic analyses based on 16S rRNA sequences extracted from metagenomic data identified >50 members of 20 different phyla (Figure 5 and Figure S1), most of which could also be affiliated with iTag sequences obtained in the amplicon study. most abundant member, respectively. Taxonomic identification was always based on the longest 16S rRNA sequence available, in conjunction with phylogenetic marker genes. Information on additional taxa and phyla can be found in the phylogenetic trees and the Supplemental Materials (Figure 5, and Figure S1, Table S1). Phylogenetic analyses based on 16S rRNA sequences extracted from metagenomic data identified >50 members of 20 different phyla (Figure 5 and Figure S1), most of which could also be affiliated with iTag sequences obtained in the amplicon study. Frontiers in Microbiology | www.frontiersin.org Armatimonadetes (OP10) Uncultivated members of the Candidate phylum OP10, now named Armatimonadetes (Tamaki et al., 2011; Lee et al., 2013), were first detected in Obsidian Pool in YNP (Hugenholtz et al., 1998b). The undermat community at Mushroom Spring also contains a considerable diversity of members of this phylum. Two of the most highly abundant OTUs, OTUs 3, and 12, were identified as members of the Armatimonadetes. In addition, two abundant (OTUs 18 and 33) and nine less abundant iTag OTUs were identified as members of this phylum (Table S1). Partial genomes were identified for OTUs-3, 12, and 18 (Table 3, Figure S1). Thermomicrobium roseum, phylum Chloroflexi, which had previously been isolated from the mats (Jackson et al., 1973), was detected in the metagenome in this study and a previous 16S rRNA cloning study (Klatt et al., 2013a), but T. roseum was only present in low numbers based on the analysis of iTag amplicons (OTU-74, 44 reads, Table S1, Figure 5A). Despite the high abundance of Armatimonadetes member OTU-3 sequences in the amplicon study and the presence of a partial 16S rRNA sequence with high coverage (951×; JGI24185J35167_1062246), no corresponding bin was obtained in the undermat metagenome. Serendipitously, a highly similar organism (99% 16S rRNA sequence identity) was identified as a chemoheterotrophic contaminant in a cyanobacterial enrichment culture obtained from these mats in the Ward laboratory at Montana State University (unpublished data). A partial genome of this enrichment contaminant was obtained by binning the assembled contigs of the corresponding enrichment culture metagenome (Bin-3, Table 3). This enrichment partial genome recruited 17,252 sequences (a total of 11 Mb of sequence data) from the undermat metagenome displaying 90.5 ± 7.5% nt id (covering min. 80% of the metagenome scaffold). OTU-3 amplicon sequences were also detected in the upper green layer in lower numbers (4.5 vs. 0.8% relative abundance; Table S1) and a partial genome of this organism was also detected as an unidentified heterotroph Cluster 7 in the upper layer metagenome (Klatt et al., 2011). The partial genome of the upper layer displayed similar identity values of 90.3 ± 7.5% to the enrichment culture metagenome bin and 94.6 ± 5.3% to sequences in the undermat metagenome, and formed a single ESOM bin with the partial genome obtained from the enrichment culture (data not shown). Chloroflexi b f h OTU-09 is represented by Bin-9 and was also identified as being derived from a member of a cluster of uncultured Chloroflexi within the Anaerolineae (Figure 5A). However, based on the absence of photosynthesis-related genes in the corresponding metagenomic bin and the absence of unassigned photosynthesis-related genes in the remaining unbinned contigs, the organisms corresponding to OTU-09 are not predicted to be chlorophototrophs. A close relative of Chloroflexus sp. strain MS-G, a chlorophototrophic member of the Chloroflexi that was previously isolated from this mat (Thiel et al., 2014b), is represented by OTU-11 and Bin-11 in this study. Like strain MS-G, OTU-11 is predicted to be an anoxygenic phototroph containing type-2 (quinone-type) photosynthetic reaction centers, light-harvesting complex 1 and chlorosomes based on a metagenomic bin of 3.1 Mb, with an average read coverage of 30× (Bin-11, Table 3). The bin contained 21 phylogenetic marker genes, all of which share amino acid sequence identity values of 98.7 to 100% with sequences from Chloroflexus sp. MS-G (Table 3). The organism representing OTU-11/Bin-11 and strain MS-G share 98.3% 16S rRNA and 94 ± 6% overall genomic nucleotide sequence identity, respectively. June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 12 Composition of the Mushroom Spring Undermat Community Thiel et al. A third anoxygenic phototrophic Chloroflexi is represented by OTU-15 and Bin-15. Phylogenetic analysis and BLAST search results indicate this organism to be only distantly related to other chlorophototrophic Chloroflexus spp., displaying 90–91% 16S rRNA sequence identity to Oscillochloris trichoides, Chloroflexus aurantiacus J-10-fland “Candidatus Chloroploca asiatica.” The organism associated with these sequences presumably represents a novel genus of chlorophototrophic Chloroflexi within the family Chloroflexaceae (Figure 5A). Based on the conserved signature indels that are specific for different groups within the Chloroflexi as described by Gupta et al. (2013), this filamentous anoxygenic phototroph is affiliated with the proposed order of “green nonsulfur bacteria,” Chloroflexales, suborder Chloroflexineae, but is distinct from all known members of the genera Chloroflexus and Oscillochloris. The functional gene content of the associated metagenome bin (Bin-15) indicates that this organism has the capacity to synthesize BChls a and c. A filamentous BChl a- and BChl c-producing isolate similar to Oscillochloris sp. has been obtained in enrichment cultures, and tentatively named “Candidatus Chloranaerofilum corporosum” (Tank et al., in press). Chloroflexi b f h of the phylogenetic marker genes were uncertain with most of the sequences only being assigned to the kingdom (“bacteria”) and phylum level (“Bacteroidetes,” “Chlorobi,” “Deinococcus- Thermus,” “Chloroflexi,” or “Thermotogae,” respectively), which indicates a high degree of novelty for this uncultured organism. Sequences similar to the ones in this metagenomic bin have previously been detected in the oxic upper green layer of the mat community (Klatt et al., 2011). The sequences formed unidentified Cluster 8 in the previous study, which were associated with an uncultivated, putatively heterotrophic bacterium. Bin-10 and Cluster 8 sequences formed a single bin when included in the analysis. A BLASTn comparison revealed an average nucleotide identity of 97 ± 3% between sequences of the previous cluster and the sequences in the bin from this study. Armatimonadetes (OP10) OTU-3 was phylogenetically identified as belonging to the “OS-L clade” within the uncharacterized group 7 of the phylum Armatimonadetes (Lee et al., 2013) (Figure S1). Clade OS-L is named after the first sequence of this clade, OS Type L, obtained from a DGGE study of enrichment cultures from microbial mats in Octopus Spring (Ward et al., Thermotogae Only two OTUs, OTU-2, and OTU-107, were identified as members of the phylum Thermotogae by the RDP classifier (Table S1). OTU-2 represents the second most abundant species-level iTag sequence and the corresponding metagenomic 16S rRNA sequence is 99% identical to that of Pseudothermotoga hypogea, formerly known as Thermotoga hypogea (Fardeau et al., 1997; Bhandari and Gupta, 2014). Bin-2 sequences, which represent this Pseudothermotoga sp. OTU-2 mat member (Table 3), show high similarities (98–100% aa sequence identities) to sequences obtained from a previous metagenomic study by Klatt et al. (2013a; IMG/M OID 2015219002), and form a single cluster with the genome sequence of Pseudothermotoga hypogea DSM 11164 in the metagenome binning analysis, which indicates the high similarity of these two genomes. OTU-107 shares 99% nt sequence identity to Fervidobacterium pennivorans strain DSM 9078 as well as to Fervidobacterium sp. isolated from YNP (Sullivan et al., unpublished, AY151268) but is represented by only 20 reads (Table S1, Figure S1). In addition, several sequences were affiliated with group EM3, which has tentatively been placed in the Thermotogae (Reysenbach et al., 2000) (Table S1, Figure S1). OTU-10 was misidentified as a member of the Chlorobi by RDP classifier, but actually represents the most abundant EM3 population and shares highest similarities with hot spring clones OPB88 (AF027006, Hugenholtz et al., 1998b) and OPS2 (AF018187, Graber et al., unpublished) from YNP with 99 and 98% 16S rRNA nt identity, respectively. Bin-10 representing this OTU was identified based on the presence of a matching 16S rRNA gene (Table 3). Phylogenetic affiliations June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 13 Composition of the Mushroom Spring Undermat Community Thiel et al. of the total iTag sequences) were assigned to cyanobacteria (Table S1). At the temperature sampled in this study (60◦C), members of Synechococcus sp. Type B’ (OS Type B’, Table 4) are the predominant organisms (Klatt et al., 2011; Liu et al., 2011) and were also detected in this study (OTU-5, Bin-5, Table 3). Synechococcus sp. A (OS Type A, Table 4) sequences were detected in lower abundance (OTU-22, Table S1). The small size of Bin-5 (Table 3) reflects a low number of long and well- assembled contigs (68 contigs, 5,005–12,792 bp; 18× to 96× coverage) in comparison to a total of 3,353 contigs identified as having their origins in members of the Cyanobacteria in the metagenome (440 to 12,792 bp). Nitrospirae iTag analysis identified seven Nitrospirae OTUs in the undermat community, of which only one, OTU-8, was abundant (Table S1). Bin-8 was assigned to this Thermodesulfovibrio sp.-like mat member based on presence of the corresponding 16S rRNA sequence (Figure 4, Table 3). OTU-8 represented ∼2.0% (3,283 reads) of all iTag sequences (Table 1), and the full 16S rRNA sequence was most closely related to a clone sequence obtained from geothermal groundwater (99%, clone: SMD-B01, NCBI acc. no. AB477993, Kimura et al., 2010) and to Thermodesulfovibrio yellowstonii strain DSM 11347, as the closest isolated relative (96%, NCBI acc. no. CP001147, Henry et al., 1994; Bhatnagar Atribacteria (OP-9/JS1) ( ) The phylum Atribacteria, formerly known as Candidate phylum OP-9/JS1, exhibited low diversity. Of two OTUs identified as belonging to members of this phylum, only OTU-7 was detected in significant numbers in the iTag analysis (Table S1, Figure S1). OTU-7 represented 2.4% of all iTag reads and was represented by only a single abundant dereplicated iTag sequence (Table 1). Bin-7 contained a partial genome of this uncultured bacterium, as identified by the full-length 16S rRNA sequence which shared 99% and 98% sequence identity to Atribacteria clones OPB72 and TP29 obtained from hot springs in YNP and Tibet, respectively (Hugenholtz et al., 1998b; Lau et al., 2009). The affiliated metagenomic bin indicates an anaerobic, fermentative lifestyle for this member of the Atribacteria (data not shown), which is similar to properties deduced from single-cell genome sequences previously obtained from members of the Atribacteria (Dodsworth et al., 2013; Nobu et al., 2016). Aquificae f f Of four OTUs identified as belonging to members of the Aquificae (Table S1), only OTU-4 was detected in significant numbers (Table S1). The corresponding 1,434-bp rRNA metagenomic sequence is 99% nt identical to clone sequences previously obtained from YNP hot spring habitats (Thermocrinis sp. clone YNP_SBC_BP2A_B2, HM448202, Meyer-Dombard et al., 2011), as well as to the YNP isolate Thermocrinis sp. P2L2B (AJ320219, Eder and Huber, 2002). The closest described relative is Thermocrinis ruber DSM 23557, which was isolated from Octopus Spring and which has a 16S rRNA sequence that shares 97% nt identity to the one found in this study (Huber et al., 1998) (Figure S1). Correlating to the high microdiversity detected for this OTU (Table 1), only a small partial genome was identified in the binning analysis of the metagenome (Bin-4, Table 3). The presence of at least two closely related populations in the undermat community is indicated by two highly similar (96% amino acid identity), Thermocrinis-like soxB genes; these genes are located on three individual scaffolds in the metagenome, each [gene-1, ∼270× coverage: JGI24185J35167_10446912, JGI24185J35167_104385 21, JGI24185J35167_10819822; gene-2, ∼70× coverage: JGI24 185J35167_10446972, JGI24185J35167_10438611, JGI24185J35 167_10820392], which also suggests problems with sequence assembly that could be related to microdiversity. Thermotogae Local BLASTn analysis and reference guided assembly using the genome sequence of Synechococcus sp. Type B’ as query (applying a 95% nt identity threshold) identified 4,898 contigs as belonging to these organisms. The low assembly quality is indicative of high microdiversity as indicated by the presence of seven abundant iTag sequences (Table 1). Recent studies have found that a high number of ecotype populations occur within this cyanobacterial population, displaying variations in gene content and sequence as well as differences in gene arrangement (Becraft et al., 2011; Olsen et al., 2015). Genome sequences of several ecotypes isolated from the dominant cyanobacteria from Mushroom Spring are now available, and these provide comprehensive insights into the physiological and metabolic capacities of the oxygenic chlorophototrophs in the mat (Bhaya et al., 2007; Nowack et al., 2015; Olsen et al., 2015). 1992), with which the 16S rRNA genes in both Bin-3 from the enrichment culture and the undermat metagenome share 98% nt identity (L04707). So far, no isolated representative has been reported for this phylogenetic group. The presence of all 31 bacterial phylogenetic marker genes in the bin suggests that it contains a nearly complete genome (Table 3). Genes encoded in the partial genome, in combination with its occurrence in an enrichment with oxygenic cyanobacteria, indicates that this organism probably exhibits an aerobic or microaerobic lifestyle, similar to the other isolated members of the Armatimonadetes (Lee et al., 2011; Tamaki et al., 2011; Im et al., 2012). A considerable microdiversity was suggested by the presence of nine abundant iTag sequences (Table 1) as well as the diversity of partial, flagellum-associated genes affiliated with this organism, which were present on short contigs in the metagenome. Additionally, thirteen closely related 16S rRNA sequences were derived from a previous undermat 16S rRNA cloning study (Klatt et al., 2013a). These sequences show high identity values (>97%) to the OTU-3 sequence as well as to each other (assembly based on 97% nt sequence identity, Figure S1A) and also reflect a high microdiversity of these organisms. Similar to the situation found for Roseiflexus spp. (see above), the high microdiversity suggested for this taxon probably caused assembly difficulties, which may explain why no metagenomic bin was recovered directly from the undermat metagenome. Acidobacteria h Thirteen OTUs representing four different members of the Acidobacteria were identified in the Mushroom Spring undermat community, and two of them were abundant with >100 reads (Table S1). OTU-17 was a member of group 4 of the Acidobacteria and was identified as Cab. aerophilum (Tank and Bryant, 2015a,b). Bin-16 (Table 3) contained a partial genome for this unique microaerophilic, chlorophototrophic member of the phylum Acidobacteria, which was first identified in the phototrophic mats of Mushroom and Octopus Spring and corresponds to the OS Type D sequences from earlier studies (Ward et al., 1990, 1992; Bryant et al., 2007; Tank and Bryant, 2015a,b). Planctomycetes Five abundant iTag OTUs were identified as belonging to members of the phylum Planctomycetes (Table S1), the very abundant OTU-14 (1,260 reads), as well as four less abundant OTUs (OTUs-16, 19, 49, and 51, Table S1). Twelve additional Planctomycetes sequences were found in very low abundance (Table S1). The fourth member of the phylum Acidobacteria corresponded to a less abundant OTU (OTU-61, 70 reads = 0.1%) and was represented by two partial 16S rRNA sequences in the metagenome. These sequences and the represented uncultured organisms were affiliated with OS Type K sequences from previous studies (Table 4, Ward et al., 1992; Weller et al., 1992). Bin-14 contained a partial genome for Planctomycetes member OTU-14 and was identified based on the corresponding full-length 16S rRNA sequence as well as nineteen phylogenetic marker genes (Table 3, Figure S1). An uncultured hot spring- associated bacterium from a neutral 61◦C geothermal hot- spring mat in Tibet, clone TP5, was identified as closest relative (EF205581, 99%, Lau et al., 2009). The microaerophilic, facultatively anaerobic, thermophilic Planctomycetes strain, Thermogutta terrifontis strain R1T (KC867694, Slobodkina et al., 2014), with 90% sequence identity, is the most closely related isolated relative (Table 1). Based on the number of phylogenetic Cyanobacteria The two major photoautotrophic primary producers of the upper green layer, Synechococcus spp. Type A and Type B’, were also abundant members of the undermat by iTag analysis (OTUs 5 and 22, Table 1, Table S1). Seventeen additional but less abundant iTag OTUs (each ≤25 reads, representing <0.05% June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 14 Composition of the Mushroom Spring Undermat Community Thiel et al. et al., 2015). Bin-8 contained scaffolds with coverage values ranging from 29 to 135, which possibly reflects two different populations with different abundances. This was also suggested by the different read numbers of two abundant, dereplicated iTag sequences (OTU-8, iTag-10, 1,721 reads; and iTag-28, 602 reads; Table S1). The partial genome suggests sulfate-reducing metabolism for this organism, similar to T. yellowstoneii, which was isolated from thermal vent water in Yellowstone Lake, Wyoming, USA (Henry et al., 1994; Bhatnagar et al., 2015). The dsrAB gene sequences associated with dissimilatory sulfate- reduction of this uncultured organism have previously been detected in the Mushroom Spring microbial mat, and the corresponding Thermodesulfovibrio-like organism was associated with the sulfate reduction activity measured in the mat (Dillon et al., 2007). OTU-8 has been detected in both the upper and lower parts of the mat (Table 5, Table S1), possibly indicating that these organisms are not restricted to the undermat; this is further supported by the finding of Thermodesulfovibrio-like sequences also in the green upper layer metagenome in a previous study (Klatt et al., 2011). marker genes present in the metagenome bin, and because of the large sizes of available Planctomycetes genomes (3.8–9.7 Mb for those in JGI/IMG as of December 2015), we expect the 1.87-Mb bin to represent no more than 60% of the genome. The presence of the iTag sequences for this OTU almost exclusively in the undermat sample (a single read was found in iTag analysis of upper green layer; Table 5, Table S1) suggests that this organism lives exclusively in the orange-colored undermat and possibly in its deeper regions below 3 mm, where mainly anoxic conditions occur and persist (Nübel et al., 2002; Jensen et al., 2011). Bin-23 was also identified as derived from a member of the Planctomycetes, but could not be directly affiliated with any iTag sequence(s) due to absence of an rRNA sequence in the bin (Table 3). Aminicenantes (OP8) The Aminicenantes (Candidate phylum OP8) was represented by only a single taxon, OTU-13, and its corresponding metagenomic Bin-13, which contains a 1,497-bp 16S rRNA gene sequence (Table 1, Table S1). Notably, OTU-13 amplicon sequences were found exclusively in the undermat community (Table S1). Although the iTag sequence shared 99% nt identity to the uncultured Aminicenantes bacterium clone OPB95 obtained from a Yellowstone hot spring (AF027060, Hugenholtz et al., 1998b), the full-length sequence showed only 95% nt identity to that sequence. No isolated bacterium shares more than 88% nt identity with this uncultured organism. 16S rRNA gene sequence surveys indicated that members of the Aminicenantes are ubiquitously present in many different habitats and across many environmental parameters (temperature, salinity, and oxygen tension) (Farag et al., 2014). They usually represent only a small fraction (<1%) of microbial communities, but have been found to be more abundant in anoxic environments (Farag et al., 2014). OTU-36, as well as the less abundant OTU-72, were members of Acidobacteria group 3 and were identified as Solibacter-like organisms. Bin-20 was associated with OTU-36 by the presence of a 16S rRNA-containing scaffold as well as by the presence of six phylogenetic marker genes (Table 3). All six phylogenetic marker genes indicated an affiliation with the Acidobacteria and four of them specifically with the candidate species, “Ca. Solibacter usitatus” (Challacombe et al., 2011). Phylogenetic analysis supported the affiliation and placed the sequence in subgroup 3 of the Acidobacteria, closely related to Yellowstone clone OPB3 (98%, AF027004, Hugenholtz et al., 1998b) and “Ca. Solibacter usitatus” Ellin6076 as the closest named relative (Table 1, Figure S1). The low number of phylogenetic marker genes indicates that this member of the Acidobacteria has a large genome, only a part of which is included in the metagenomic bin. This correlates well with the fact that “Ca. Solibacter usitatus” Ellin6076 has an exceptionally large, 9.97-Mb genome (Challacombe et al., 2011). Frontiers in Microbiology | www.frontiersin.org Proteobacteria Sequences for 16S rRNAs of two Alpha-, two Beta- and one Delta-Proteobacteria were found in the metagenome (Figure S1C). The abundant deltaproteobacterial sequence (OTU-44) was closely affiliated to a sequence obtained in a previous metagenome study (Figure S1C, Klatt et al., 2013a). Although the Deltaproteobacteria are commonly known to include members with sulfate-reducing metabolism, and sulfate-reduction has been shown in the microbial mat at Mushroom Spring (Dillon et al., 2007), deltaproteobacterial dsrAB genes were not identified in this nor any previous study. No metagenomic bin was affiliated with a Deltaproteobacterium. Brevinema-like member of the Spriochaeta (OTU-35), two of which were Deltaproteobacteria (OTUs-40 and 44), and one of which was an Alphaproteobacterium (OTU-46). Twenty- nine additional, low-abundance OTUs were affiliated with Proteobacteria by RDP classifier (Table S1). Sequences for 16S rRNAs of two Alpha-, two Beta- and one Delta-Proteobacteria were found in the metagenome (Figure S1C). The abundant deltaproteobacterial sequence (OTU-44) was closely affiliated to a sequence obtained in a previous metagenome study (Figure S1C, Klatt et al., 2013a). Although the Deltaproteobacteria are commonly known to include members with sulfate-reducing metabolism, and sulfate-reduction has been shown in the microbial mat at Mushroom Spring (Dillon et al., 2007), deltaproteobacterial dsrAB genes were not identified in this nor any previous study. No metagenomic bin was affiliated with a Deltaproteobacterium. The abundant Alphaproteobacterium (OTU-46) was identified as an Elioraea sp. within the Rhodospirilliales, which corresponds to OS Type O obtained in previous studies (Figure S1C, Table 4, Ward et al., 1992). The corresponding partial genome (Bin-22, Figure 4, Table 3) as well as the genome for the closest relative, Elioraea tepidiphila DSM 17972 (NCBI acc. no. NZ_KB899965.1), contain genes for anoxygenic photosynthesis. Although chlorophototrophy has not been described for Elioraea tepidiphila (Albuquerque et al., 2008), the ability to synthesize BChl a is predicted for the OTU-46 population in the undermat community. A BChl a containing strain, “Candidatus Elioraea thermophilum,” was isolated from the mat, which shares 99.8% and 99.2% sequence identity with the 16S rRNA sequences from the metagenome and amplicon study, respectively (Figure S1C, Tank et al., in press). A low abundance Alphaproteobacterium sequence (OTU-121, 16 reads) was identified as belonging to a Roseomonas/Rhodovarius-like organism, for which an isolate has been obtained from Mushroom Spring and which has tentatively been named “Candidatus Roseovibrio tepidum” (Figure S1C, Tank et al., in press). Proteobacteria The isolate exhibits BChl a autofluorescence suggesting a phototrophic lifestyle, which is further strengthened by the presence of low coverage, unidentified alphaproteobacterial pufLM sequences in the metagenome (scaffold JGI24185J35167_1024732, genes 2 and 3, 20× coverage). Only a single described Roseomonas sp., R. aestuarii, has been reported to produce BChl a, but no pufLM sequences are available for that isolate (Venkata Ramana et al., 2010). Furthermore, two low-abundance OTUs (OTUs-101 and 154) showed the same phylogenetic affiliation (Hydrogenophilius sp., Betaproteobacteria) as OS type G from previous studies (Ward et al., 1990, 1992). The OS Type R sequence (NCBI acc. no. U46750, unpublished) represented an unidentified Betaproteobacterium and a similar, low- abundance iTag sequence (OTU-172) was detected in this study (Table 4, Figure S1C). Bin-24 (Table 3) does not contain a 16S rRNA sequence, but was affiliated with a putative member of the Bacteroidetes- Chlorobi group based on phylogenetic marker genes. It is most closely related to heterotrophic members of the Chlorobi, in the family Ignavibacteriaceae (Liu et al., 2012; Kadnikov et al., 2013) and is presumably affiliated with OTUs-34 or 45 in the Chlorobi Lineage 5/group SM1H02 (Figure 5B). All genes needed for dissimilatory sulfate reduction are present in the partial genome and indicate that this organism is putatively the first sulfate-reducing member of the Bacteroidetes-Chlorobi group. These results will be described in detail elsewhere (Thiel et al., in preparation). The OS Type M sequences obtained in previous studies (Ward et al., 1992) are affiliated with OTU-34 as well as with two partial 16S rRNA sequences from the metagenome (Table 4) within the SM1H02 (Chlorobi Lineage 2) group. Only low abundance OTUs were affiliated with the Bacteroidetes (Table S1). Many of them were closely related to clone sequences obtained in a previous undermat study, and some also represented partial 16S rRNA sequences from the metagenome (Figure 5B, Klatt et al., 2013a). Schleiferia thermophila, a strain of which has been isolated from Octopus Spring microbial mats (Thiel et al., 2014a), was not detected in this study. Proteobacteria Four abundant OTUs were affiliated with the phylum Proteobacteria by the RDP classifier, one of which was misidentified as Proteobacteria and rather represents a June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 15 Composition of the Mushroom Spring Undermat Community Thiel et al. Chlorobi were abundant with read numbers >100, and one was very abundant with >1,000 reads (Table S1). However, the most abundant “Chlorobi” sequence (OTU-10) was mis-classified and represents an Thermotogae/EM3 group member (see above, Table 1, Figure 5B). The other abundant Chlorobi sequences were affiliated with the proposed family Thermochlorobacteriaceae (OTU-38) (Liu et al., 2012), “Chlorobi lineage 5” = “OPB56 group” (OTUs 24, 27, and 29) (Iino et al., 2010; Hiras et al., 2015) and “Chlorobi lineage 2” = “SM1H02 group” (OTUs 34 and 45) (Iino et al., 2010; http://www.arb-silva. de/browser/ssu-121/AY555793, named after clone SM1H02, Genbank acc. no. AF445702). Bin-19 (Table 3) was identified as a partial genome representing OTU-24, a representative of OPB56, a subgroup of the Chlorobi with predicted chemoheterotrophic lifestyle that was first detected in YNP (Hugenholtz et al., 1998b; Hiras et al., 2015, Table 3). A low abundance OTU in the OPB56, OTU-262, was identified as a probable representative of the OS Type F sequences from previous studies (Table 4, Ward et al., 1990, 1992). The first aerobic, phototrophic member of the Chlorobi, “Ca. Tcb. aerophilum,” which belongs to the proposed family Thermochlorobacteriaceae and was identified in the upper green layer of the microbial mat by previous metagenomic analyses (Liu et al., 2012), is represented by OTU-38 (Table 1), and was identified as OS Type E in previous studies (Ward et al., 1990, 1992; Ferris et al., 1996b). Bin-21 is derived from this novel phototroph (Table 3) and supports its characterization as a chlorophototroph that synthesizes type-1 reaction centers and chlorosomes, similar to cultivated relatives among the green sulfur bacteria, but which is otherwise very different physiologically. “Ca. Tcb. aerophilum” is proposed to be an aerobic photoheterotroph that cannot oxidize sulfur compounds, cannot fix N2, and does not fix CO2 (Liu et al., 2012). Brevinema-like member of the Spriochaeta (OTU-35), two of which were Deltaproteobacteria (OTUs-40 and 44), and one of which was an Alphaproteobacterium (OTU-46). Twenty- nine additional, low-abundance OTUs were affiliated with Proteobacteria by RDP classifier (Table S1). Archaea l h h Although methanogenesis has been demonstrated in several mats of alkaline siliceous hot springs, including Mushroom Spring (Ward, 1978; Sandbeck and Ward, 1982), and methane has been shown to accumulate in the water above the Mushroom Spring mat in darkness (Kim et al., 2015), iTag sequencing only identified a few partial 16S rRNA sequences as potentially derived from methanogenic Archaea (OTUs-143, 151, 162, 192, and 244; ≤11 reads = ≤0.01%, Table S1). Phylogenetic analysis confirmed affiliation to the Euryarchaeota for four of them (OTUs-143, 151, 162, and 192, Figure S1A) and three of the sequences were detected in a cloning experiment from a previous study (Klatt et al., 2013a); thus, methanogenic archaea seem to be present in the mat over time, although in very low abundance. One OTU, OTU-151 with 10 reads but no representative sequence in the metagenome, shows high similarity (99% nt id) with the 16S rRNA sequence of the methanogenic archaeon Methanothermobacter thermoautotrophicus, strains of which have been isolated from these mats previously (former Methanobacter thermoautotrophicum; Sandbeck and Ward, 1982). Further, a single, low coverage mcrA gene encoding a methyl-coenzyme M reductase alpha subunit was present in the metagenome (JGI24185J35167_11200021, 7× coverage) possibly indicating methanogenic metabolism in at least one of the archaeal mat members. Two slightly more abundant 16S rRNA sequences affiliated with ammonia-oxidizing Archaea were detected (Table S1). One (OTU-60, 72 reads) was related to “Candidatus Nitrosocaldus yellowstonii,” which was also identified in an enrichment culture from Octopus Spring mat in previous studies (De La Torre et al., 2008). The other, OTU-67 represents a member of a putatively novel archaeal phylum/division, related to “Candidatus Caldiarchaeum subterranum” (Nunoura et al., 2011). Another less abundant Firmicutes Although Anoxybacillus spp. are common members of cyanobacterial enrichment cultures from these environments (e.g., Nowack, 2014; Olsen et al., 2015; Tank and Bryant, 2015b), no evidence for this organism was found in the metagenome nor the iTag analysis. Twenty-four OTUs were classified as belonging to members of the Firmicutes, of which two (OTUs-251 and 255) were predicted to be Bacillus sp.; however, they shared highest sequence similarity to the type strains of Syntrophothermus lipocalidus and Acetomicrobium faecale (both clostridia). None of the 16S rRNA genes retrieved from the metagenome could be affiliated with the Firmicutes. In addition, none of the metagenomic scaffolds were affiliated with Anoxybacillus spp. No sequence from an Anoxybacillus sp. was identified by BLASTn analysis of the metagenome using the partial genome sequence obtained from the Anoxybacillus sp. MT isolated from an enrichment culture from Octopus Spring (Thiel et al. in prep), nor the “phylogenetic distribution of genes by BLAST percent identities” tool implemented in the JGI/IMG website. Deinococcus-Thermus/Thermi Deinococcus-Thermus/Thermi Of two different members of the phylum Thermi identified in this study, only Meiothermus sp. was abundant in the undermat community (OTU-21, 656 reads), whereas sequences of Thermus spp. were only present in low numbers in the iTag study (Table S1, Figure S1C). Members of both genera have been isolated from these mat communities (Brock and Freeze, 1969; Ward et al., 1997; Thiel et al., 2015). OTU-21 was identified as a relative of Meiothermus ruber, a member of which, strain A, has previously been isolated from an enrichment culture originally obtained from the microbial mats at Octopus Spring and whose genome has been sequenced (Thiel et al., 2015). Tetranucleotide frequency-based binning of contigs >10 kb led to a 1.3-Mb partial genome (Bin-18, Table 3) for this moderately thermophilic, aerobic, and heterotrophic bacterium. The Meiothermus sp. 16S rRNA sequences obtained from the metagenome share 96.7% nt sequence identity with M. ruber strains A and DSM1279T. Sequences of Bin-18 shared 84.5% (±4.5%) with the M. ruber strain A genome and 84.2% (±4.5%) with M. ruber DSM1279T. Although the (partial) genome sequences of the isolate and the metagenome bin clusters overlap, some separation was visible when the sequences of both organisms were included in the binning analyses (data not shown). Bacteroidetes-Chlorobi The RDP classifier identified twenty and eight different OTU sequences belonging to members of the phyla Chlorobi and Bacteroidetes, respectively. Seven OTUs affiliated with the June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 16 Composition of the Mushroom Spring Undermat Community Thiel et al. iTag sequence, similar to that of an archaeal 16S rRNA sequence recovered from the undermat metagenome previously (Klatt et al., 2013a), was also detected in the iTag analysis (OTU-125, 15 reads), but not in the metagenome of this study (Figure S1A). None of the metagenomic bins could be identified as belonging to Archaea, and only a few contigs with low coverage values, showed high identities to known archaeal sequences. Thus, our metagenomic and 16S rRNA gene amplicon studies indicate a very low abundance of Archaea, of which sequences related to ammonia-oxidizing Archaea seem to be more abundant than possible methanogenic Archaea. The low abundance of archaeal sequences is consistent with the low relative abundance of archaeal lipids in previous studies, which had been discussed to be related to the energy flows through the trophic structure of the community (Ward et al., 1989). Frontiers in Microbiology | www.frontiersin.org DISCUSSION In this study we analyzed the orange undermat of the microbial mat community at 60◦C in Mushroom Spring YNP by 16S rRNA gene amplicon and metagenomic sequencing. Only eight major organismal populations were identified in the upper green layer by genomic, metagenomic and metatranscriptomic analysis (Klatt et al., 2011; Liu et al., 2011). A higher diversity had been speculated to occur in the undermat community (Klatt et al., 2013a). In this study the undermat was found to be a highly diverse but uneven bacterial community, which could be related to the trophic structure associated with mat-decomposing organisms, as hypothesized to explain the variable abundances of lipid biomarkers (Ward et al., 1989) and 16S rRNA sequences (Ward et al., 1998). Out of 317 OTUs, the 15 most abundant ones represent 87% of all iTag sequences, and the single most abundant OTU comprises nearly half of all iTag reads. More than 44 abundant taxa, as defined by read numbers of >100 in the iTag analysis, were detected in the orange-colored undermat at Mushroom Spring. The phylum Chloroflexi displayed the highest diversity with nine abundant and 41 total taxon-specific 16S June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 17 Composition of the Mushroom Spring Undermat Community Thiel et al. by the relative number of 16S rRNA gene amplicon reads between the upper layer and undermat samples. For example, Pseudothermotoga spp. OTU-2, Armatimonadetes member OTU- 3, Thermocrinis spp. OTU-4, Chloroflexi members OTU-6, 9, and 15, as well as the Atribacteria member OTU-7, the Aminicenantes member OTU-13, and Planctomycetes member OTU-14, are found in much higher relative abundance in the undermat (Table 5, Table S1). Future transcriptomic studies will assess which of the detected populations correspond to the highest transcriptional activities based on gene expression. The presence of aerobic, microaerobic and anaerobic organisms detected in this study indicate a possible layered distribution along the steep and fluctuating oxygen gradient and shows that some oxygen is available during the day below a depth of 2 mm in the microbial mat, as previously suggested by microelectrode measurements (Revsbech and Ward, 1984; Nübel et al., 2002; Jensen et al., 2011). Whereas aerobic bacteria and facultative anaerobes are expected to live in the transition zone adjacent to the upper green layer, abundant anaerobic members of the undermat community, e.g., Pseudothermotoga sp. DISCUSSION Studies with more rapidly evolving protein-encoding loci led to the prediction of numerous ecotypes with identical or nearly identical 16S rRNA sequences (Ferris et al., 2003; Becraft et al., 2011, 2015; Melendrez et al., 2011). The existence of temperature- and light-adapted Synechococcus ecotypes has been demonstrated by obtaining representative strains and studying their temperature and light preferences as well as their genomes, (Allewalt et al., 2006; Nowack et al., 2015; Olsen et al., 2015). A similar microdiversity and existence of putative ecotypes is suggested by this study for members of the undermat community, and in particular for Roseiflexus spp., the most dominant member in the undermat. The presence of unique 16S rRNA genotypes in the undermat (this study) and at different temperatures (Ferris and Ward, 1997), supports this inference. In addition to the high diversity of OTUs within the phylum Chloroflexi, a high microdiversity was found for Roseiflexus spp. by the presence of 24 abundant and a total of 6,193 dereplicated Roseiflexus sp. iTag sequences, which is further supported by a preliminary analysis of pufLM amplicon sequence data (J. Wood and D. Ward, unpublished data). The microbial mat as a living and active biological system has been shown to be constantly growing (Doemel and Brock, 1977). In this study we observed phototrophic taxa known from the upper layer in the undermat. Analyses of psaA sequences sampled in this metagenomic study suggest that the Synechococcus populations observed match species found in the upper mat and thus likely occur in the undermat as a consequence of burial. In contrast, similar analyses of pufLM sequences as well as oligotyping suggest that Roseiflexus populations in the undermat are a mixture of those found in the upper green mat layers and those uniquely found in the undermat (Table 5, Figure S2, Wood et al., unpublished). The detection of identical dereplicated iTag and oligotype sequences in both layers might indicate burial. However, the detection of oligotypes and dereplicated iTag sequences with higher relative abundance in the undermat strongly suggests the existence of putative ecotypes specifically adapted to niches in the undermat. Further it is important to note that specifically adapted ecotypes can be so closely related that they have the identical 16S rRNA gene sequence, and can only be detected using more rapidly evolving genes (Becraft et al., 2011, 2015). DISCUSSION OTU-2 and Atribacteria member OTU-7 can be expected to be active members mainly in the community below a depth of 3 mm, where anoxic conditions are expected to persist throughout the day (Nübel et al., 2002; Becraft et al., 2011; Jensen et al., 2011). Despite the anaerobic lifestyle of sulfate reduction, Thermodesulfovibrio sp. OTU-8 was detected in higher abundance in the upper layer, which might indicate some degree of oxygen tolerance and diel activity patterns, i.e., primary sulfate-reducing activity under anoxic conditions in the afternoon or at night as measured by Dillon et al. (2007). An Aminicenantes (OP8) member (OTU-13), a Planctomycetes member (OTU-14) and an Oscillochloris-like chlorophototrophic member of the Chloroflexi, “Ca. Chloranaerofilum corporosum” (OTU-15) (Tank et al., in press) were exclusively detected in the undermat by iTag analysis, which suggests that they have an anaerobic lifestyle in the deeper layers of the undermat. However, “Ca. Chloranaerofilum corporosum” is expected to be a phototroph, and only a limited amount of light reaches deep into the undermat. Thus, a layered structure of the microbial community, as has been demonstrated in the upper green layer (Ramsing et al., 2000; Becraft et al., 2011), can only be hypothesized for the undermat at this time. Further studies are needed to determine the distribution of the members of the undermat community. rRNA sequences (OTUs) found. All of the taxa found in the upper mat by Klatt et al. (2011) were also identified in the undermat. rRNA sequences (OTUs) found. All of the taxa found in the upper mat by Klatt et al. (2011) were also identified in the undermat. y ( ) In this study we analyzed the composition and diversity of the microbial community based on 16S rRNA gene sequences, which cannot easily be translated into species populations. However, relatively high 16S rRNA sequence diversity was found in this study, not only on the OTU level but particularly within the dereplicated iTags, which suggests that this microbial mat community is not simple. Previous observations that closely related cyanobacterial 16S rRNA sequences were differently distributed along environmental gradients (Ferris and Ward, 1997; Ramsing et al., 2000) prompted consideration of the Stable Ecotype Model of species and speciation (Cohan and Perry, 2007), which postulates that some microorganisms exist as ecological species occupying distinct niches (Ward, 1998; Ward and Cohan, 2005). Frontiers in Microbiology | www.frontiersin.org DISCUSSION For other organisms, a greater relative abundance, or exclusive presence in the lower part of the mat, is indicated y All seven chlorophototrophs identified in previous genomic and metagenomic studies of the upper green layer were also present in the undermat metagenome (Table 5; Klatt et al., 2011; Liu et al., 2011). Roseiflexus spp. and “Candidatus Roseilinea gracile” showed higher relative abundance in the undermat, whereas the other phototrophs are present in lower relative abundance in comparison to the upper green layer of the mat (Table 5, Table S1). Three additional phototrophic bacteria were detected in the microbial mat for the first time in this study (“Candiatus Chloranaerofilum corporosum” OTU-15, as well as two phototrophic Alphaproteobacteria, “Candidatus Elioraea thermophila” OTU-46, and “Candidatus Roseovibrio tepidum” OTU-121; Tank et al., in press). A total of sixteen phototrophic bacterial taxa representing six different phyla have now been June 2016 | Volume 7 | Article 919 18 Composition of the Mushroom Spring Undermat Community Thiel et al. TABLE 5 | Overview of community composition detected by the different methods used in this study (iTag, metagenome 16S rRNA, metagenome binni and relative abundances in undermat and upper layer iTag sequencing study. iTag OTU Identity Undermat metagenome 16S rRNA Undermat metagenomic bin iTag MS undermat (%) iTag MS upper green layer (%) Upper green la metagenomic b OTU-01 Chloroflexi, Roseiflexus sp., OS Type C Yes, scaffold 166812 Yes, bin-1 [very small] 49.1 33.9 Yes OTU-02 Thermotogae, Pseudothermotoga sp. Yes, scaffold 336 Yes, bin-2 10.4 1.5 No OTU-03 OP10/Armatimonadetes_Gp7, OS Type L Yes, scaffold 622461 No [enrichment bin-3] 4.5 0.8 Yes OTU-04 Aquificae, Thermocrinis sp. Yes, scaffold 2657 Yes, bin-4 4.4 0.3 No OTU-05 Cyanobacteria, Synechococcus sp. B’, OS Type B Yes, scaffold 8881 Yes, bin-5 3.6 37.4 Yes OTU-06 Chloroflexi, Anaerolineae-like’ phototroph Yes, scaffold 1696 Yes, bin-6 2.6 1.2 Yes OTU-07 OP9/Atribacteria Yes, scaffold 14288 Yes, bin-7 2.4 0.7 No OTU-08 Nitrospirae, Thermodesulfovibrio sp. Yes, scaffold 00748 Yes, bin-8 2.4 2.7 (Yesb) OTU-09 Chloroflexi, Anerolineae Yes, scaffold 273 Yes, bin-9 1.4 0.7 No OTU-10 Thermotogae, EM3/OPS-2 Yes, scaffold 1962 Yes, bin-10 1.2 3.1 Yes OTU-11 Chloroflexus sp. DISCUSSION MS-G Yes, scaffold 301461 Yes, bin-11 1.1 1.2 Yes OTU-12 OP10/Armatimonadetes_Gp6 Yes, scaffold 3586 Yes, bin-12 1.1 0.5 No OTU-13 OP-8/Aminicenantes Yes, scaffold 32931 Yes, bin-13 1.0 0.0 No OTU-14 Planctomycetes Yes, scaffold 3293 Yes, bin-14 0.9 0.0 No OTU-15 Chloroflexi Yes, scaffold 218671 Yes, bin-15 0.7 0.0 No OTU-16 Planctomycetes, Gemmata Yes, scaffold 261011 Maybe, bin-23 0.7 0.2 No OTU-17 Chloracidobacterium thermophilum Yes, scaffold 32584 Yes, bin-16 0.7 5.2 No OTU-18 Armatimonadetes_Gp 2 Yes, scaffold 584 Yes, bin-17 0.6 0.0 No OTU-19 Planctomycetes, uncultured Yes, scaffold 11289 No 0.6 0.0 No OTU-20 Elusimicrobia, uncultured Yes, scaffold 20130 No 0.5 0.1 Maybe OTU-21 Deinococcus-Thermus, Meiothermus sp. Yes, scaffolds 8341 and 25957 Yes, bin-18 0.5 0.4 No OTU-22 Cyanobacteria, Synechococcus sp. A, OS Type A Yes, scaffold 85825 No 0.5 0.5 No OTU-23 Chloroflexi, Anaerolineae, OPB12 Yes, scaffold 18877 No 0.5 0.0 No OTU-24 Chlorobi, Lineage 5: OPB56 Yes, scaffold 2638 Yes, bin-19 0.5 2.0 No OTU-25 Spirochaetae, Leptospiraceae Yes, scaffold 4665 No 0.4 0.1 No OTU-26 Thermodesulfobacteria, Caldimicrobium Yes, scaffold 193547 Yes, bin-32 0.4 0.4 No OTU-27 Chlorobi, Lineage 5: OPB56 Yes, scaffold 104947 No 0.4 1.0 No OTU-28 Thermotogae, EM3 Yes, scaffold 49539 No 0.4 0.0 No OTU-29 Chlorobi, Lineage 5: OPB56 Yes, scaffold 6663 No 0.4 0.3 No OTU-30 Thermotogae, EM3 Yes, scaffold 26263 No 0.4 0.0 No OTU-31 Chloroflexi, Bellilinea Yes, scafffold 10483 Yes, bin-25 0.3 0.1 No OTU-32 Spirochaetae, Exilispira Yes, scaffolds 5322 and 20220 No 0.2 1.1 No OTU-33 OP10/Armatimonadetes_Gp7, OS Type L Yes, scaffold 62246 No 0.2 0.0 No OTU-34 Chlorobi, Ignavibacteriaceae Yes, scaffolds 10292 and 68906 Maybe, bin-24 0.2 0.2 No OTU-35 Spirochaetae, Brevinema No No 0.2 0.3 No OTU-36 Acidobacterium, OPB3 Yes, scaffolds 1343 and 2292 Yes, bin-20 0.2 0.0 No (Continu position detected by the different methods used in this study (iTag, metagenome 16S rRNA, metagenome binning) nd upper layer iTag sequencing study. TABLE 5 | Overview of community composition detected by the different methods used in this study (iTag, metagenome 16S rRNA, metagenome binning) and relative abundances in undermat and upper layer iTag sequencing study. June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 19 Composition of the Mushroom Spring Undermat Community Thiel et al. CONCLUSIONS 16S rRNA gene sequences of iTag OTUs as well as assembled clone sequences have been deposited in GenBank (Acc. nos. KU860141–KU860455 [iTag OTUs]; KX213895–KX214032 [clone OTUs]). Complete metagenome data are available in the Integrated Microbial Genomes with Microbiome Samples (IMG/M, https://img.jgi.doe.gov/) database, taxon object IDs 3300002493, 3300005452 and 2015219002. In this study we analyzed the community composition and diversity of the orange-colored undermat of Mushroom Spring, an alkaline hot spring in YNP (WY, USA) by 16S rRNA gene amplicon and metagenomic analyses. Despite a long history of research on the microbial mats at Mushroom and Octopus Springs (Brock, 1967; Ward et al., 1998, 2012; Kim et al., 2015), these mats still harbor the potential for many novel discoveries. Members of the genus Roseiflexus dominated a fairly diverse but uneven microbial community, and metagenomic analysis identified several novel organisms with unusual traits. Many unidentified 16S rRNA sequences recovered from these environments in previous studies were detected and phylogenetically identified. Other organisms, which have been cultured from either Mushroom or Octopus Spring, DISCUSSION The second unidentified heterotroph previously detected in the upper layer metagenome, Cluster 7 (Klatt et al., 2011), was identified as an Armatimonadetes member OTU-3. Due to a high microdiversity of this organism in the microbial mat sample, identification was only possible by a serendipitous finding of a closely related organism in an enrichment culture. detected in the Mushroom Spring microbial mat (Tank et al., in press). Additionally, the discovery of multiple organisms with genes encoding xanthorhodopsin raises new questions about the role of retinal-based phototrophy (retinalophototrophy; Bryant and Frigaard, 2006) or signaling in the undermat. This will be addressed in more detail elsewhere (Thiel et al., in preparation). The unidentified Cluster 8 previously detected in the upper layer metagenome was identified again here as OTU-10, an organism affiliated with the group EM3, which has tentatively been placed in the phylum Thermotogae (Reysenbach et al., 1994; Klatt et al., 2013a). The second unidentified heterotroph previously detected in the upper layer metagenome, Cluster 7 (Klatt et al., 2011), was identified as an Armatimonadetes member OTU-3. Due to a high microdiversity of this organism in the microbial mat sample, identification was only possible by a serendipitous finding of a closely related organism in an enrichment culture. Frontiers in Microbiology | www.frontiersin.org DISCUSSION TABLE 5 | Continued iTag OTU Identity Undermat metagenome 16S rRNA Undermat metagenomic bin iTag MS undermat (%) iTag MS upper green layer (%) Upper green layer metagenomic bina OTU-37 Verrucomicrobia, uncultured Yes, scaffold 25955 No 0.2 0.0 No OTU-38 Chlorobi, “Ca. Thermochlorobacter aerophilum” Yes, scaffold 761 Yes, bin-21 0.2 2.2 No OTU-39 Chloroflexi, Anaerolineae Yes, scaffold 145123 No 0.2 0.1 No OTU-40 Deltaproteobacteria, Desulfarculales, uncultured Yes, scaffold 112567 No 0.2 0.0 No OTU-41 Spirochaetae, Spirochaeta Yes, scaffold 19076 No 0.2 0.1 No OTU-42 Acetothermia, uncultured (Yes, scaffold 169700)* No 0.1 0.0 No OTU-43 Spirochaetae, Leptospiraceae, uncultured (Yes, scaffold 205406)* No 0.1 0.0 No OTU-44 Deltaproteobacteria, Synthroporhabdus-like Yes, scaffolds 233149 and 241554 No 0.1 0.0 No OTU-45 Chlorobi, Ignavibacteriaceae Yes, scaffolds 104127 and 141772 Maybe, bin-24 0.1 0.0 No OTU-46 Elioraea sp. Yes, scaffold 23894 Yes, bin-22 0.1 0.0 No *based on phylogenetic analysis, no overlap of sequences. aKlatt et al. (2011). bno metagenomic bin, but related sequences recruited by reference genomes. were not detected, once again illustrating the inherent bias of untargeted cultivation experiments. A more detailed analysis of the metagenome, focusing on the metabolic potential of the mat members and their putative interactions, will be published elsewhere (Thiel et al., in preparation). Studies of microbial ecology, diversity, species evolution and interspecies interactions are still subjects of ongoing research with many open questions to be addressed. Comparisons of species in both upper and lower mat and a diel-transcriptomic analysis that will hopefully reveal gene expression activity within the undermat community that will allow us to distinguish between active and inactive members of the community defined in this study, and should provide information on the temporal pattern of gene expression in the undermat. Depth-dependent distributions of OTU populations that may represent putative ecotypes will also be addressed in future studies. detected in the Mushroom Spring microbial mat (Tank et al., in press). Additionally, the discovery of multiple organisms with genes encoding xanthorhodopsin raises new questions about the role of retinal-based phototrophy (retinalophototrophy; Bryant and Frigaard, 2006) or signaling in the undermat. This will be addressed in more detail elsewhere (Thiel et al., in preparation). The unidentified Cluster 8 previously detected in the upper layer metagenome was identified again here as OTU-10, an organism affiliated with the group EM3, which has tentatively been placed in the phylum Thermotogae (Reysenbach et al., 1994; Klatt et al., 2013a). AUTHOR CONTRIBUTIONS VT conducted sequence analysis after assembly for both amplicon and metagenome sequences, including phylogenetic analysis and phylogenetic marker genes analysis of metagenome bins. JW conducted initial tetranucleotide binning analyses, June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 20 Composition of the Mushroom Spring Undermat Community Thiel et al. reference targeted mapping studies and contributed to discussion and manuscript. Sampling and DNA extraction from the hot- spring microbial mat and enrichment cultures was conducted by MO, who also wrote corresponding sections in the manuscript and contributed to the discussion of results. MT isolated and identified all cultures mentioned in the manuscript, contributed to writing the manuscript and discussing the results. CK conducted 16S rRNA cloning and sequencing from undermat samples from a previous time point, analyzed those sequences and contributed to manuscript and discussion. Sequencing, quality check, assembly and dereplication of amplicon and the metagenome was conducted by JGI staff. DW and DB planned the experiments, acquired funding, organized and led field excursions and provided scientific infrastructure. VT, DW, and DB wrote the manuscript. used in this study were collected under permit #YELL-SCI-0129 held by DW and administered under the authority of Yellowstone National Park. The authors especially thank Christie Hendrix and Stacey Gunther for their advice and assistance. FUNDING The trees were generated based on the Maximum Likelihood method using the phyML software included in the ARB package. Percentage numbers on nodes refer to 100 bootstrap pseudoreplicates conducted. Only values >50% are shown. Bold sequences were obtained from Mushroom or Octopus Spring in this or previous studies. Red bold labels indicate sequences obtained in this study. Blue bold labels indicate “OS type” sequences from previous studies. OTU numbers shown refer to the most abundant OTU represented by the sequence. Only sequences with length >1,000 bp were used for phylogenetic calculations. Sequence length <1,000 bp are given in (gray) in the labels and corresponding sequences were added using the Parsimony method without changing tree topology. This study was partly funded by the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the Department of Energy through Grant DE-FG02- 94ER20137. DB and DW additionally acknowledge support from the NASA Exobiology program (NX09AM87G). This work was also partly supported by the U. S. Department of Energy (DOE), Office of Biological and Environmental Research (BER), as part of BER’s Genomic Science Program 395 (GSP). This contribution originates from the GSP Foundational Scientific Focus Area (FSFA) at the Pacific Northwest National Laboratory (PNNL) under a subcontract to DB. The nucleotide sequencing was performed as part of a Community Sequencing Program (Project CSP-411) and was performed by the U.S. Department of Energy Joint Genome Institute, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Figure S2 | Entropy distribution in Roseiflexus-like 16S rRNA gene amplicon sequences in the combined dataset (A), and the undermat (B), and upper layer (C). The difference in the entropy figures from upper layer (C) and undermat (B) analyzed separately, specifically the considerably lower entropy at pos. 104 and 109 in upper layer, are indicative of a lower abundance of two oligotypes in the upper layer, namely “CCCCGCGTGC” (2.13% in undermat, 0.19% in upper layer) and “CCCCGCGGGC” (1.02 vs. 0.21%) (Table S2). Table S1 | OTUs obtained from 16S rRNA V4 iTag sequencing. Read numbers, relative abundance and number of total and abundant dereplicated iTag sequences are stated. Classification are based on RDP classifier. ACKNOWLEDGMENTS Table S2 | Read counts and relative abundance of the 23 most abundant Roseiflexus-like oligotypes in undermat and upper layer as determined in the combined amplicon dataset (>100 reads total). The authors would like to thank all of the JGI staffmembers who contributed to obtaining the sequence data. The materials SUPPLEMENTARY MATERIAL The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fmicb. 2016.00919 Figure S1 | Phylogenetic tree based on 16S rRNA gene sequences showing the phylogenetic relationship between sequences obtained from the Mushroom Spring microbial undermat community and cultivated and uncultivated relatives in the phyla Armatimonadetes OP10, Aminicenantes OP8, Nitrospirae, Thermodesulfobacteria, Microgenomates OP11, Aquificae, SM2F11 and Archaea (A), Planctomycetes, Verrucomicrobia, Spirochaeta, Acidobacteria, Atribacteria OP9/JS1, Elusimicrobia and Cyanobacteria (B), and Proteobacteria, Thermotogae/EM3 and Thermi (C). The trees were generated based on the Maximum Likelihood method using the phyML software included in the ARB package. Percentage numbers on nodes refer to 100 bootstrap pseudoreplicates conducted. Only values >50% are shown. Bold sequences were obtained from Mushroom or Octopus Spring in this or previous studies. Red bold labels indicate sequences obtained in this study. Blue bold labels indicate “OS type” sequences from previous studies. OTU numbers shown refer to the most abundant OTU represented by the sequence. Only sequences with length >1,000 bp were used for phylogenetic calculations. Sequence length <1,000 bp are given in (gray) in the labels and corresponding sequences were added using the Parsimony method without changing tree topology. Figure S1 | Phylogenetic tree based on 16S rRNA gene sequences showing the phylogenetic relationship between sequences obtained from the Mushroom Spring microbial undermat community and cultivated and uncultivated relatives in the phyla Armatimonadetes OP10, Aminicenantes OP8, Nitrospirae, Thermodesulfobacteria, Microgenomates OP11, Aquificae, SM2F11 and Archaea (A), Planctomycetes, Verrucomicrobia, Spirochaeta, Acidobacteria, Atribacteria OP9/JS1, Elusimicrobia and Cyanobacteria (B), and Proteobacteria, Thermotogae/EM3 and Thermi (C). REFERENCES Anderson, K. L., Tayne, T. A., and Ward, D. M. (1987). Formation and fate of fermentation products in hot spring cyanobacterial mats. Appl. Environ. Microbiol. 53, 2343–2352. Albuquerque, L., Rainey, F. A., Nobre, M. F., and da Costa, M. S. (2008). Elioraea tepidiphila gen. nov., sp. nov., a slightly thermophilic member of the Alphaproteobacteria. Int. J. Syst. Evol. Microbiol. 58, 773–778. doi: 10.1099/ijs.0.65294-0 Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T., Edwards, R. A., et al. (2008). The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75 Allewalt, J. P., Bateson, M. M., Revsbech, N. P., Slack, K., and Ward, D. M. (2006). Effect of temperature and light on growth of and photosynthesis by Synechococcus isolates typical of those predominating in the Octopus Spring microbial mat community of Yellowstone National Park. Appl. Environ. Microbiol. 72, 544–550. doi: 10.1128/AEM. 72.1.544 Bateson, M. M., and Ward, D. M. (1988). Photoexcretion and fate of glycolate in a hot spring cyanobacterial mat. Appl. Environ. Microbiol. 54, 1738–1743. Bauld, J., and Brock, T. D. (1973). Ecological studies of Chloroflexis, a gliding photosynthetic bacterium. Arch. Mikrobiol. 92, 267–284. doi: 10.1007/BF00409281 Becraft, E. D., Cohan, F. M., Kuehl, M., Jensen, S. I., and Ward, D. M. (2011). Fine- scale distribution patterns of Synechococcus ecological diversity in the microbial mat of Mushroom Spring, Yellowstone National Park. Appl. Env. Microbiol. 77, 7689–7697. doi: 10.1128/AEM.05927-11 Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403–410. doi: 10.1016/S0022- 2836(05)80360-2 Amann, R. I., Ludwig, W., and Schleifer, K. H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143–169. Becraft, E. D., Wood, J. M., Rusch, D. B., Kühl, M., Jensen, S. I., Bryant, D. A., et al. (2015). The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 21 Composition of the Mushroom Spring Undermat Community Thiel et al. ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park. Front. Microbiol. 6:590. doi: 10.3389/fmicb.2015.00590 genome sequence signatures. Genome Biol. 10, R85. doi: 10.1186/gb-2009- 10-8-r85 genome sequence signatures. Genome Biol. 10, R85. doi: 10.1186/gb-2009- 10-8-r85 Dillon, J. G., Fishbain, S., Miller, S. R., Bebout, B. M., Habicht, K. S., Webb, S. REFERENCES Characterization of novel bacteriochlorophyll a-containing red filaments from alkaline hot springs in Yellowstone National Park. Arch. Microbiol. 174, 152–161. doi: 10.1007/s002030000189 Ferris, M. J., Kopczynski, E. D., Bateson, M. M., and Ward, D. M. (1996a). Enrichment culture and microscopy conceal diverse thermophilic Synechococcus populations in a single hot spring mat habitat. Microbiology 62, 1045–1050. Brock, T. D. (1967). Micro-organisms adapted to high temperatures. Nature 214, 882–885. Ferris, M. J., Kuehl, M., Wieland, A., and Ward, D. M. (2003). Cyanobacterial ecotypes in different optical microenvironments of a 68◦C hot spring mat community revealed by 16S-23S rRNA internal transcribed spacer region variation. Appl. Environ. Microbiol. 69, 2893–2898. doi: 10.1128/AEM.69.5. 2893 Brock, T. D., and Freeze, H. (1969). Thermus aquaticus gen. nov. and sp. nov., a non-sporulating extreme thermophile. J. Bacteriol. 98, 289–297. Bryant, D. A., Costas, A. M. G., Maresca, J. A., Chew, A. G. M., Klatt, C. G., Bateson, M. M., et al. (2007). “Candidatus Chloracidobacterium thermophilum”: an aerobic phototrophic Acidobacterium. Science 317, 523–526. doi: 10.1126/science.1143236 Ferris, M. J., Muyzer, G., and Ward, D. M. (1996b). Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 62, 340–346. Bryant, D. A., and Frigaard, N.-U. (2006). Prokaryotic photosynthesis and phototrophy illuminated. Trends Microbiol. 14, 488–496. doi: 10.1016/j.tim.2006.09.001 Ferris, M. J., Nold, S. C., Revsbech, N. P., and Ward, D. M. (1997). Population structure and physiological changes within a hot spring microbial mat community following disturbance. Appl. Environ. Microbiol. 63, 1367–1374. Caporaso, J. G., Bittinger, K., and Bushman, F. D., et al. (2010b). PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266–267. doi: 10.1093/bioinformatics/btp636 Ferris, M. J., and Ward, D. M. (1997). Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 63, 1375–1381. Caporaso, J. G., Kuczynski, J., and Stombaugh, J., et al. (2010a). QUIME allows analysis of high-throughput community sequencing data. Nat Methods 7, 335–336. doi: 10.1038/nmeth.f.303.QIIME Garcia Costas, A. M., Liu, Z., Tomsho, L. P., Schuster, S. C., Ward, D. M., and Bryant, D. A. (2012a). Complete genome of “Candidatus Chloracidobacterium thermophilum”, a chlorophyll-based photoheterotroph belonging to the phylum Acidobacteria. Environ. Microbiol. 14, 177–190. doi: 10.1111/j.1462- 2920.2011.02592.x Castenholz, R. W. (1969). Thermophilic blue-green algae and the thermal environment. Bacteriol. Rev. 33, 476–504. Challacombe, J. F., Eichorst, S. REFERENCES M., et al. (2007). High rates of sulfate reduction in a low-sulfate hot spring microbial mat are driven by a low level of diversity of sulfate-respiring microorganisms. Appl. Environ. Microbiol. 73, 5218–5226. doi: 10.1128/AEM. 00357-07 Bhandari, V., and Gupta, R. S. (2014). Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations. Antonie van Leeuwenhoek 105, 143–168. doi: 10.1007/s10482-013-0062-7 Dodsworth, J. A., Blainey, P. C., Murugapiran, S. K., Wesley, D., Ross, C. A., Tringe, S. G., et al. (2013). Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for member of the OP9 lineage. Nat Commun. 4, 1854. doi: 10.1038/ncomms2884 Bhatnagar, S., Badger, J. H., Madupu, R., Khouri, H. M., Connor, E. M. O., Robb, F. T., et al. (2015). Genome sequence of the sulfate- reducing thermophilic bacterium Thermodesulfovibrio yellowstonii strain DSM 11347T (Phylum Nitrospirae). Genome Announc. 3, e01489–e01414. doi: 10.1128/genomeA.01489-14 Doemel, W. N., and Brock, T. D. (1977). Structure, growth, and decomposition of laminated algal-bacterial mats in alkaline hot springs. Appl. Environ. Microbiol. 34, 433–452. Eder, W., and Huber, R. (2002). New isolates and physiological properties of the Aquificales and description of Thermocrinis albus sp. nov. Extremophiles 6, 309–318. doi: 10.1007/s00792-001-0259-y Bhaya, D., Grossman, A. R., Steunou, A.-S., Khuri, N., Cohan, F. M., Hamamura, N., et al. (2007). Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses. ISME J. 1, 703–713. doi: 10.1038/ismej.2007.46 Farag, I. F., Davis, J. P., Youssef, N. H., and Elshahed, M. S. (2014). Global patterns of abundance, diversity and community structure of the Aminicenantes (Candidate phylum OP8). PLoS ONE 9:e92139. doi: 10.1371/journal.pone.0092139 Boomer, S. M., Lodge, D. P., Dutton, B. E., and Pierson, B. (2002). Molecular characterization of novel red green nonsulfur bacteria from five distinct hot spring communities in Yellowstone National Park. Appl. Environ. Microbiol. 68, 346–355. doi: 10.1128/AEM.68.1.346-355.2002 Fardeau, M.-L., Ollivier, B., Patel, B. K. C., Magot, M., Thomas, P., and Rimbault, A. (1997). Thermotoga hypogea sp. nov., a xylanolytic, thermophilic bacterium from an oil-producing well. Int. J. Syst. Bacteriol. 47, 1013–1019. Boomer, S. M., Pierson, B. K., Austinhirst, R., and Castenholz, R. W. (2000). REFERENCES A., Hauser, L., Land, M., Xie, G., and Kuske, C. R. (2011). Biological consequences of ancient gene acquisition and duplication in the large genome of “Candidatus Solibacter usitatus” Ellin6076. PLoS ONE 6:e24882. doi: 10.1371/journal.pone.0024882 Garcia Costas, A. M., Tsukatani, Y., Rijpstra, W. I. C., Schouten, S., Welander, P. V., Summons, R. E., et al. (2012b). Identification of the bacteriochlorophylls, carotenoids, quinones, lipids, and hopanoids of “Candidatus Chloracidobacterium thermophilum.” J. Bacteriol. 194, 1158–1168. doi: 10.1128/JB.06421-11 Chao, A. (1984). Nonparametric estimation of the number of classes in a population. Scand. J. Stat. 11, 265–270. Choi, A. R., Shi, L., Brown, L. S., and Jung, K.-H. (2014). Cyanobacterial light-driven proton pump, Gloeobacter rhodopsin: complementarity between rhodopsin-based energy production and photosynthesis. PLoS ONE 9:e110643. doi: 10.1371/journal.pone.0110643 Grégoire, P., Fardeau, M.-L., Joseph, M., Guasco, S., Hamaide, F., Biasutti, S., et al. (2011). Isolation and characterization of Thermanaerothrix daxensis gen. nov., sp. nov., a thermophilic anaerobic bacterium pertaining to the phylum Chloroflexi, isolated from a deep hot aquifer in the Aquitaine Basin. Syst. Appl. Microbiol. 34, 494–497. doi: 10.1016/j.syapm.2011.02.004 doi: 10.1371/journal.pone.0110643 Cohan, F. M., and Perry, E. B. (2007). A systematics for discovering the fundamental units of bacterial diversity. Curr. Biol. 17, 373–386. doi: 10.1016/j.cub.2007.03.032 Gupta, R., Chander, P., and George, S. (2013). Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades: proposal for division of the class Chloroflexi class. nov. into the suborder Chloroflexineae subord. nov., consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. nov., and the suborder Roseiflexinae subord. nov., containing the family Roseiflexaceae fam. nov. Antonie van Leeuwenhoek 103, 99–119. doi: 10.1007/s10482-012-9790-3 Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., et al. (2009). The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucl. Acids Res. 37, D141–D145. doi: 10.1093/nar/gkn879 De La Torre, J. R., Walker, C. B., Ingalls, A. E., Könneke, M., and Stahl, D. A. (2008). Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ. Microbiol. 10, 810–818. doi: 10.1111/j.1462-2920.2007.01506.x Henry, E. A., Devereux, R., Maki, J. S., Gilmour, C. C., Woese, C. R., Mandelco, L., et al. (1994). Characterization of a new thermophilic sulfate-reducing bacterium Thermodesulfovibrio yellowstoneii, gen. nov. and sp. nov.: its Dick, G. J., Andersson, A. F., Baker, B. J., Simmons, S. L., Thomas, B. C., Yelton, A. P., et al. (2009). REFERENCES Hydrothermal ecotones and streamer biofilm communities in the Lower Geyser Basin, Yellowstone National Park. Environ. Microbiol. 13, 2216–2231. doi: 10.1111/j.1462-2920.2011.02476.x Nobu, M. K., Dodsworth, J. A., Murugapiran, S. K., Rinke, C., Gies, E. A., Webster, G., et al. (2016). Phylogeny and physiology of candidate phylum “Atribacteria” (OP9/JS1) inferred from cultivation-independent genomics. ISME J. 10, 273–286. doi: 10.1038/ismej.2015.97 Kerepesi, C., Bánky, D., and Grolmusz, V. (2014). AmphoraNet: the webserver implementation of the AMPHORA2 metagenomic workflow suite. Gene 533, 538–540. doi: 10.1016/j.gene.2013.10.015 Nold, S. C., and Ward, D. M. (1996). Photosynthate partitioning and fermentation in hot spring microbial mat communities. Appl. Environ. Microbiol. 62, 4598–4607. Kim, Y.-M., Nowack, S., Olsen, M. T., Becraft, E. D., Wood, J. M., Thiel, V., et al. (2015). Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms. Front. Microbiol. 6:209. doi: 10.3389/fmicb.2015.00209 Nowack, S., Olsen, M. T., Schaible, G. A., Becraft, E. D., Shen, G., Klapper, I., et al. (2015). The molecular dimension of microbial species: 2. Synechococcus strains representative of putative ecotypes inhabiting different depths in the Mushroom Spring microbial mat exhibit different adaptive and acclimative responses to light. Front. Microbiol. 6:626. doi: 10.3389/fmicb.2015. 00626 Kimura, H., Nashimoto, H., Shimizu, M., Hattori, S., Yamada, K., Koba, K., et al. (2010). Microbial methane production in deep aquifer associated with the accretionary prism in Japan. ISME J. 4, 531–541. doi: 10.1038/ismej.2009.132 Klatt, C. G., Bryant, D. A., and Ward, D. M. (2007). Comparative genomics provides evidence for the 3-hydroxypropionate autotrophic pathway in filamentous anoxygenic phototrophic bacteria and in hot spring microbial mats. Environ. Microbiol. 9, 2067–2078. doi: 10.1111/j.1462-2920.2007. 01323.x Nowack, S. P. (2014). Niche Character in a Temporally Varying Environment. Ph. D. thesis, Montana State University. doi: 10.1017/CBO9781107415324.004 Nübel, U., Bateson, M. M., Vandieken, V., Kühl, M., and Ward, D. M. (2002). Microscopic examination of distribution and phenotypic properties of phylogenetically diverse Chloroflexaceae-related bacteria in hot spring microbial mats. Appl. Environ. Microbiol. 68, 4593–4603. doi: 10.1128/AEM.68.9.4593 Klatt, C. G., Inskeep, W. P., Herrgard, M. J., Jay, Z. J., Rusch, D. B., Tringe, S. G., et al. (2013a). Community structure and function of high- temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. Front. Microbiol. 4:106. doi: 10.3389/fmicb.2013.00106 Nunoura, T., Hirai, M., Miyazaki, M., Kazama, H., Makita, H., Hirayama, H., et al. (2013). REFERENCES Community-wide analysis of microbial June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 22 Composition of the Mushroom Spring Undermat Community Thiel et al. phylogenetic relationship to Thermodesulfobacterium commune and their origins deep within the bacterial domain. Arch. Microbiol. 161, 62–69. phylogenetic relationship to Thermodesulfobacterium commune and their origins deep within the bacterial domain. Arch. Microbiol. 161, 62–69. Koeppel, A. F., and Wu, M. (2013). Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units. Nucl. Acids Res. 41, 5175–5188. doi: 10.1093/nar/gkt241 g p Hiras, J., Wu, Y.-W., Eichorst, S. A., Simmons, B. A., and Singer, S. W. (2015). Hiras, J., Wu, Y.-W., Eichorst, S. A., Simmons, B. A., and Singer, S. W. (2015). Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage. ISME J. 9, 1751–7370. doi: 10.1038/ismej.2015.158 g Lau, M. C. Y., Aitchison, J. C., and Pointing, S. B. (2009). Bacterial community composition in thermophilic microbial mats from five hot springs in central Tibet. Extremophiles 13, 139–149. doi: 10.1007/s00792-008-0205-3 Huber, R., Eder, W., Heldwein, S., Huber, H., Rachel, R., Karl, O., et al. (1998). Thermocrinis ruber gen. nov., sp. nov., a pink-filament-forming hyperthermophilic bacterium isolated from Yellowstone National Park. Appl. Environ. Microbiol. 64, 3576–3583. Lee, K. C.-Y., Dunfield, P. F., Morgan, X. C., Crowe, M. A., Houghton, K. M., Vyssotski, M., et al. (2011). Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate candiate division OP1. Int. J. Syst. Evol. Microbiol. 61, 2482–2490. doi: 10.1099/ijs.0.02 7235-0 Hugenholtz, P., Goebel, B. M., and Pace, N. R. (1998a). Impact of culture- independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180, 4765–4774. Hugenholtz, P., and Pace, N. R. (1996). Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Trends Biotechnol. 14, 190–197. doi: 10.1016/0167-7799(96)10025-1 Lee, K. C.-Y., Herbold, W., Dunfield, P. F., Morgan, X. C., McDonald, I. R., and Stott, M. B. (2013). Phylogenetic delineation of the novel phylum Armatimonadetes (former candidate division OP10) and definition of two novel candidate divisions. Appl. Environ. Microbiol. 79, 2484–2487. doi: 10.1128/AEM.03333-12 Hugenholtz, P., Pitulle, C., Hershberger, K. L., and Pace, N. R. (1998b). Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180, 366–376. Liu, Z., Klatt, C. REFERENCES G., Ludwig, M., Rusch, D. B., Jensen, S. I., Kühl, M., et al. (2012). “Candidatus Thermochlorobacter aerophilum:” an aerobic chlorophotoheterotrophic member of the phylum Chlorobi defined by metagenomics and metatranscriptomics. ISME J. 6, 1869–1882. doi: 10.1038/ismej.2012.24 Iino, T., Mori, K., Uchino, Y., Nakagawa, T., Harayama, S., and Suzuki, K.-I. (2010). Ignavibacterium album gen. nov., sp. nov., a moderately thermophilic anaerobic bacterium isolated from microbial mats at a terrestrial hot spring and proposal of Ignavibacteria classis nov., for a novel lineage at the periphery of green sulfur bacteria. Int. J. Syst. Evol. Microbiol. 69, 1376–1382. doi: 10.1099/ijs.0.012484-0 Liu, Z., Klatt, C. G., Wood, J. M., Rusch, D. B., Ludwig, M., Wittekindt, N., et al. (2011). Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat. ISME J. 5, 1279–1290. doi: 10.1038/ismej.2011.37 Im, W.-T., Hu, Z.-Y., Kim, K.-H., Rhee, S.-K., Meng, H., Lee, S.-T., et al. (2012). Description of Fimbriimonas ginsengisoli gen. nov., sp. nov. within the Fimbriimonadia class nov., of the phylum Armatimonadetes. Antonie Van Leeuwenhoek 102, 307–317. doi: 10.1007/s10482-012-9739-6 Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, et al. (2004). ARB: a software environment for sequence data. Nucl. Acids Res. 32, 1363–1371. doi: 10.1093/nar/gkh293 Markowitz, V. M., Chen, I. M. A., Chu, K., Szeto, E., Palaniappan, K., Pillay, M., et al. (2014). IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Res. 42, 568–573. doi: 10.1093/nar/gkt919 Jackson, T. J., Ramaley, R. F., and Meinschein, W. G. (1973). Thermomicrobium, a new genus of extremely thermophilic bacteria. Int. J. Syst. Bacteriol. 23, 28–36. doi: 10.1099/00207713-23-1-28 Jensen, S. I., Steunou, A.-S., Bhaya, D., Kühl, M., and Grossman, A. R. (2011). In situ dynamics of O2, pH and cyanobacterial transcripts associated with CCM, photosynthesis and detoxification of ROS. ISME J. 5, 317–328. doi: 10.1038/ismej.2010.131 Melendrez, M. C., Lange, R. K., Cohan, F. M., and Ward, D. M. (2011). Influence of molecular resolution on sequence-based discovery of ecological diversity among Synechococcus populations in an alkaline siliceous hot spring microbial mat. Appl. Environ. Microbiol. 77, 1359–1367. doi: 10.1128/AEM.02032-10 Kadnikov, V. V., Mardanov, A. V., Podosokorskaya, O. A., Gavrilov, S. N., Kublanov, I. V., Beletsky, A. V., et al. (2013). Genomic analysis of Melioribacter roseus, facultatively anaerobic organotrophic bacterium representing a novel deep lineage within Bacteriodetes/Chlorobi group. PLoS ONE 8:e53047. doi: 10.1371/journal.pone.0053047 Meyer-Dombard, D. R., Swingley, W., Raymond, J., Havig, J., Shock, E. L., and Summons, R. E. (2011). REFERENCES L., Tomsho, L. P., Burhans, R., Gay, S. E., Ramaley, R. F., et al. (2014a). Draft genome sequence of the moderately thermophilic bacterium Schleiferia thermophila strain Yellowstone (Bacteroidetes). Genome Announc. 2, e00860–e00814. doi: 10.1128/genomeA.00 860-14 Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., et al. (2014). The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 42, 1–9. doi: 10.1093/nar/gkt1226 Technology (RAST). Nucleic Acids Res. 42, 1–9. doi: 10.1093/nar/ Thiel, V., Hamilton, T. L., Tomsho, L. P., Burhans, R., Gay, S. E., Schuster, S. C., et al. (2014b). Draft genome sequence of a sulfide-oxidizing, autotrophic filamentous anoxygenic phototrophic bacterium, Chloroflexus sp. strain MS-G (Chloroflexi). Genome Announc. 2, e00872–e00814. doi: 10.1128/genomeA.00872-14 Pace, N. R. (2009). Mapping the tree of life: progress and prospects. Microbiol. Mol. Biol. Rev. 73, 565–576. doi: 10.1128/MMBR.00033-09 Ramsing, N. B., Ferris, M. J., and Ward, D. M. (2000). Highly ordered vertical structure of Synechococcus populations within the one-millimeter-thick photic zone of a hot spring cyanobacterial mat. Appl. Environ. Microbiol. 66, 1038–1049. doi: 10.1128/AEM.66.3.1038-1049.2000 Thiel, V., Tomsho, L. P., Burhans, R., Gay, S. E., Schuster, S. C., Ward, D. M., et al. (2015). Draft genome sequence of the Deinococcus-Thermus bacterium Meiothermus ruber strain A. Genome Announc. 3, e00202–e00215. doi: 10.1128/genomeA.00202-15 Revsbech, N. P., and Ward, D. M. (1984). Microelectrode studies of interstitial water chemistry and photosynthetic activity in a hot spring microbial mat. Appl. Environ. Microbiol. 48, 270–275. Reysenbach, A., Longnecker, K., and Kirshtein, J. (2000). Novel bacterial and archaeal lineages from an in situ growth chamber deployed at a Mid- Atlantic Ridge hydrothermal vent. Appl. Environ. Microbiol. 66, 3798–3806. doi: 10.1128/AEM.66.9.3798-3806.2000 van der Meer, M. T. J., Klatt, C. G., Wood, J., Bryant, D. A., Bateson, M. M., Lammerts, L., et al. (2010). Cultivation and genomic, nutritional, and lipid biomarker characterization of Roseiflexus strains closely related to predominant in situ populations inhabiting Yellowstone hot spring microbial mats. J. Bacteriol. 192, 3033–3042. doi: 10.1128/JB.01610-09 Reysenbach, A., Wickham, G. S., and Pace, N. R. (1994). Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park. Appl. Environ. Microbiol. 60, 2113–2119. van der Meer, M. T. J., Schouten, S., Damsté, J. S. S., and Ward, D. M. (2007). REFERENCES Isolation and characterization of a thermophilic, obligately anaerobic and heterotrophic marine Chloroflexi bacterium from a Chloroflexi-dominated microbial community associated with a Japanese shallow hydrothermal system, and proposal for Thermomarinilinea lacunofontalis gen. nov., sp. nov. Microbes Environ. 28, 228–235. doi: 10.1264/jsme2.ME12193 Klatt, C. G., Liu, Z., Ludwig, M., Kühl, M., Jensen, S. I., Bryant, D. A., et al. (2013b). Temporal metatranscriptomic patterning in phototrophic Chloroflexi inhabiting a microbial mat in a geothermal spring. ISME J. 7, 1775–1789. doi: 10.1038/ismej.2013.52 Klatt, C. G., Wood, J. M., Rusch, D. B., Bateson, M. M., Hamamura, N., Heidelberg, J. F., et al. (2011). Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential. ISME J. 5, 1262–1278. doi: 10.1038/ismej.2011.73 Nunoura, T., Takaki, Y., Kakuta, J., Nishi, S., Sugahara, J., Kazama, H., et al. (2011). Insights into the evolution of Archaea and eukaryotic protein modifier June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 23 Composition of the Mushroom Spring Undermat Community Thiel et al. systems revealed by the genome of a novel archaeal group. Nucl. Acids Res. 39, 3204–3223. doi: 10.1093/nar/gkq1228 Tank, M., and Bryant, D. A. (2015b). Nutrient requirements and growth physiology of the photoheterotrophic acidobacterium, Chloracidobacterium thermophilum. Front. Microbiol. 6:226. doi: 10.3389/fmicb.2015.00226 systems revealed by the genome of a novel archaeal group. Nucl. Acids Res. 39, 3204–3223. doi: 10.1093/nar/gkq1228 g Olsen, G. J., Lane, D. J., Giovannoni, S. J., Pace, N. R., and Stahl, D. A. (1986). Olsen, G. J., Lane, D. J., Giovannoni, S. J., Pace, N. R., and Stahl, D. A. (1986). Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40, 337–365. Tank, M., Thiel, V., Ward, D. M., and Bryant, D. A. (in press). “A panoply of phototrophs: a photomicrographic overview of chlorophototrophs found in the microbial mats of alkaline siliceous hot springs in Yellowstone National Park, WY, USA,” in Modern Topics in the Phototrophic Prokaryotes: Environmental and Applied Aspects, ed P. C. Hallenbeck (Berlin: Springer). Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40, 337–365. Olsen, M. T., Nowack, S., Wood, J. M., Becraft, E. D., LaButti, K., Lipzen, A., et al. (2015). The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat. Front. Microbiol. 6:604. doi: 10.3389/fmicb.2015.00604 Thiel, V., Hamilton, T. REFERENCES Impact of carbon metabolism on 13C signatures of cyanobacteria and green non-sulfur-like bacteria inhabiting a microbial mat from an alkaline siliceous hot spring in Yellowstone National Park (USA). Environ. Microbiol. 9, 482–491. doi: 10.1111/j.1462-2920.2006.01165.x Sandbeck, K. A., and Ward, D. M. (1981). Fate of immediate methane precursors in low-sulfate, hot-spring algal-bacterial mats. Appl. Environ. Microbiol. 41, 775–782. van der Meer, M. T. J., Schouten, S., Jaap, S., Damsté, S., Leeuw, J. W., De Ward, D. M., et al. (2003). Compound-specific isotopic fractionation patterns suggest different carbon metabolisms among Chloroflexus-like bacteria in hot-spring microbial mats. Appl. Environ. Microbiol. 69, 6000–6006. doi: 10.1128/AEM.69.10.6000-6006.2003 Sandbeck, K. A., and Ward, D. M. (1982). Temperature adaptations in the terminal processes of anaerobic decomposition of yellowstone national park and icelandic hot spring microbial mats. Appl. Environ. Microbiol. 44, 844–851. Schloss, P. D., and Handelsman, J. (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71, 1501–1506. doi: 10.1128/AEM.71. 3.1501 van der Meer, M. T. J., Schouten, S., Mary, M., Nübel, U., Wieland, A., Kühl, M., et al. (2005). Diel variations in carbon metabolism by green nonsulfur-like bacteria in alkaline siliceous hot spring microbial mats from Yellowstone National Park. Appl. Environ. Microbiol. 71, 3978–3986. doi: 10.1128/AEM.71.7.3978-3986.2005 Sekiguchi, Y., Yamada, T., Hanada, S., Ohashi, A., Harada, H., and Kamagata, Y. (2003). Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int. J. Syst. Evol. Microbiol. 53, 1843–1851. doi: 10.1099/ijs.0. 02699-0 Venkata Ramana, V., Sasikala, C., Takaichi, S., and Ramana, C. V. (2010). Roseomonas aestuarii sp. nov., a bacteriochlorophyll-a containing alphaproteobacterium isolated from an estuarine habitat of India. Syst. Appl. Microbiol. 33, 198–203. doi: 10.1016/j.syapm.2009.09.004 Slobodkina, G. B., Kovaleva, O. L., Miroshnichenko, M. L., Slobodkin, A. I., Kolganova, T. V., Novikov, A. A., et al. (2014). Thermogutta terrifontis gen. nov., sp. nov. and Thermogutta hypogea sp. nov., thermophilic anaerobic representatives of the phylum Planctomycetes. Int. J. Syst. Evol. Microbiol. 65, 760–765. doi: 10.1099/ijs.0.000009 Wang, Q., Garrity, G. M., Tiedje, J. M., and Cole, J. R. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267. doi: 10.1128/AEM. 00062-07 Ward, D. M. (1978). Thermophilic methanogenesis in a hot-spring algal-bacterial mat (71 to 30 degrees C). Appl. Environ. Microbiol. 35, 1019–1026. REFERENCES Stackebrandt, E., and Goebel, B. M. (1994). Taxonomic Note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44, 846–849. doi: 10.1099/00207713-44-4-846 Ward, D. M. (1998). A natural species concept for prokaryotes. Curr. Opin. Microbiol. 1, 271–277. Ward, D. M., Bateson, M. M., Weller, R., and Ruff-Roberts, A. L. (1992). “Ribosomal RNA analysis of microorganisms as they occur in nature,” in Advances in Microbial Ecology, ed K. C. Marshall (New York, NY: Springer US), 219–286. Steunou, A.-S., Jensen, S. I., Brecht, E., Becraft, E. D., Bateson, M. M., Kilian, O., et al. (2008). Regulation of nif gene expression and the energetics of N2 fixation over the diel cycle in a hot spring microbial mat. ISME J. 2, 364–378. doi: 10.1038/ismej.2007.117 Ward, D. M., Brassell, S. C., and Eglinton, G. (1985). Archaebacterial lipids in hot-spring microbial mats. Nature 318, 162–163. doi: 10.1038/31 4731a0 Tamaki, H., Tanaka, Y., Matsuzawa, H., Muramatsu, M., Meng, X.-Y., Hanada, S., et al. (2011). Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10. Int. J. Syst. Evol. Microbiol. 61, 1442–1447. doi: 10.1099/ijs.0.0 25643-0 Ward, D. M., Castenholz, R. W., and Miller, S. R. (2012). “Ecology of cyanobacteria II: cyanobacteria in geothermal habitats,” in Ecology of Cyanobacteria II, ed B. A. Whitton (Dordrecht: Springer), 39–63. Tank, M., and Bryant, D. A. (2015a). Chloracidobacterium thermophilum gen. nov., sp. nov.: an anoxygenic microaerophilic chlorophotoheterotrophic acidobacterium. Int. J. Syst. Evol. Microbiol. 65, 1426–1430. doi: 10.1099/ijs.0.000113 Ward, D. M., and Cohan, F. M. (2005). “Microbial diversity in hot spring cyanobacterial mats: pattern and prediction,” in Geothermal Biology and Geochemistry in Yellowstone National Park, eds W. P. Inskeep and T. McDermott (Bozeman: Thermal Biology Institute), 185–202. June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 24 Composition of the Mushroom Spring Undermat Community Thiel et al. Ward, D. M., Ferris, M. J., Nold, S. C., and Bateson, M. M. (1998). A natural view of microbial biodiversity within hot spring cyanobacterial mat communities. Microbiol. Mol. Biol. Rev. 62, 1353–1370. spirochete-like inhabitants of a hot spring microbial mat. Appl. Environ. Microbiol. 58, 3964–3969. spirochete-like inhabitants of a hot spring microbial mat. Appl. Environ. Microbiol. 58, 3964–3969. Wu, D., Raymond, J., Wu, M., Chatterji, S., Ren, Q., Graham, J. E., et al. (2009). Frontiers in Microbiology | www.frontiersin.org June 2016 | Volume 7 | Article 919 REFERENCES Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS ONE 4:e4207. doi: 10.1371/journal.pone.0004207 Ward, D. M., Santegoeds, C. M., Nold, S. C., Ramsing, N. B., Ferris, M. J., and Bateson, M. M. (1997). Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures. Antonie van Leeuwenhoek 71, 143–150. doi: 10.1023/A:10001314 26164 Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Ward, D. M. J., Shiea, J., Zeng, Y. B., Dobson, G., Brassell, S., and Eglinton, G. (1989). “Lipid biochemical markers and the composition of microbial mats,” in Microbial Mats: Physiological Ecology of Benthic Microbial Communities, eds Y. Cohen and E. Rosenburg (Washington, DC: American Society For Microbiology), 439–454. Copyright © 2016 Thiel, Wood, Olsen, Tank, Klatt, Ward and Bryant. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Ward, D. M., Weller, R., and Bateson, M. M. (1990). 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 346, 183–187. doi: 10.1038/346183a0 Weller, R., Bateson, M. M., Heimbuch, B. K., Kopczynski, E. D., and Ward, D. M. (1992). Uncultivated cyanobacteria, Chloroflexus-like inhabitants, and June 2016 | Volume 7 | Article 919 Frontiers in Microbiology | www.frontiersin.org 25
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Utilization of Mineral Wools as Alkali-Activated Material Precursor
Materials
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Received: 15 March 2016; Accepted: 20 April 2016; Published: 26 April 2016 Received: 15 March 2016; Accepted: 20 April 2016; Published: 26 April 2016 Abstract: Mineral wools are the most common insulation materials in buildings worldwide. However, mineral wool waste is often considered unrecyclable because of its fibrous nature and low density. In this paper, rock wool (RW) and glass wool (GW) were studied as alkali-activated material precursors without any additional co-binders. Both mineral wools were pulverized by a vibratory disc mill in order to remove the fibrous nature of the material. The pulverized mineral wools were then alkali-activated with a sodium aluminate solution. Compressive strengths of up to 30.0 MPa and 48.7 MPa were measured for RW and GW, respectively, with high flexural strengths measured for both (20.1 MPa for RW and 13.2 MPa for GW). The resulting alkali-activated matrix was a composite-type in which partly-dissolved fibers were dispersed. In addition to the amorphous material, sodium aluminate silicate hydroxide hydrate and magnesium aluminum hydroxide carbonate phases were identified in the alkali-activated RW samples. The only crystalline phase in the GW samples was sodium aluminum silicate. The results of this study show that mineral wool is a very promising raw material for alkali activation. Keywords: geopolymer; alkali activation; mineral wool; rock wool; glass wool; mmmf: man-made mineral fibre materials materials materials Materials 2016, 9, 312; doi:10.3390/ma9050312 Utilization of Mineral Wools as Alkali-Activated Material Precursor Juho Yliniemi *, Paivo Kinnunen, Pasi Karinkanta and Mirja Illikainen Fiber and Particle Engineering Research Unit, University of Oulu, Oulu 90014, Finland; paivo.kinnunen@oulu.fi(P.K.); pasi.karinkanta@oulu.fi(P.K.); mirja.illikainen@oulu.fi(M.I.) * Correspondence: juho.yliniemi@oulu.fi; Tel.: +358-443120686 Academic Editor: Claudio Ferone 1. Introduction Alkali-activated materials (AAM), also called geopolymers or inorganic polymers, have received a lot of attention lately because they have the potential to partly replace ordinary Portland cement (OPC) as a construction material. Studies have shown that AAMs have mechanical properties as good as, or even better than, OPC concrete [1]. In addition, other beneficial properties, such as fire resistance and their typically light weight, make it possible to use them for such purposes as constructing panels or making ceramics [2,3]. The increased interest in AAMs lies in the fact that they can be produced from waste materials, such as fly ash, mine tailings, and slags. In 2012, OPC production was estimated to account for 8% of global CO2 emissions [4], and government policies worldwide strongly encourage reducing OPC use. This explains the recent interest in finding alternative construction materials and binders. Proper thermal insulation is needed throughout the world, because it is the most effective way to save energy used for heating and cooling buildings. Mineral wools—a general term for rock wool and glass wool—are the most common insulation materials in the world. They are produced at high temperatures by melting quartz sand, basalt, dolomite, and glass [5]. The molten mixture is fiberized by a high-speed spinning process. A small quantity of organic resin, typically phenol-formaldehyde, is used as an additive to bind the fibers together. As old buildings are torn down or renovated, a large amount of construction and demolition waste is generated, including the waste from mineral wools. Globally, 2.3 million tons of mineral wool waste was generated in 2010, and the amount is expected Materials 2016, 9, 312; doi:10.3390/ma9050312 www.mdpi.com/journal/materials Materials 2016, 9, 312 2 of 12 to rise to 2.5 million tons by the year 2020 [6]. Unfortunately, mineral wool is often unrecyclable [6]. The problems in recycling arise from the fibrous nature and low density of the material. Despite many attempts [7–17], the utilization of mineral wool waste in post-consumer production remains very low. Both glass wool and rock wool have high contents of Si and X-ray amorphous mineralogy and, thus, have potential as AAM precursors. However, there has been to date only one preliminary study of utilizing rock wool as raw material for alkali activation [18]. Alkali activation of glass wool has not been previously studied. 1. Introduction Mineral wools also have very consistent chemical and physical compositions, which make them even more attractive as raw materials for alkali activation. This study experimented with the utilization of rock wool and glass wool as alkali-activation precursors. Both mineral wools were pulverized and activated with sodium aluminate. The effects of heat curing and organic resin removal on the physical and mineralogical properties of the mineral wools were analyzed. Note: n.d represents “not detectable”. Note: n.d represents “not detectable”. 2. Materials and Methods Two types of virgin mineral wool were purchased from a hardware store for this study: rock wool (RW, Paroc, Paroc eXtra) and glass wool (GW, Saint Gobain, Isover KL37-100). The chemical composition of both mineral wools was determined with 4 kV X-ray fluorescence (XRF, PANalytical Omnian Axiosmax). For the XRF analyses, it was necessary to prepare melt-fused tablets from both mineral wool samples. The melt-fused tablets were produced from 1.5 g of sample melted at 1150 ˝C with 7.5 g of X-ray Flux Type 66:34 (66% Li2B4O7 and 34% LiBO2). The concentration of trace elements was determined by microwave-assisted wet digestion using a 3:1 mixture of HNO3 and HCl for 0.5 g of mineral wool and measured using an inductively coupled, plasma-optical emission spectrometer (ICP-OES, Thermo Electron IRIS Intrepid II XDL Duo, Thermo Scientific). The moisture content and loss-on-ignition at 350 and 525 ˝C were determined using thermo-gravimetric analysis equipment (PrepAsh, Precisa). The RW consisted mainly of silicon, aluminum, calcium, magnesium, and iron. The GW contained 62.4 wt % of SiO2, but only 1.8 wt % of Al2O3 (Table 1). However, the Na2O content in the GW was high (16.8 wt %) in contrast to that of the RW (1.4 wt %). Table 2 shows the chemical compositions of the RW and GW determined using the ICP-OES method. The composition is in line with the XRF results (Table 1). However, the content of boron in the GW was significant, and it is possible that this was the result of the use of waste glass as a raw material in the GW manufacturing process. Table 1. The chemical composition, dry matter content, and loss-on-ignition of rock wool (RW) and glass wool (GW), determined by XRF and TGA. Chemical Component Rock Wool (RW) Glass Wool (GW) CaO 17.4 7.1 SiO2 40.4 62.4 Al2O3 15.8 1.8 Fe2O3 9.2 0.6 Na2O 1.4 16.8 K2O 0.4 0.9 MgO 12.6 2.2 P2O5 0.1 n.d TiO2 0.8 n.d SO3 n.d 0.9 Cl n.d 0.1 Dry matter content (%) 100.0 100.0 Loss-on-ignition 350 ˝C (%) 1.8 5.0 Loss-on-ignition 525 ˝C (%) 2.4 5.1 Note: n.d represents “not detectable”. Table 1. The chemical composition, dry matter content, and loss-on-ignition of rock wool (RW) and glass wool (GW), determined by XRF and TGA. 3 of 12 Materials 2016, 9, 312 Table 2. The chemical composition of rock wool (RW) and glass wool (GW), determined by ICP-OES. 2. Materials and Methods In total, there were 140 g of RW and 150 g of GW in each sample. The mixture was vibrated in order to remove air bubbles and was then cast into molds, which were then sealed into a plastic bag until testing (28 days). Three batches were prepared from each type of mineral wool. Table 3 shows the molar ratios of the alkali-activated samples. The molar ratios were set as close to 1:1:4:11 (Na2O:Al2O3:SiO2:H2O) [19] as possible. In order to obtain these ratios, both mineral wools had to be alkali-activated with sodium aluminate solution because of their lack of aluminum aluminate solution and mixing it in a mixer (ARE-250, Thinky Corporation) at 2000 rpm for 60 s. The mineral wools were added in 15–40 g portions to 63 g of sodium aluminate solution and mixed after each addition until the desired consistency was reached. In total, there were 140 g of RW and 150 g of GW in each sample. The mixture was vibrated in order to remove air bubbles and was then cast into molds, which were then sealed into a plastic bag until testing (28 days). Three batches were prepared from each type of mineral wool. Table 3 shows the molar ratios of the alkali-activated samples. The molar ratios were set as close to 1:1:4:11 (Na2O:Al2O3:SiO2:H2O) [19] as possible. In order to obtain these ratios, both mineral wools The alkali-activated samples were prepared by adding the pulverized RW or GW to the sodium aluminate solution and mixing it in a mixer (ARE-250, Thinky Corporation) at 2000 rpm for 60 s. The mineral wools were added in 15–40 g portions to 63 g of sodium aluminate solution and mixed after each addition until the desired consistency was reached. In total, there were 140 g of RW and 150 g of GW in each sample. The mixture was vibrated in order to remove air bubbles and was then cast into molds, which were then sealed into a plastic bag until testing (28 days). Three batches were prepared from each type of mineral wool. had to be alkali activated with sodium aluminate solution because of their lack of aluminum. However, sodium aluminate is not stable in liquid form at certain sodium-aluminum ratios [20], so optimal ratios were not achieved. In the GW samples in particular, the low quantity of aluminum yielded seemingly high Na2O, SiO2, and H2O ratios. 2. Materials and Methods Chemical Component Rock Wool (RW) Glass Wool (GW) Ca, ICP (g/kg) 125 20.1 Si, ICP partial solution (g/kg) 0.4 0.4 Al, ICP (g/kg) 85.6 0.3 Fe, ICP (g/kg) 61.3 0.9 Na, ICP (g/kg) 10.4 68.2 K, ICP (g/kg) 3.7 3.7 Mg, ICP (g/kg) 75.8 3.9 P, ICP (g/kg) 0.3 <0.020 Ti, ICP (g/kg) 3.5 <0.050 S, ICP (g/kg) 0.1 3.8 Ba, ICP (g/kg) 0.2 1.3 Mn, ICP (g/kg) 1 0.5 As, ICP (mg/kg) <3 <3 Cd, ICP (mg/kg) <0.3 <0.3 Cr, ICP (mg/kg) 280 2.3 Cu, ICP (mg/kg) 34 8.8 Hg, CVAAS (mg/kg) <0.04 <0.04 Ni, ICP (mg/kg) 49 1.8 Pb, ICP (mg/kg) <3 3.7 Zn, ICP (mg/kg) 47 430 B, ICP (mg/kg) 8.9 6260 Be, ICP (mg/kg) <1 <1 Co, ICP (mg/kg) 21 2 Mo, ICP (mg/kg) <1 <1 Sb, ICP (mg/kg) <3 <3 Se, ICP (mg/kg) <3 <3 Sn, ICP (mg/kg) <3 <3 V, ICP (mg/kg) 170 <2 Note: CVAAS represents “cold-vapor atomic absorption spectrometry”. Table 2. The chemical composition of rock wool (RW) and glass wool (GW), determined by ICP-OES. The GW and RW samples were pulverized with RS200 vibratory disc mill (Retsch). Pulverizing was accomplished by milling mineral wool in 10 g patches for 30 s at a milling speed of 1500 min´1. This procedure was repeated several times to obtain a sufficient amount of pulverized mineral wool for further experiments and analyses. The particle size distributions of the pulverized mineral wools were measured with a LS 13320 (Beckman Coulter), using the universal liquid module and applying the Fraunhofer model in calculations. Prior to the particle size measurements, the pulverized mineral wool was diluted with distilled water by using sodium pyrophosphate as a dispersing agent. The diluted sample was held in an ultrasonic bath for three minutes to ensure comprehensive dispersion before measurements were taken. The appearances of the RW and GW before and after grinding are shown in Figure 1. Figure 2 presents the differential particle size distribution of the RW and GW after pulverization. The grinding was a very efficient means of pulverization, as the median size of both pulverized wools was approximately 7 microns, and 90% particles by volume (d90) was less than 34 microns in both cases (Figure 2). Although the pulverized wools had similar median particle sizes, there were slight differences between the differential particle size distributions (Figure 2). 4 of 12 Materials 2016, 9, 312 Figure 1. 2. Materials and Methods Photograph and FESEM images of (a) rock wool (RW); and (b) glass wool (GW) before and after grinding. Figure 1. Photograph and FESEM images of (a) rock wool (RW); and (b) glass wool (GW) before and after grinding. Materials 2016, 9, 312 4 of 12 Figure 1. Photograph and FESEM images of (a) rock wool (RW); and (b) glass wool (GW) before and after grinding. Figure 1. Photograph and FESEM images of (a) rock wool (RW); and (b) glass wool (GW) before and after grinding. Figure 1. Photograph and FESEM images of (a) rock wool (RW); and (b) glass wool (GW) before and after grinding. Figure 1. Photograph and FESEM images of (a) rock wool (RW); and (b) glass wool (GW) before and after grinding. Figure 2. Particle size distributions of pulverized rock wool (RW) and glass wool (GW). The sodium aluminate solution was prepared by mixing sodium aluminate (Sigma-Ald Figure 2. Particle size distributions of pulverized rock wool (RW) and glass wool (GW). Figure 2. Particle size distributions of pulverized rock wool (RW) and glass wool (GW). g p ( ) g ( ) The sodium aluminate solution was prepared by mixing sodium aluminate (Sigma-Ald Figure 2. Particle size distributions of pulverized rock wool (RW) and glass wool (GW). Figure 2. Particle size distributions of pulverized rock wool (RW) and glass wool (GW). 13404), sodium hydroxide (VWR Merck, 1.06498.1000) and deionized water, using weight ratios of 14.3 wt %, 22.2 wt %, and 63.5 wt %, respectively. The alkali-activated samples were prepared by adding the pulverized RW or GW to the sodium aluminate solution and mixing it in a mixer (ARE-250, Thinky Corporation) at 2000 rpm for 60 s. The The sodium aluminate solution was prepared by mixing sodium aluminate (Sigma-Aldrich, 13404), sodium hydroxide (VWR Merck, 1.06498.1000) and deionized water, using weight ratios of 14.3 wt %, 22.2 wt %, and 63.5 wt %, respectively. The alkali-activated samples were prepared by adding the pulverized RW or GW to the sodium The sodium aluminate solution was prepared by mixing sodium aluminate (Sigma-Aldrich, 13404), sodium hydroxide (VWR Merck, 1.06498.1000) and deionized water, using weight ratios of 14.3 wt %, 22.2 wt %, and 63.5 wt %, respectively. g ( y p ) p mineral wools were added in 15–40 g portions to 63 g of sodium aluminate solution and mixed after each addition until the desired consistency was reached. 2. Materials and Methods Another thing to keep in mind is that a sodium aluminate solution can contain both 4-coordinated and 6-coordinated aluminum species depending on the [OH]/[Al] ratio [21], which can have an effect on the formation of aluminosilicate phases. In the molar ratio calculations, it was assumed that all elements dissolve from the mineral wools in the same proportions. Table 3 shows the molar ratios of CaO and MgO, because it is known that calcium and magnesium can participate in alkali activation [22–24]. ( ) p had to be alkali-activated with sodium aluminate solution because of their lack of aluminum. However, sodium aluminate is not stable in liquid form at certain sodium-aluminum ratios [20], so optimal ratios were not achieved. In the GW samples in particular, the low quantity of aluminum yielded seemingly high Na2O, SiO2, and H2O ratios. Another thing to keep in mind is that a sodium aluminate solution can contain both 4-coordinated and 6-coordinated aluminum species depending on the [OH]/[Al] ratio [21], which can have an effect on the formation of aluminosilicate phases. In the molar ratio calculations, it was assumed that all elements dissolve from the mineral wools in the same proportions. Table 3 shows the molar ratios of CaO and MgO, because it is known that calcium and magnesium can participate in alkali activation [22–24]. Table 3 shows the molar ratios of the alkali-activated samples. The molar ratios were set as close to 1:1:4:11 (Na2O:Al2O3:SiO2:H2O) [19] as possible. In order to obtain these ratios, both mineral wools had to be alkali-activated with sodium aluminate solution because of their lack of aluminum. However, sodium aluminate is not stable in liquid form at certain sodium-aluminum ratios [20], so optimal ratios were not achieved. In the GW samples in particular, the low quantity of aluminum yielded seemingly high Na2O, SiO2, and H2O ratios. Another thing to keep in mind is that a sodium aluminate solution can contain both 4-coordinated and 6-coordinated aluminum species depending on the [OH]/[Al] ratio [21], which can have an effect on the formation of aluminosilicate phases. In the molar ratio calculations, it was assumed that all elements dissolve from the mineral wools in the same proportions. Table 3 shows the molar ratios of CaO and MgO, because it is known that calcium and magnesium can participate in alkali activation [22–24]. 5 of 12 Materials 2016, 9, 312 Table 3. 2. Materials and Methods The sample name, binder molar ratio composition, and curing temperature and time. Sample Name RW1 GW1 RW2 GW2 RW3 GW3 Mineral wool type Pulverized rock wool Pulverized glass wool Pulverized rock wool Pulverized glass wool Pulverized and resin removed rock wool Pulverized and resin removed glass wool Na2O (mol) 0.7 7.6 0.7 7.6 0.7 7.5 Al2O3 (mol) 1.0 1.0 1.0 1.0 1.0 1.0 SiO2 (mol) 3.6 20.5 3.6 21.2 3.6 21.1 H2O (mol) 8.4 29.5 8.4 30.3 8.5 30.4 CaO (mol) 1.7 2.5 1.7 2.6 1.7 2.6 MgO (mol) 1.7 1.1 1.7 1.1 1.7 1.1 Curing (temp. and time) 28 days in 22 ˝C 28 days in 22 ˝C 4 days in 50 ˝C and then 24 days in 22 ˝C 4 days in 50 ˝C and then 24 days in 22 ˝C 4 days in 50 ˝C and then 24 days in 22 ˝C 4 days in 50 ˝C and then 24 days in 22 ˝C Table 3. The sample name, binder molar ratio composition, and curing temperature and time. After a total 28 days of curing, the Z100 testing machine (Zwick Roell) and TestXpert II software (Zwick Roell) were used to determine the unconfined compressive strength. Compressive force was increased at 2.4 kN/s until failure, and the maximum force was used to calculate the compressive strength. Flexural strength was measured with the Instron 5544 (Instron) (2 kN max force). A Siemens 5000 X-ray diffractometer (Siemens) with CuKaα radiation (40 mA and 40 kV) and a graphite monochromator were used to identify the main crystalline phases of the pulverized mineral wools and prepared samples. The step interval, integration time, and angle interval used were 0.04˝/step, 2.5 s/step, and 10˝–60˝ 2θ, respectively. The International Center for Diffraction Data (ICDD) database was used for the identification of crystalline phases [25]. A Zeiss Ultra Plus field emission scanning electron microscope (FESEM, Zeiss) was used to analyze the original and pulverized mineral wools and the fracture surface of the prepared samples. The samples were attached to a sample holder on a carbon tape and coated with carbon. The acceleration voltage was 5 kV. 3.1. Physical Properties of the Alkali-Activated Mineral Wools The bars show the average of at least three samples measured and the error represent the confidence interval for means at 95% Figure 3. The compressive and flexural strength of each prepared sample. The bars show the average of at least three samples measured and the error represent the confidence interval for means at 95% confidence level. Figure 3. The compressive and flexural strength of each prepared sample. The bars show the average of at least three samples measured and the error represent the confidence interval for means at 95% confidence level. Figure 3. The compressive and flexural strength of each prepared sample. The bars show the average of at least three samples measured and the error represent the confidence interval for means at 95% whereas the GW samples stayed in more or less one piece and were merely compressed (Figure 4). Especially peculiar behavior was observed for GW3, which was compressed by a mechanism called strain hardening (see Appendix Figure A1). In strain hardening, the material requires an ever- increasing amount of stress to continue straining [26]. The GW1 sample cured at room temperature was a bit moist even after 28 days, but all other GW and RW samples were dry. There was no sign of the formation of salts (i.e., efflorescence) on the surface of the samples during the first four months of hardening. It was observed that the RW samples broke into several pieces in the compressive strength tests, whereas the GW samples stayed in more or less one piece and were merely compressed (Figure 4). Especially peculiar behavior was observed for GW3, which was compressed by a mechanism called strain hardening (see Appendix Figure A1). In strain hardening, the material requires an ever-increasing amount of stress to continue straining [26]. The GW1 sample cured at room temperature was a bit moist even after 28 days, but all other GW and RW samples were dry. There was no sign of the formation of salts (i.e., efflorescence) on the surface of the samples during the first four months of hardening. confidence level. It was observed that the RW samples broke into several pieces in the compressive strength tests, whereas the GW samples stayed in more or less one piece and were merely compressed (Figure 4). Especially peculiar behavior was observed for GW3, which was compressed by a mechanism called strain hardening (see Appendix Figure A1). 3.1. Physical Properties of the Alkali-Activated Mineral Wools The alkali-activated RW samples had an apparent density of approximately 2000 kg/m3, regardless of the curing conditions or resin removal (Table 4). The apparent density of samples GW1 and GW2 was roughly 1800 kg/m3, but the sample with organic resin removed had a density of 2037 kg/m3. Table 4. The apparent density of each prepared sample. Table 4. The apparent density of each prepared sample. Sample Code Density (kg/m3) RW1 2093 GW1 1779 RW2 2003 GW2 1802 RW3 1956 GW3 2037 The compressive and flexural strengths of the alkali-activated samples are presented in Figure 3. The stressing curves of each measurement are presented in the Appendix (Figure A1). The RW samples gained high compressive strength (~28 MPa), regardless of the curing temperature or presence of the resin. All samples, except GW1, had a very high flexural strength. The highest flexural strength (20.1 MPa) was in the heat-treated sample in which resin remained (RW2). The compressive and The compressive and flexural strengths of the alkali-activated samples are presented in Figure 3. The stressing curves of each measurement are presented in the Appendix (Figure A1). The RW samples gained high compressive strength (~28 MPa), regardless of the curing temperature or presence of the resin. All samples, except GW1, had a very high flexural strength. The highest flexural strength (20.1 MPa) was in the heat-treated sample in which resin remained (RW2). The compressive and 6 of 12 Materials 2016, 9, 312 flexural strengths of the GW samples were low without the heat treatment (GW1). GW2 gained the highest compressive strength (48.7 MPa) of all of the prepared samples. Materials 2016, 9, 312 6 of 12 flexural strengths of the GW samples were low without the heat treatment (GW1). GW2 gained the highest compressive strength (48.7 MPa) of all of the prepared samples. Materials 2016, 9, 312 6 of 12 Figure 3. The compressive and flexural strength of each prepared sample. The bars show the average of at least three samples measured and the error represent the confidence interval for means at 95% confidence level. Figure 3. The compressive and flexural strength of each prepared sample. The bars show the average of at least three samples measured and the error represent the confidence interval for means at 95% confidence level. Materials 2016, 9, 312 6 of 12 Figure 3. The compressive and flexural strength of each prepared sample. 3.1. Physical Properties of the Alkali-Activated Mineral Wools In strain hardening, the material requires an ever- increasing amount of stress to continue straining [26]. The GW1 sample cured at room temperature was a bit moist even after 28 days, but all other GW and RW samples were dry. There was no sign of the formation of salts (i.e., efflorescence) on the surface of the samples during the first four months of hardening. Figure 4. The deformation type of the alkali activated rock wool (RW) and glass wool (GW) samples. 3.2. FESEM Analysis Figure 5 presents the typical look of the fracture surfaces of the alkali-activated rock wool (RW) Figure 4. The deformation type of the alkali activated rock wool (RW) and glass wool (GW) samples. Figure 4. The deformation type of the alkali activated rock wool (RW) and glass wool (GW) samples. 3. . ESEM Analysis Figure 5 presents the typical look of the fracture surfaces of the alkali-activated rock wool (RW) Figure 4. The deformation type of the alkali activated rock wool (RW) and glass wool (GW) samples. Figure 4. The deformation type of the alkali activated rock wool (RW) and glass wool (GW) samples. 3.3. XRD Analysis 3.3. XRD Analysis the right sid Both mineral wools were completely X-ray amorphous (Figure 6). The amorphous hump was observed between 20° and 38° 2θ for RW, whereas it was wider for GW, starting from 14° and ending around 40° 2θ. The shift of the amorphous hump is considered to be an indicator of newly-formed nanocrystalline zeolites [27]. It can be observed that the shift of the amorphous hump is more notable for GW. This is mainly because the center of the hump in GW is around 25° 2θ before the alkali activation and 30° 2θ after the activation. For RW, the center of the hump is around 30° 2θ before alkali activation; thus, the shift is not as clearly observable. Both mineral wools were completely X-ray amorphous (Figure 6). The amorphous hump was observed between 20˝ and 38˝ 2θ for RW, whereas it was wider for GW, starting from 14˝ and ending around 40˝ 2θ. The shift of the amorphous hump is considered to be an indicator of newly-formed nanocrystalline zeolites [27]. It can be observed that the shift of the amorphous hump is more notable for GW. This is mainly because the center of the hump in GW is around 25˝ 2θ before the alkali activation and 30˝ 2θ after the activation. For RW, the center of the hump is around 30˝ 2θ before alkali activation; thus, the shift is not as clearly observable. 3.3. XRD Analysis Both mineral wools were completely X-ray amorphous (Figure 6). The amorphous hump was observed between 20° and 38° 2θ for RW, whereas it was wider for GW, starting from 14° and ending around 40° 2θ. The shift of the amorphous hump is considered to be an indicator of newly-formed nanocrystalline zeolites [27]. It can be observed that the shift of the amorphous hump is more notable for GW. This is mainly because the center of the hump in GW is around 25° 2θ before the alkali activation and 30° 2θ after the activation. For RW, the center of the hump is around 30° 2θ before alkali activation; thus, the shift is not as clearly observable. Figure 6. X-ray diffractograms of the (a) rock wool (RW); (b) glass wool (GW), and the alkali-activated Figure 6. X-ray diffractograms of the (a) rock wool (RW); (b) glass wool (GW), and the alkali-activated samples. Figure 6. and glass wool (GW fibers is shown. Th 3.2. FESEM Analys Figure 5 prese 3.2. FESEM Analysis than the heat-cured samples. The pieces of pulverized mineral wools can be observed to be bound together by the matrix. g p yp ( ) and glass wool (GW) samples. On the right side of the images, a magnification of the partly-dissolved fibers is shown. The samples cured at room temperature had a significantly more porous structure than the heat-cured samples. The pieces of pulverized mineral wools can be observed to be bound together by the matrix. Figure 5 presents the typical look of the fracture surfaces of the alkali-activated rock wool (RW) and glass wool (GW) samples. On the right side of the images, a magnification of the partly-dissolved fibers is shown. The samples cured at room temperature had a significantly more porous structure than the heat-cured samples. The pieces of pulverized mineral wools can be observed to be bound together by the matrix. 7 of 12 7 of 12 Materials 2016, 9, 312 Figure 5. Secondary electron image of the fracture surface of (a) the rock wool (RW); and (b) glass wool (GW) geopolymer samples. On the left side of the images is a general look of the surface and on the right side of the images is a more detailed image showing the composite-type structure. Figure 5. Secondary electron image of the fracture surface of (a) the rock wool (RW); and (b) glass wool (GW) geopolymer samples. On the left side of the images is a general look of the surface and on the right side of the images is a more detailed image showing the composite-type structure. Materials 2016, 9, 312 7 of 12 Figure 5. Secondary electron image of the fracture surface of (a) the rock wool (RW); and (b) glass wool (GW) geopolymer samples. On the left side of the images is a general look of the surface and on the right side of the images is a more detailed image showing the composite type structure Materials 2016, 9, 312 Materials 20 Figure 5. Secondary electron image of the fracture surface of (a) the rock wool (RW); and (b) glass wool (GW) geopolymer samples. On the left side of the images is a general look of the surface and on the right side of the images is a more detailed image showing the composite-type structure. Figure 5. and glass wool (GW fibers is shown. Th 3.2. FESEM Analys Figure 5 prese 3.2. FESEM Analysis Secondary electron image of the fracture surface of (a) the rock wool (RW); and (b) glass wool (GW) geopolymer samples. On the left side of the images is a general look of the surface and on the right side of the images is a more detailed image showing the composite-type structure. Figure 5. Secondary electron image of the fracture surface of (a) the rock wool (RW); and (b) glass wool (GW) geopolymer samples. On the left side of the images is a general look of the surface and on h h d f h d l d h h 4. Discussion The relationship between the molar ratios and physical properties of AAMs is often discussed. According to a study by Duxson et al. [19], the molar ratio of Si/Al should be around two and that of Na/Al should be one in order to complete the charge balancing of the negatively-charged tetrahedral aluminum centers. The amount of water should be as low as possible, because water is not usually considered to be part of the structure but acts merely as a medium in which the reactions occur and serves to maintain workability. However, recent studies [29–31] have shown that C-(N)-A-S-H gels can have bound water in the structure. Regardless of the far-from-optimum molar ratios for GW, GW2 gained the highest compressive strength of all of the samples. Theoretically, Si-O-Si are stronger bonds than Si-O-Al or Al-O-Al bonds [32], and the very high Si/Al ratio of GW2 could explain its high compressive strength. However, boron, which was present in GW, has also been noticed to increase the strength of the AAMs [33,34]. One possibility is that silicon and aluminum do not dissolve at the same proportions, as they are present in the mineral wools and, thus, the calculated molar ratios would not represent the real molar ratios of the binder system. This note is supported by the aforementioned fact that Si-O-Si are stronger bonds than Si-O-Al or Al-O-Al bonds, which would result in aluminum dissolving in higher proportions than silicon. One other difficulty in explaining the compressive strength differences using molar ratios arises from the XRD analysis, because this analysis shows only the crystalline phases, which may not be the main strength-increasing aluminosilicate structure. Instead, the newest phases are X-ray amorphous, and, thus, the chemical composition of the new nanocrystalline phases remains undetermined. The main difference between the RW and GW, in addition to the aluminum content, was the high content of Ca and Mg in the RW. Both have been shown to be reactive in alkali activation [22–24], but only the formation of a new Mg phase was identified in the RW samples. The formation of a hydrotalcite-type magnesium phase shows that Mg from RW reacts with CO2, thus acting as a CO2 sorbent in the formation of these binders. A similar hydrotalcite-type phase has been observed in the alkali activation of blast furnace slag (BFS) [23]. 3.3. XRD Analysis 3.3. XRD Analysis the right sid X-ray diffractograms of the (a) rock wool (RW); (b) glass wool (GW), and the alkali-activated samples. Fi X diff f h ( ) k l (RW) (b) l l (GW) d h lk li i d Figure 6. X-ray diffractograms of the (a) rock wool (RW); (b) glass wool (GW), and the alkali-activated samples. Figure 6. X-ray diffractograms of the (a) rock wool (RW); (b) glass wool (GW), and the alkali-activated samples. Materials 2016, 9, 312 8 of 12 In alkali-activated RW samples (RW1-3), sodium aluminate silicate hydroxide hydrate (00-041-0009) and magnesium aluminum hydroxide carbonate (01-070-2151) phases were found, in addition to the amorphous phase. A similar sodium aluminum silicate hydrate (NASH) phase was found in a previous study of RW alkali activation by sodium aluminate solution [18]. Additionally, Van Riessen et al. [28] found a NASH phase when coal fly ash was activated with a sodium aluminate solution. A sodium aluminate silicate (00-042-0217) phase was identified in GW1-3. A remark about the identification of these phases should be made. The identification was not absolute, because there were other similar aluminosilicate phases that had signals at the same 2θ positions. Also, the relatively wide signals indicate the presence of other similar type of phases than identified. However, the phase signals that fitted the best to the X-ray diffractograms were chosen and are presented here. 4. Discussion In CaO-rich systems, the strongly alkaline activating solution can favor the pozzolanic reaction between CaO and SiO2, producing calcium silicate hydrate (CSH). If present, this phase can give broad peaks at about 30˝ and 50˝ 2θ. The former is clearly visible in the XRD traces (Figure 6) of the RW1, RW2, and RW3 samples and barely visible in those of the GW2 and GW3 samples (the CaO content of GW is lower than that of RW, but not negligible). It has been shown that in low-Ca binder systems, heat treatment accelerates the hardening and increases early mechanical strength [35–37]. However, for high-Ca systems, heat curing has been observed to negatively affect the mechanical strength [38,39]. The severe drying shrinkage of the specimens with high-Ca type gels may be one reason for the lower strength. The phenomenon has been also explained by the fast calcium reactions, which are then accelerated by the elevated temperature, thus inhibiting further reactions (formation of secondary phases). However, for low-Ca binder systems, the binding of water into NASH gel is slow and/or weak; thus, heat curing speeds up the reaction (but only if the samples are sealed, as this prevents the evaporation of water). This could partly explain the Materials 2016, 9, 312 9 of 12 high increase in compressive strength of the heat-cured GW samples and the negligible increase in strength with heat-cured RW samples. The studies that have considered binder structure with a high or low calcium content have mostly used a (sodium) hydroxide or (sodium) silicate activator [22,40], and there are only a few studies in which sodium aluminate is the activator of choice [21,28,41,42]. Additionally, the high-Ca studies have been mostly conducted with BFS as a precursor, so the observations found in the literature may not be directly applicable with our binder system. However, both the BFS and mineral wools are manufactured in high temperatures and from similar precursors, so it might be appropriate to consider them as similar types of AAM precursors. yp p The presence of organic resin in the mineral wools had a positive effect on the strengths; thus, it is not necessary to remove it prior to the alkali activation. The reason for this is either that the organic resin physically strengthens the aluminosilicate matrix or that it reacts chemically with the other binder components. 4. Discussion During the preparation of the samples, it was observed that the samples in which the organic resin was present had a very strong smell, but samples RW3 and GW3 were odorless. This indicated the success of organic resin removal in samples RW3 and GW3, but also signaled possible reactions with Na-Alu and organic resin in samples RW1, RW2, GW1, and GW2. The effect of the organic resin on these binder systems will be studied further The high flexural strength of the samples can be explained by their composite-type matrix, as shown in Figure 5. However, as the fibers are dissolved and chemically bound to the matrix, the long-term mechanical performance must be carefully determined, because if the mineral wool fibers will eventually dissolve fully, the matrix will consist only of aluminosilicate gel. The dissolution of mineral wool fibers could yield a better or worse mechanical strength depending on whether the formatting aluminosilicate structure is stronger or weaker than the fibers. Conflicts of Interest: The authors declare no conflict of interest. 5. Conclusions Each of the graphs show results of three or four different samples, which are indicated by different color. Figure A1. Stressing curves of studied mineral wool-based geopolymers under bending and compression. Each of the graphs show results of three or four different samples, which are indicated by different color Figure A1. Stressing curves of studied mineral wool-based geopolymers under bending and compression. Each of the graphs show results of three or four different samples, which are indicated by different color. Figure A1. Stressing curves of studied mineral wool-based geopolymers under bending and compression. Each of the graphs show results of three or four different samples, which are indicated by different color. 5. Conclusions This study shows that mineral wools have great potential as precursors to alkali activation, because they have suitable chemical and mineralogical compositions. Heat curing and the presence of organic resin increased the mechanical properties. Maximum compressive strengths of 48.7 and 30.0 MPa were measured for GW and RW, respectively. The binder matrix consisted of aluminosilicate gel with partly-dissolved mineral wool fibers. The maximum flexural strength was 13.2 MPa for GW and 20.1 MPa for RW. The sodium aluminate silicate phase was the only crystalline phase in the GW samples. In RW samples, sodium aluminate silicate hydroxide hydrate and magnesium aluminum hydroxide carbonate were identified, in addition to the X-ray amorphous material. The apparent density of all the samples varied between 1750 and 2100 kg/m3. The results of this study show that high-strength AAMs can be obtained without any additional co-binders by alkali activating them with sodium aluminate solution. Acknowledgments: The authors would like to thank the Ekokem Environmental Stipend Fund for its financial support. Kalle Hyypiö, is acknowledged for his completion of a part of the experimental work as a part of his bachelor’s thesis. Jarno Karvonen, Elisa Wirkkala and Jani Österlund are acknowledged for their contributions to the laboratory analyses. The personnel of the Center of Microscopy and Nanotechnology are acknowledged for their contributions to the FESEM and XRD analyses. Special thanks to Arie van Riessen for the valuable advice for the experiments. Author Contributions: Juho Yliniemi, Paivo Kinnunen, Pasi Karinkanta and Mirja Illikainen conceived and designed the experiments; Juho Yliniemi and Pasi Karinkanta performed the experiments; Juho Yliniemi, Paivo Kinnunen and Pasi Karinkanta analyzed the data; Juho Yliniemi, Paivo Kinnunen, Pasi Karinkanta and Mirja Illikainen wrote the paper. Conflicts of Interest: The authors declare no conflict of interest. 10 of 12 Materials 2016, 9, 312 Appendix Materials 2016, 9, 312 10 of 12 Appendix Appendix Materials Appendix Appendix Figure A1. Stressing curves of studied mineral wool-based geopolymers under bending and compression. Each of the graphs show results of three or four different samples, which are indicated by different color. Figure A1. Stressing curves of studied mineral wool-based geopolymers under bending and compression. Each of the graphs show results of three or four different samples, which are indicated by different color. Figure A1. Stressing curves of studied mineral wool-based geopolymers under bending and compression. cement based concrete binders. In Handbook of Alkali Activated Cement, Mortars and Concretes; Woodhead Publishing Series in Civil and Structural Engineering: Cambridge, UK, 2015; Volume 2015, pp. 423–461. 3. Pacheco-Torgal, F.; Labrincha, J.A.; Leonelli, C.; Chindaprasirt, P. The fire resistance of alkali-activated cement-based concrete binders. In Handbook of Alkali-Activated Cement, Mortars and Concretes; Woodhead Publishing Series in Civil and Structural Engineering: Cambridge, UK, 2015; Volume 2015, pp. 423–461. development of “green concrete”. Cem. Concr. Res. 2007, 37, 1590–1597. 2. Bell, J.L.; Driemeyer, P.E.; Kriven, W.M. Formation of Ceramics from Metakaolin-Based Geopolymers. Part II: K-Based Geopolymer. J. Am. Ceram. Soc. 2009, 92, 607–615. 3. Pacheco-Torgal, F.; Labrincha, J.A.; Leonelli, C.; Chindaprasirt, P. The fire resistance of alkali-activated b d bi d I H db k f Alk li A i d C M d C W dh d 1. Duxson, P.; Provis, J.L.; Lukey, G.C.; van Deventer, J.S.J. The role of inorganic polymer technology in the development of “green concrete”. Cem. Concr. Res. 2007, 37, 1590–1597. [CrossRef] 2. Bell, J.L.; Driemeyer, P.E.; Kriven, W.M. Formation of Ceramics from Metakaolin-Based Geopolymers. Part II: K-Based Geopolymer. J. Am. Ceram. Soc. 2009, 92, 607–615. [CrossRef] II: K-Based Geopolymer. J. Am. Ceram. Soc. 2009, 92, 607–615. 3. Pacheco-Torgal, F.; Labrincha, J.A.; Leonelli, C.; Chindaprasirt, P. The fire resistance of alkali-activat cement-based concrete binders In Handbook of Alkali-Activated Cement Mortars and Concretes; Woodhe p g 2. Bell, J.L.; Driemeyer, P.E.; Kriven, W.M. Formation of Ceramics from Metakaolin-Based Geopolymers K-Based Geopolymer. J. Am. Ceram. Soc. 2009, 92, 607–615. [CrossRef] , ; , J ; y, ; , J J g p y gy development of “green concrete”. Cem. Concr. Res. 2007, 37, 1590–1597. 2. Bell, J.L.; Driemeyer, P.E.; Kriven, W.M. Formation of Ceramics from Metakaolin-Based Geopolymers. Part II: K-Based Geopolymer. J. Am. Ceram. Soc. 2009, 92, 607–615. 3. Pacheco-Torgal, F.; Labrincha, J.A.; Leonelli, C.; Chindaprasirt, P. The fire resistance of alkali-activated cement-based concrete binders. In Handbook of Alkali-Activated Cement, Mortars and Concretes; Woodhead Publishing Series in Civil and Structural Engineering: Cambridge, UK, 2015; Volume 2015, pp. 423–461. 1. Duxson, P.; Provis, J.L.; Lukey, G.C.; van Deventer, J.S.J. The role of inorganic polymer technology in the development of “green concrete”. Cem. Concr. Res. 2007, 37, 1590–1597. [CrossRef] 2. Bell, J.L.; Driemeyer, P.E.; Kriven, W.M. Formation of Ceramics from Metakaolin-Based Geopolymers. Part II: K-Based Geopolymer. J. Am. Ceram. Soc. 2009, 92, 607–615. [CrossRef] 3. Pacheco-Torgal, F.; Labrincha, J.A.; Leonelli, C.; Chindaprasirt, P. The fire resistance of alkali-activated cement-based concrete binders. In Handbook of Alkali-Activated Cement, Mortars and Concretes; Woodhead Publishing Series in Civil and Structural Engineering: Cambridge, UK, 2015; Volume 2015, pp. 423–461. development of “green concrete”. Cem. Concr. Res. 2007, 37, 1590–1597. 2. Bell, J.L.; Driemeyer, P.E.; Kriven, W.M. Formation of Ceramics from Metakaolin-Based Geopolymers. P II K B d G l J A C S 2009 92 607 615 1. Duxson, P.; Provis, J.L.; Lukey, G.C.; van Deventer, J.S.J. The role of inorganic polymer technolog development of “green concrete”. Cem. Concr. Res. 2007, 37, 1590–1597. [CrossRef] 1. Dux References cement based concrete binders. In Handbook of Alkali Activated Cement, Mortars and Concretes; Woodhead Publishing Series in Civil and Structural Engineering: Cambridge, UK, 2015; Volume 2015, pp. 423–461. 3. Pacheco-Torgal, F.; Labrincha, J.A.; Leonelli, C.; Chindaprasirt, P. The fire resistance of alkali-activated cement-based concrete binders. In Handbook of Alkali-Activated Cement, Mortars and Concretes; Woodhead Publishing Series in Civil and Structural Engineering: Cambridge, UK, 2015; Volume 2015, pp. 423–461. Materials 2016, 9, 312 11 of 12 4. Olivier, J.G.; Janssens-Maenhout, G.; Peters, J.A.H. PBL Netherlands Environmental Assessment Agency Trends in Global CO2 Emissions 2012 Report; European Commission, Joint Research Centre, Institute for Environment and Sustainability: Luxembourg, Luxembourg, 2012. 5. Papadopoulos, A.M. State of the art in thermal insulation materials and aims for future develo Energy Build. 2005, 37, 77–86. [CrossRef] 6. Väntsi, O.; Kärki, T. Mineral wool waste in Europe: A review of mineral wool waste quantity, quality, and current recycling methods. J. Mater. Cycles Waste Manag. 2013, 16, 62–72. [CrossRef] 7. Ali, M.H. Fire Resistant Gypsum Board Containing Mineral Wool Fibers and Method. Patent US4557973, 7 July 1987. 8. Cadotte, J. Production of Water-Laid Felted Mineral Fiber Panels Including Use of Flocculating Agent. Patent 3510394, 5 May 1970. 9. Cheng, A.; Lin, W.-T.; Huang, R. Application of rock wool waste in cement-based composites. Mater. Des. 2011, 32, 636–642. [CrossRef] 10. Felegi, J.; Kehrer, K. Composite Fiberboard and Process of Manufacture. Patent US5134179, 1 October 1990. 11 H R Mi l W l W t C t P t t US4662941 5 M 1987 0. Felegi, J.; Kehrer, K. Composite Fiberboard and Process of Manufacture. Patent US5134179, 1 October 1 10. Felegi, J.; Kehrer, K. Composite Fiberboard and Process of Manufacture. Patent US5134179, 1 October 1990. 11. Hagerman, R. Mineral Wool Waste Cement. Patent US4662941, 5 May 1987. Felegi, J.; Kehrer, K. Composite Fiberboard and Process of Manufacture. Patent US5134179, 1 October 1990 Hagerman, R. Mineral Wool Waste Cement. Patent US4662941, 5 May 1987. 1. Hagerman, R. Mineral Wool Waste Cement. Patent US4662941, 5 May 1987. 11. Hagerman, R. Mineral Wool Waste Cement. Patent US4662941, 5 May 1987. 12. Kizinieviˇc, O.; Balkeviˇcius, V.; Pranckeviˇcien˙e, J.; Kizinieviˇc, V. Investigation of the usage of centrifuging waste of mineral wool melt (CMWW), contaminated with phenol and formaldehyde, in manufacturing of ceramic products. Waste Manag. 2014, 34, 1488–1494. [CrossRef] [PubMed] 13. Lin, W.-T.; Han, T.-Y.; Huang, C.-C.; Cheng, A.; Huang, R. 1. Dux References [CrossRef] 12 of 12 Materials 2016, 9, 312 28. Van Riessen, A.; Jamieson, E.; Kealley, C.S.; Hart, R.D.; Williams, R.P. Bayer-geopolymers: An exploration of synergy between the alumina and geopolymer industries. Cem. Concr. Compos. 2013, 41, 29–33. [CrossRef] 29. Myers, R.J.; L’Hôpital, E.; Provis, J.L.; Lothenbach, B. Effect of temperature and aluminium on calcium (alumino) silicate hydrate chemistry under equilibrium conditions. Cem. Concr. Res. 2015, 68, 83–93. [CrossRef] 30. Myers, R.J.; Bernal, S.A.; San Nicolas, R.; Provis, J.L. Generalized structural description of calcium-sodium aluminosilicate hydrate gels: The cross-linked substituted tobermorite model. Langmuir 2013, 29, 5294–5306. [CrossRef] [PubMed] 31. Provis, J.L.; Myers, R.J.; White, C.E.; Rose, V.; van Deventer, J.S.J. X-ray microtomography shows pore structure and tortuosity in alkali-activated binders. Cem. Concr. Res. 2012, 42, 855–864. [CrossRef] 32. De Jong, B.H.W.S.; Brown, G.E., Jr. Polymerization of silicate and aluminate tetrahedra in glasses, melts, and aqueous solutions—I. Electronic structure of H6Si2O7, H6AlSiO71´, and H6Al2O72´. Geochim. Cosmochim. Acta 1980, 44, 491–511. [CrossRef] 33. Nazari, A.; Maghsoudpour, A.; Sanjayan, J.G. Characteristics of boroaluminosilicate geopolymers. Constr. Build. Mater. 2014, 70, 262–268. [CrossRef] 34. Williams, R.P.; van Riessen, A. Development of alkali activated borosilicate inorganic polymers (AABSIP). J. Eur. Ceram. Soc. 2011, 31, 1513–1516. [CrossRef] 35. Alonso, S.; Palomo, A. Alkaline activation of metakaolin and calcium hydroxide mixtures: Influence of temperature, activator concentration and solids ratio. Mater. Lett. 2001, 47, 55–62. [CrossRef] 36. Rovnaník, P. Effect of curing temperature on the development of hard structure of metakaolin-based geopolymer. Constr. Build. Mater. 2010, 24, 1176–1183. [CrossRef] 37. Sindhunata; van Deventer, J.S.J.; Lukey, G.C.; Xu, H. Effect of Curing Temperature and Silicate Concentration on Fly-Ash-Based Geopolymerization. Ind. Eng. Chem. Res. 2006, 45, 3559–3568. [CrossRef] 38. Bakharev, T.; Sanjayan, J.G.; Cheng, Y.-B. Effect of elevated temperature curing on properties of alkali-activated slag concrete. Cem. Concr. Res. 1999, 29, 1619–1625. [CrossRef] 39. Fernández-Jiménez, A.; Palomo, J.G.; Puertas, F. Alkali-a behaviour. Cem. Concr. Res. 1999, 29, 1313–1321. [CrossRef] 39. Fernández-Jiménez, A.; Palomo, J.G.; Puertas, F. Alkali-activated slag mortars: Mechanical strength behaviour. Cem. Concr. Res. 1999, 29, 1313–1321. [CrossRef] 40. Provis, J.; Fernández-Jiménez, A.; Kamseu, E.; Leonelli, C.; Palomo, A. Binder Chemistry—Low-Calcium Alkali-Activated Materials. In Alkali Activated Materials—State-of-the Art Report; Springer: Rotterdam, The Netherlands, 2014; Volume 2014, pp. 93–123. 41. Nugteren, H.W.; Ogundiran, M.B.; Witkamp, G.J.; Kreutzer, M. Coal Fly Ash Activated by Waste Sodium Aluminate Solutions as an Immobilizer for Hazardous Waste. 1. Dux References Using Rock Wool Wastes as Partial Replacement of Cement in Cement-Based Composites. Adv. Sci. Lett. 2012, 8, 489–494. [CrossRef] 14. Long, W. Mineral Fiber-Containing Paper for the Production of Gypsum Wallboard and Wallboard Product Prepared Therewith. Patent CA1192709A1, 3 September 1984. 15. Pranckeviˇcien˙e, J. Impact of Mineral Wool Production Waste on Properties of Sintered Ceramics. Ph.D. Thesis, Vilnius Gediminas Technical University, Vilna, Lithuania, 11 November 2011. 16. Talling, B.L.O.; Sarudis, M. Raw Material Briquette for Mineral Wool Production and Process for Its Preparation and Its Use. Patent US5472917, 5 December 1995. 17. Wei-Ting Lin, A.C. Rock wool wastes as a supplementary cementitious material replacement in cement-based composites. Comput. Concr. 2013, 11. [CrossRef] 18. Kinnunen, P.; Yliniemi, J.; Talling, B.L.O.; Illikainen, M. Rockwool waste in fly ash geopolymer composites. Mater. Cycles Waste Manag. 2015. under review. 19. Duxson, P.; Provis, J.L.; Lukey, G.C.; Mallicoat, S.W.; Kriven, W.M.; van Deventer, J.S.J. Understanding the relationship between geopolymer composition, microstructure and mechanical properties. Colloids Surf. Physicochem. Eng. Asp. 2005, 269, 47–58. [CrossRef] 20. Nugteren, H.W. Secondary Industrial Minerals from Coal Fly Ash and Aluminum Anodising Waste Solutions. Ph.D. Thesis, Technical University of Delft, Delft, The Netherlands, 10 January 2010. 21. Phair, J.W.; van Deventer, J.S.J. Characterization of Fly-Ash-Based Geopolymeric Binders Activated with Sodium Aluminate. Ind. Eng. Chem. Res. 2002, 41, 4242–4251. [CrossRef] 22. Bernal, S.; Provis, J.; Fernández-Jiménez, A.; Krivenko, P.; Kavalerova, E.; Palacios, M.; Shi, C. Binder Chemistry—High-Calcium Alkali-Activated Materials. In Alkali Activated Materials—State-of-the Art Report; Springer: Rotterdam, The Netherlands, 2014; Volume 2014, pp. 59–91. 23. Bernal, S.A.; San Nicolas, R.; Myers, R.J.; Mejía de Gutiérrez, R.; Puertas, F.; van Deventer, J.S.J.; Provis, J.L. MgO content of slag controls phase evolution and structural changes induced by accelerated carbonation in alkali-activated binders. Cem. Concr. Res. 2014, 57, 33–43. [CrossRef] 24. Walling, S.A.; Kinoshita, H.; Bernal, S.A.; Collier, N.C.; Provis, J.L. Structure and properties of binder gels formed in the system Mg(OH)2-SiO2-H2O for immobilisation of Magnox sludge. Dalton Trans. Camb. Engl. 2015, 44, 8126–8137. [CrossRef] [PubMed] 25. The International Centre for Diffraction Data (ICDD). The Powder Diffraction File; The International Centre for Diffraction Data (ICDD): Philadelphia, PA, USA, 2006. 26. Roylance, D. Stress-Strain Curves. Available online: http://www.saylor.org/site/wp-content/uploads/2012/ 09/ME1022.2.4.pdf (accessed on 14 December 2015). 27. Provis, J.L.; Lukey, G.C.; van Deventer, J.S.J. Do Geopolymers Actually Contain Nanocrystalline Zeolites? A Reexamination of Existing Results. Chem. Mater. 2005, 17, 3075–3085. 1. Dux References In Proceedings of the 2011 World Coal Ash WOCA Conference, Denver, CO, USA, 9–11 May 2011. y 42. Ogundiran, M.B.; Nugteren, H.W.; Witkamp, G.J. Immobilisation of lead smelting slag within spent aluminate—Fly ash based geopolymers. J. Hazard. Mater. 2013, 248–249, 29–36. [CrossRef] [PubMed] © 2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/).
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Like ships passing in the night? Nonstandard work schedules and spousal satisfaction in Finland, the Netherlands and the United Kingdom
Journal of family research
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Year: 2020 Rights url: https://creativecommons.org/licenses/by/4.0/ This is a self-archived version of an original article. This version may differ from the original in pagination and typographic details. Author(s): Malinen, Kaisa; Rönkä, Anna; Sevón, Eija Author(s): Malinen, Kaisa; Rönkä, Anna; Sevón, Eija Title: Like ships passing in the night? Nonstandard work schedules and spousal satisfaction in Finland, the Netherlands and the United Kingdom Title: Like ships passing in the night? Nonstandard work schedules and spousal satisfaction in Finland, the Netherlands and the United Kingdom This is a self-archived version of an original article. This version may differ from the original in pagination and typographic details. Please cite the original version: Malinen, K., Rönkä, A., & Sevón, E. (2020). Like ships passing in the night? Nonstandard work schedules and spousal satisfaction in Finland, the Netherlands and the United Kingdom. Journal of Family Research, 32(2), 192-213. https://doi.org/10.20377/jfr-359 Like ships passing in the night? Nonstandard work schedules and spousal satisfaction in Finland, the Netherlands and the United Kingdom Kaisa Malinen1, Anna Rönkä2, and Eija Sevón2 1 JAMK University of Applied Scienes, Jyväskylä. 2 University of Jyväskylä, Jyväskylä 1 JAMK University of Applied Scienes, Jyväskylä. 2 University of Jyväskylä, Jyväskylä Address correspondence to: Kaisa Malinen, School of Health and Social Studies, JAMK University of Applied Sciences, Piippukatu 2, FI-40100 Jyväskylä (Finland). Email: kai- sa.malinen@jamk.fi JFR – Journal of Family Research, 2020, Early View, 1–22 doi: 10.20377/jfr-359 1. Introduction Working spouses spend a considerable proportion of their time at work. One of the as- pects of work affecting the lives of spouses is the scheduling of work, that is, when the work is done. This frames family timetables, rhythms and experiences (see e.g., Presser 2003; Wright, Raley & Bianchi 2008). When working outside so-called office hours, em- ployees may find themselves in a situation where their schedules are often out of sync with the timetables of their partners, children and society. In contrast to the standard 8 am to 4 pm (or 9 am to 5 pm) Monday to Friday working day, nonstandard work schedules re- fer to work times that fall outside these hours (e.g., Presser 2003). ( g , ) This study examined whether working nonstandard work schedules is associated with spousal satisfaction. The study extends the existing research literature, which has mainly been conducted in the US, by investigating these phenomena in three European coun- tries: Finland, the Netherlands and the United Kingdom. The study used a dataset that oversamples the proportion of nonstandard workers and thus enables comparisons be- tween different types of nonstandard work schedules, as suggested by Presser (2003, 2004; see also Maume & Sebastian 2012). The study also took into account the multidimension- al nature of working time and examined the roles of other work time-related factors, namely, changes in and influence over one’s work times and one’s partner’s work sched- ules. In addition to quantitatively examining whether connections exist between different aspects of working time and spousal satisfaction, this study addressed the qualitative ques- tion of how. Namely, the study examined what meanings parents attribute to their working times from the viewpoint of their spousal relationships. The study focused on workers with children, whose spousal relationship is mingled with parental duties. Abstract This study examined the associations of work schedules and spousal satisfaction among Finnish (n = 347), Dutch (n = 304) and British (n = 337) parents. In addition to comparing parents with nonstandard schedule with parents in regular day work, the study examined separately the roles played in spousal satisfaction of morning, evening, night and weekend work and other working time-related variables (working hours, changes in and influence over one’s work schedules and spouse’s work schedule). The three-country data were ana- lyzed using structural equation modeling with a multigroup procedure in Mplus. Little ev- idence for negative associations of work schedules and related factors with spousal satis- faction was found among the present European employees. No between-country differ- ences were found in the examined associations. The quantitative analyses were supple- mented with content analysis of parents’ descriptions of the experienced effects of their working times on their spousal relationship. Parents described their working times mostly as having a negative influence on their possibilities of being together, organization of daily life, psychological and physiological reactions and spousal communication. Some, howev- er, also mentioned benefits and finding solutions to problems related to their working times. Key words: content analysis, cross-cultural, nonstandard working times, spousal satisfac- tion, structural equation modeling, work schedules JFR – Journal of Family Research, 2020, Early View, 1–22 doi: 10.20377/jfr-359 2 1.1 Earlier research on the associations between work schedules and spousal relationship well-being Research on how nonstandard work schedules affect family life has mainly been atheoret- ical. Grzywacz (2016), however, identifies four distinct, albeit interrelated, frameworks for considering the possible impacts of nonstandard work schedules on the balance of work and family life. Although originally created to understand the mechanisms relating to work-family reconciliation, these frameworks may also increase understanding on the ef- fects of working time on spousal well-being. According to Grzywacz (2016), the effects of nonstandard work schedules on family life may be related to disturbed circadian rhythm and its physiological consequences (e.g., impaired sleep; biobehavioral framework) and/or specific psychological costs of working nonstandard times (e.g., irritability, distractedness and social detachment; social-cognitive framework). Nonstandard working times may also affect family life through the physical absence from home (social disruption framework) and an individual’s beliefs that s/he can- not be a good spouse or parent because of her/his working times (socialization framework). These beliefs may act as a self-fulfilling prophecy, leading to social withdrawal or other harmful behavior. Such consequences may cause individuals to feel inadequate and una- 3 ble to meet their family responsibilities. These frameworks all share the assumption that the consequences of work at nonstandard times are mainly negative in nature. ble to meet their family responsibilities. These frameworks all share the assumption that the consequences of work at nonstandard times are mainly negative in nature. q y g Earlier empirical research findings on the associations of nonstandard working times and family life accord with the above-mentioned theoretical frameworks, especially the bi- obehavioral, social-cognitive and social disruptive frameworks. Nonstandard work times are known to have negative consequences for employees’ mental and physical health and to disturb the quantity and quality of sleep (Peruzzi et al. 2007; Totterdell 2005; Vogel et al. 2012). Nonstandard work times also affect parents’ time use. Parents working nonstand- ard times are known to protect their time with children at the cost of spousal and personal time (Wight et al. 2008; see also Gracia & Kalmijn 2016). It is thus unsurprising that pre- vious studies have found engagement in this type of a work to be linked to an increased probability of relationship break-down (e.g., Presser 2000; Täht 2011; White & Keith 1990) and diminished relationship quality (e.g., White & Keith 1990). The longitudinal study by Jekielek (2003) further confirmed that nonstandard work schedules are a cause of deterio- ration in relationship quality over time. 1.1 Earlier research on the associations between work schedules and spousal relationship well-being However, other studies suggests that working nonstandard work schedules is associated with a diminished gender gap in the division of housework and parenting (Barnett & Gareis 2007; Presser 2003), a finding which could positively affect the spousal relationship. This overall picture of the effects of nonstandard work becomes more complex when account is taken of the type of nonstandard work performed. Research suggests that work- ing evenings and nights and, especially for women, rotating or varying shifts seem to be most harmful types of nonstandard work for spousal relationship quality or stability (Da- vis et al. 2008; Kalil, Ziol-Guest & Epstein 2010; Maume & Sebastian 2012; Mills & Täht 2010; Perry-Jenkins et al. 2007). Perry-Jenkins and colleagues (2007) propose that rotating shifts may be harmful for family life because they make it difficult to establish regular routines. In addition to negative associations between night work and rotating or varying shifts, Täht (2011; see also Mills & Täht 2010) found weekend work to be a risk for the quality and stability of spousal relationships among Dutch couples. q y y p p g p The diversity of research findings on the effects of different types of nonstandard work led Presser (2003, 2004) to emphasize the need to compare schedule types rather than examining nonstandard work as a unified phenomenon. Earlier studies have pre- dominantly treated nonstandard work as a set of exclusion categories (e.g., evening work, rotating shifts, and regular day work) and defined a person’s type of work schedule as the schedule most frequently worked by that person. In practice, however, the boundaries be- tween standard day work and nonstandard work are blurred (see also, Grzywacz 2016). Dunifon, Kalil, Crosby, Sy and DeLeire (2013) found that half of the participating mothers worked only either nonstandard or standard schedules, whereas other half reported that they worked both standard and nonstandard working hours. Moreover, Eurostat (2014) sta- tistics show that a notable proportion of European employees occasionally work evenings, nights and weekends. Consequently, a study procedure that obliges a participant to de- scribe her or his work situation by selecting only one type of work schedule may not re- flect reality. y Several other factors also introduce variability into parents’ work schedules. For ex- ample, working long hours may complicate spousal and family life (see Hostetler et al. 2012). 1.1 Earlier research on the associations between work schedules and spousal relationship well-being On the other hand, the negative influences of nonstandard work may not be pre- 4 sent when the employee has control over her or his nonstandard work times (Jekielek 2003; see also Pedersen & Jeppesen 2012). Experiencing changes in work schedules is a central feature of varying and rotating work times, which, as already stated, is linked with challenges in spousal relationships. Also, as Craig and Brown (2017) state, “time is both an individual and a family resource” (p. 225). This means that in dual-earner families, the partner’s type of work schedule may also influence spousal experiences. Davis and col- leagues (2008) found that individuals reported greater marital instability when one or oth- er partner worked nights. In contrast, both Mills and Täht (2010) and Perry-Jenkins and colleagues (2007) found that partnership quality was linked only with the individual’s own and not her or his partner’s work schedules. p If, as the current literature suggests, the impacts of nonstandard work may be highly individual and vary along many dimensions of work characteristics, a more qualitative ap- proach is called for. Such an approach could reveal, for example, whether and, if so, how individuals with similar working time arrangements perceive their situation differently, for example, as either a problem or a benefit. 1.2 Work and family in Finland, the Netherlands and the United Kingdom 1.2 Work and family in Finland, the Netherlands and the United Kingdom Nonstandard working times are widely prevalent in Europe, including in Finland, the Netherlands and the United Kingdom (Eurostat 2014). For example, evening work is done at least sometimes by more than half of Finnish and Dutch men, whereas more than half of Dutch men work on Saturdays. Despite the high prevalence of nonstandard work schedules in Europe, most of what is known about the impact of work schedules in family life is based on studies conducted in the US context. This study focuses on parents in three European countries with different working time practices, care policies and welfare regimes. Finland represents a social democratic, the Netherlands a corporatist and the UK a liberal welfare regime (Esping-Andersen 1990). g ( p g ) Finland has high rates of maternal employment and full-time work, although the number of weekly working hours is below the European mean (OECD 2014). With respect to nonstandard working times, shift work is more common among mothers in Finland than elsewhere in Europe (Eurostat 2014). However, the life of Finnish families with non- standard work schedules is facilitated by a broad range of social security measures (Forsberg 2005; Pfau-Effinger 2004). The accessibility of high-quality municipal early childhood education and care is guaranteed by law, and flexibly scheduled early childhood education and care for children whose parents work nonstandard schedules is widely available (Kröger 2011; Rönkä et al. 2019). Many mothers of young children also work in the Netherlands (OECD 2014), where part-time work is largely supported by the state as a way of reconciling work and parenthood (Pfau-Effinger 2004), and thus Dutch mothers, especially, and fathers work part-time more often than their European counterparts (OECD 2014). Public childcare is widely available in the Netherlands, some centers having extended opening hours, and is largely subsidized by a state childcare allowance (De Schipper et al. 2003; Statistics Neth- erlands 2014). Given the part-time working culture and the value placed on home-based care for children, child care in the Netherlands is commonly part-time only (Kröger 2011) 5 with “tag-team parenting” and parental working time desynchronization as alternative strategies for Dutch families (Mills & Täht 2010). with “tag-team parenting” and parental working time desynchronization as alternative strategies for Dutch families (Mills & Täht 2010). In the United Kingdom, the maternal employment rate is slightly below the EU aver- age and clearly lower than in the two other countries studied here (OECD 2014). 1.2 Work and family in Finland, the Netherlands and the United Kingdom The UK, with its liberal regime, favors unregulated markets and individual responsibility for work- family reconciliation (Abendroth & Den Dulk 2011). The costs of childcare services for families in the UK are high, and the average number of hours children attend public childcare services are very low (Kröger 2011). Although these cross-country differences do not provide precise information on the impact of work schedules on spousal satisfaction in these three countries, they illustrate the considerable diversity in the spousal life of parents with nonstandard schedules. For example, in Finland, where families working nonstandard schedules are supported by the availability of public, flexibly scheduled early childhood education and care, the full-time dual-earner model may put pressure on the spousal relationship. In the Netherlands, pa- rental part-time work and flexible work arrangements encourage parents to take turns in parenting; however, this may also diminish couple time. In the UK, while the home- mother culture may ease work-family reconciliation, parents may feel they lack institu- tional support for their family life. 1.3 This study This study contributes to the literature on the associations of work schedules and spousal satisfaction by examining parents in three European countries, utilizing both multifaceted measures of work schedules and parents’ descriptions on experienced effects of their working times. The following questions were addressed: Research question 1: How are parents’ work schedules associated with their evaluations of spousal satisfaction? In addition to investigating the associations of work schedules and spousal satisfaction by comparing those who work nonstandard schedules and those in regular day work, the study examined in more detail whether different amounts of work performed during early mornings, evenings, nights and weekends is associated with spousal satisfaction. p Hypothesis 1: In all three countries, we expected working nonstandard schedules, es- pecially working nights, to be connected with lower spousal satisfaction than working a regular day-work schedule. Due to the conflicting and weak links found in previous re- search, we expected to find only weak associations. Research question 2: How are other work time-related factors associated with spousal satisfaction? Hypothesis 2: We hypothesized that, in all three countries, working more hours, hav- ing less influence on and experiencing more changes in one’s work schedules and having a partner with a nonstandard work schedule would be associated with low spousal satisfac- tion. Research question 3: How do parents describe the experienced effects of their working times on spousal satisfaction? Hypothesis 3: We expected parents’ descriptions to overlap but also go beyond Grzywacz’s (2016) frameworks on the impact of nonstandard working time on family life. 6 In addition to parents attaching negative meanings to nonstandard schedules we expected to find parents attaching positive meanings to working non-standard hours, as findings on, for example, tag-team parenting (see Mills & Täht 2010) suggests that nonstandard work schedules may be well suited to the needs of some families. The hypothesis was also based on the conflicting findings earlier reported on the link between work schedules and spousal life. p Research question 4: Do the associations between work schedules and other work time- related factors and spousal satisfaction differ between the Finnish, Dutch and British par- ents? In the absence of previous research comparing European countries and owing to the complexity of the various country-specific aspects that could influence the associations be- tween work schedules and spousal satisfaction, we set no specific hypotheses on cross- country differences in these associations. 2. Method 2.1 Data collection 2.1 Data collection The data of the present study were drawn from data collected for the Families 24/7 re- search project investigating nonstandard work schedules from the perspectives of parents, children and day care personnel in Finland, the Netherlands and the UK. The project fo- cused on families with children under age 13. In addition to parents working so-called nonstandard schedules, web-questionnaire data were also collected from parents working in regular day work to enable comparison between the two groups. In all three countries, participants were recruited through work organizations, childcare centers, trade unions and word of mouth. In contrast to the Netherlands and the UK, almost all the child care centers in Finland involved in the study had extended hours or operated 24/7 (i.e., flexibly scheduled early childhood education and care centers), and almost all the parents of the families using these day care centers worked a nonstandard schedule. Consequently, the recruitment process reached more workers with a nonstandard schedule in Finland than in the other two countries. To be selected for the subsample used in this study, partici- pants were required to have a heterosexual (cohabiting or marital) spousal relationship and to be employed. Applying these selection criteria resulted in a data set of 988 partici- pants. Participant background information is presented in Table 1. As described later, the analyses were controlled for these between-country differences. Owing to the recruitment procedures used, evaluation of the survey response rate was not possible. For example, day care centers do not supply information about their client families, and the exact number of employees who have children aged 0–12 years is not re- ported by work organizations or trade unions. Thus, evaluation of the number of parents who received information about the survey but declined to participate could not be per- formed. 2.1 Data collection 7 Table 1: Background information on the Finnish, Dutch and British participants Finns (n = 347) Dutch (n = 304) British (n = 337) Difference test M (SD) or % M (SD) or % M (SD) or % Background variables % of females 74.64 86.18 81.60 χ2(2) = 14.14, p = .001 Age in years 35.72 (5.67) 35.54 (5.29) 37.97 (5.75) F(2,972) = 19.11, p < .001, UK > FIN, NL % of tertiary education 41.91 71.29 79.34 χ2(2) = 113.92, p < .001 % of married 72.91 72.70 78.04 ns Length of spousal rela- tionship in years 11.25 (5.78) 11.69 (5.10) 12.59 (5.60) F(2, 977) = 5.14, p = .006, UK > FIN Number of children at home 1.98 (0.92) 1.85 (0.88) 1.76 (0.72) F(2, 986) = 5.89, p = .003, FIN > UK Age of youngest child in years 3.94 (2.50) 2.48 (2.55) 3.87 (2.91) F(2, 980) = 30.30, p < .001, FIN, UK > NL Financial situation (0 = worst, 10 = best) 5.61 (2.15) 6.39 (1.86) 5.34 (2.13) F(2,980) = 21.77, p > .001, NL > FIN, UK Work schedule % with nonstandard work schedule 71.01 30.00 24.10 χ2(2) = 177.82, p < .001 Morning work χ2(4) = 75.69, p < .001 0 times / month 54.39 81.61 74.24 1–2 times / month 12.28 8.36 12.42 >2 times / month 33.33 10.03 13.33 Evening work χ2(4) = 66.21, p < .001 0 times / month 16.91 32.11 27.68 1–2 times / month 17.20 33.44 26.79 >2 times / month 65.89 34.45 45.54 Night work χ2 (4) = 18.65, p = .001 0 times / month 63.85 76.43 70.21 1–2 times / month 11.95 11.45 13.98 >2 times / month 24.20 12.12 15.81 Number of weekend shifts / month 3.00 (2.25) 1.20 (1.79) 1.46 ( 2.06) F(2, 967) = 73.76, p < .001, FIN > NL, UK Table 1: Background information on the Finnish, Dutch and British participants 8 Table 1: Background information on the Finnish, Dutch and British participants (continued) g p p (continued) Other work time variables Working hours per week 37.10 (8.35) 30.39 (8.79) 36.21 (10.87) F(2, 965) = 47.11, p < .001, FIN, UK > NL % having influence on schedules 44.71 68.60 75.60 χ2(2) = 74.97, p < .001 % experiencing chan- ges in schedules 37.50 12.12 34.94 χ2(2) = 58.37, p < .001 Spouse’s work schedule (only for those with an em- ployed spouse) % of spouses with nonstandard schedule 52.67 22.13 28.67 χ2(2) = 59.59, p < .001 Note: Effects were tested with ANOVAs and Tukey’s post-hoc tests (continuous variables) and crosstabulations, χ2-tests and adjusted standardized residuals (categorical variables) Note: Effects were tested with ANOVAs and Tukey’s post-hoc tests (continuous variables) and crosstabulations χ2-tests and adjusted standardized residuals (categorical variables) 2.2 Measures The questionnaire was prepared in English. In the Finnish and Dutch questionnaires, questions for which official translations did not already exist were back-translated. In the back translations, the English version was first translated into Finnish/Dutch by the re- search team and then back into English by an independent official translator. Relationship satisfaction. Spousal relationship quality was assessed from the perspec- tive of spousal satisfaction and measured using a four-item version of the Couple Satisfac- tion Index (CSI) developed by Funk and Rogge (2007). For each item (“Please indicate the degree of happiness, all things considered, of your relationship”) a 7-point scale from 0 (extremely unhappy) to 6 (perfect) was used, whereas with the three other items (“I have a warm and comfortable relationship with my partner”; “How rewarding is your relation- ship with your partner?”; “In general, how satisfied are you with your relationship?”) a 6- point scale (0 = not at all/ not at all true, 5 = completely / completely true) was used. In Gra- ham and Diebels’s (2011) reliability-generalization meta-analysis, the CSI proved to be a promising measure, showing a mean α of .94. In the present study, αs for the composite score were .95 (FIN), .88 (NL), and .95 (UK). Work schedules. Work schedules were measured in two ways. First, participants’ self- identified work schedule was measured with the question “What is your working time pat- tern?” The original seven response alternatives were dichotomized into regular day work schedule (= 0) and nonstandard schedule (= 1; including evening/night/morning work, ir- regular work, shift work and other work schedules). Second, participants were asked how often they worked during specific hours of the day or on specific days per month. The questions measuring evening and night work were drawn from the European Working Conditions Survey 2010 (EWCS; Eurofound 2010). For evening work, the question was 9 “How many times a month do you work (including overtime work) in the evening, for at least 2 hours (between 18.00 and 22.00)?” Working nights was similarly measured with the time frame 22.00 to 05.00 and morning work with the time frame 05.00 to 07.00). The response options were never (= 1), once (= 2), twice (= 3) and more than twice (= 4). In the present analyses, the categories once and twice were combined. 2.2 Measures As morning, evening and night work were each measured with three ordinal categories (0 times/month, 1–2 times/month, more than 2 times/month), two dichotomous variables were created for each of these types of nonstandard work time. The reference category was 0 times/month. To measure weekend work, the answers to the questions on Saturday and Sunday work (“How many times on average a month do you work on Saturdays (Sundays)?” (EWCS; Euro- found 2010) were summed. Other work time-related variables. The question on working hours was “How many hours do you normally work a week in your main job, including any paid or unpaid overtime (regardless of your contracted hours)?”. Influence over one’s work schedules was measured with a structured question: “How are your working time arrangements set?”. For the pur- poses of this article, the response option They are set by the company /organization with no possibility for changes was coded as 0 and the other options (I can choose between several fixed work schedules determined by the company /organization, I can adapt my working hours within certain limits [e.g. flexitime] and My working hours are entirely determined by myself) as 1. In addition, to evaluate changes in work schedules, participants were asked “Do changes to your work schedule occur regularly?” (1= yes, 0= no). The variable measuring spouse’s work schedule included those whose spouse was employed, that are, dual-earners. The question and response categories were similar to those on the participant’s own work schedule. The analyses did not include participants with unemployed or self-employed spouses as the number of these participants was rela- tively low (spouse unemployed: FIN n = 38, NL n = 5, UK n = 23; spouse self-employed: FIN n = 39, NL n = 42, UK n = 30). Background variables. Information about several background factors was gathered with questionnaires: gender (1 = woman, 0 = man), participant’s age in years, highest education (1 = tertiary, 0 = lower than tertiary), marital status (1 = married, 0 = not married), length of the spousal relationship in years, number of children living at home, and age of the youngest child in years. Self-rated financial situation of the family was elicited with the question “How would you rate your family’s financial situation these days?” Answers were given on an 11-point scale from the worst possible financial situation (= 0) to the best possible financial situation (= 10). 2.3 Statistical Analyses Multigroup procedure in structural equation modeling (SEM) was used to analyze the data from all three countries. The analyses were conducted with the Mplus statistical package (version 7.11.; Muthén & Muthén 2004). The estimation method used was MLR, which produces maximum likelihood parameter estimates with standard errors and a chi-square test statistic that are robust to the nonnormality and nonindependence of observations (Muthén & Muthén). Model fit was assessed using chi-square, Tucker-Lewis index (TLI), root mean square error of approximation (RMSEA), and standardized root mean square residual (SRMR). Nonsignificant chi-square p-values, RMSEA with values ≤.06, SRMR with values ≤.08 and TLI with values ≥.95 indicated good model fit (Hu & Bentler 1999). The significance of the differences in chi-square values between the nested models was evaluated using a scaled chi-square difference test (Satorra & Bentler 1994). g q ( ) The analysis was started by testing the invariance of the latent variable. When compar- ing different sociocultural groups (e.g., countries) in psychological constructs, similarity in the measurement level of the latent constructs in each group is a prerequisite for mean- ingful comparisons (Little 1997; Milfont & Fischer 2010). For this purpose, the measure- ment models for couple satisfaction were first estimated separately for each of the three countries to examine whether the proposed factor structure fits the empirical data for each group. Next, to test metric invariance, a freely estimated (i.e., no requirements for invari- ant loadings) multi-group model was compared with the model in which the item load- ings were constrained to be equal between the groups using the Satorra-Bentler chi-square difference test. To answer RQ1 and RQ2, exogenous variables were added to the model in a stepwise procedure. In step 1 the background variables, in step 2 the dichotomous, self-identified work schedule variable, in step 3 the other work schedule variables, and in step 4 the other work time-related variables were added to the model. At each step, exogenous variables with nonsignificant (using p < .10 as a limit here) path coefficients in all three countries were omitted from the analysis before proceeding to the next step. To answer RQ 4, invar- iance of the path coefficients between the countries was tested with the Satorra-Bentler test. Finally, variables with nonsignificant path coefficients (using p < . 05 as a limit here) in all three countries were omitted from the final model. 2.3 Statistical Analyses The analysis on the associations of spouse’s work schedule with spousal satisfaction (RQ2) was only performed for parents with an employed spouse, that is, participants with a spouse who did not work or was self-employed were excluded from this analysis. The di- chotomous variable of spouse’s work schedule was included in the above-mentioned un- constrained model in step 5. Country differences in this association (RQ4) were tested with a procedure similar to that described above. 2.2 Measures Qualitative open-ended question on the experienced effects of working times on the spousal relationship. All participants irrespective of their work schedules were asked the open- ended question “How do the working hours of you or your spouse affect your spousal rela- tionship?” The answers given by the Dutch participants were translated into English by a professional translator. Invalid answers were removed from the analysis (no answer or dash n = 277; unclear answer n = 11, answer clearly not related to working times n = 17), yielding a total of 683 valid descriptions. Of these, 64 (9.37%) directly stated that working times had no effect on the spousal relationship and hence were excluded from the anal- yses. 10 2.4 Analysis of the qualitative data Content analysis was applied to the open-ended questionnaire data, utilizing Grzywacz’s (2016) frameworks where applicable. Data were reviewed to identify two aspects, content and appraisal. First, two researchers independently reviewed the data to identify relevant 11 contents of each description and to group these contents into overarching themes. Second, the data were also reviewed to identify how parents evaluated the impact of working time, that is, to identify appraisals. For example, the content of the description “My spouse works long hours, participates little in domestics” (id 562, a British mother) would be “or- ganization of daily life” and the appraisal “negative”. The researchers then met to discuss and compare their tentative versions of the con- tent themes and appraisals and settled on the final versions presented in the Results sec- tion. The data were then quantified by coding the descriptions by both their identified con- tents and appraisals. Both content and appraisal were treated as non-exclusive, that is, sev- eral contents and several appraisals could be coded for each description. Data were coded by two researchers and in cases of disagreement the researchers reached consensus through discussion. Cross-tabulations were used to compare parents with different work schedule situa- tions in the family (i.e., both spouses in regular day work vs. at least one partner with non- standard work schedule; this analysis included dual-earners only) and parents from differ- ent countries in the prevalence of specific contents and appraisals. 3. Results 3.1 Preliminary analyses: Structure of the CSI in the three countries Among the Finnish, British and Dutch samples, all the items loaded significantly on the latent factor (standardized factor loadings in freely estimated model .56–.95). All loadings except for the item “How rewarding is your relationship with your partner?” among the Dutch participants could be set equal between the countries based on the Satorra-Bentler significance test (constrained model: χ² (11) = 27.49, p = .004, TLI = 0.99, RMSEA = .07, SRMR = .04). Consequently, the requirement of metric invariance between the countries was fulfilled. 3.2 Associations of participants’ work schedules and other work time-related factors with spousal satisfaction in the three countries In step 1, age, marital status, number of children and financial situation were associated (p < .10) with the latent variable of spousal satisfaction in at least one of the countries. Other background variables showed no statistically significant paths with the latent varia- ble in any of the countries and were thus removed from the model. In step 2, self- identified work schedule was not associated with the latent variable. In step 3, the only work schedule variable connected with the latent variable was the dichotomous variable for occasional (1–2 times/month) night work, and hence both dichotomous variables for night work were retained in the model. In step 4, changes in and influence over work schedules were connected with the latent variable, and hence these variables were retained in the model. 12 The Satorra-Bentler test showed that all path coefficients could be set equal between the countries. After so doing, number of children, influence over work schedules and changes in work schedules were no longer associated (p > .10) with the latent variable and were thus removed from the model (constrained model: χ² (66) = 99.14, p = .005, TLI = 0.99, RMSEA = .04, SRMR = .04; see Figure 1). High spousal satisfaction was associated with being younger, being married and a better self-reported financial situation. In addi- tion, occasional night work (1–2 times/month) showed a negative association with the la- tent variable. The difference between occasional and more frequent night work was not statistically significant as the 95 % confidence intervals of the path coefficients of occa- sional, 95 % CI [-.46, -.07], and more frequent night work, 95 % CI [-.24, .08], were over- lapping. g The analyses on spouse’s work schedule were performed for only the subsample of the participants who had an employed spouse. When the variable of spouse’s schedule was added to the unconstrained model described above in step 5, this variable was associ- ated with the CSI in the Dutch sample (spouse’s nonstandard schedule was associated with lower satisfaction), and thus the variable was retained in the model. After constrain- ing all the path coefficients to be equal between the countries, as indicated by the Satorra- Bentler test, spouse’s work schedule was not associated (p > .05) with the latent variable and was thus removed from the model. 3.3 Parents’ descriptions of the meaning of working time in spousal relationship 3.3 Parents’ descriptions of the meaning of working time in spousal relationship 3.3 Parents’ descriptions of the meaning of working time in spousal relationship Content. Table 2 presents the five content themes identified in the data. Many descriptions contained several themes, and these were often presented as a chain of events (e.g., “Tiredness from work sometimes causes tension”; id 1116, a Dutch mother). The theme most often mentioned in the parents’ descriptions, absence/presence, focused on the amount of time and/or (lack of) possibilities for being present. The theme organization of daily life included descriptions of how working times affected the activities of daily family life, such as the division of labor, housework, parenting and hobbies. Working times were also seen to affect the spousal relationship through different kind of psychological reactions, such as irritability, promoting an understanding attitude, habituation and appreciation. Parents reported that their working times also caused physical reactions; that is, they men- tioned the physical consequences of their working times, most commonly tiredness. Ef- fects related to spousal interaction and the intimate spousal relationship, such as disputes, discussions and closeness were classified as spousal communication and intimacy. The cat- egory Other included descriptions in which the content was either not mentioned or not included in any of the other themes. When families with diverse working schedules and parents from different countries were compared, cross-tabulations showed some differences in the prevalence of content themes (see Table 2). Absence/presence was more often mentioned by parents in families where one or both parents worked nonstandard schedules whereas physical reactions and the organization of daily life were more often described in families where both parents worked a regular day schedule. Physical and psychological reactions were more often de- scribed by the British than Finnish and, in case of physical reactions, Dutch parents. The Finnish parents more often described absence/presence than the British parents, and the Dutch parents more often referred to the organization of daily family life than the Finnish parents. p Appraisal. The vast majority of the parents’ descriptions (n = 497, 80.3%) portrayed working times as a problem for their spousal relationship (e.g., “I work Monday-Friday days, and he works shifts of 6 days on and 4 days off of various patterns. We can sometimes be passing ships in the night! 3.2 Associations of participants’ work schedules and other work time-related factors with spousal satisfaction in the three countries Figure 1: Multigroup SEM model explaining spousal satisfaction, unstandardized coeffi- cients (standardized coefficients for Finland/the Netherlands/and the United Kingdom in parentheses) ∗p < .05; ∗∗p < .01; ∗∗∗p < .001 Figure 1: Multigroup SEM model explaining spousal satisfaction, unstandardized coeffi- cients (standardized coefficients for Finland/the Netherlands/and the United Kingdom in parentheses) Figure 1: Multigroup SEM model explaining spousal satisfaction, unstandardized coeffi- cients (standardized coefficients for Finland/the Netherlands/and the United Kingdom in parentheses) ∗p < .05; ∗∗p < .01; ∗∗∗p < .001 13 3.3 Parents’ descriptions of the meaning of working time in spousal relationship This means we have few evenings to do social activities and sometimes feel like single parents.”; id 841, a British mother). Nevertheless, a notable proportion of parents (n = 108, 17.4 %) also described their working times as benefiting their spousal relationship (e.g., “Positively. The father can also have a moment alone with the children without the mother being present”; id 57, a Finnish mother). In addition, rather than just focusing on either positive or negative effects, many parents mentioned solutions and coping strategies used to tackle the negative effects of parental working times (n = 52, 8.4%; e.g., “We don’t get much family time and even less time for just being together as a couple. When sensibly organized, everyday life, however, runs smoothly enough and it doesn’t seem to have a specially adverse effect on our relationship as a couple.”; id 474, a Finnish mother). Appraisals were unclear in 4.0 per cent (n = 25) of cases. 14 Table 2: Content themes Note: NS = parents in families where either or both parents work nonstandard schedules; DW = parents in fami- lies where both parents work in regular daywork Content theme Example Prevalence Differences between family work schedule situations Differences between countries n % Absence/ presence “Allows us to spend more day time together as a couple. 4. Discussion This study examined whether and, if so, how parents’ working schedules are associated with their satisfaction with their spousal relationship. Utilizing quantitative and qualita- tive data from three European countries - Finland, the Netherlands and the United King- dom - various aspects of work schedules were analyzed with the aim of broadening under- standing of the associations of work schedules and spousal relationship quality. Based on earlier research, it was hypothesized that working nonstandard schedules, working more hours and having less influence on and experiencing more changes in one’s work sched- ules would be negatively associated with spousal satisfaction. We also expected that par- ents would not only describe the experienced effects of work schedules on their spousal relationship in line with Grzywacz’s (2016) framework but they would also describe effects not observed by earlier studies. No specific hypotheses on cross-country differences were set. With respect to hypotheses 1 and 2, the results showed weak support for the quantita- tive connections between different aspects of work schedules and spousal satisfaction among parents in three European countries. When parents in regular day work were compared with those working nonstandard times, no associations were found between work times and spousal satisfaction, except for night work. Specifically, working nights occasionally was associated with diminished spousal satisfaction. Night work has also earlier been shown to pose unique challenges for the social life and well-being of parents (Su & Dunifon 2017) by, for example, causing physiological stress and disturbance of the sleep-wake rhythm (Totterdell 2005; Vogel et al. 2012; see al- so Grzywacz 2016). The present study extends the research literature by taking into ac- count the amount of work done outside office hours. When night work is done only occa- sionally, families may not have established well-functioning practices for ensuring that a parent has sufficient sleep after a night at work. Another explanation relates to the nature of the jobs that involve occasional night work. It is possible that these jobs have important features which our control variables did not reflect but which – rather than occasional night work per se – relate to low spousal satisfaction. In this study, in comparison to the findings of earlier research, which has mainly been conducted in the US, relatively few quantitative associations were observed between work schedules and spousal satisfaction. 3.3 Parents’ descriptions of the meaning of working time in spousal relationship Sometimes it means we can't attend evening functions as a couple”; id 1417, a British mother 367 59.3 ꭓ2 (1) = 15.534, p < .001; adj.res: NS 3.9, DW -3.9 ꭓ2(2) = 12.32, p = .002; adj.res: FIN 3.3, UK -2.9 Organization of daily life “When a busy wife has to take care of driving children to their hobbies, preparing food, cleaning…”; id 597, a Finnish father 199 32.1 ꭓ2 (1) = 6.583, p = .010; adj.res: NS -2.6, DW 2.6 ꭓ2 (2) = 23.33, p < .001; adj.res: FIN -4.6, NL 3.2 Psychological reactions “Sometimes a lot of alternating shifts mean we appreciate it all the more when we are together.”; id 1584, a British mother 133 21.5 ns ꭓ2 (2) = 19.49, p < .001; adj.res: FIN -3.7, UK 4.2 Physical reactions “If my partner regularly has work via the temping agency, he is often tired in the evening, and the weekends I have to work are quite a challenge for him.”; id 285, a Dutch mother 94 15.2 ꭓ2 (1) = 3.971, p = .046; adj.res: NS -2.0, DW 2.0 ꭓ2 (2) = 34.76, p < .001; adj.res: FIN -3.1, NL -3.2, UK 5.9 Spousal communica- tion and intimacy “Often a source of conflict due to competing demands”; id 260, a British father 81 13.1 ns ns Other “Badly”; id 1984, a British father 52 8.4 ns ns 15 The results of the cross-tabulations showed no difference in how families with diverse working time arrangements evaluated the effects of working time. However, Dutch par- ents (adjusted residual = 8.6) described their working times as a benefit more often than their Finnish (-2.9) and British counterparts (-4.7), ꭓ2 (2) = 75.22, p < .001. They also re- ported working time-related problems less often (adjusted residual = -7.2) than the British parents (4.8), ꭓ2 (2) = 54.69, p < .001. 4. Discussion Together with Täht’s (2011) findings, this study sug- gests that in the three European countries studied, nonstandard work schedules may not be as strongly associated with spousal satisfaction as appears to be the case in the US. To our knowledge, the only study comparing European and US employees on the associa- 16 tions between nonstandard schedules and family life Täht (2011) showed that nonstand- ard work schedules were less strongly associated with relationship dissolution among the Dutch than US participants. For example, in the areas of employment protection and ma- ternal and paternal leaves, the parents in the three European countries represented in this study are in a stronger position than their US counterparts (OECD 2014; Täht 2011), a factor which may ease the spousal life of parents working nonstandard schedules. y p p g Our qualitative findings showed a clear overlap with Grzywacz’s (2016) frameworks as proposed by our hypothesis 3. According to the parents, working times affected their spousal relationship via their physical and psychological well-being, organization of daily life and possibilities to be present in daily family life. Broadening Grzywacz’s frameworks, we also found that the effects of working times, as reported by parents, were on spousal communication and intimacy. Working times were described as a source of conflict, but also of agreement and discussion. Most parents appraised the impact their working times on their spousal relationship as detrimental. A notable proportion, however, mentioned that their working times also had benefits for their spousal relationship, thereby illustrating the diversity in parents’ ex- periences. Also in line with our quantitative results was the finding that whether parents described their working times as problematic or beneficial or as something they were able to accommodate to was not found to be conditional on their work schedules. The results of our content analysis may reveal a further possible explanation for the scarcity of quantitative associations found between work schedules and spousal relation- ship quality. Many parents, rather than just listing the pros or cons of their working times, reported having found effective solutions and coping strategies to counter the negative ef- fects. For example, adopting an accepting attitude towards one’s own life situation or uti- lizing flexible childcare may act as a protective factor against the risk presented by non- standard working times. 4. Discussion It is important to note that the parents in the study had relatively long relationship histories and thus it is possible that during their relationship they had learned to cope with the possible challenges caused by their working times. Those suffer- ing most from the negative effects of their working times may have separated earlier in their relationship history and thus are not represented in this study. y y Interestingly, with respect to research question 4, although the structural equation modelling revealed no quantitative differences between the three countries, the content analysis showed some differences between the countries in how parents evaluated the ef- fects of working time on their spousal relationship. Namely, the Dutch parents described these effects as beneficial more often than either the Finnish or British parents. Previous studies utilizing the present data set also suggest that nonstandard working times are more positively experienced by Dutch parents than their British and Finnish counterparts (Rönkä, Malinen, Sevón, Metsäpelto & May 2017; Tammelin, Malinen, Verhoef, & Rönkä 2017). ) In reviewing the results of this study, it should be remembered that the study utilized cross-sectional data and thus research using a longitudinal design would be needed to complement the present findings. Another limitation of this study is the relatively limited sample size. To verify that the lack of significant findings in the SEM analyses was not ex- plained by the relatively limited sample size, simpler analyses were also run. For each type of nonstandard work time (i.e., morning, evening, night and weekend work) a separate 17 analysis in which only the nonstandard work variables in question were used as exoge- nous variables (i.e., omitting background or other work-related variables) was run. These analyses showed no significant findings in addition to that related to occasional night work, a result that strengthens the reliability of the present findings. It should also be noted that the samples of Finnish, Dutch and British parents were not randomly selected and therefore not representative, which makes cross-national com- parisons and generalization of the results difficult. Due to these data-related constraints, it is not possible to reliably evaluate whether the results of the study relate to the characteris- tics of our data set or reflect the more general situation in these countries, a problem commonly encountered in cross-national studies (see Yu, 2015). 4. Discussion The country samples dif- fered from each other in some background factors such as financial and work situation. Although all the differences detected were controlled for in the analyses, it is nevertheless possible that all meaningful differences between the samples were not captured. p g p p Rather than indicating that the timing of partners’ work only plays a small role in spousal well-being, the results of this study suggest that working early mornings, eve- nings, nights and weekends have both advantages and disadvantages for the spousal rela- tionship. Families also appear to be active in finding solutions to their problems of work- family reconciliation. Thus, research in this field could benefit from focusing more on the possible moderating and mediating factors as well as examining whether and how the timing of spouses’ work affects the organization of family life. For example, although it is often assumed that working nonstandard times reduces spousal time, in a situation where both parents of school-aged children work evenings and have free time during school- hours, extensive possibilities exist for one-on-one spousal time. Since nonstandard work schedules take several different forms, a simple categorization of individuals’ work times is not adequate for addressing questions of this kind. In future studies, more emphasis, both quantitative and qualitative, should be put on understanding the complex nature of work schedules. Further research is also needed on the solutions and good practices fami- lies have come up with in response to problems caused by their work schedules. References Abendroth, A. & Den Dulk, L. (2011). Support for the work–life balance in Europe: The impact of state, workplace and family support on work-life balance satisfaction. Work, employment and society, 25, 2, 234–256. https://doi.org/10.1177/0950017011398892 Barnett, R.C. & Gareis, K.C. (2007). Shift work, parenting behaviors, and children’s socio- emotional well-being: A within-family study. Journal of Family Issues, 28, 6, 727–748. https://doi.org/10.1177/0192513X06298737 p // g/ / Craig, L. & Brown, J.E. (2017). Feeling rushed: gendered time quality, work hours, non- standard work schedules, and spousal crossover. Journal of Marriage and Family, 79, 1, 225–242. https://doi.org/10.1111/jomf.12320 18 Davis, K.D., Goodman, W.B., Pirretti, A.E. & Almeida, D.M. (2008). Non-standard work schedules, perceived family well-being, and daily stressors. Journal of Marriage and Family, 70, 4, 991–1003. https://doi.org/10.1111/j.1741-3737.2008.00541.x De Schipper, J.C., Tavecchio, L.W.C., Van IJzendoorn, M.H. & Linting, M. (2003). The re- lation of flexible child care to quality of center day care and children’s socio-emotional functioning: a survey and observational study. Infant Behavior & Development, 26, 3, 300–325. https://doi.org/10.1016/S0163-6383(03)00033-X Dunifon, R., Kalil, A., Crosby, D.A., Su, J.H. & DeLeire, T. (2013). Measuring maternal non-standard work in survey data. Journal of Marriage and Family, 75, 3, 523–532. https://doi.org/10.1111/jomf.12017 p // g/ /j Esping-Andersen, G. (1999). Social foundations of postindustrial economies. Oxford, UK: Ox- ford University Press. Eurofound (2010). Fifth European Survey on Working Conditions (2010) Questionnaire. https://www.eurofound.europa.eu/surveys/european-working-conditions- surveys/fifth-european-working-conditions-survey-2010/ewcs-2010-questionnaire [re- trieved December 10, 2019] Eurostat (2014). Labour Force Survey. https://ec.europa.eu/eurostat/web/microdata/labour-force-survey [retrieved Decem- ber 10, 2019] Forsberg, H. (2005). Finland’s families. In: Adams, B.N. & Trost, J. (Eds.), Handbook of World Families. Thousand Oaks, CA: Sage, 262–282. Funk, J.L. & Rogge, R.D. (2007). Testing the ruler with item response theory: Increasing precision of measurement for relationship satisfaction with the Couples Satisfaction Index. Journal of Family Psychology, 21, 4, 572–583. https://doi.org/10.1037/0893-3200.21.4.572 Gracia, P. & Kalmijn, M. (2016). Parents’ family time and work schedules: the split-shift schedule in Spain. Journal of Marriage and Family, 78, 2, 401–441. https://doi.org/10.1111/jomf.12270 Graham, J.M. & Diebels, K.J. (2011). The reliability of relationship satisfaction: a reliability generalization meta-analysis. Journal of Family Psychology, 25, 1, 39–48. https://doi.org/10.1037/a0022441 Grzywacz, J.G. (2016). Shift work and its implications for everyday work and family life: a foundation and summary. In: Iskra-Golec, I., Barnes-Farrell, J. & Bohle, P. (Eds.), So- cial and family issues in shift work and non standard working hours. Cham, Switzerland: Springer, 3–17. Hostetler, A.J., Desrochers, S., Kopko, K. & Moen, P. (2012). References Marital and family satisfac- tion as a function of work-family demands and community resources: Individual- and couple-level analyses. Journal of Family Issues, 33, 3, 316–340. https://doi.org/10.1177/0192513X11413877 p // g/ / Hu, L., & Bentler, P.M. (1999). Cutoff criteria for fit indexes in covariance structure analy- sis: Conventional criteria versus new alternatives. Structural Equation Modeling, 6, 1, 1–55. https://doi.org/10.1080/10705519909540118 19 Jekielek, S.M. (2003). Non-standard work hours and the relationship quality of dual-earner parents. Dissertation Abstracts International Section A: Humanities and Social Sciences, 64(6-A), 2272. Kalil, A., Ziol-Guest, K. & Epstein, J.L. (2010). Non-standard work and marital instability: Evidence from the national longitudinal survey of youth. Journal of Marriage and Fami- ly, 72, 5, 1289–1300. https://doi.org/10.1111/j.1741-3737.2010.00765.x Kröger, T. (2011). Defamilisation, dedomestication and care policy: Comparing childcare service provisions of welfare states. International Journal of Sociology and Social Policy, 31, 7/8, 424–440. https://doi.org/10.1108/01443331111149860 Little, T.D. (1997). Mean and covariance structures (MACS) analyses of cross-cultural data: Practical and theoretical issues. Multivariate Behavioral Research, 32, 1, 53–76. https://doi.org/10.1207/s15327906mbr3201_3 Maume, D.J. & Sebastian, R.A. (2012). Gender, non-standard work schedules, and marital quality. Journal of Family and Economic Issues, 33, 4, 477–490. https://doi.org/10.1007/s10834-012-9308-1 Milfont, T.L. & Fischer, R. (2010). Testing measurement invariance across groups: Appli- cations in crosscultural research. International Journal of Psychological Research, 3, 1, 111–121. https://doi.org/10.21500/20112084.857 Mills, M. & Täht, K. (2010). Non-standard work schedules and partnership quality: Quanti- tative and qualitative findings. Journal of Marriage and Family, 72, 4, 860–875. https://doi.org/10.1111/j.1741-3737.2010.00735.x Muthén, L.K. & Muthén, B. (2004). Mplus user’s guide. Los Angeles: Authors (3rd edition Muthén, L.K. & Muthén, B. (2004). Mplus user’s guide. Los Angeles: Authors (3rd edition). OECD (2014). OECD Family Database. Muthén, L.K. & Muthén, B. (2004). Mplus user’s guide. Los Angeles: Authors (3rd edition). OECD (2014). OECD Family Database. http://www.oecd.org/social/family/database [retrieved November 5, 2019] Pedersen, V.B. & Jeppesen, H.J. (2012). Contagious flexibility? A study on whether sched- ule flexibility facilitates work-life enrichment. Scandinavian Journal of Psychology, 53, 4, 347–359. https://doi.org/10.1111/j.1467-9450.2012.00949.x Perrucci, R., MacDermid, S., King, E., Tang, C., Brimeyer, T., Ramadoss, K., Kiser, S.J. & Swanberg, J. (2007). The significance of shift work: Current status and future direc- tions. Journal of Family and Economic Issues, 28, 4, 600–617. https://doi.org/10.1007/s10834-007-9078-3 Perry-Jenkins, M., Goldberg, A., Pierce, C. & Sayer, A. (2007). Shift work, role overload and the transition to parenthood. Journal of Marriage and the Family, 69, 1, 123–138. https://doi.org/10.1111/j.1741-3737.2006.00349.x g j Pfau-Effinger, B. (2004). References Development of culture, welfare states and women’s employment in Europe. Aldershot, UK: Ashgate. Presser, H.B. (2000). Non-standard work schedules and marital instability. Journal of Mar- riage and the Family, 62, 1, 93–110. Presser, H.B. (2000). Non-standard work schedules and marital instability. Journal of Mar- riage and the Family, 62, 1, 93–110. https://doi.org/10.1111/j.1741-3737.2000.00093.x Presser, H.B. (2003). Working in a 24/7 economy: Challenges for American families. New York: Russell Sage Foundation. Presser, H.B. (2003). Working in a 24/7 economy: Challenges for American families. New York: Russell Sage Foundation. 20 Presser, H.B. (2004). Employment in a 24/7 Economy: challenges for the family. In: Ep- stein, C.F. & Kalleberg, A.L. (Eds.), Fighting for time: shifting boundaries of work and so- cial life. New York: Russell Sage Foundation, 46–76. Rönkä, A., Malinen, K., Sevón, E., Metsäpelto, R.-L., & May, V. (2017). Positive parenting and parenting stress among working mothers in Finland, the UK and the Nether- lands: Do working time patterns matter? Journal of Comparative Family Studies, 48, 2, 175–196. https://doi.org/10.3138/jcfs.48.2.175 Rönkä, A., Turja, L., Malinen, K., Tammelin, M., & Kekkonen, M. (2019). Flexibly sched- uled early childhood education and care: experiences of Finnish parents and educa- tors. Early Years: An International Research Journal, 39, 4, 376–391. https://doi.org/10.1080/09575146.2017.1387519 Satorra, A. & Bentler, P.M. (1994). Corrections to test statistics and standard errors in co- variance structure analysis. In: von Eye, A. & Clogg, C.C. (Eds.), Latent variables analy- sis: Applications for developmental research. Thousand Oaks, CA: Sage, 399–419. Statistics Netherlands (2014). Fewer children in day care centres. http://www.cbs.nl/en-GB/menu/themas/dossiers/vrouwen-en- mannen/publicaties/artikelen/archief/2014/2014-4024-wm.htm [retrieved November 5, 2019] Su, J.H. & Dunifon, R. (2017). Nonstandard work schedules and private safety nets among working mothers. Journal of Marriage and Family, 79, 3, 597–613. Su, J.H. & Dunifon, R. (2017). Nonstandard work schedules and private safety nets among working mothers. Journal of Marriage and Family, 79, 3, 597–613. https://doi.org/10.1111/jomf.12358 https://doi.org/10.1111/jomf.12358 Tammelin, M., Malinen, K., Verhoef, M. & Rönkä, A. (2017). Work-family conflict and nonstandard working time in Finland, the Netherlands and the United Kingdom. Journal of Family Issues, 38, 1, 3–24. https://doi org/10 1177/0192513X15585810 Totterdell, P. (2005). Work schedules. In: Barling, J.B., Kelloway, E.K. & Frone, M.R. (Eds). Handbook of work stress. California: Sage, 35–62. Täht, K. (2011). Out of sync? The determinants and consequences of non-standard schedules for family cohesion: The Netherlands within a comparative perspective (Doctoral Dissertation). http://dare.ubvu.vu.nl/handle/1871/24038 [retrieved July 5, 2019] Vogel, M., Braungardt, T., Meyer, W. & Schneider, W. (2012). The effects of shift work on physical and mental health. Journal of Neural Transmission, 119, 10, 1121–1132. https://doi.org/10.1007/s00702-012-0800-4 White, L. & Keith, B. (1990). The effect of shift work on the quality and stability of marital relations. Journal of Marriage and the Family, 52, 2, 453–462. https://doi.org/10.2307/353039 Wright, V.R., Raley, S.B. & Bianchi, S.M. (2008). Time for children, one's spouse and one- self among non-standard workers. Social Forces, 87, 1, 243–271. https://doi.org/10.1353/sof.0.0092 Yu, W.H. (2015). Placing families in context: Challenges for cross-national family re- search. Journal of Marriage and Family, 77, 1, 23–39. https://10.1111/jomf.12152 21 Deutscher Titel Deutscher Titel Eine Nacht – zwei Schiffe? Unregelmäßige Arbeitszeiten und Zufriedenheit in der Ehe in Finnland, den Niederlanden und dem Vereinigten Königreich Schlagwörter: Inhaltsanalyse, interkulturell, unregelmäßige Arbeitszeiten, eheliche Zu- friedenheit, Strukturgleichungsmodell, Arbeitspläne Zusammenfassung Diese Studie untersucht den Zusammenhang von Arbeitszeiten und Zufriedenheit in der Ehe unter finnischen (n = 347), niederländischen (n = 304) und britischen (n = 337) El- tern. Neben dem Vergleich von Eltern mit außergewöhnlichen Arbeitszeiten und Eltern mit regulären Tagesarbeitszeiten, wurde gesondert untersucht, welche Rolle Morgen-, Abend-, Nacht- und Wochenendarbeit und andere arbeitszeitbezogenen Variablen (Ar- beitsstunden, Änderungen der eigenen Arbeitszeiten und der des Ehepartners und deren Einfluss auf die eigenen Arbeitszeiten bzw. die des Ehepartners) spielen. Die Daten aus drei Ländern wurden mithilfe des Strukturgleichungsmodells durch einen Mehrgruppen- vergleich in Mplus analysiert. Unter den anwesenden europäischen Arbeitnehmern wur- den nur wenige Hinweise für eine Korrelation zwischen negativen Assoziationen zu Ar- beitszeiten (damit zusammenhängenden Faktoren) und der Zufriedenheit in der Ehe festgestellt. Bei den untersuchten Assoziationen wurden keine Unterschiede zwischen den Ländern gefunden. Die quantitativen Analysen wurden durch Inhaltsanalysen der El- tern ergänzt, in denne sie beschreiben, wie sie die Auswirkungen der Arbeitszeiten auf ihre eheliche Beziehung erleben. Die Eltern beschrieben ihre Arbeitszeiten meist so, dass diese einen negativen Einfluss auf die Möglichkeiten zur gemeinsamen Zeitnutzung, auf die Organisation des Alltags sowie auf die psychologischen und physiologischen Reaktio- nen und die eheliche Kommunikation haben. Einige gaben jedoch auch Vorteile und Problemlösungen an, die in Verbindung zu ihren Arbeitszeiten stehen. Schlagwörter: Inhaltsanalyse, interkulturell, unregelmäßige Arbeitszeiten, eheliche Zu- friedenheit, Strukturgleichungsmodell, Arbeitspläne 22 JFR – Journal of Family Research, 2020, Early View, pp. 1–22. doi: 10.20377/jfr-359 Submitted: April 30, 2019 Accepted: January 16, 2020 Published online: March 02, 2020 This work is licensed under a Creative Commons Attribution 4.0 International License. doi: 10.20377/jfr-359 Submitted: April 30, 2019 Accepted: January 16, 2020 Published online: March 02, 2020 This work is licensed under a Creative Commons Attribution 4.0 International License.
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OmbriaNet—Supervised Flood Mapping via Convolutional Neural Networks Using Multitemporal Sentinel-1 and Sentinel-2 Data Fusion
IEEE journal of selected topics in applied earth observations and remote sensing
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I. INTRODUCTION Abstract—Regions around the world experience adverse climate-change-induced conditions that pose severe risks to the normal and sustainable operations of modern societies. Extreme weather events, such as floods, rising sea levels, and storms, stand as characteristic examples that impair the core services of the global ecosystem. Especially floods have a severe impact on human activities, hence, early and accurate delineation of the disaster is of top priority since it provides environmental, economic, and societal benefits and eases relief efforts. In this article, we introduce OmbriaNet, a deep neural network architecture, based on convolutional neural networks, that detects changes between permanent and flooded water areas by exploiting the temporal differences among flood events extracted by different sensors. To demonstrate the potential of the proposed approach, we generated OMBRIA, a bitemporal and multimodal satellite imagery dataset for image segmentation through supervised binary classification. It consists of a total number of 3.376 images, synthetic aperture radar imagery from Sentinel-1, and multispectral imagery from Sentinel-2, accompanied with ground-truth binary images produced from data derived by experts and provided from the Emergency Management Service of the European Space Agency Copernicus Program. The dataset covers 23 flood events around the globe, from 2017 to 2021. We collected, co-registrated and preprocessed the data in Google Earth Engine. To validate the performance of our method, we performed different benchmarking experiments on the OMBRIA dataset and we compared with several competitive state-of-the-art techniques. The experimental analysis demonstrated that the proposed formulation is able to producehigh-qualityfloodmaps,achievingasuperiorperformance over the state-of-the-art. We provide OMBRIA dataset, as well as OmbriaNet code at: https://github.com/geodrak/OMBRIA. F F LOODS are natural disasters that have a great impact on human societies, affecting economic activity at both local and regional scales. Their main driver on such extreme events is meteorological phenomena with an increase in frequency and magnitude observed during the last decades due to climate change [1]. Communities are pushed to poverty as agriculture production output is reduced and infrastructure is damaged. Studies from insurance companies show that between 1980 and 2019, hydrological disasters caused overall losses of approxi- mately 1 billion U.S. dollars [2]. Detecting flooded areas is a tedious task that requires hu- man expertise and many work hours. Remote sensing data are used to delimit flood extents and integrated with GIS to produce maps [3]. 2341 2341 IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 OmbriaNet—Supervised Flood Mapping via Convolutional Neural Networks Using Multitemporal Sentinel-1 and Sentinel-2 Data Fusion Georgios I. Drakonakis , Grigorios Tsagkatakis , Konstantina Fotiadou , and Panagiotis Tsakalides , Member, IEEE Manuscript received May 30, 2021; revised October 13, 2021 and January 11, 2022; accepted February 12, 2022. Date of publication March 1, 2022; date of current version March 23, 2022. This work was supported by the Marie Skłodowska-Curie project CALCHAS project under Grant 842560 within the H2020 Framework Program of the European Commission. (Corresponding author: Georgios I. Drakonakis.) This work is licensed under a Creative Commons Attribution 4.0 License. For more information, see https://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 License. For more information, see https://creativecomm A. Computer Vision and Image segmentation There are many applications in remote sensing that require assigning a label to every pixel in an image. This classification task is addressed with semantic segmentation algorithms. Com- puter vision is contributing significantly in remote sensing tasks such as cloud detection [26], urban planning [27], and land cover classification [28]. During the last years, semantic segmentation algorithms with three channels or multispectral imagery have been developed employing machine learning and especially deep learning [29]. Pretrained networks like VGG-16 [30] and ResNet [31] have been used not for segmentation per se, but for scene understanding in a coarse scale classification [32]. The DeepLab network [33] improves segmentation performance and produces sharp boundaries by substituting convolution layers with atrous convolutions. Atrous filters have zeros between sample points resulting in increased filter sizes with a constant number of parameters. Synthetic aperture radar (SAR) is proven to provide more reliable information on flood extent [46]. Precipitation events have as a result long-lasting cloud coverage periods and SAR sensors’ ability to penetrate clouds both day and night make them more suitable for the task. Lidar technologies can give precise digital elevation models that can be combined with SAR toestimatefloodextendalongwithprecisedepth[47].Sentinel-2 multispectral imagery and CNN’s have been used in supervised classification producing good results but in limited spatial scale (national) and water segmentation for labeling was produced by visual interpretation with results relative to a human analyst and not in absolute ground truth [48]. Deep learning frameworks for classifying multispectral im- ages have been explored thoroughly in the community. How- ever the scarcity of annotated data has limited most work to unsupervised methods [34], [35]. Lack of supervised data has an impact on model generalization between different datasets. Stacked autoencoders are unsupervised neural networks that encode efficiently the training data and learn high feature repre- sentations [36], [37]. In [38], a hybrid autoencoder—multilayer perceptron is introduced to map floods in two study areas in Iran and India. The autoencoder was used to reduce the feature count, enhance the training process, and increase the performance compared to the traditional MLP. IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 2342 Experiments on the International Society of Photogrammetry and Remote Sensing (ISPRS) Vahingen benchmark test set showed that the overall accuracy is among the top performers ac- cording to [39]. Transfer learning was used in [40] fusing a U-net baseddeep,1 calledTL-DenseUNet,withanencodersubnetwork transferring pretrained DenseNet to fuse multiscale informa- tion, performing multiobject semantic segmentation with an imbalanced class distribution. Experimental results showed that transfer learning is effective and achieves a better performance than other models. In this article, we address two challenges. The first is to compensate for the lack of ground-truth data and flooded area annotations and to provide to the scientific community a new dataset for supervised classification. Second, we propose a novel deep learning architecture for supervised segmentation that is able to detect changes in water presence using a bitemporal set of high-resolution 3-D imagery. The main novelties of this article include the following. The main novelties of this article include the following. 1) OMBRIA: The generation of a new dataset for addressing the problem of flood mapping. the problem of flood mapping. 2) OmbriaNet: A novel multimodal and bitemporal CNN designed for supervised image segmentation and change detection. B. Remote Sensing and Flood Detection Remote sensing technologies have evolved rapidly during the recent years and their advantages in analyzing the Earth surface by its spectral properties have been utilized in environmental monitoring and emergency and disaster relief [41]. Automated methods for waterbodies segmentation with satellite imagery can be divided in two categories, namely rule-based systems and machine learning models. Thresholding a water index such as themodifiednormalizeddifferencewaterindex(MNDWI)orthe multiband water index (MBWI) [8], [42] is a simple rule-based approach. Less commonly used by remote sensing community techniques that include expert systems, with visual analysis combining human cognitive abilities and evidential reasoning to deal with problems related to both uncertainties and quality issues in the dataset are used in [43]. While these methods pro- duce accurate results, this comes under specific conditions and it lacks generalization ability and transferability. Machine learning methods can learn flood characteristics given a set of labeled samples [44]. CNNs are able to learn features from images and segment water from land, outperforming hand-crafted features, and report higher accuracy and generalization ability [45]. The rest of this article is organized as follows. In Section II, we present the state-of-the-art on image segmentation with deep learning and flood detection in remote sensing. In Section III, the OMBRIA dataset creation is discussed. In Section IV, we present some theoretical background of deep learning and the proposed OmbriaNet network is presented. Furthermore, in Section V, the experimental results are shown. In Section VI, discussionovertheanalysisresultsanddirectionsforfuturesteps is made. Finally, Section VII concludes this article. 1Convolutional neural network (CNN). I. INTRODUCTION Satellite systems constitute the most widely used platform for large area mapping and emergency manage- ment [4], with Coperincus Emergency Management Service being a prime example. Earth observation satellites are equipped with instruments operating in wavelengths extending from the visible to microwave range. Traditional approaches exploit the capacity of water to absorb light at certain wavelengths [5], [6]. Early and current works use indicators, such as the normal- ized difference water index (NDWI) [7] and its improved ver- sion [8], which are suitable for enhancing and extracting water information. Recently, the combination of the satellite imagery infras- tructure with artificial intelligence technologies has provided a new path toward successfully addressing the problem of flood detection and mapping. Traditional machine learning techniques have been employed in Earth observation (EO) data analysis, including support vector machines (SVMs) [9] and random forests [10]. convolutional neural networks (CNNs), as partic- ular types of deep learning architectures, represent the most promising and prolific machine learning models, and have be- come a predominate tool due to their efficiency in learning data representations [11]. Advances in the fields of deep learning and computer vision have taken remote sensing to a new level [12] and are proven to be more accurate in tasks such as land cover classification [13]–[16] and object detection [17]–[19], outper- formingthetraditionalmethods[20]–[22].Althoughmostworks focus on land applications, there is an increasing interest in water applications, such as water detection [23]–[25]. Index Terms—Convolutional neural network (CNN), deep learning, flood mapping, remote sensing, Sentinel-1, Sentinel-2. Georgios I. Drakonakis, Konstantina Fotiadou, and Panagiotis Tsakalides are with the Department of Computer Science, University of Crete, 700 13 Herak- lion, Greece, and also with the Institute of Computer Science and Foundation of Research and Technology Hellas, University of Crete, 70013 Heraklion, Greece (e-mail: drakonakis@ics.forth.gr; kfot@ics.forth.gr; tsakalid@ics.forth.gr). Grigorios Tsagkatakis is with the Institute of Computer Science and Founda- tion of Research and Technology Hellas, University of Crete, 70013 Heraklion, Greece (e-mail: greg@ics.forth.gr). g g g Digital Object Identifier 10.1109/JSTARS.2022.3155559 This work is licensed under a Creative Commons Attribution 4.0 License. For more information, see https://creativec III. OMBRIA DATASET Imagery from Sentinel-1 was acquired at Level-1 Ground Range Detected (GRD), with VV polarization (single copolar- ization, vertical transmit/vertical receive). Level-1, GRD prod- ucts consist of focused SAR data, that has been detected, multi- looked and projected to ground range using the Earth ellipsoid model WGS ‘84. The ellipsoid projection of the GRD products is corrected using the terrain height from the SRTM Digital Elevation Model [59]. Ground range coordinates correspond to the slant range coordinates projected onto the ellipsoid of the Earth. Additionally, pixel values represent the detected am- plitude, while phase information is lost. To reduce the speckle effect, morphological filtering was applied with a 30 × 30 me- ters median value kernel. As a result, the resulting patches have dimensions of 256 × 256 × 1. The Copernicus program [52] provides data with global cov- erage, high temporal frequency, and high spatial resolution. The European Space Agency (ESA) launched the Sentinel-2 mission in July 2015, putting into orbit two twin satellites with a better resolution and a more frequent acquisition, compared to previ- ous missions, e.g., NASA’s LANDSAT 8. The ESA satellites provide Copernicus Emergency Management Service (EMS) with data necessary for mapping products to support emergency activities immediately following a disaster [53]. In addition, LANDSAT 8 constellation, the longest record of global scale EO providing data since 1972 [54], is widely used in delineating flood extents with change detection approaches [55]. Active EO sensors can also be utilized for flood mapping. SAR instruments have been used in several studies to create inundation maps [56]–[58]. The Sentinel-2 MSI instrument bands that were exploited are: Band 3—Green (0.560 μm), Band 8—Near Infrared (0.842 μm), and Band 11—SWIR (1.610 μm). Bands 3 and 8 have a spatial resolution of 10 m, while band 11 has a spatial resolution of 20 m. Additionally, the bottom-of-atmosphere reflectance in carto- graphic geometry product (i.e., Level 2 A) was selected, since it is atmospherically corrected and orthorectified with the SRTM. The resulting patches have dimensions of 256 × 256 × 3. The Emergency Management Service of the Copernicus Pro- gramme provides data packages of delineation and grading products for emergency situations and natural disasters. These products have been produced by field experts in semiautomated procedures. For the creation of the dataset, 20 flood event acti- vations around the globe were picked between 2017 and 2020. C. Flood Mapping With Deep Learning Machine learning models have not been utilized extensively in flood mapping problems because there is a lack of available datasets. Sen1Floods11 is the first dataset for flood detection. It was introduced to assist efforts to operationalize deep learn- ing algorithms for flood mapping in global scale. It contains Sentinel-1 imagery and is trained with a fully CNN to perform multiple classifications and compare performance with common remote sensing algorithms like backscatter thresholding [49]. Fusion of high-resolution imagery with digital surface models in a fully convolutional network has achieved state-of-the-art performance on a multimodal semantic segmentation scheme. DRAKONAKIS et al.: OMBRIANET—SUPERVISED FLOOD MAPPING VIA CONVOLUTIONAL NEURAL NETWORKS 2343 TABLE I TABLE I TABLE WITH FLOOD EVENTS USED IN OMBRIA DATASET AS EMERGENCY MANAGEMENT SERVICE RAPID MAPPING ACTIVATIONS Fig. 1. Map of emergency management service activations for flood events. TABLE I TABLE WITH FLOOD EVENTS USED IN OMBRIA DATASET AS EMERGENCY MANAGEMENT SERVICE RAPID MAPPING ACTIVATIONS Fig. 1. Map of emergency management service activations for flood events. Deep learning architectures tailored for water segmentation are also numbered. H20-Net is the first to our knowledge to address the problem. The network learns SWIR signal synthesis in low resolution data as a domain adaptation mechanism for accurate flood segmentation. It uses as input red, green, blue, and near infrared channels in a self-supervised classification and achieves high accuracy [50]. Besides EO, unmanned aerial vehicles (UAVs) constitute another source of data that makes observation easy and more frequent. High-resolution UAV im- agery has been used for postnatural disaster damage assessment using state-of-the-art deep learning algorithms [51]. data collection. More details regarding the data collection and preproccessing is given in Section V-A. III. OMBRIA DATASET Vector files were converted into raster images and used as ground truth. In Fig. 1, we present a world map with all flood events used in this article. In Table I, the flood events are categorized in a chronological order from the oldest to the most recent. The table includes the EMS Activation ID, the name of the country, the corresponding geographic zone, and the two dates used for Imagery from every flood event were divided into nonover- lapping tiles of size 256 × 256. This division led to 844 tiles for each timestamp (preevent and postevent) and each modality (Sentinel-1 and Sentinel-2) creating 1.688 optical and 1688 SAR images adding up to of 3.376 input image patches. Given that the ground sample distance is 10 m the total cover area is 553 km2. IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 2344 Fig. 2. OMBRIA Dataset samples. From left to right: Sentinel-1 preevent, Sentinel-1 postevent, Sentinel-2 preevent, Sentinel-2 postevent, and ground truth (white pixels is flood). Fig. 2. OMBRIA Dataset samples. From left to right: Sentinel-1 preevent, Sentinel-1 postevent, Sentinel-2 preevent, Sentinel-2 postevent, and ground truth (white pixels is flood). Fig. 2. OMBRIA Dataset samples. From left to right: Sentinel-1 preevent, Sentinel-1 postevent, Sentinel-2 preevent, S (white pixels is flood). The equations for reprojecting latitude and longitude to the cartesian coordinates as presented in [61] are formulated as In Fig. 2, selected samples are presented. During or after a flood event, there is a high probability of cloud presence. We took that into consideration during data collection and included cloudy samples (Sentinel-2 only as SAR has the ability to penetrate clouds) to simulate realistic data capture scenarios. x = k0N  A + (1 −T + C)A3 6 +(5 −18T + T 2 + 72C −58e ′2)A5 120  x = k0N  A + (1 −T + C)A3 6 +(5 −18T + T 2 + 72C −58e ′2)A5 120  y = k0  M −M0 + N tan φ A2 2 +(5 −T + 9C + 4C2)A4 24 + (61 −148T + 16T 2)A6 720  (1) The coordinate reference system of the imagery is the World Geodetic System 1984 [60], the so-called WGS ‘84, which stands as a gold standard in geodesy, satellite navigation, and cartography. B. Deep Learning Architectures 1) Baseline Architecture: U-Net: The majority of visual clas- sification tasks target to assign a label to a provided image. Nevertheless, in remote sensing applications, a key objective also concerns the localization of the labels, i.e., the correspond- ing class that is assigned to each pixel. In this article, we use U-Net, a state-of-the-art image segmentation neural network, as the baseline and we further develop novel multimodal and multitemporal DL architectures designed specifically for the problem of flood mapping change detection. L =  0, if not flooded 1, if flooded. L =  0, if not flooded 1, if flooded. Classic machine learning approach to this problem is by means of SVMs. SVMs build a discriminating function that simulates the optimal discriminating surface between classes, using training data [9]. When linear separation is impossible, kernel techniques are used so that the hyperplane defining the SVMs corresponds to a nonlinear decision boundary in the input space that is mapped to a linearized higher dimensional space [63]. U-Net [65] is a fully connected CNN architecture particularly applied on biomedical segmentation problems. It consists of a contracting path to imprint context and an expanding path, which is symmetric and enables precise localization. The U-Net architecture has also been exploited in various remote sensing tasks. Over the last years, deep learning (DL) has revolutionized several remote sensing analysis tasks, including the challenging problem of change detection, among others. Due to its fully data-driven structure, DL-based approaches learn automatically higher level features providing more faithful and representative approximations of input feature space. DL architectures with several intermediate hidden layers efficiently encode the internal representations of the raw data, and thus, they exhibit a superior performancecomparedtothetraditional,shallowmachinelearn- ing (ML)-based techniques. Additionally, DL techniques are quite robust and effective in remote sensing image segmentation tasks. In our analysis, we perform adjustments on the basic U-Net architecture to perform flood mapping, and we further use it in our experimental setup as a baseline evaluation. The new proposed contracting path consists of a repeated pattern of two 3 × 3 convolutions activated via a Leaky ReLU function [66], instead of the ReLU activation that is used in the original implementation of U-Net. Additionally, a 2 × 2 max pooling operation with stride 2 is used for down sampling. III. OMBRIA DATASET It consists of an ellipsoid that is an oblate spheroid, a geodetic datum (horizontal and vertical), and the geographical coordinates, which are the angles measured in terms of latitude (φ), north or south of the equatorial plane, and longitude (λ), east or west of the prime meridian. The coordinate reference system utilizedbytheEMSistheUniversalTransverseMercator(UTM) that divides the Earth into 60 longitudinal and 20 latitudinal segments. For the coregistration task of the flooded areas, it is necessary to reproject the Sentinel-2 imagery. A map projection is defined as a systematic transformation of ellipsoidal coordi- nates to a plane coordinate system (x, y) = (f1(φ, λ), f2(φ, λ)).  (1) where e ′2 = e2 1 −e2 , N = α (1 −e2 sin2 φ)1/2, T = tan2 φ C = eι2cos2φ, A = (λ −λ0) cos φ DRAKONAKIS et al.: OMBRIANET—SUPERVISED FLOOD MAPPING VIA CONVOLUTIONAL NEURAL NETWORKS 2345 M = α  1 −e2 4 −3e4 64 −5e6 256  φ − 3e2 8 + 3e4 32 + 45e6 1024  sin2 φ+ 15e4 256 + 44e6 1024  sin4 φ  . (2) the inp Y where M = α  1 −e2 4 −3e4 64 −5e6 256  φ − 3e2 8 + 3e4 32 + 45e6 1024  sin2 φ+ 15e4 256 + 44e6 1024  sin4 φ  . (2) the input depth or channel, and it is expressed as Y (l) = I(k) ∗K(l,k) =  m  n  k I(m, n, k)K(i −m, j −n, l, k) (3) where K(l,k) ∈Rm,n is the convolution kernel of size m × n the input depth or channel, and it is expressed as Y (l) = I(k) ∗K(l,k) =  m  n  k I(m, n, k)K(i −m, j −n, l, k) (3) (3)  (2) where K(l,k) ∈Rm,n is the convolution kernel of size m × n, associated with input channel k and output channel l. Latitude and longitude are expressed in radians, M is the true distance from the Equator to φ along the central meridian, and M0 is computed with respect to the latitude φ0 that crosses the central meridian at the origin of the (x, y) coordinates. For these equations, k0 is specified for a 6◦longitude window at 0.9996 [61]. Features generated from convolving the inputs are passed through a nonlinear function, the activation function. IV. PROPOSED METHOD: OMBRIANET where α is a hyperparameter to be tuned. Leaky ReLU can assist to overcome the vanishing gradient problem and avoid network saturation. III. OMBRIA DATASET We use the leaky rectified linear unit (ReLU) [64], expressed as yi =  x, ifx ≥0 x α, ifx < 0 (4) (4) A. Problem Formulation and Theoretical Background The goal in semantic segmentation has several variations from scene prediction to dense, fine-grained predictions and instance separation [62]. In this article, we focused on dense prediction, i.e., per-pixel class segmentation. To that end, we formulate the pixel labeling problem as assigning a class from a label space L = {ℓ1, ℓ2, . . ., ℓk} to each pixel of a set of 2-D or high-dimensional images X = {x1, x2, . . ., xN}. For the problem addressed in this article, there is one class for “water” and another for “not water.” Therefore, To determine the optimal values for the weights during train- ing, it is necessary to select the proper loss function. The loss function is defined as L = E(ˆy −y), where ˆy is the predicted value and y the ground truth. One common loss function that is widely used is the binary cross-entropy loss function L(y, ˆy) = −(y log(ˆy) + (1 −y) log(1 −ˆy)). (5) (5) B. Deep Learning Architectures p g p p p p 2) Bitemporal OmbriaNet: Creating meaningful feature maps from multitemporal images improves the change detection accuracy because the network detects modifications based on the temporal information from the feature maps generated from temporal images. Bitemporal OmbriaNet takes as input two images of a region in two different timestamps. The first is before the event and the second is right after the event. Three blocks of double 3 × 3 Convolutions, with a 2 × 2 max pooling factor and Leaky ReLU activations, encode the input data into the deepest point of the network. The resulting feature maps are concatenated, and then, a dropout layer with a 0.3 probability value is applied for regularization. Additionally, three blocks of double 3 × 3 convolutions and a 2 × 2 up-sampling factor are combined with skip connections and are activated via a sigmoid activation layer for obtaining the final predictions. Regarding the loss function, we utilize the binary cross entropy, as it was also used in the original U-Net implementation. Additionally, the exploited optimizer is the Adam. Finally, the Bitemporal OmbriaNet architecture has a total of 10796485 parameters. In Fig. 3, we depict the detailed Bitemporal OmbriaNet scheme. To compensate the inability of U-Net in detecting accurately flooded areas, we introduce the novel OmbriaNet architecture. The intuition behind our approach is that there are three sources of water: main water bodies such as sea oceans and rivers, temporal streams only in winter seasons, and flood water. Tem- poral streams and flood water present a periodicity. This event periodicity may be captured if the proposed DL architecture is fed with the same area of interest in two different chronological moments that represent characteristic timestamps before and after the event. Intense precipitation is related to dense cloud coverage. These clouds cause severe obstructions and heavy shadowing effects to satellite optical sensors resulting in significant data information loss. We leverage this discrepancy by introducing multimodal input in the proposed DL architecture. For this purpose, we exploit SAR data, since it is not limited by illumination or cloud coverage conditions. Additionally, SAR technology is proved to be a valuable source of information due to its higher probability of capturing imagery right after the flood event. In our proposed OmbriaNet architecture, two different approaches were designed: the Bitemporal OmbriaNet and the Multimodal OmbriaNet. B. Deep Learning Architectures In the ex- pansive path, the feature maps are up-sampled, followed by a 2 × 2 convolution that halves the number of feature maps. Then, a concatenation with the corresponding cropped feature maps from the contracting path is implemented, followed by two 3 × 3 convolutions activated with the Leaky ReLU func- tion. Moreover, a final 1 × 1 convolution layer is exploited that maps each feature vector to the desired class. Regarding the loss function, the binary cross-entropy was selected, since we An efficient DL approach is based on CNNs. CNNs are composed of convolutional layers that alternate with nonlinear activation and possibly subsampling (pooling) layers, resulting in a hierarchy of increasingly abstract features. CNNs involve the mathematical operation of convolution. For the case of 2-D imagery, the convolution is applied on input features I(i, j, k), where (i, j) represent the input image height and width and k is IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 2346 Fig. 3. Bitemporal OmbriaNet architecture. Two input images of the same region in different timestamps are imported into our proposed two-branch architecture attempting to take advantage of the bitemporality in detecting the change that is present. Fig. 3. Bitemporal OmbriaNet architecture. Two input images of the same region in different timestamps are imported into our proposed two-branch architecture attempting to take advantage of the bitemporality in detecting the change that is present. address a binary classification task. Concerning the optimization algorithm, the Adam optimizer [67] was selected. Finally, the total number of parameters is 31032837. different sensor and different timestamp. In the first instance, the network is referred as Multitemporal OmbriaNet and in the second is referred as Multimodal OmbriaNet. The following paragraphs provide their complete description. Despite U-Net’s superior performance in several remote sens- ing tasks and its promise for the proposed flood detection task, a major drawback still remains that the traditional U-Net con- siders single input imagery. This limitation makes the network incapable of distinguishing permanent from flooded water ter- ritories. Consequently, the basic U-Net formulation results in misclassification of water bodies (i.e., lakes, rivers, oceans, etc.) as flooded water areas resulting in the deterioration of the overall system detection accuracy. B. Deep Learning Architectures OmbriaNet’s intuition is based the U-Net frame- work but designed to receive multiple input. Different input is categorized as same sensor and different timestamp or both 3) Multimodal OmbriaNet: To fully exploit multimodal data fusion, we constructed the so-called Multimodal OmbriaNet ar- chitecture, as an improved version of the Bitemporal OmbriaNet that considers four input images, corresponding to one pre- and one postevent image acquired by Sentinel-1, and one pair of pre- and postevent images acquired by Sentinel-2, depicting the same spatial territory. Similar to the Bitemporal OmbriaNet architecture, three convolutional 3 × 3 blocks followed by 2 × 2 max-pooling layers were exploited and activated via the Leaky ReLU function. The resulting feature maps are concatenated, while the dropout regularization term is also set to 0.3. Re- garding the inverse process, three 3 × 3 convolutional blocks DRAKONAKIS et al.: OMBRIANET—SUPERVISED FLOOD MAPPING VIA CONVOLUTIONAL NEURAL NETWORKS 2347 Fig. 4. Multimodal OmbriaNet architecture. In our final proposed method, four input images of different modalities and different timestamps are exploited in a multibranch architecture and utilized to segment the flood. Fig. 4. Multimodal OmbriaNet architecture. In our final proposed method, four input images of different modalities in a multibranch architecture and utilized to segment the flood. Fig. 4. Multimodal OmbriaNet architecture. In our final proposed method, four input images of different modalities and different timestamps are exploited in a multibranch architecture and utilized to segment the flood. B. Evaluation Metrics followed by 2 × 2 up-sampling layers are combined with two more skip connections, for completeness purposes. The final layer is a fully connected activated using the sigmoid function and is responsible for the segmentation task. The Multimodal OmbriaNet architecture resolves a total of 18 108 101 trainable parameters. In Fig. 4, we present the proposed Multimodal OmbriaNet architecture. Evaluation using standard and well-known metrics is of critical importance, since it enables fair comparisons with the state-of-the-art. Additionally, the context of the application de- termines the importance of the metrics. We also provide exe- cution time as an evaluation parameter, bearing in mind that computation times depend on the available hardware resources. Insemanticsegmentation,themostpopularperformancemetrics are pixel accuracy and intersection over union (IoU). In our case, we have a total of two classes (ℓ0 and ℓ1). Let pij be the number ofpixelsoftheclassiinferredtobelongtotheclassj.Then,pii is the number of correctly classified or true positives, while pij and pji represent the false positives and true negatives, respectively. 1) Pixel accuracy (PA): PA is defined as the ratio of the 3) Frequency weighted intersection over union (FWIoU): FWIoU is an improved version of the IoU metric that takes into consideration class appearance frequencies and A. Analysis Ready Dataset (7) (7) 3) Frequency weighted intersection over union (FWIoU): FWIoU is an improved version of the IoU metric that takes into consideration class appearance frequencies and 3) Frequency weighted intersection over union (FWIoU): FWIoU is an improved version of the IoU metric that takes into consideration class appearance frequencies and IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 2348 Fig. 5. Data preproccessing flowchart. All preproccessing was performed in Google Earth Engine API. Fig. 5. Data preproccessing flowchart. All preproccessing was performed in Google Earth Engine API. TABLE II TABLE II U-NET BASELINE SCHEME: QUANTITATIVE PERFORMANCE OF TRAINING AND VALIDATION PHASES weighs their importance weighs their importance the best case scenario is achieved using 50 epochs, a batch size of 8 for Sentinel-2, and a batch size of 12 for Sentinel-1. FWIoU = 1 1 i=0 1 j=0 pij × 1  i=0 1 j=0 piipij 1 j=0 pij+1 j=0 pji−pii . (8) Table II presents the quantitative performance regarding the trainingandvalidationphases of theU-Net baselinearchitecture. We observe, that using Sentinel-2 input data, the highest training accuracy is achieved with a batch size of 6, and it is 82.05%, while the highest validation accuracy is 84.93%, using a batch size of 8. Additionally, using Sentinel-1 input data, the highest training accuracy is 76.31% using a batch size of 8, while the best validation accuracy of 85.58% is achieved using a batch size 6. We also observe that the validation score is higher than the training score, especially in Sentinel-1, probably due to the sampling batch during the training process. (8) A. Analysis Ready Dataset Data preprocessing was conducted on the widely utilized Google Earth Engine [68] platform for geo-spatial science data and analysis. Data collections from Sentinel-1 and Sentinel-2 were accessed via this platform. In order to implement our proposed bitemporal approach, we selected two time stamps as follows. The Date 1 ranges from the 1st to the 31st of May of the year before the flood event. In this window, available pixels with cloud coverage below a threshold between 10% and 30% were averaged to yield the final input intensities. The Date 2 ranges from the date that the event has occurred until 15 days after it. The same cloud coverage threshold was applied and instead of pixel averaging, the first available pixels were selected. All pixels were reprojected to the corresponding UTM zone, de- pending on the region that is illustrated in Table I. We consider a significant preprocessing step by adopting a generalized data augmentation approach. We apply in each patch of the input EO imagery the following set of transformations:left-right flip, horizontal and vertical shift, shearing, and random rotations. Via thisapproach,ourdatasetsizeincreasedbyafactorof2,covering the dominant possible scenarios regarding data transformation. The dataset was then shuffled and further divided into training (80%), validation (10%), and testing (10%). All preproccessing steps are visualized as a flow chart in Fig. 5. pji p p g p y 1) Pixel accuracy (PA): PA is defined as the ratio of the amount of correctly classified pixels to their total number: PA = 1 i=0 pii 1 i=0 1 j=0 pij . (6) (6) 2) Intersection over union (IoU): IoU is the most frequently used metric for image segmentation. It stands as the ratio between the intersection and the union of two sets. In our formulation, it represents the prediction and the ground truth. It is formulated as the number of true positives over the sum of true positives, false negatives, and false positives. It is computed in a per-class basis and averaged. For the binary problem, it is written as IoU = 1 2 1  i=0 pii 1 j=0 pij + 1 j=0 pji −pii . C. Evaluation InthisSection,weprovidethecompleteexperimentalanalysis that has been benchmarked on the developed OMBRIA dataset. Specifically, we provide a detailed experimental setup corre- sponding to various training parameters, including different batch sizes and number of epochs. Additionally, we evaluate the proposed DL methods in terms of the training, validation, and testing accuracy. Moreover, we provide quantitative and qualitative results of our proposed Bitemporal and Multimodal architectures and we compare with competitive state-of-the-art ML and DL algorithmic formulations. In Table III, we report the scores of the trained models on the testing set. We observe that the highest overall score is achieved with Sentinel-2 for a batch size of 8, and it is 84.67% in PA, 43.46% in IoU, and 75.51% in FW IoU. The results indicate that Sentinel-2 slightly outperforms Sentinel-1 when examined in terms of accuracy. In Fig. 6, a sample from the test set is illustrated that highlights the advantage of using SAR over optical imagery. Due to a large concentration of clouds, Sentinel-2 was not able to capture any flooded water areas, which is demonstrated by the relatively low value for the classification accuracy. 1) Baseline: U-Net: The initial experiments were conducted using the U-Net architecture on both Sentinel-1 and Sentinel-2 data, separately. Since U-Net allows single input data, only post- flood event imagery was utilized. For the specific architecture, 1) Baseline: U-Net: The initial experiments were conducted using the U-Net architecture on both Sentinel-1 and Sentinel-2 data, separately. Since U-Net allows single input data, only post- flood event imagery was utilized. For the specific architecture, DRAKONAKIS et al.: OMBRIANET—SUPERVISED FLOOD MAPPING VIA CONVOLUTIONAL NEURAL NETWORKS DRAKONAKIS et al.: OMBRIANET—SUPERVISED FLOOD MAPPING VIA CONVOLUTIONAL NEURAL NETWORKS 2349 TABLE III QUANTITATIVE PERFORMANCE COMPARISON OF U-NET WITH SENTINEL-1 AND SENTINEL-2 IN TERMS OF PIXEL ACCURACY, IOU, FW IOU, AND TRAINING TIME FOR 50 EPOCHS Fig. 6. U-Net baseline scheme: Qualitative comparison of selected samples, in terms of both visual perception and the corresponding IoU metric. (a) Sentinel-1 Input. (b) Sentinel-2 Input. (c) Ground Truth (White pixelsis flood). (d) Sentinel-1 Output (58.19%). (e) Sentinel-2 Output (9.24%). TABLE III QUANTITATIVE PERFORMANCE COMPARISON OF U-NET WITH SENTINEL-1 AND SENTINEL-2 IN TERMS OF PIXEL ACCURACY, IOU, FW IOU, AND TRAINING TIME FOR 50 EPOCHS Fig. 6. U-Net baseline scheme: Qualitative comparison of selected samples, in terms of both visual perception and the corresponding IoU metric. (a) Sentinel-1 Input. (b) Sentinel-2 Input. (c) Ground Truth (White pixelsis flood). (d) Sentinel-1 Output (58.19%). (e) Sentinel-2 Output (9.24%). TABLE III QUANTITATIVE PERFORMANCE COMPARISON OF U-NET WITH SENTINEL-1 AND SENTINEL-2 IN TERMS OF PIXEL ACCURACY, IOU, FW IOU, AND TRAINING TIME FOR 50 EPOCHS Fig. 6. U-Net baseline scheme: Qualitative comparison of selected samples, in terms of both visual perception and the corresponding IoU metric. (a) Sentinel-1 Input. (b) Sentinel-2 Input. (c) Ground Truth (White pixelsis flood). (d) Sentinel-1 Output (58.19%). (e) Sentinel-2 Output (9.24%). Fig. 6. U-Net baseline scheme: Qualitative comparison of selected samples, in terms of both visual perception and the corresponding IoU metric. (a) Sentinel-1 Input. (b) Sentinel-2 Input. (c) Ground Truth (White pixelsis flood). (d) Sentinel-1 Output (58.19%). (e) Sentinel-2 Output (9.24%). TABLE IV QUANTITATIVE PERFORMANCE OF TRAINING AND VALIDATION FOR BITEMPORAL OMBRIANET TABLE IV TABLE IV QUANTITATIVE PERFORMANCE OF TRAINING AND VALIDATION FOR BITEMPORAL OMBRIANET IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 2350 IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 TABLE VI NTITATIVE PERFORMANCE COMPARISON ON TESTING SET FOR BITEMPORAL AND MULTIMODAL OMBRIANET IN TERMS OF PIXEL ACCURACY, IOU, FW, AND IOU (100 EPOCHS) TABLE VII OMBRIANET PERFORMANCE COMPARISON ON OMBRIA DATASET ON 90%/10% TRAINING/TESTING SPLIT ualitative comparison of selected samples with Bitemporal OmbriaNet and their corresponding IoU metric. (a) Sentinel-1 (Pre-event). (b) Sentinel-2 . (c) Ground Truth (White pixels is flood). (d) Sentinel-1 (Post-event). (e) Sentinel-2 (Post-event). (f) Bitemporal Output (94.64%). a significant improvement in the IoU metric (about 5%). nedindividually, therangeof IoUvalues for thedifferent es is far larger for the U-Net (i.e., approximately 10%) ared to the OmbriaNet (i.e., approximately 4%). This on indicates a higher model robustness. Additionally, hibi ll i i l 2 3% toward its performance, when increasing the number of epochs. Specifically increasing the training epochs yields into a limited gain (i.e., approximately 1%), while the training time is almost doubled when doubling the training iterations. In this scenario, the best evaluation metrics values are achieved using a batch size f 8 di i l d FW I U Th l i TABLE VI UANTITATIVE PERFORMANCE COMPARISON ON TESTING SET FOR BITEMPORAL AND MULTIMODAL OMBRIANET IN TERMS OF PIXEL ACCURACY, IOU, FW, AND IOU (100 EPOCHS) TABLE VII OMBRIANET PERFORMANCE COMPARISON ON OMBRIA DATASET ON 90%/10% TRAINING/TESTING SPLIT TABLE VII TABLE VII OMBRIANET PERFORMANCE COMPARISON ON OMBRIA DATASET ON 90%/10% TRAINING/TESTING SPLIT Fig. 7. Qualitative comparison of selected samples with Bitemporal OmbriaNet and their corresponding IoU metric. (a) Sentinel-1 (Pre-event). (b) Sentinel-2 (Pre-event). (c) Ground Truth (White pixels is flood). (d) Sentinel-1 (Post-event). (e) Sentinel-2 (Post-event). (f) Bitemporal Output (94.64%). Fig. 7. Qualitative comparison of selected samples with Bitemporal OmbriaNet and their corresponding IoU metric. (a) Sentinel-1 (Pre-event). (b) Sentinel-2 (Pre-event). (c) Ground Truth (White pixels is flood). (d) Sentinel-1 (Post-event). (e) Sentinel-2 (Post-event). (f) Bitemporal Output (94.64%). toward its performance, when increasing the number of epochs. Specifically increasing the training epochs yields into a limited gain (i.e., approximately 1%), while the training time is almost doubled when doubling the training iterations. TABLE IV QUANTITATIVE PERFORMANCE OF TRAINING AND VALIDATION FOR BITEMPORAL OMBRIANET QUANTITATIVE PERFORMANCE OF TRAINING AND VALI TABLE V QUANTITATIVE PERFORMANCE OF TRAINING, VALIDATION ACCURACY, AND COMPUTATIONAL TIME FOR MULTIMODAL OMBRIANET TABLE V CE OF TRAINING, VALIDATION ACCURACY, AND COMPUTATIONAL TIME FOR MULTIMODAL OMBRIANET TABLE V TABLE V QUANTITATIVE PERFORMANCE OF TRAINING, VALIDATION ACCURACY, AND COMPUTATIONAL TIME FOR MULTIMODAL OM In Table IV, the quantitative performance comparison of training and validation metrics for the Bitemporal OmbriaNet architecture is demonstrated. In this scenario, for a fixed batch value of 4, the best validation accuracy that is achieved is 84.92% for 50 epochs and 85.66% for 100 epochs. Multimodal OmbriaNet quantitive performance comparison is shown in Ta- ble V. Fora batch size of 12 the validation accuracy is 86.59% and 85.96% for 50 and 100 epochs respectively. 2) OmbriaNet—Bitemporal: In this subsection, we report on experiments meant to evaluate the improvement in our overall systemaccuracywhenintroducingbitemporalimagery.Thegoal is to demonstrate that the proposed OmbriaNet architecture described in Section IV, which takes as input preevent and postevent images, is capable of “learning” the change between the absence of water in normal conditions and the presence of water when the region is flooded. In our experiments, we experimented with different batch sizes, as with the traditional U-Net case. 2) OmbriaNet—Bitemporal: In this subsection, we report on experiments meant to evaluate the improvement in our overall systemaccuracywhenintroducingbitemporalimagery.Thegoal is to demonstrate that the proposed OmbriaNet architecture described in Section IV, which takes as input preevent and postevent images, is capable of “learning” the change between the absence of water in normal conditions and the presence of water when the region is flooded. In our experiments, we experimented with different batch sizes, as with the traditional U-Net case. In Table VI, we illustrate the quantitative performance com- parison on the testing set with the OmbriaNet architecture. We IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 A significant improvement in overall accuracy is observed, especially in the IoU score, in which Multimodal OmbriaNet outperforms the Bitemporal OmbriaNet by about 10%. The highest score is achieved for batch size of 12, and that is the model used in Table VII. In Fig. 8, a sample comparison between different experi- ments is presented. The Multimodal OmbriaNet improves the prediction performance about 21% compared to Multitemporal OmbriaNet achieving an IoU score 81.90% over 60.96%. A remarkable note is that although in the Sentinel-2 postevent instance, there is extensive cloud coverage over the flooded areas, our multimodal network manages a very good delineation of the event. Table VI gives the quantitative results over the test set for Multimodal OmbriaNet. A significant improvement in overall accuracy is observed, especially in the IoU score, in which Multimodal OmbriaNet outperforms the Bitemporal OmbriaNet by about 10%. The highest score is achieved for batch size of 12, and that is the model used in Table VII. Regarding all DL architectures, the batch sizes and number of epochs were chosen for best performance, resulting in a batch size of 12 for the U-Net with Sentinel-1, a batch size of 8 for the U-Net with Sentinel-2, and 50 epochs for both schemes. Concerning the Bitemporal OmbriaNet, both with Sentinel-1 and Sentinel-2, the batch size number was set to 8, while the number of epochs is fixed to 100. Finally, for the Multimodal OmbriaNet, the batch size was fixed to 12 and the number of epochs to 100. The corresponding results are presented in Table IX. 4) Overall Comparison: In this paragraph, we illustrate the final comparisons among the proposed architectures and the related state-of-the-art approaches. In order to obtain a fair comparison, we retrained all models (i.e., the baseline U-Net, proposed Multimodal, and proposed Bitemporal) with 90% of the OMBRIA dataset, and we tested on the resulting 10% test set. Regarding the state-of-the-art approaches, we com- pared against Otsu’s method for completeness in benchmarking Performance scores show that networks trained with Sentinel- 2 imagery perform better than Sentinel-1 in both U-Net and Bitemporal OmbriaNet. Sentinel-2 data utilize three reflectance channels (Band 3, Band 8, and Band 11). These channels were selected due to their high response on water, according to lit- erature. IR (Band8) and SWIR (Band11) are infrared channels and water absorbs infrared radiation. IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 In this scenario, the best evaluation metrics values are achieved using a batch size of 8, regarding pixel accuracy and FW IoU.The resulting pre- dictions in Table VII were implemented from the corresponding models that were trained with a batch size of 8. observe a significant improvement in the IoU metric (about 5%). If examinedindividually, therangeof IoUvalues for thedifferent batch sizes is far larger for the U-Net (i.e., approximately 10%) as compared to the OmbriaNet (i.e., approximately 4%). This observation indicates a higher model robustness. Additionally, pixel accuracy exhibits a small increase, approximately 2–3% when comparing the different architectures, and demonstrates similar variations when examined for different batch sizes (i.e., about 10% for U-Net and only 2% for OmbriaNet). Experiments showed that the model behavior presents minimum change observe a significant improvement in the IoU metric (about 5%). If examinedindividually, therangeof IoUvalues for thedifferent batch sizes is far larger for the U-Net (i.e., approximately 10%) as compared to the OmbriaNet (i.e., approximately 4%). This observation indicates a higher model robustness. Additionally, pixel accuracy exhibits a small increase, approximately 2–3% when comparing the different architectures, and demonstrates similar variations when examined for different batch sizes (i.e., about 10% for U-Net and only 2% for OmbriaNet). Experiments showed that the model behavior presents minimum change In Fig. 7, a sample of inundated areas with rivers is illustrated to demonstrate the model ability to segregate permanent water DRAKONAKIS et al.: OMBRIANET—SUPERVISED FLOOD MAPPING VIA CONVOLUTIONAL NEURAL NETWORKS 2351 Fig. 8. Qualitative comparison of selected sample with Multimodal OmbriaNet and their corresponding IoU metric. (a) Sentinel-1 (Pre-event). (b) Sentinel-1 (Post-event). (c) Sentinel-2 (Pre-event). (d) Sentinel-2 (Post-event). (e) Sentinel-1 U-Net (22.19%). (f) Sentinel-2 U-Net (59:13%). (g) Bitemporal OmbriaNet (60:96%). (h) Multimodal OmbriaNet (81:90%). (i) Ground Truth (White pixels is flood). Fig. 8. Qualitative comparison of selected sample with Multimodal OmbriaNet and their corresponding IoU metric. (a) Sentinel-1 (Pre-event). (b) Sentinel-1 (Post-event). (c) Sentinel-2 (Pre-event). (d) Sentinel-2 (Post-event). (e) Sentinel-1 U-Net (22.19%). (f) Sentinel-2 U-Net (59:13%). (g) Bitemporal OmbriaNet (60:96%). (h) Multimodal OmbriaNet (81:90%). (i) Ground Truth (White pixels is flood). evaluation. Since Otsu’s algorithm input is based on a single value pixel intensity, we derive the modified normalized differ- ence water index (MNDWI) [69] from the Sentinel-2 imagery, provided by from flooded territories. IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 As we may observe, the Bitemporal OmbriaNet depicts a high classification IoU score of 96.64%, validating its better robustness compared to the traditional U-Net scheme. 3) OmbriaNet—Multimodal: Bitemporal OmbriaNet show- ed a significant improvement over the baseline of U-Net mo- tivating the fusion of Sentinel-1 and Sentinel-2 preevent and postevent imagery via our proposed multimodal OmbriaNet, which indeed gave the best results. Specifically, running the experiments with the same hyperparameters as in Section V-C2, Multimodal OmbriaNet outperforms the baseline of U-Net by over 10% and Bitemporal OmbriaNet by 7% in IoU score achieving a value of 70.93%. Increasing the number of epochs did not show a significant increase in accuracy. MNDWI = BGREEN −BSWIR BGREEN + BSWIR MNDWI = BGREEN −BSWIR BGREEN + BSWIR where BGREEN and BSWIR are reflectance values of the corre- sponding channels. Additionally, for the ML-based SVM algo- rithm, we choose a linear kernel over the RBF as it results in a smaller time complexity and converges much faster on large datasets (i.e., about 45 million pixels). The Hinge loss function was selected, L2 norm for penalization, while the parameter C is set to 10. Feature selection was performed on raw pixel values and no complex features were constructed, but different sets of features were tested depending on sensor and timestamp. The multimodal combination was selected for the SVM. where BGREEN and BSWIR are reflectance values of the corre- sponding channels. Additionally, for the ML-based SVM algo- rithm, we choose a linear kernel over the RBF as it results in a smaller time complexity and converges much faster on large datasets (i.e., about 45 million pixels). The Hinge loss function was selected, L2 norm for penalization, while the parameter C is set to 10. Feature selection was performed on raw pixel values and no complex features were constructed, but different sets of features were tested depending on sensor and timestamp. The multimodal combination was selected for the SVM. g y In Fig. 8, a sample comparison between different experi- ments is presented. The Multimodal OmbriaNet improves the prediction performance about 21% compared to Multitemporal OmbriaNet achieving an IoU score 81.90% over 60.96%. A remarkable note is that although in the Sentinel-2 postevent instance, there is extensive cloud coverage over the flooded areas, our multimodal network manages a very good delineation of the event. Table VI gives the quantitative results over the test set for Multimodal OmbriaNet. IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 Sentinel-1 one channel (VV polarization) has a similar response as the emitting signal 4) Overall Comparison: In this paragraph, we illustrate the final comparisons among the proposed architectures and the related state-of-the-art approaches. In order to obtain a fair comparison, we retrained all models (i.e., the baseline U-Net, proposed Multimodal, and proposed Bitemporal) with 90% of the OMBRIA dataset, and we tested on the resulting 10% test set. Regarding the state-of-the-art approaches, we com- pared against Otsu’s method for completeness in benchmarking IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 2352 TABLE VIII QUANTITATIVE PERFORMANCE OF TRAINING/VALIDATION AND TESTING OF OMBRIANET WITH MISSING INPUT TABLE IX OMBRIANET PERFORMANCE COMPARISON ON NEW FLOOD EVENTS TABLE VIII QUANTITATIVE PERFORMANCE OF TRAINING/VALIDATION AND TESTING OF OMBRIANET WITH MISSING INPUT Fig. 9. Comparison of selected sample from ID492 flood in France (IoU metric score). (a) Sentinel-1 (Pre-event). (b) Sentinel-1 (Post-event). (c) Sentinel-2 (Pre-event). (d) Sentinel-2 (Post-event). (e) Sentinel-1 U-Net (66:98%). (f) Sentinel-2 U-Net (63:19%). (g) Multimodal OmbriaNet (90:03%). (h) Ground Truth (White pixels is flood). Fig. 9. Comparison of selected sample from ID492 flood in France (IoU metric score). (a) Sentinel-1 (Pre-event). (b) Sentinel-1 (Post-event). (c) Sentinel-2 (Pre-event). (d) Sentinel-2 (Post-event). (e) Sentinel-1 U-Net (66:98%). (f) Sentinel-2 U-Net (63:19%). (g) Multimodal OmbriaNet (90:03%). (h) Ground Truth (White pixels is flood). 5) Case of Missing Input: As it is discussed in previous sections, OMBRIA dataset was constructed taking into account realistic conditions as the purpose is for the network to be used in real data. Clouds and drained parts of land are present in the dataset. For completeness reasons, we performed several experiments replacing successively each modality postevent in Multimodal OmbriaNet with black imagery to simulate missing input. We conducted experiments for two different batch sizes, 8 and 12, and we trained the networks for 50 epochs. The results 5) Case of Missing Input: As it is discussed in previous sections, OMBRIA dataset was constructed taking into account realistic conditions as the purpose is for the network to be used in real data. Clouds and drained parts of land are present in the dataset. For completeness reasons, we performed several experiments replacing successively each modality postevent in Multimodal OmbriaNet with black imagery to simulate missing input. We conducted experiments for two different batch sizes, 8 and 12, and we trained the networks for 50 epochs. The results reflects away on the water’s smooth surface. The higher channel number in Sentinel-2 leads to information surplus, thus increas- ing performance. Experimental results for Bitemporal OmbriaNet are lower thantheU-NetwhenusingSentinel-1data.Thiscanbeexplained by the speckle effect that is present in a number of preevent im- agery. This effect creates problems in predictions in Bitemporal OmbriaNet. Although this is not a setback for the Multimodal OmbriaNet. DRAKONAKIS et al.: OMBRIANET—SUPERVISED FLOOD MAPPING VIA CONVOLUTIONAL NEURAL NETWORKS 2353 Fig. 10. Comparison of selected sample from ID501 flood in Albania (IoU metric score). (a) Sentinel-1 (Pre-event). (b) Sentinel-1 (Post-event). (c) Sentinel-2 (Pre-event). IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 (d) Sentinel-2 (Post-event). (e) Sentinel-1 U-Net (63.82%). (f) Sentinel-2 U-Net (78:30%). (g) Multimodal OmbriaNet (89:14%). (h) Ground Truth (White pixels is flood). Fig. 10. Comparison of selected sample from ID501 flood in Albania (IoU metric score). (a) Sentinel-1 (Pre-event). (b) Sentinel-1 (Post-event). (c) Sentinel-2 (Pre-event). (d) Sentinel-2 (Post-event). (e) Sentinel-1 U-Net (63.82%). (f) Sentinel-2 U-Net (78:30%). (g) Multimodal OmbriaNet (89:14%). (h) Ground Truth (White pixels is flood). Fig. 11. Comparison of selected sample from ID507 flood in Timor (IoU metric score). (a) Sentinel-1 (Pre-event). (b) Sentinel-1 (Post-event). (c) Sentinel-2 (Pre-event). (d) Sentinel-2 (Post-event). (e) Sentinel-1 U-Net (69:50%). (f) Sentinel-2 U-Net (79:08%). (g) Multimodal OmbriaNet (79:44%). (h) Ground Truth (White pixels is flood). Fig. 11. Comparison of selected sample from ID507 flood in Timor (IoU metric score). (a) Sentinel-1 (Pre-event). (b) Sentinel-1 (Post-event). (c) Sentinel-2 (Pre-event). (d) Sentinel-2 (Post-event). (e) Sentinel-1 U-Net (69:50%). (f) Sentinel-2 U-Net (79:08%). (g) Multimodal OmbriaNet (79:44%). (h) Ground Truth (White pixels is flood). experiments on new flood events that are not included in the training process. These events are the EMS ID 492 (France) 501 (Albania), 507 (Timor), and 514 (Guyana). Event ID 492 took place in France in 2021 and includes regions that have flooded in 2019 and mapped in event ID 416. The rest are completely new events. For each flood, we used the pretrained models of the U-Net with Sentinel-1, U-Net with Sentinel-2, and Multimodal OmbriaNet that were used in Section V-C4. The results are presented in Table IX. Multimodal OmbriaNet again surpassed U-Net both with Sentinel-1, by about 20%–30% in IoU score, and with Sentinel-2, by about 15%–25%. This are shown on Table VIII. For the case of missing Sentinel-1 postevent data, the network scores 86.07% in PA, 63.25% in IoU, and 77.74% in FW IoU. For the case of missing Sentinel-2 postevent data, the scores are 75.69% in PA, 53.15% in IoU, and 65.69% in FW IoU. Both cases achieve almost equal scores with Bitemporal OmbriaNet. 6) Testing OmbriaNet Performance in New Floods: Samples in OMBRIA dataset have spatial-temporal relationships as they were produced from same regions. This relationship can result two neighboring regions to share similar semantic segmen- tation information and leading to overfitting. We performed 6) Testing OmbriaNet Performance in New Floods: Samples in OMBRIA dataset have spatial-temporal relationships as they were produced from same regions. VII. CONCLUSION In this article, we presented a novel approach to address the problem of flood delineation, allowing detection of floods with satellite imagery. We introduced the OmbriaNet network that employs multimodal and multitemporal satellite imagery for semantic segmentation using supervised learning under realistic conditions. Our hope is that this article will contribute to the efforts of flood disaster management. Our approach showed that new platforms such as Google Earth Engine can be employed to construct a supervised dataset for remote sensing applications. IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 This relationship can result two neighboring regions to share similar semantic segmen- tation information and leading to overfitting. We performed IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 2354 Fig. 12. Comparison of selected sample from ID514 flood in Guyana (IoU metric score). (a) Sentinel-1 (Pre-event). (b) Sentinel-1 (Post-event). (c) Sentinel-2 (Pre-event). (d) Sentinel-2 (Post-event). (e) Sentinel-1 U-Net (58.19%). (f) Sentinel-2 U-Net (53:72%). (g) Multimodal OmbriaNet (79:97%). (h) Ground Truth (White pixels is flood). Fig. 12. Comparison of selected sample from ID514 flood in Guyana (IoU metric score). (a) Sentinel-1 (Pre-event). (b) Sentinel-1 (Post-event). (c) Sentinel-2 (Pre-event). (d) Sentinel-2 (Post-event). (e) Sentinel-1 U-Net (58.19%). (f) Sentinel-2 U-Net (53:72%). (g) Multimodal OmbriaNet (79:97%). (h) Ground Truth (White pixels is flood). The closest work that includes fused data from Sentinel-1 and Sentinel-2 is [49], which we outperform by more than 30% in IoU. We also outperform [50] by 3% in PA and by 6% in FW IoU, which are, to our knowledge, the highest scores in flood delineation with remote sensing data. proves the network’s superiority on change detection for flood events. U-Net with Sentinel-2 outperformed the U-Net with Sentinel-1 in all cases. The scores indicate that our proposed model is robust and effective on new and “unseen” flood events as the performance is at least equal or better than Table VII. Figs. 9–12 show the qualitative results on selected samples with their respective IoU score for each flood event. REFERENCES Gao, “NDWI—A normalized difference water index for remote sensing of vegetation liquid water from space,” Remote Sens. Environ., vol. 58, no. 3, pp. 257–266, 1996. [32] J. Long, E. Shelhamer, and T. Darrell, “Fully convolutional networks for semantic segmentation,” in Proc. IEEE Conf. Comput. Vis. Pattern Recognit., 2015, pp. 3431–3440. pp [8] H. Xu, “Modification of normalised difference water index (NDWI) to enhance open water features in remotely sensed imagery,” Int. J. Remote Sens., vol. 27, no. 14, pp. 3025–3033, 2006. [33] L.-C. Chen, G. Papandreou, I. Kokkinos, K. Murphy, and A. L. Yuille, “Deeplab: Semantic image segmentation with deep convolutional nets, atrous convolution, and fully connected CRFs,” IEEE Trans. Pattern Anal. Mach. Intell., vol. 40, no. 4, pp. 834–848, Apr. 2018. [9] B. E. Boser, I. M. Guyon, and V. N. Vapnik, “A training algorithm for optimal margin classifiers,” in Proc. 5th Annu. Workshop Comput. Learn. Theory, 1992, pp. 144–152. Mach. Intell., vol. 40, no. 4, pp. 834–848, Apr. 2018. [34] A. Romero, C. Gatta, and G. Camps-Valls, “Unsupervised deep feature extraction for remote sensing image classification,” IEEE Trans. Geosci. Remote Sens., vol. 54, no. 3, pp. 1349–1362, Mar. 2016. y pp [10] T. K. Ho, “Random decision forests,” in Proc. 3rd Int. Conf. Document Anal. Recognit., vol. 1, 1995, pp. 278–282. [35] R. Kemker and C. Kanan, “Self-taught feature learning for hyperspectral image classification,” IEEE Trans. Geosci. Remote Sens., vol. 55, no. 5, pp. 2693–2705, May 2017. [11] Y. LeCun, Y. Bengio, and G. Hinton, “Deep learning,” Nature, vol. 521, no. 7553, pp. 436–444, 2015. [12] X. X. Zhu et al., “Deep learning in remote sensing: A comprehensive review and list of resources,” IEEE Geosci. Remote Sens. Mag., vol. 5, no. 4, pp. 8–36, Dec. 2017. [36] A. Mughees and L. Tao, “Hyperspectral image classification based on deep auto-encoder and hidden Markov random field,” in Proc. 13th Int. Conf. Natural Comput., Fuzzy Syst. Knowl. Discov., 2017, pp. 59–65. [13] C. Karakizi, K. Karantzalos, M. Vakalopoulou, and G. Antoniou, “Detailed land cover mapping from multitemporal landsat-8 data of different cloud cover,” Remote Sens., vol. 10, no. 8, 2018, Art. no. 1214. [37] M. Ahmad, A. M. Khan, M. Mazzara, and S. Distefano, “Multi-layer extreme learning machine-based autoencoder for hyperspectral image classification,” in Proc. Int. Joint Conf. Comput. Vis., Imag. Comput. Graph., 2019, pp. 75–82. [14] M. Mahdianpari, B. Salehi, M. Rezaee, F. Mohammadimanesh, and Y. REFERENCES [25] A. Rango and V. V. Salomonson, “Regional flood mapping from space,” Water Resour. Res., vol. 10, no. 3, pp. 473–484, 1974. [1] Y. Hirabayashi et al., “Global flood risk under climate change,” Nature Climate Change, vol. 3, no. 9, pp. 816–821, 2013. [26] F. Xie, M. Shi, Z. Shi, J. Yin, and D. Zhao, “Multilevel cloud detec- tion in remote sensing images based on deep learning,” IEEE J. Sel. Topics Appl. Earth Observ. Remote Sens., vol. 10, no. 8, pp. 3631–3640, Aug. 2017. [2] MunuchRE, “Risks from floods, storm surges and flash floods,” 2019. [Online]. Available: https://www.munichre.com [Online]. Available: https://www.munichre.com [3] P. Brivio, R. Colombo, M. Maggi, and R. Tomasoni, “Integration of remote sensing data and GIS for accurate mapping of flooded areas,” Int. J. Remote Sens., vol. 23, no. 3, pp. 429–441, 2002. [27] I. Masser, “Managing our urban future: The role of remote sensing and geographic information systems,” Habitat Int., vol. 25, no. 4, pp. 503–512, 2001. [4] A. Goffi, D. Stroppiana, P. A. Brivio, G. Bordogna, and M. Boschetti, “Towards an automated approach to map flooded areas from Sentinel-2 MSI data and soft integration of water spectral features,” Int. J. Appl. Earth Observ. Geoinf., vol. 84, 2020, Art. no. 101951. [28] K. Karantzalos, D. Bliziotis, and A. Karmas, “A scalable geospatial web service for near real-time, high-resolution land cover mapping,” IEEE J. Sel. Topics Appl. Earth Observ. Remote Sens., vol. 8, no. 10, pp. 4665–4674, Oct. 2015. [5] Y. Du, Y. Zhang, F. Ling, Q. Wang, W. Li, and X. Li, “Water bodies’ mapping from Sentinel-2 imagery with modified normalized difference water index at 10-m spatial resolution produced by sharpening the SWIR band,” Remote Sens., vol. 8, no. 4, p. 354, 2016, Art. no. 354. [29] K.Fotiadou,G.Tsagkatakis,andP.Tsakalides,“Deepconvolutionalneural networks for the classification of snapshot mosaic hyperspectral imagery,” Electron. Imag., vol. 2017, no. 17, pp. 185–190, 2017. [6] R. Brakenridge and E. Anderson, “Modis-based flood detection, mapping and measurement: The potential for operational hydrological applica- tions,” in Transboundary Floods: Reducing Risks Through Flood Man- agement. Berlin, Germany: Springer, 2006, pp. 1–12. [30] K. Simonyan and A. Zisserman, “Very deep convolutional networks for large-scale image recognition,” 2014, arXiv:1409.1556. [31] O. Russakovsky et al., “ImageNet large scale visual recognition chal- lenge,” Int. J. Comput. Vis., vol. 115, no. 3, pp. 211–252, 2015. [7] B.-C. REFERENCES Zhang, “Very deep convolutional neural networks for complex land cover mapping using multispectral remote sensing imagery,” Remote Sens., vol. 10, no. 7, 2018, Art. no. 1119. [38] M. Ahmadlou et al., “Flood susceptibility mapping and assessment using a novel deep learning model combining multilayer perceptron and au- toencoder neural networks,” J. Flood Risk Manage., vol. 14, no. 1, 2020, Art. no. e12683. [15] R. Stivaktakis, G. Tsagkatakis, and P. Tsakalides, “Deep learning for multilabel land cover scene categorization using data augmentation,” IEEE Geosci. Remote Sens. Lett., vol. 16, no. 7, pp. 1031–1035, Jul. 2019. [39] W. Sun and R. Wang, “Fully convolutional networks for semantic seg- mentation of very high resolution remotely sensed images combined with DSM,” IEEE Geosci. Remote Sens. Lett., vol. 15, no. 3, pp. 474–478, Mar. 2018. [16] G. Tsagkatakis, A. Aidini, K. Fotiadou, M. Giannopoulos, A. Pen- tari, and P. Tsakalides, “Survey of deep-learning approaches for re- mote sensing observation enhancement,” Sensors, vol. 19, no. 18, 2019, Art. no. 3929. [40] B. Cui, X. Chen, and Y. Lu, “Semantic segmentation of remote sensing images using transfer learning and deep convolutional neural network with dense connection,” IEEE Access, vol. 8, pp. 116744–116755, 2020. [17] M. Vakalopoulou, K. Karantzalos, N. Komodakis, and N. Paragios, “Build- ing detection in very high resolution multispectral data with deep learn- ing features,” in Proc. IEEE Int. Geosci. Remote Sens. Symp., 2015, pp. 1873–1876. [41] S. Van Ackere, J. Verbeurgt, L. De Sloover, S. Gautama, A. De Wulf, and P. De Maeyer, “A review of the internet of floods: Near real-time detection of a flood event and its impact,” Water, vol. 11, no. 11, 2019, Art. no. 2275. pp [18] Z. Deng, H. Sun, S. Zhou, J. Zhao, L. Lei, and H. Zou, “Multi-scale object detection in remote sensing imagery with convolutional neural networks,” ISPRS J. Photogramm. Remote Sens., vol. 145, pp. 3–22, 2018. [42] X. Wang et al., “A robust multi-band water index (MBWI) for automated extraction of surface water from landsat 8 OLI imagery,” Int. J. Appl. Earth Observ. Geoinf., vol. 68, pp. 73–91, 2018. [19] Y. Long, Y. Gong, Z. Xiao, and Q. Liu, “Accurate object localization in remote sensing images based on convolutional neural networks,” IEEE Trans. Geosci. Remote Sens., vol. 55, no. 5, pp. 2486–2498, May 2017. [43] J.-F. Pekel, A. Cottam, N. Gorelick, and A. S. DRAKONAKIS et al.: OMBRIANET—SUPERVISED FLOOD MAPPING VIA CONVOLUTIONAL NEURAL NETWORKS DRAKONAKIS et al.: OMBRIANET—SUPERVISED FLOOD MAPPING VIA CONVOLUTIONAL NEURAL NETWORKS 2355 constellation. Finally, it is worth exploring the transfer learning possibility on data from unmanned aerial vehicles, which can provide high-resolution imagery and will greatly improve the mapping accuracy. [22] C. Huang, L. Davis, and J. Townshend, “An assessment of support vector machines for land cover classification,” Int. J. Remote Sens., vol. 23, no. 4, pp. 725–749, 2002. [23] F. Isikdogan, A. C. Bovik, and P. Passalacqua, “Surface water mapping by deep learning,” IEEE J. Sel. Topics Appl. Earth Observ. Remote Sens., vol. 10, no. 11, pp. 4909–4918, Nov. 2017. [24] Y. Wang, J. Colby, and K. Mulcahy, “An efficient method for mapping flood extent in a coastal floodplain using landsat TM and DEM data,” Int. J. Remote Sens., vol. 23, no. 18, pp. 3681–3696, 2002. VI. DISCUSSION The experimental results reveal that machine learning and deep learning methods outperform the traditional thresholding algorithms by at least 25% in IoU. SVMs perform decently if both optical and SAR data are given. One remarkable note is that bitemporality in our SAR data does not necessarily improve the performance. Examining Sentinel-1 VV band, we observed that the results are better with postevent imagery rather than combined with preevent. This is caused by the speckle effect that is inevitably present. The best model is Multimodal Om- briaNet that outperforms the SVM by 10% in IoU, Bitemporal OmbriaNet with Sentinel-2 by 8%, Bitemporal OmbriaNet with Sentinel-1 by 20%, and U-Net by more than 20%. Results also suggest that OmbriaNet is robust and effective in flood mapping under realistic conditions where input data are not ideal, cloudy, or even missing. OMBRIA dataset includes ref- erence imagery that has already masked out permanent water bodies resulting our proposed architectures to learn how to automatically distinguish flooded from permanent water. This ability eliminates the necessity for manual permanent water body annotation and drastically reduces the workload. OMBRIA is an analysis ready dataset, which is introduced in this article. It is the first fused dataset comprising both optical and Radar imagery with different timestamps, and conducts a complete comparison with other state-of-the art methods not subjective. Ground-truth annotations provided by ESA can be of crucial importance for tackling the flood mapping problem, as hand labeling such types of data requires expertise in remote sensing photointerpretation and is time consuming. Computer vision contributessignificantlytoremotesensingproblemssuchasland cover classification and cloud detection. There are few datasets available for training flood detection algorithms using publicly available satellite imagery. In this article, we focused on flooded water detection in an effort to operationalize monitoring for crisis situations. We formed and provided the OMBRIA dataset to the research community in order to train deep learning algo- rithms for flood detection without the overhead of generating training and validation datasets. Future plans include the expansion of the dataset with more samples so that it generalizes better. Furthermore, we will inves- tigate the expansion of the architecture to include more spectral bands in order to exploit the full potential of the Sentinel satellite IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 Since 2012, she has been a Research Assistant with the Signal Processing Laboratory, Institute of Com- puter Science, Foundation for Research and Technol- ogy Hellas, Heraklion, Greece. From the past four years, she has been working in the industry domain in the fields of machine learning and big data analytics. Her main research interests include machine learning, image processing, and computational photography applications with an emphasis on satellite imaging systems. pp [56] S. Long, T. E. Fatoyinbo, and F. Policelli, “Flood extent mapping for Namibia using change detection and thresholding with SAR,” Environ. Res. Lett., vol. 9, no. 3, 2014, Art. no. 035002. [57] L. Pulvirenti, N. Pierdicca, M. Chini, and L. Guerriero, “An algorithm for operational flood mapping from synthetic aperture radar (SAR) data using fuzzy logic,” Natural Hazards Earth Syst. Sci., vol. 11, no. 2, pp. 529–540, 2011. [58] D. Amitrano, G. Di Martino, A. Iodice, D. Riccio, and G. Ruello, “Unsu- pervised rapid flood mapping using Sentinel-1 GRD SAR images,” IEEE Trans. Geosci. Remote Sens., vol. 56, no. 6, pp. 3290–3299, Jun. 2018. [59] F. Gascon et al., “Copernicus Sentinel-2A calibration and products vali- dation status,” Remote Sens., vol. 9, no. 6, 2017, Art. no. 584. [60] M. Kumar, “World geodetic system 1984: A modern and accurate global reference frame,” Mar. Geodesy, vol. 12, no. 2, pp. 117–126, 1988. pp [61] J. P. Snyder, Map Projections-A Working Manual, vol. 1395. Washington, DC, USA: U.S. Government Printing Office, 1987. Panagiotis Tsakalides (Member, IEEE) received the Diploma in electrical engineering from the Aristotle University of Thessaloniki, Thessaloniki, Greece, in 1990, and the Ph.D. degree in electrical engineering from the University of Southern California, Los An- geles, CA, USA, in 1995. [62] A. Garcia-Garcia, S. Orts-Escolano, S. Oprea, V. Villena-Martinez, and J. Garcia-Rodriguez, “A review on deep learning techniques applied to semantic segmentation,” 2017, arXiv:1704.06857. g [63] V. N. Vapnik, “An overview of statistical learning theory,” IEEE Trans. Neural Netw., vol. 10, no. 5, pp. 988–999, Sep. 1999. [64] A. L. Maas, A. Y. Hannun, and A. Y. Ng, “Rectifier nonlinearities improve neural network acoustic models,” in Proc. Int. Conf. Mach. Learn., vol. 30, no. 1, 2013, p. 3. He is currently a Professor in computer science with the University of Crete, Heraklion, Greece, and the Head with the Signal Processing Laboratory, In- stitute of Computer Science, Foundation for Research and Technology Hellas (FORTH-ICS), Heraklion. IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 2356 IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 [45] Y. Li, S. Martinis, and M. Wieland, “Urban flood mapping with an active self-learning convolutional neural network based on TerraSAR-X intensity and interferometric coherence,” ISPRS J. Photogramm. Remote Sens., vol. 152, pp. 178–191, 2019. Georgios I. Drakonakis received the Diploma (M. Eng.) in rural, surveying and geoinformatics engineering from the National Technical University of Athens, Athens, Greece, in 2016, and the M.Sc. degree in computer science and engineering from Computer Science Department, University of Crete, Heraklion, Greece, in 2021. [46] A. Refice et al., “SAR and inSAR for flood monitoring: Examples with cosmo-skymed data,” IEEE J. Sel. Topics Appl. Earth Observ. Remote Sens., vol. 7, no. 7, pp. 2711–2722, Jul. 2014. [47] F. Cian, M. Marconcini, P. Ceccato, and C. Giupponi, “Flood depth esti- mation by means of high-resolution SAR images and lidar data,” Natural Hazards Earth Syst. Sci., vol. 18, no. 11, pp. 3063–3084, 2018. Since June 2020, he has been with the Institute of Computer Science of the Foundation for Re- search and Technology Hellas (FORTH-ICS), Her- aklion, as a Graduate Research Assistant with the Signal Processing Laboratory. His main research interests include machine/deep learning applications in the fields of remote sensing, computer vision, and photogrammetry [48] M. Wieland and S. Martinis, “Large-scale surface water change observed by Sentinel-2 during the 2018 drought in Germany,” Int. J. Remote Sens., vol. 41, no. 12, pp. 4742–4756, 2020. [49] D. Bonafilia, B. Tellman, T. Anderson, and E. Issenberg, “Sen1floods11: A georeferenced dataset to train and test deep learning flood algorithms for Sentinel-1,” in Proc. IEEE/CVF Conf. Comput. Vis. Pattern Recognit. Workshops, Jun. 2020, pp. 835–845. [50] P. Akiva, M. Purri, K. Dana, B. Tellman, and T. Anderson, “H2O-Net: Self-supervised flood segmentation via adversarial domain adaptation and label refinement,” in Proc. IEEE/CVF Winter Conf. Appl. Comput. Vis., 2021, pp. 111–122. Grigorios Tsagkatakis received the B.Sc. and M.Sc. degrees in electronics and computer engineering from the Technical University of Crete, Chania, Greece, in 2005 and 2007, respectively, and the Ph.D. degree in imaging science from the Center of Imaging Science, Rochester Institute of Technology, Rochester, NY, USA, in 2011. [51] M. Rahnemoonfar, T. Chowdhury, A. Sarkar, D. Varshney, M. Yari, and R. Murphy, “Floodnet: A high resolution aerial imagery dataset for post flood scene understanding,” IEEE Access, vol. 9, pp. 89644–89654, 2020. REFERENCES Belward, “High-resolution mapping of global surface water and its long-term changes,” Nature, vol. 540, no. 7633, pp. 418–422, 2016. [20] S. Ahmad, A. Kalra, and H. Stephen, “Estimating soil moisture using remote sensing data: A machine learning approach,” Adv. Water Resour., vol. 33, no. 1, pp. 69–80, 2010. [44] A. Hollstein, K. Segl, L. Guanter, M. Brell, and M. Enesco, “Ready-to-use methods for the detection of clouds, cirrus, snow, shadow, water and clear sky pixels in Sentinel-2 MSI images,” Remote Sens., vol. 8, no. 8, 2016, Art. no. 666. [21] M. Pal and P. Mather, “Support vector machines for classification in remote sensing,” Int. J. Remote Sens., vol. 26, no. 5, pp. 1007–1011, 2005. IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 g pp [52] M. Berger, J. Moreno, J. A. Johannessen, P. F. Levelt, and R. F. Hanssen, “ESA’s Sentinel missions in support of Earth system science,” Remote Sens. Environ., vol. 120, pp. 84–90, 2012. He is an Associate Researcher with the Signal Processing Laboratory, Institute of Computer Sci- ence, Foundation for Research and Technology Hel- las (FORTH-ICS), Heraklion, Greece. He is currently a Marie Skłodowska-Curie Fellow with the University of Southern California and FORTH on the CALCHAS project. His research interests include the domains of signal/image processing and machine learning for remote sensing and astrophysics. pp [53] I. Caballero, J. Ruiz, and G. Navarro, “Sentinel-2 satellites provide near- real time evaluation of catastrophic floods in the west Mediterranean,” Water, vol. 11, no. 12, 2019, Art. no. 2499. [54] M. C. Hansen and T. R. Loveland, “A review of large area monitoring of land cover change using landsat data,” Remote Sens. Environ., vol. 122, pp. 66–74, 2012. [55] S. Schlaffer, P. Matgen, M. Hollaus, and W. Wagner, “Flood detection from multi-temporal SAR data using harmonic analysis and change detection,” Int. J. Appl. Earth Observ. Geoinf., vol. 38, pp. 15–24, 2015. Konstantina Fotiadou received the B.Sc. degree in applied mathematics from the Department of Ap- plied Mathematics, University of Crete (UoC), Crete, Greece, in 2011, the M.Sc. and Ph.D. degrees in computer science from the Computer Science Depart- ment, UoC in 2014 and 2019, respectively. Since 2012, she has been a Research Assistant with the Signal Processing Laboratory, Institute of Com- puter Science, Foundation for Research and Technol- ogy Hellas, Heraklion, Greece. From the past four years, she has been working in the industry domain in the fields of machine learning and big data analytics. Her main research interests include machine learning, image processing, and computational photography applications with an emphasis on satellite imaging systems. Konstantina Fotiadou received the B.Sc. degree in applied mathematics from the Department of Ap- plied Mathematics, University of Crete (UoC), Crete, Greece, in 2011, the M.Sc. and Ph.D. degrees in computer science from the Computer Science Depart- ment, UoC in 2014 and 2019, respectively. Konstantina Fotiadou received the B.Sc. degree in applied mathematics from the Department of Ap- plied Mathematics, University of Crete (UoC), Crete, Greece, in 2011, the M.Sc. and Ph.D. degrees in computer science from the Computer Science Depart- ment, UoC in 2014 and 2019, respectively. IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING, VOL. 15, 2022 He has an extended experience of transferring research and interacting with the industry. During the last ten years, he has been the Project Coordinator in seven European Commission and 12 national research and innovation projects totaling more than 5.5 Meuros in actual funding for FORTH-ICS and the University of Crete. His research interests include the fields of statistical signal processing and machine learning with emphasis in non-Gaussian estimation and detection theory, sparse representations, and applications in sensor networks, audio, imaging, and multimedia systems. He has co-authored more than 200 technical publications in these areas. [65] O. Ronneberger, P. Fischer, and T. Brox, “U-Net: Convolutional networks for biomedical image segmentation,” in Proc. Int. Conf. Med. Image Comput. Comput.-Assist. Interv., 2015, pp. 234–241. [66] B. Xu, N. Wang, T. Chen, and M. Li, “Empirical evaluation of rectified activations in convolutional network,” 2015, arXiv:1505.00853. [67] D. P. Kingma and J. Ba, “Adam: A method for stochastic optimization,” 2014, arXiv:1412.6980. [68] N. Gorelick, M. Hancher, M. Dixon, S. Ilyushchenko, D. Thau, and R. Moore, “Google Earth Engine: Planetary-scale geospatial analysis for everyone,” Remote Sens. Environ., vol. 202, pp. 18–27, 2017. [Online]. Available: https://doi.org/10.1016/j.rse.2017.06.031 [69] X. Han-Qiu, “A study on information extraction of water body with the modified normalized difference water index (MNDWI),” J. Remote Sens., vol. 5, pp. 589–595, 2005.
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https://ieeexplore.ieee.org/ielx7/6287639/9668973/09757136.pdf
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A Flow-Based Generative Network for Photo-Realistic Virtual Try-on
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Received March 28, 2022, accepted April 10, 2022, date of publication April 14, 2022, date of current version April 21, 2022. Digital Object Identifier 10.1109/ACCESS.2022.3167509 Digital Object Identifier 10.1109/ACCESS.2022.3167509 TAO WANG, XIAOLING GU , (Member, IEEE), AND JUNKAI ZHU Key Laboratory of Complex Systems Modeling and Simulation, School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou 310005, China Corresponding author: Xiaoling Gu (guxl@hdu.edu.cn) Corresponding author: Xiaoling Gu (guxl@hdu.edu.cn) This work was supported in part by the Zhejiang Provincial Natural Science Foundation of China under Grant LY21F020019, a by the National Science Foundation of China under Grant 61802100. ABSTRACT Image-based virtual try-on systems aim at transferring the try-on clothes onto a target person. Despite making considerable progress recently, such systems are still highly challenging for real-world applications because of occlusion and drastic spatial deformation. To address the issues, we propose a novel Flow-based Virtual Try-on Network (FVTN). It consists of three modules. Firstly, the Parsing Alignment Module (PAM) aligns the source clothing to the target person at the semantic level by predicting a semantic parsing map. Secondly, the Flow Estimation Module (FEM) learns a robust clothing deformation model by estimating multi-scale dense flow fields in an unsupervised fashion. Thirdly, the Fusion and Rendering Module (FRM) synthesizes the final try-on image by effectively integrating the warped clothing features and human body features. Extensive experiments on a public fashion dataset demonstrate that our FVTN qualitatively and quantitatively outperforms the state-of-the-art approaches. The source code and trained models are available at https://github.com/gxl-groups/FVNT. INDEX TERMS Image-based virtual try-on, image synthesis, appearance flow. INDEX TERMS Image-based virtual try-on, image synthesis, appearance flow. is work is licensed under a Creative Commons Attribution 4.0 License. For more information, see https://creativecommons.org/licenses/by/4.0/ The associate editor coordinating the review of this manuscript and approving it for publication was Inês Domingues . 1https://viubox.com/ 2https://www.trimirror.com/ II. RELATED WORK A. VIRTUAL TRY-ON or TPS transformation for warping the source clothing [6], [14], [36], [43] fail to generate precise appearance details because such methods cannot deal with the transformations of non-rigid objects such as clothes. Recently, flow-based methods [13], [30], [46] show advantages in learning complex non-rigid geometric deformation in comparison to the affine transformation approaches. Inspired by it, we propose a novel flow-based spatial alignment scheme for precisely capturing the clothing deformation. The second one is how to render the final try-on image by effectively fusing the contents of body parts and warped clothes? The quality of try-on look highly depends on the appearances of garments (e.g. texture, logo and color) as well as the characteristics of the target person (e.g. hair, face and arms). Previous approaches [14], [36] using a composition mask to integrate clothing and human body bring obvious boundary artifacts in the intersection regions. These approaches overlook the occluded regions and fail to synthesize the body parts flexibly. Conventional approaches for virtual try-on works are based on graphics models. For instance, Sekine et al. [32] intro- duced a virtual fitting system that adjusts 2D clothing images to users by estimating their 3D body shape models from single-shot depth images. Yang et al. [41] computed a 3D model of a human body and outfits from a single-view image. Pons-Moll et al. [28] used a multi-cloth 3D model of the body and clothing for capturing a clothed person in motion and retargeting the clothing to new body shapes. Patel et al. [27] proposed TailorNet for estimating clothing deformation in 3D as a function of three factors: body shape, body pose and garment style. Mir [26] proposed Pix2Surf to digitally map the texture of clothing images to the 3D surface of virtual garment items, which enables 3D virtual try-on in real-time. 3D methods can generate good results for virtual try-on, but usually, they require additional 3D measurements. y y p y In this paper, we propose a novel Flow-based Virtual Try-on Network (FVTN), which consists of three modules. The first one is the Parsing Alignment Module (PAM), aligning the source clothing to the posture of the target person at the semantic level. This module provides accurate spatial information for subsequent modules. The second one is the Flow Estimation Module (FEM), which learns clothing deformation by estimating multi-scale dense flow fields in an unsupervised fashion. I. INTRODUCTION try-on methods using generative models provide a more economical solution, the goal of which is to naturally warp the try-on clothes on a target person without leveraging any 3D information. Although image-based virtual try-on makes considerable progress recently, generating perceptu- ally convincing virtual try-on images is highly challenging for the real-world scenario. The main challenges lie in: (1) Occlusion occurs in the target person. For example, the target person’s arms may cross over the chest and occlude the clothing region. (2) Varying deformation exists among different human poses and shapes of the target person (e.g., limbs from non-overlapping to overlapping), which makes it extremely hard to deform the garments and well fit the posture and body shape of the target person. (3) Due to the drastic spatial deformation from source clothing to the target person, generating the try-on image that maintains the detailed visual features of the original garment such as texture and color is a non-trivial task. As online shopping has continued to grow in popularity, virtually trying on clothes in an online fitting room has achieved much attention in recent years. A photo-realistic virtual try-on system will not only enhance the user shopping experience by fitting different clothes without changing them physically but also improve sales for retailers. This motivates many companies to develop various virtual fitting technologies, such as SenseMi,1 triMirror,2 etc. Classical virtual try-on methods primarily rely on com- puter graphics to synthesize the try-on looks for users based on their 3D body shapes, desired poses and target clothing items [2], [28], [44], which can well control clothing deformation and material performance. However, the huge labor costs for 3D data annotation and upfront costs for scanning equipment inhibit their large-scale deployment [14]. Motivated by the rapid development of image synthesis methods [10]–[12], [19], [21], the image-based virtual The aforementioned challenges can be ultimately summed up as two key problems for tackling image-based virtual try-on. The first one is how to design a robust geometric deformation scheme to warp the source clothing for fitting the target person? Existing approaches relying on the affine The associate editor coordinating the review of this manuscript and The associate editor coordinating the review of this manuscript and approving it for publication was Inês Domingues . 1https://viubox.com/ 2https://www.trimirror.com/ 40899 40899 T. Wang et al.: Flow-Based Generative Network for Photo-Realistic Virtual Try-On II. RELATED WORK A. VIRTUAL TRY-ON II. RELATED WORK A. VIRTUAL TRY-ON The predicted multi-scale flows are used to establish visual correspondence between the source clothing and the target try-on clothing in the feature domain. The learned flow fields do not directly warp the source clothing at the pixel level but the feature level. This is because warping clothing at the pixel level would result in the model having difficulty extracting large motions and generating new contents [30]. The final part is the Fusion and Rendering Module (FRM), aligning the source clothing to the target person at the pixel level. By effectively integrating the warped source clothing features and the body features, the proposed FRM can generate accurate clothing appearances and fine details of the human body. Experiments on the VITON dataset [14] demonstrate that the proposed FVTN can produce photo-realistic and perceptually convincing try-on images. y y y q Compared to graphics models, image-based generative models are more computationally efficient and broadly appli- cable. For example, VITON [14] first proposed image-based virtual try-on method, which generates warped clothes using Thin Plate Spline (TPS) transformation and maps the texture to the refined result with a composition mask. CP-VTON [36] improves VITON by using neural networks to directly learn the parameters of TPS for clothing warping, and thus achieves more accurate alignment results. CP-VTON+ [25] outperforms CP-VTON by improving the clothing warping stage and blending stage. VTNFP [43] achieves better try-on results than CP-VTON and VITON by concatenating the high-level features extracted from the body parts and the bottom garment, since CP-VTON and VITON only focus on the upper garment. ACGPN [40] synthesizes try-on images preserving both the characteristics of clothes and details of the human identity by using three modules. Xintong et al. proposed ClothFlow [13] for handling pose-guided synthesis and image-based virtual try-on. Similarly, ClothFlow and our proposed FVTN both learn clothing deformation by using flow-based methods. However, different from ClothFlow, we leverage an unsupervised flow training scheme relying on the photometric loss [42]. Furthermore, our FVTN uses the learned flow to warp the garments at the feature level instead of at the pixel level for extracting the large motions and generate new contents. The main contributions of our work can be summarized as follows: • We propose a new flow-based generative network with three tailored modules for image-based virtual try-on. B. OPTICAL FLOW • We design a novel spatial alignment scheme in the flow estimation module to precisely capture clothing deformation by estimating multi-scale dense flow fields in an unsupervised fashion. Optical flow [16], [17] is the task of estimating dense pixel- to-pixel correspondence between two input images, which is widely used in many applications such as action recognition, motion tracking, video segmentation and 3D reconstruc- tion. Optical flow has traditionally been approached as a hand-crafted optimization problem, the objective of which is defined as a trade-off between a data term and a regularization term [1]. Recently, deep learning has been shown as a promising alternative to traditional methods. FlowNet [7] is the first trainable CNN for optical flow estimation. • We propose a novel image synthesis network to synthesize the final try-on images by integrating the warped clothing features and the body features. • Experimental results on VITON [14] verify that our method qualitatively and quantitatively outperforms the state-of-the-art methods. VOLUME 10, 2022 40900 VOLUME 10, 2022 T. Wang et al.: Flow-Based Generative Network for Photo-Realistic Virtual Try-On FIGURE 1. The overall network architecture of the proposed FVTN, which consists of three modules. Given the source clothing image Is and the target person image It , Parsing Alignment Module (PAM) first aligns the source clothing to the posture of the target person at the semantic level by predicting the target semantic parsing map Mt . With the predicted parsing map Mt , we obtain the semantic mask of target clothing Mc t . Based on Mcs (the semantic mask of source clothing) and Mc t , Flow Estimation Module (FEM) learns clothing deformation by estimating multi-scale flow fields {F1, F2, . . . , FN } in an unsupervised fashion. Relying on the estimated multi-scale flow fields, Fusion and Rendering Module (FRM) renders the final try-on image I′ t by effectively integrating the features of warped clothes and features of the human body. FIGURE 1. The overall network architecture of the proposed FVTN, which consists of three modules. Given the source clothing image Is and the target person image It , Parsing Alignment Module (PAM) first aligns the source clothing to the posture of the target person at the semantic level by predicting the target semantic parsing map Mt . With the predicted parsing map Mt , we obtain the semantic mask of target clothing Mc t . A. PARSING ALIGNMENT MODULE (PAM) To disentangle the generation of shape and appearance, PAM aligns the source clothing Is to the target person It at the semantic level. It takes the semantic mask of source clothing Mc s , the segmented source clothing Ic s , the pose of the target person Pt and the binary mask of the target person’s head Mh t as input to predict the target semantic parsing map Mt. The predicted parsing map is required to retain the body parts and the pose of the target person as well as accurately show the shapes and categories of the transformed source clothing. To avoid annotating labels, Meister et al. [24] proposed an end-to-end unsupervised learning approach by designing a bidirectional flow-based loss function. Wang et al. [38] further proposed an unsupervised learning framework that models occlusion and large motions. Liu et al. [23] pro- posed SelFlow that distills reliable flow estimations from non-occluded pixels using self-supervised training. Unsuper- vised optical flow estimation is closer to our setting. However, different from these works, we focus on learning a flow for establishing correspondence between the source clothing and target try-on clothing. We use a human parser [9] to compute the parsing map with 20 semantic labels for Is and It. Each parsing map is represented as a one-hot tensor with 20 channels. On the other hand, we use a state-of-the-art pose estimator [3] to estimate the pose of the target person. Following [36], Pt is represented as 18-channels heat maps that each one encodes one joint of a human body. B. OPTICAL FLOW Based on Mcs (the semantic mask of source clothing) and Mc t , Flow Estimation Module (FEM) learns clothing deformation by estimating multi-scale flow fields {F1, F2, . . . , FN } in an unsupervised fashion. Relying on the estimated multi-scale flow fields, Fusion and Rendering Module (FRM) renders the final try-on image I′ t by effectively integrating the features of warped clothes and features of the human body. FlowNet2 [18] improves the flow accuracy of FlowNet by cascading several variants of it. Subsequently, Ranjan and Black introduced SpyNet [29], a compact spatial image pyramid network, which warps images at multiple scales to cope with large displacements. Recent notable contributions to end-to-end trainable optical flow include PWC-Net [34] and LiteFlowNet [18]. They proposed to use the feature warping and cost volume at multiple pyramid levels in a coarse-to-fine estimation, yielding more compact and effective networks. We draw inspiration from those coarse- to-fine flow estimation methods. fuses the warped features of source clothing and the features of the human body for rendering the final try-on image. Fig. 2 illustrates details of these three modules. Ideally, we need an image triplet ⟨Is, It, Ir⟩to train the FVTN, where Is is the source clothing image, It is the target person image, and Ir stands for the ground-truth image. However, such a dataset is hard to obtain. Therefore, Ir is replaced with It to train the FVTN in our implementation. III. PROPOSED METHOD As shown in Fig. 1, our FVTN is composed of three modules. The first one is the Parsing Alignment Module (PAM), which transfers the source clothing onto the target person at the semantic level. The proposed PAM provides accurate spatial and semantic information for subsequent modules. The second one is the Flow Estimation Module (FEM), which learns diverse spatial deformation between the source clothing and the target try-on clothing by estimating multi-scale dense flow fields in an unsupervised way. The final part is the Fusion and Rendering Module (FRM), which In this module, we simply adopt a conditional generative adversarial network [37], in which a U-Net structure is used as the generator while a discriminator is utilized to distinguish generated parsing map from the ground-truth parsing map. The overall objective function for PAM is formulated as: (1) LPAM = λadvLadv + λsegLseg 40901 VOLUME 10, 2022 T. Wang et al.: Flow-Based Generative Network for Photo-Realistic Virtual Try-On FIGURE 2. (a) Parsing Alignment Module (PAM). (b) Flow Estimation Module (FEM). (c) Fusion and Rendering Module (FRM). 2. (a) Parsing Alignment Module (PAM). (b) Flow Estimation Module (FEM). (c) Fusion and Rendering Module (FRM). where Ladv is the adversarial loss [37] and Lseg is the pixel-wise cross-entropy loss. λadv and λseg are the trade-off parameters for these two loss terms, which are set to 0.2 and 1, respectively, in our experiments. the flow fields in an iterative manner, where the flow is first estimated at low resolution followed by upsampled and refined at high resolution. Specially, we deploy a two-stream weight-sharing Feature Pyramid Network (FPN) to extract two feature pyramids from Mc s and Mc t , that is, {fs(1), fs(2),..., fs(N)} and {ft(1), ft(2),..., ft(N)}, respectively, where N corresponds to the lowest spatial resolution (in our case N = 5) and 1 corresponds to the highest spatial resolution. The extracted multi-scale features will be used to estimate the flow from the source clothing to the target one in an unsupervised way. Beginning with the lowest spatial resolution, after concatenating fs(N) and ft(N), a flow estimation layer initially infers a coarse flow FN. III. PROPOSED METHOD Formally, The pixel-wise cross-entropy loss Lseg constrains pixel-level accuracy during semantic parsing map generation, which is defined as: Lseg(Mt, ˜Mt) = −1 HW HW X m=1 C X c=1 ˜Mt log(Mt) (2) (2) where H, W and C are height, width and the number of channels of the parsing map, respectively. Mt is the generated parsing map and ˜Mt is the ground-truth. FN = Def fs(N), ft(N)  (3) (3) B. FLOW ESTIMATION MODULE (FEM) As we’ve discussed, building a robust clothing deformation model is crucial for image-based virtual try-on. Early methods of image-based virtual try-on [14], [25], [36], [43] warp clothes by computing a Thin Plane Spline (TPS) trans- formation. However, because of its low degree of freedom, TPS transformation can only model limited geometric trans- formations and is inflexible to achieve complex and non-rigid deformation [46]. Considering that flow-based methods can capture complex non-rigid geometric deformation [13], [30], [46], we design an unsupervised flow-based clothing deformation scheme without using explicit correspondence annotation. where Def denotes the deformable convolution [4] layer. l h d d l i i h h d f bl where Def denotes the deformable convolution [4] layer. We replace the standard convolution with the deformable convolution in the flow estimation layer for improving the network’s ability to handle drastic spatial deformation, since the standard convolution is limited by the lack of ability to spatially transform the inputs [4]. At a higher spatial resolution, the flow estimation layer gets a refined flow FN−1 by computing a residue flow RN−1 and adding the upscaled flow field F↑2 N , as illustrate in Fig. 2(b). RN−1 is computed based on the upscaled flow field F↑2 N , fs(N −1) and ft(N −1). Formally, FN−1 = RN−1 + 2F↑2 N (4) RN−1 = Def  W fs(N −1), 2F↑2 N  , ft(N −1)  (5) With the predicted parsing map Mt, we first obtain the semantic mask of target clothing Mc t . FEM takes Mc s and Mc t as input to predict multi-scale dense flow fields for establishing visual correspondence between the source clothing and the target try-on clothing in the feature domain. To deal with the drastic spatial deformation existing between the source clothing and the target try-on clothing, we estimate (4) (5) where W is warping operation with bilinear interpolation when the flow field falls into a sub-pixel coordinate. This allows end-to-end training via stochastic gradient 40902 VOLUME 10, 2022 T. Wang et al.: Flow-Based Generative Network for Photo-Realistic Virtual Try-On hyper-parameter that controls the contributions of different layers and is set by following [14]. descent [47]. Note that the resolution of FN is upsampled with bilinear interpolation and its value is doubled. Such process will be repeated until inferring the finest flow F1 from the two pyramial features with the highest spatial resolution fs(1) and ft(1). C. FUSION AND RENDERING MODULE (FRM) Going beyond the clothing deformation model, it is another great challenge to render the final try-on image by fusing the contents of the human body and warped clothes. FRM accepts the segmented source clothing Ic s , the body parts of the target person Ib t , the head region of the target person Ih t , the parsing map of the target person Mt and the pose of the target person Pt as input to synthesize the photo-realistic try-on image I′ t . Since we do not have the ground-truth flow, we leverage an unsupervised flow training scheme relying on the photomet- ric loss [42] with the clothing images. The overall objective function for FEM is formulated as: Specifically, FRM adopts three encoders of the same architecture, i.e., ENCc, ENCb and ENCh, to encode the features for the source clothing, the body of the target person, the head of the target person, respectively. Note that the three encoders do not share weights during training. ENCc extracts source clothing features from Ic s through N downsampling layers. Formally, LFEM = λphotLphot + λTV LTV + +λperc1Lperc1 (6) (6) where Lphot is a multi-scale photometric loss, LTV is a flow regularization loss and Lperc1 is the perceptual loss [20]. λphot, λTV and λperc1 are the trade-off parameters for these three loss terms, which are set to 5, 2 and 1, respectively, in our experiments. ENCc(Ic s ) = {fc(1), fc(2), . . . , fc(N)} (10) (10) where fc(n), n = 1, . . . , N denotes the extracted clothing features after n downsampling layers. The multi-scale photometric loss Lphot sums the photomet- ric loss between the source clothing regions and the target one at multiple scales for fast convergence [46], which is defined as: ENCh extracts the head features of the target person separately from the body parts to enhance the siginals of facial features and hair features. Formally, Lphot(Ic t , Ic s , F) = N X i=0 ||ρ(Ic t (i) −W(Ic s (i), Fi))||1 (7) ENCh(Ih t ) = {fh(1), fh(2), . . . , fh(N)} (11) (11) where fh(n), n = 1, . . . , N denotes the extracted head features after n downsampling layers. where fh(n), n = 1, . . . , N denotes the extracted head features after n downsampling layers. C. FUSION AND RENDERING MODULE (FRM) where ρ(x) = (x2 + ϵ2)α is a penalty function for mitigating the effects of outliers [42]. Ic t and Ic s is the segment image with the clothing regions of the target clothing and the source clothing, respectively. And i represents the spatial resolution of images and flows. Note that Ic t (i), Ic s (i) and Fi have the same spatial resolution. Likewise, ENCb extracts the body features of the target person conditioned on Ib t , Mt and Pt, ENCb(Ib t , Mt, Pt) = {fb(1), fb(2), . . . , fb(N)} (12) (12) where fb(n), n = 1, . . . , N denotes the extracted body features after n downsampling layers. With the removed clothing and head regions, the arms and legs are represented as body parts. where fb(n), n = 1, . . . , N denotes the extracted body features after n downsampling layers. With the removed clothing and head regions, the arms and legs are represented as body parts. The flow regularization loss LTV is a total variation- based (TV) smoothness penalty term to regularize the flow prediction, which is defined as: Next, the final try-on result I′ t is generated through N decoding blocks, where each decoding block accepts the concatenated warped clothing features, body features and head features. Formally, LTV (FN, R) = ||1FN||1 + N−1 X i=1 ||1Ri||1 (8) (8) Unlike previous methods [13], [46] that regularize the multi- scale flows, we apply smoothness loss on the coarse flow FN and the multi-scale residue flows. f (1) dec = DEC fb(N), W(fc(N), FN), fh(N)  f (2) dec = DEC f (1) dec, W(fc(N −1), FN−1), fh(N −1)  In order to preserve realistic details and textures of source clothing, we add the perceptual loss between Ic t and the warped source clothing segment image (i.e., W(Ic s ) = W(Ic s , F0)). Specifically, the perceptual loss Lperc1 models the distance between Ic t and W(Ic s ) in a feature space, which is defined as: f (N) dec = DEC f (N−1) dec , W(fc(1), F1), fh(1)  (13) (13) where the clothing feature fc(n) is warped via the predicted flow Fn from previous module. Note that fc(n) and Fn is ensured to have the same spatial resolution. Tanh function is applied after f (N) dec to generate the normalized image, i.e. B. FLOW ESTIMATION MODULE (FEM) Finally, F1 is upsampled and its value is doubled to F0 = 2F↑2 1 . Inspired by [35], the flow estimation layers share weights between iterations for speeding up model training and reducing the amount of model parameters. C. FUSION AND RENDERING MODULE (FRM) I′ t = tanh(f (N) dec ). Lperc1(Ic t , W(Ic s )) = Nl X i=0 βi||φi(Ic t ) −φi(W(Ic s ))||1 (9) (9) Besides, to enhance the robustness of the mapping in FRM, we introduce a body mask Mb t for Ib t to randomly remove some regions of the human body, where Nl is the number of chosen layers. And φi(Ic t ) denotes the feature map of image Ic t at the i-th layer in a VGG-19 [33] network pre-trained on ImageNet [5]. βi is the Ib t = (1 −Mb t ) ∗Ib t (14) 40903 Ib t = (1 −Mb t ) ∗Ib t (14) (14) 40903 VOLUME 10, 2022 VOLUME 10, 2022 The reconstruction loss is the L1 loss between the synthesized image I′ t and the ground-truth image Ir, which is defined as: LL1(I′ t , Ir) = ||I′ t −Ir||1 (16) (16) The perceptual loss Lperc2 models the distance between the synthesized image I′ t and the ground-truth image Ir in a The perceptual loss Lperc2 models the distance between the synthesized image I′ t and the ground-truth image Ir in a feature space, i.e., Lperc2(I′ t , Ir) = Nl P i=0 βi||φi(I′ t ) −φi(Ir)||1. feature space, i.e., Lperc2(I′ t , Ir) = Nl P i=0 βi||φi(I′ t ) −φi(Ir)||1. 1) QUANTITATIVE RESULTS Table 1 reports the quantitative comparison between our approach and the baselines. Except for SSIM and IS, our method significantly outperforms all baselines on FID and LPIPS. The IS metric provides a proxy to evaluate the performance but it is not a good measurement of how well the model is performing our task. Although our method gets the second-highest SSIM score, the FID and LPIPS A. IMPLEMENTATION DETAILS We conduct the experiments on the VITON dataset [14] to evaluate the proposed FVTN on virtual try-on task. We follow [36] to split 16,253 image pairs into a training set and a validation set with 14,221 and 2,032 pairs, respectively. Each image pair includes a front-view woman image and a top clothing image. Resolution for all images in VITON is 256 × 192. Note that the images of the validation set are rearranged into unmatched pairs as the test set. B. EVALUATIONS We mainly perform visual comparison of our method with recent proposed virtual try-on networks [13], [25], [36], [40]. VOLUME 10, 2022 T. Wang et al.: Flow-Based Generative Network for Photo-Realistic Virtual Try-On TABLE 1. Quantitative comparison results of our proposed method and the baselines on the virtual try-on task. A higher score of SSIM/IS is better. A lower score of FID/LPIPS is better. TABLE 1. Quantitative comparison results of our proposed method and the baselines on the virtual try-on task. A higher score of SSIM/IS is better. A lower score of FID/LPIPS is better. where Mb t is sampled from the Irregular Mask Dataset [22]. Without Mb t , FRM tends to learn an identity mapping for the body parts (i.e., arms and legs). For example, when transferring a long-sleeve garment to the target person in a short-sleeve one, the arm parts should be rendered with clothing textures instead of retaining the original arms. In the opposite case, when transferring a short-sleeve garment to the target person in a long-sleeve one, the arm parts should be synthesized instead of retaining the original clothing textures. By introducing Mb t , FRM can adaptively determine the generation or preservation of the body parts. The overall objective function for FRM is formulated as: LFRM = λL1LL1 + λperc2Lperc2 + λstyLstyle (15) (15) and a learning rate of 0.0001 for 15 epochs. FEM is trained with a minibatch of size 8 and a learning rate of 0.00005 for 20 epochs. In FEM, the FPN consists of five encoding layers where each layer is a convolution layer with kernel 3 and stride 2 followed by one residual block. Besides, we use a deformable convolution with kernel 3 and stride 1 as the flow estimation layer. FRM is trained with a minibatch of size 8 and a learning rate of 0.0001 for 20 epochs. In FRM, three encoders share the same architecture, consisting of five downsampling layers where each layer contains two convolution layers with kernel 3 and stride 2 and with kernel 3 and stride 1, respectively. where LL1 is the reconstruction loss, Lperc2 is the perceptual loss [20] and Lstyle is the style loss [8]. λL1, λperc2 and λsty are the trade-off parameters for these three loss terms, which are set to 1, 1 and 400, respectively, in our experiments. 3) EVALUATION METRICS i=0 Lstyle is the style loss that matches style information between the synthesized image and the ground-truth image, which is defined as: We adopt four widely used evaluation metrics to evaluate the quality of the synthesized images. Inception Score (IS) [31] is used to measure the quality and diversity of the generated images. Structural Similarity (SSIM) [39] is used to measure the similarity between the generated images and ground- truth images. Fréchet Inception Distance (FID) [15] is used to measure the realism of the generated images by computing the Wasserstein-2 distance between distributions of the generated images and ground-truth images. Learned Perceptual Image Patch Similarity (LPIPS) [45] is used to measure how similar are two images by computing the distance between the generated images and generated images at the perceptual domain. Lstyle(I′ t , Ir) = Nl X i=1 γi||ψi(I′ t ) −ψi(Ir)||1 (17) (17) where ψi(I′ t ) denotes the Gram matrix [8] of image I′ t at the i-th layer in a VGG-19 [33] network pre-trained on ImageNet [5]. γi is the hyper-parameter that controls the contributions of different layers and is set by following [13]. 2) TRAINING DETAILS We train three modules of the proposed FVTN separately. We use the Adam optimizer with β1 = 0.9 and β2 = 0.999 in all experiments. PAM is trained with a minibatch of size 16 VOLUME 10, 2022 40904 T. Wang et al.: Flow-Based Generative Network for Photo-Realistic Virtual Try-On FIGURE 3. Comparison visual results of different approaches on the virtual try-on task. FIGURE 3. Comparison visual results of different approaches on the virtual try-on task. more accurately reflect the similarity between the synthesized images and the ground-truth images. more accurately reflect the similarity between the synthesized images and the ground-truth images. the second column is the target person image and the other columns are the synthesized virtual try-on images with different approaches. We observe that CP-VTON produces the worst visual effects, which fails to handle clothing deformation and generate the fine details of the human body. This observation verifies the inefficiency of 2) QUALITATIVE RESULTS Figure 3 presents a visual comparison of the evaluated methods, where the first column is the garment image, VOLUME 10, 2022 2) QUALITATIVE RESULTS Figure 3 presents a visual comparison of the evaluated methods, where the first column is the garment image, 40905 T. Wang et al.: Flow-Based Generative Network for Photo-Realistic Virtual Try-On FIGURE 4. More visual try-on results of the proposed FVTN. FIGURE 4. More visual try-on results of the proposed FVTN. outperforms these three methods because of its proposed second-order spatial transformation constraint and inpainting module. However, we notice visible high-frequency artifacts in the collar regions of try-on images generated by ACGPN. By contrast, our proposed FVTN generates more perceptually convincing synthetic results which warp the garments more naturally and align them with the human body more accurately. TPS for modeling the highly non-rigid transformation like clothing. What’s more, the composition mask of CP-VTON cannot flexibly synthesize the body parts. By improv- ing the clothing warping stage and the blending stage, CP-VTON+ gets better visual results than CP-VTON, especially in the case of body occlusion. Compared with CP-VTON and CP-VTON+, ClothFlow achieves much better try-on results, especially in the clothing regions. Such comparison demonstrates the advantages of the flow-based methods during learning clothing deformation. However, ClothFlow gets unsatisfactory human body parts because of its simple try-on image rendering model. ACGPN Figure 4 displays more synthetic examples of our FVTN in which different target persons under arbitrary poses virtually try on various garments. Notably, our method preserves the fine-grained appearance details of the garments (such as the 40906 VOLUME 10, 2022 VOLUME 10, 2022 T. Wang et al.: Flow-Based Generative Network for Photo-Realistic Virtual Try-On FIGURE 5. Ablation study: synthesis quality evaluation on the virtual try-on task. T. Wang et al.: Flow-Based Generative Network for Photo-Realistic Virtual Try-On FIGURE 5. Ablation study: synthesis quality evaluation on the virtual try-on task. Several variants of the FVTN are trained: (1) w.o/iter, the model using a direct flow estimation scheme instead of an iterative flow estimation scheme in FEM. (2) w.o/deconv, the model using the standard convolution instead of deformable convolution in the flow estimation layer. (3) w.o/multi, the model using conventional single-scale photometric loss in FEM. (4) w.o/fwarp, the model accepting the warped clothing as input instead of the warped feature in FRM. (5) w.o/mask, the model accepting the body parts of the target person Ib t without the body mask Mb t as input in FRM. logos and clothing textures) along with the body parts under complex posture changes and occlusion. 2) QUALITATIVE RESULTS Our FVTN can handle different types of body shapes because PAM provides accurate spatial information by aligning the source clothing to the posture of the target person at the semantic level. To sum up, these quantitative and qualitative results verify the effectiveness of our FVTN. 4) USER STUDY We further evaluate the image quality of our synthesized images via a human subjective study involving 20 partic- ipants. Following [40], given two generated images, each participant is asked to choose a better and more realistic image meeting three criteria: (1) how well the target clothing characteristics of the source clothing image are preserved; (2) how photo-realistic the whole image is; (3) how good the whole person seems. Our FVTN achieves significantly better human evaluation scores on the image-based virtual try-on, as shown in Table 2. The results of the user study are consistent with those of qualitative and quantitative experiments, which demonstrate the effectiveness of the proposed FVTN. [8] L. A. Gatys, A. S. Ecker, and M. Bethge, ‘‘Image style transfer using convolutional neural networks,’’ in Proc. IEEE Conf. Comput. Vis. Pattern Recognit. (CVPR), Jun. 2016, pp. 2414–2423. [9] K. Gong, X. Liang, Y. Li, Y. Chen, M. Yang, and L. Lin, ‘‘Instance-level human parsing via part grouping network,’’ in Proc. ECCV, in Lecture Notes in Computer Science, vol. 11208, 2018, pp. 805–822. [10] I. J. Goodfellow, J. Pouget-Abadie, M. Mirza, B. Xu, D. Warde-Farley, S. Ozair, A. C. Courville, and Y. Bengio, ‘‘Generative adversarial nets,’’ in Proc. NIPS, 2014, pp. 2672–2680. [11] X. Gu, J. Yu, Y. Wong, and M. S. Kankanhalli, ‘‘Toward multi-modal conditioned fashion image translation,’’ IEEE Trans. Multimedia, vol. 23, pp. 2361–2371, 2021. [12] Y. Guo, Q. Chen, J. Chen, Q. Wu, Q. Shi, and M. Tan, ‘‘Auto-embedding generative adversarial networks for high resolution image synthesis,’’ IEEE Trans. Multimedia, vol. 21, no. 11, pp. 2726–2737, Nov. 2019. [13] X. Han, W. Huang, X. Hu, and M. Scott, ‘‘ClothFlow: A flow-based model for clothed person generation,’’ in Proc. IEEE/CVF Int. Conf. Comput. Vis. (ICCV), Oct. 2019, pp. 10470–10479. 3) ABLATION STUDY We train several ablation experiments on the VITON dataset to assess the contribution of each component of the FVTN. 40907 VOLUME 10, 2022 T. Wang et al.: Flow-Based Generative Network for Photo-Realistic Virtual Try-On TABLE 2. User study results on the VITON dataset. The results indicate the proportion of images that human subjects regard our method are better and more realistic than the compared method. FIGURE 6. Failure cases of our method on the virtual try-on task. TABLE 2. User study results on the VITON dataset. The results indicate the proportion of images that human subjects regard our method are better and more realistic than the compared method. TABLE 2. User study results on the VITON dataset. The results indicate the proportion of images that human subjects regard our method are better and more realistic than the compared method. view. Besides, our FVTN relies on human segmentation of different body parts to enable the learning procedure. Thus, wrong segmentation would lead to highly-unrealistic try-on images. REFERENCES [1] Q. Chen and V. Koltun, ‘‘Full flow: Optical flow estimation by global optimization over regular grids,’’ in Proc. IEEE Conf. Comput. Vis. Pattern Recognit. (CVPR), Jun. 2016, pp. 4706–4714. FIGURE 6. Failure cases of our method on the virtual try-on task. The quantitative evaluation results are shown in Table 1. From the results, we find that our model outperforms all the variants on all metrics and all components improve performances in different degrees. The qualitative evalua- tion results are visualized in Fig. 5. Consistent with the quantitative evaluations, our model surpasses all the variants with the highest quality of visual results. Besides, we obtain the following observations: (1) w.o/mask cannot adaptively determine the generation or preservation of the body parts. (2) w.o/iter generates very poor appearances of the garments. (3) w.o/deconv, w.o/multi and w.o/fwarp all bring visual artifacts in the synthesized clothing regions. Those findings prove the necessity of each component of our FVTN. [2] W. Chen, H. Wang, Y. Li, H. Su, Z. Wang, C. Tu, D. Lischinski, D. Cohen-Or, and B. Chen, ‘‘Synthesizing training images for boosting human 3D pose estimation,’’ in Proc. 4th Int. Conf. 3D Vis. (3DV), Oct. 2016, pp. 479–488. [3] Y. Chen, Z. Wang, Y. Peng, Z. Zhang, G. Yu, and J. Sun, ‘‘Cascaded pyramid network for multi-person pose estimation,’’ in Proc. IEEE/CVF Conf. Comput. Vis. Pattern Recognit., Jun. 2018, pp. 7103–7112. [4] J. Dai, H. Qi, Y. Xiong, Y. Li, G. Zhang, H. Hu, and Y. Wei, ‘‘Deformable convolutional networks,’’ in Proc. IEEE Int. Conf. Comput. Vis. (ICCV), Oct. 2017, pp. 764–773. [5] J. Deng, W. Dong, R. Socher, L.-J. Li, K. Li, and L. Fei-Fei, ‘‘ImageNet: A large-scale hierarchical image database,’’ in Proc. IEEE Conf. Comput. Vis. Pattern Recognit., Jun. 2009, pp. 248–255. [6] H. Dong, X. Liang, X. Shen, B. Wang, H. Lai, J. Zhu, Z. Hu, and J. Yin, ‘‘Towards multi-pose guided virtual try-on network,’’ in Proc. IEEE/CVF Int. Conf. Comput. Vis. (ICCV), Oct. 2019, pp. 9025–9034. [7] A. Dosovitskiy, P. Fischer, E. Ilg, P. Hausser, C. Hazirbas, V. Golkov, P. V. D. Smagt, D. Cremers, and T. Brox, ‘‘FlowNet: Learning optical flow with convolutional networks,’’ in Proc. IEEE Int. Conf. Comput. Vis. (ICCV), Dec. 2015, pp. 2758–2766. V. CONCLUSION In this work, we propose a novel Flow-based Virtual Try-on Network (FVTN), which aims at generating photo-realistic try-on results. We present three tailored modules, i.e., Parsing Alignment Module (PAM), Flow Estimation Module (FEM) and Fusion and Rendering Module (FRM). Specifically, we design an unsupervised flow-based spatial alignment scheme in FEM to precisely capture clothing deformation. We propose an image synthesis network in FRM to synthesize the try-on look by integrating information from the warped clothing and the human body. The results clearly show the great superiority of our proposed FVTN in terms of quantitative metrics, visual quality and user study. [1] Q. Chen and V. Koltun, ‘‘Full flow: Optical flow estimation by global optimization over regular grids,’’ in Proc. IEEE Conf. Comput. Vis. Pattern Recognit. (CVPR), Jun. 2016, pp. 4706–4714. 5) FAILURE CASES AND LIMITATIONS ECCV, in Lecture Notes in Computer Science, vol. 9906, 2016, pp. 694–711. [44] M. Yuan, I. R. Khan, F. Farbiz, S. Yao, A. Niswar, and M.-H. Foo, ‘‘A mixed reality virtual clothes try-on system,’’ IEEE Trans. Multimedia, vol. 15, no. 8, pp. 1958–1968, Dec. 2013. p pp [21] C. Lassner, G. Pons-Moll, and P. V. Gehler, ‘‘A generative model of people in clothing,’’ in Proc. IEEE Int. Conf. Comput. Vis. (ICCV), Oct. 2017, pp. 853–862. [45] R. Zhang, P. Isola, A. A. Efros, E. Shechtman, and O. Wang, ‘‘The unreasonable effectiveness of deep features as a perceptual metric,’’ in Proc. IEEE/CVF Conf. Comput. Vis. Pattern Recognit., Jun. 2018, pp. 586–595. [22] G. Liu, A. F. Reda, J. K. Shih, T. Wang, A. Tao, and B. Catanzaro, ‘‘Image inpainting for irregular holes using partial convolutions,’’ in Proc. ECCV, in Lecture Notes in Computer Science, vol. 11215, Sep. 2018, pp. 89–105. [46] H. Zheng, L. Chen, C. Xu, and J. Luo, ‘‘Unsupervised pose flow learning for pose guided synthesis,’’ CoRR, vol. abs/1909.13819, pp. 1–12, Sep. 2019. [23] P. Liu, M. Lyu, I. King, and J. Xu, ‘‘SelFlow: Self-supervised learning of optical flow,’’ in Proc. IEEE/CVF Conf. Comput. Vis. Pattern Recognit. (CVPR), Jun. 2019, pp. 4571–4580. [47] T. Zhou, S. Tulsiani, W. Sun, J. Malik, and A. A. Efros, ‘‘View synthesis by appearance flow,’’ in Proc. ECCV, in Lecture Notes in Computer Science, vol. 9908, 2016, pp. 286–301. [24] S. Meister, J. Hur, and S. Roth, ‘‘UnFlow: Unsupervised learning of optical flow with a bidirectional census loss,’’ in Proc. AAAI, 2018, pp. 7251–7259. [25] M. Minar, T. Tuan, H. Ahn, P. Rosin, and Y. Lai, ‘‘CP-VTON+: Clothing shape and texture preserving image-based virtual try-on,’’ in Proc. CVPRW, 2020, pp. 1–4. [26] A. Mir, T. Alldieck, and G. Pons-Moll, ‘‘Learning to transfer texture from clothing images to 3D humans,’’ in Proc. IEEE/CVF Conf. Comput. Vis. Pattern Recognit. (CVPR), Jun. 2020, pp. 7021–7032. TAO WANG is currently pursuing the master’s degree with Hangzhou Dianzi University. His research interests include computer vision and deep learning. [27] C. Patel, Z. Liao, and G. Pons-Moll, ‘‘TailorNet: Predicting clothing in 3D as a function of human pose, shape and garment style,’’ in Proc. IEEE/CVF Conf. Comput. Vis. Pattern Recognit. (CVPR), Jun. 2020, pp. 7363–7373. [28] G. Pons-Moll, S. Pujades, S. Hu, and M. J. Black, ‘‘ClothCap: Seamless 4D clothing capture and retargeting,’’ ACM Trans. Graph., vol. 36, no. 5) FAILURE CASES AND LIMITATIONS 4, pp. 73:1–73:15, 2017. [29] A. Ranjan and M. J. Black, ‘‘Optical flow estimation using a spatial pyramid network,’’ in Proc. IEEE Conf. Comput. Vis. Pattern Recognit. (CVPR), Jul. 2017, pp. 2720–2729. [30] Y. Ren, X. Yu, J. Chen, T. H. Li, and G. Li, ‘‘Deep image spatial transformation for person image generation,’’ in Proc. IEEE/CVF Conf. Comput. Vis. Pattern Recognit. (CVPR), Jun. 2020, pp. 7687–7696. [31] T. Salimans, I. J. Goodfellow, W. Zaremba, V. Cheung, A. Radford, and X. Chen, ‘‘Improved techniques for training GANs,’’ in Proc. NIPS, 2016, pp. 2226–2234. XIAOLING GU (Member, IEEE) received the Ph.D. degree in computer science from Zhejiang University, in 2017. She is currently an Associate Professor at the School of Computer Science and Technology, Hangzhou Dianzi University. She has published several top-tier conferences and journal papers, such as SIGIR, ACM Multimedia, and the IEEE TRANSACTIONS ON MULTIMEDIA. Her current research interests include computer vision, machine learning, and fashion data analysis. [32] M. Sekine, K. Sugita, F. Perbet, B. Stenger, and M. Nishiyama, ‘‘Virtual fitting by single-shot body shape estimation,’’ in Proc. 5th Int. Conf. 3D Body Scanning Technol., Oct. 2014, pp. 406–413. [33] K. Simonyan and A. Zisserman, ‘‘Very deep convolutional networks for large-scale image recognition,’’ CoRR, vol. abs/1409.1556, pp. 1–14, Sep. 2014. [34] D. Sun, X. Yang, M.-Y. Liu, and J. Kautz, ‘‘PWC-Net: CNNs for optical flow using pyramid, warping, and cost volume,’’ in Proc. IEEE/CVF Conf. Comput. Vis. Pattern Recognit., Jun. 2018, pp. 8934–8943. [35] Z. Teed and J. Deng, ‘‘RAFT: Recurrent all-pairs field transforms for optical flow,’’ in Proc. Eur. Conf. Comput. Vis. (ECCV), in Lecture Notes in Computer Science, vol. 12347, 2020, pp. 402–419. [36] B. Wang, H. Zheng, X. Liang, Y. Chen, L. Lin, and M. Yang, ‘‘Toward characteristic-preserving image-based virtual try-on network,’’ in Proc. ECCV, in Lecture Notes in Computer Science, vol. 11217, 2018, pp. 607–623. JUNKAI ZHU is currently pursuing the master’s degree with Hangzhou Dianzi University. His research interests include computer vision and deep learning. [37] T.-C. Wang, M.-Y. Liu, J.-Y. Zhu, A. Tao, J. Kautz, and B. Catanzaro, ‘‘High-resolution image synthesis and semantic manipulation with condi- tional GANs,’’ in Proc. IEEE/CVF Conf. Comput. Vis. Pattern Recognit., Jun. 2018, pp. 8798–8807. [38] Y. Wang, Y. Yang, Z. Yang, L. Zhao, P. Wang, and W. Xu, ‘‘Occlusion aware unsupervised learning of optical flow,’’ in Proc. IEEE/CVF Conf. Comput. Vis. Pattern Recognit., Jun. 2018, pp. 4884–4893. 5) FAILURE CASES AND LIMITATIONS [14] X. Han, Z. Wu, Z. Wu, R. Yu, and L. S. Davis, ‘‘VITON: An image-based virtual try-on network,’’ in Proc. IEEE/CVF Conf. Comput. Vis. Pattern Recognit., Jun. 2018, pp. 7543–7552. Fig. 6 displays two failure cases of our proposed FVTN on the virtual try-on task. The example of the top row is caused by the rarely-seen human poses while another example is due to the viewpoint transformation from the front view to the back [15] M. Heusel, H. Ramsauer, T. Unterthiner, B. Nessler, and S. Hochreiter, ‘‘GANs trained by a two time-scale update rule converge to a local Nash equilibrium,’’ in Proc. NIPS, 2017, pp. 6626–6637. 40908 VOLUME 10, 2022 T. Wang et al.: Flow-Based Generative Network for Photo-Realistic Virtual Try-On [16] B. K. P. Horn and B. G. Schunck, ‘‘Determining optical flow,’’ Artif. Intell., vol. 17, nos. 1–3, pp. 185–203, Aug. 1980. [40] H. Yang, R. Zhang, X. Guo, W. Liu, W. Zuo, and P. Luo, ‘‘Towards photo-realistic virtual try-on by adaptively generating↔preserving image content,’’ in Proc. IEEE/CVF Conf. Comput. Vis. Pattern Recognit. (CVPR), Jun. 2020, pp. 7847–7856. [17] P. Hu, G. Wang, and Y.-P. Tan, ‘‘Recurrent spatial pyramid CNN for optical flow estimation,’’ IEEE Trans. Multimedia, vol. 20, no. 10, pp. 2814–2823, Oct. 2018. [41] S. Yang, T. Amert, Z. Pan, K. Wang, L. Yu, T. L. Berg, and M. C. Lin, ‘‘Detailed garment recovery from a single-view image,’’ CoRR, vol. abs/1608.01250, pp. 1–13, Aug. 2016. [18] E. Ilg, N. Mayer, T. Saikia, M. Keuper, A. Dosovitskiy, and T. Brox, ‘‘FlowNet 2.0: Evolution of optical flow estimation with deep networks,’’ in Proc. IEEE Conf. Comput. Vis. Pattern Recognit. (CVPR), Jul. 2017, pp. 1647–1655. [42] J. J. Yu, A. W. Harley, and K. G. Derpanis, ‘‘Back to basics: Unsupervised learning of optical flow via brightness constancy and motion smoothness,’’ in Proc. ECCV Workshops, in Lecture Notes in Computer Science, vol. 9915, 2016, pp. 3–10. [19] P. Isola, J.-Y. Zhu, T. Zhou, and A. A. Efros, ‘‘Image-to-image translation with conditional adversarial networks,’’ in Proc. IEEE Conf. Comput. Vis. Pattern Recognit. (CVPR), Jul. 2017, pp. 5967–5976. [43] R. Yu, X. Wang, and X. Xie, ‘‘VTNFP: An image-based virtual try-on network with body and clothing feature preservation,’’ in Proc. IEEE/CVF Int. Conf. Comput. Vis. (ICCV), Oct. 2019, pp. 10510–10519. [20] J. Johnson, A. Alahi, and L. Fei-Fei, ‘‘Perceptual losses for real-time style transfer and super-resolution,’’ in Proc. JUNKAI ZHU is currently pursuing the master’s degree with Hangzhou Dianzi University. His research interests include computer vision and deep learning. TAO WANG is currently pursuing the master’s degree with Hangzhou Dianzi University. His research interests include computer vision and deep learning. 5) FAILURE CASES AND LIMITATIONS [39] Z. Wang, A. C. Bovik, H. R. Sheikh, and E. P. Simoncelli, ‘‘Image quality assessment: From error visibility to structural similarity,’’ IEEE Trans. Image Process., vol. 13, no. 4, pp. 600–612, Apr. 2004. 40909 VOLUME 10, 2022 VOLUME 10, 2022 VOLUME 10, 2022
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Interventions, outcomes and outcome measurement instruments in stillbirth care research: A systematic review to inform the development of a core outcome set
BJOG
2,023
cc-by
14,768
Danya Bakhbakhi1  | Dimitrios Siassakos2  | Anna Davies3   | Abi Merriel1   | Katie Barnard4   | Emma Stead5  | Clare Shakespeare1  | James M. N. Duffy6  | Lisa Hinton7  | Karolina McDowell4  | Anna Lyons8  | Abigail Fraser1  | Christy Burden1  | iCHOOSE Collaborative Group Danya Bakhbakhi1  | Dimitrios Siassakos2  | Anna Davies3   | Abi Merriel1   | Katie Barnard4   | Emma Stead5  | Clare Shakespeare1  | James M. N. Duffy6  | Lisa Hinton7  | Karolina McDowell4  | Anna Lyons8  | Abigail Fraser1  | Christy Burden1  | iCHOOSE Collaborative Group 1University of Bristol, Bristol, UK 2Institute for Women's Health, University College London, London, UK 3Centre for Academic Child Health, University of Bristol, Bristol, UK 4North Bristol NHS Trust, Bristol, UK 5Liverpool University Hospitals Foundation Trust, Liverpool, UK 6North Middlesex University Hospital NHS Trust, London, UK 7THIS Institute, University of Cambridge, Cambridge, UK 8Northern General Hospital, Sheffield, UK 1University of Bristol, Bristol, UK 2Institute for Women's Health, University College London, London, UK 3Centre for Academic Child Health, University of Bristol, Bristol, UK 4North Bristol NHS Trust, Bristol, UK 5Liverpool University Hospitals Foundation Trust, Liverpool, UK 6North Middlesex University Hospital NHS Trust, London, UK 7THIS Institute, University of Cambridge, Cambridge, UK 8Northern General Hospital, Sheffield, UK Background: A core outcome set could address inconsistent outcome reporting and improve evidence for stillbirth care research, which have been identified as an im- portant research priority. p p y Objectives: To identify outcomes and outcome measurement instruments reported by studies evaluating interventions after the diagnosis of a stillbirth. Search strategy: Amed, BNI, CINAHL, ClinicalTrials.gov, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, Embase, MEDLINE, PsycINFO, and WHO ICTRP from 1998 to August 2021. y g Selection criteria: Randomised and non-­randomised comparative or non-­ comparative studies reporting a stillbirth care intervention. g Data collection and analysis: Interventions, outcomes reported, definitions and outcome measurement tools were extracted. Correspondence Danya Bakhbakhi, Department of Translational Health Sciences, Bristol Medical School, University of Bristol, Faculty of Health Sciences, Bristol, UK. Email: danya.bakhbakhi@bristol.ac.uk Funding information Research Trainees Coordinating Centre, Grant/Award Number: NIHR DRF-­2017-­10-­130 Main results: Forty randomised and 200 non-­randomised studies were included. Fifty-­eight different interventions were reported, labour and birth care (52 studies), hospital bereavement care (28 studies), clinical investigations (116 studies), care in a multiple pregnancy (2 studies), psychosocial support (28 studies) and care in a sub- sequent pregnancy (14 studies). A total of 391 unique outcomes were reported and organised into 14 outcome domains: labour and birth; postpartum; delivery of care; investigations; multiple pregnancy; mental health; emotional functioning; grief and bereavement; social functioning; relationship; whole person; subsequent pregnancy; subsequent children and siblings and economic. S Y S T E M A T I C R E V I E W S Y S T E M A T I C R E V I E W Accepted: 26 October 2022 DOI: 10.1111/1471-0528.17390 Accepted: 26 October 2022 DOI: 10.1111/1471-0528.17390 |  1 wileyonlinelibrary.com/journal/bjo This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2023 The Authors. BJOG: An International Journal of Obstetrics and Gynaecology published by John Wiley & Sons Ltd. Abigail Fraser and Christy Burden: Joint Last Authors. See Appendix 1 for iCHOOSE Collaborative Group members. Danya Bakhbakhi1  | Dimitrios Siassakos2  | Anna Davies3   | Abi Merriel1   | Katie Barnard4   | Emma Stead5  | Clare Shakespeare1  | James M. N. Duffy6  | Lisa Hinton7  | Karolina McDowell4  | Anna Lyons8  | Abigail Fraser1  | Christy Burden1  | iCHOOSE Collaborative Group A total of 242 outcome measure- ment instruments were used, with 0–­22 tools per outcome. Conclusions: Heterogeneity in outcome reporting, outcome definition and meas- urement tools in care after stillbirth exists. Considerable research gaps on specific intervention types in stillbirth care were identified. A core outcome set is needed to standardise outcome collection and reporting for stillbirth care research. BJOG. 2023;00:1–17. Abigail Fraser and Christy Burden: Joint Last Authors. 2.1 As very few randomised trials of care after stillbirth exist, we felt it was necessary to include observational studies in our methods. This approach was designed to facilitate the development of a comprehensive long-­list of potential out- comes for inclusion in a core outcome set for stillbirth care research. With assistance from a clinical librarian (KB), elec- tronic searches of Amed, BNI, CINAHL, ClinicalTrials.gov, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, Embase, MEDLINE, PsycINFO and WHO ICTRP databases were conducted with a date limit of 1998 to 2019, updated in August 2021. For pragmatic reasons, the research team decided to limit the search to a generation's worth of research data (approxi- mately 20 years) to ensure results included seminal stillbirth care research and relevant contemporary outcomes. Free text and subject heading terms were searched, such as still- birth, fetal death, perinatal mortality and fetal mortality, and methodological filters were applied. A detailed search strat- egy is included in Appendix S1. Reference lists of extracted articles and relevant systematic reviews were searched. There is a range of potential interventions that tackle dif- ferent aspects of care after a stillbirth across the life course, from the initial diagnosis of the death of a baby, bereavement care and interventions to understand why a baby has died, to long-­term psychosocial support and care in a subsequent pregnancy. Cochrane reviews exploring these aspects of care have unanimously found few randomised controlled trials to guide clinical practice and improve care after a stillbirth has been diagnosed.8–­10 The lack of evidence is further com- pounded by heterogeneity in outcome reporting, leading to a difficulty in synthesising and appraising the results of pre- viously conducted studies. Perhaps it is unsurprising that heterogeneity exists, given the array of interventions available at different timepoints, addressing different aspects of the stillbirth. Nonetheless, it is important to identify and measure outcomes consistently when investigating mental, physical and social healthcare and impacts associated with the experience of stillbirth care.2 This is particularly important in order to build a comprehensive evidence base on the interventions that are most likely to be effective. 2.3 The identified publications were uploaded to Covidence systematic review software and duplicates removed.15 Prior to abstract and full-­text screening, all review authors had training on the study's objectives, eligibility criteria and outcome extraction. All titles and abstracts were screened independently by at least two members of the review team (two of DB, AM, AD, CS, KB) with previous experience of systematic review methodology. Full text articles identified from the screening process were then assessed for eligibility by two reviewers. Due to the large number of studies, a team of reviewers were involved in the full text review and data extraction process (DB, AM, AD, CS, KD, KB, ES, AL, CB). An international survey in 2019 nominated the devel- opment of a core outcome set for stillbirth research as an important and urgent, top-­five priority to inform clini- cal practice in a pregnancy subsequent to stillbirth.12 The iCHOOSE study is addressing and expanding these pri- orities by developing a core outcome set for stillbirth care research.13 Here we report on a systematic review that aims to identify what interventions and outcomes have been reported as an initial step in core outcome set development. 2.2  |  Study eligibility 2.2 See Table 1 for inclusion and exclusion criteria for systematic review. 1  |  INTRODUCTION In 2019, an estimated 2 million babies were stillborn.1 Previous research has documented the devastating negative medical, social and psychological impact of stillbirth on families.2,3 Studies have found that the care parents receive after the diagnosis stillbirth is inconsistent and often subop- timal.4,5 There is a consensus among the stillbirth research community and bereaved parents that there needs to be more evidence-­based care available to improve care follow- ing stillbirth for families worldwide.4,6,7 2.1 By developing a core outcome set, a minimum set of outcomes that should be collected and reported in a given study, the same outcomes could be measured using the same measurement tools, minimising outcome reporting bias.11 Similar outcomes can therefore can be compared and combined, thus strengthening the ev- idence base and statistical power to inform best practice and improve care.11 K E Y W O R D S core outcome set, patient and public involvement, stillbirth, stillbirth care, systematic review This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2023 The Authors. BJOG: An International Journal of Obstetrics and Gynaecology published by John Wiley & Sons Ltd. Abigail Fraser and Christy Burden: Joint Last Authors. See Appendix 1 for iCHOOSE Collaborative Group members. 2  |      1  |  INTRODUCTION BAKHBAKHI et al. checklist).14 The full protocol for the development of the core outcome set for stillbirth care research has been published elsewhere.13 2.5 Data were extracted into a standardised data extraction sheet using Google FORMS, which was directly input into a Microsoft EXCEL spreadsheet. The data extraction form was developed and piloted with members of the review team prior to its use. Extracted data were: basic publication details (author and date of publication); study setting; study popula- tion; details of intervention; study methodology; outcomes measured; their definition (if stated); their relevant outcome measurement tool (if applicable); and patient and public in- volvement in the research design. Outcomes were extracted 2.6  | Quality assessment The systematic review was prospectively registered on PROSPERO International prospective register of systematic reviews (CRD42018087748) and adheres to the Preferred Reporting Items for Systematic Reviews and Meta-­Analyses (PRISMA) guidelines (see Appendix  S2 for the PRISMA Risk of bias assessment was initially included in the protocol; however, quality assessment was not relevant in the context of identifying reported outcomes, as the aim of this study was to create a long-­list of outcomes and identify outcome SYSTEMATIC REVIEW OF STILLBIRTH CARE OUTCOMES 1  Inclusion and exclusion criteria for systematic review of interventions, outcomes and measurement instruments. • Systematic reviews, case reports, editorials, review articles, abstracts, protocols and grey literature • Systematic reviews, case reports, editorials, review articles, abstracts, protocols and grey literature • Randomised controlled trials • Non-­randomised comparative and non-­comparative studies (e.g. cohort, case–­control, cross-­sectional studies) • English-­language studies • Qualitative studies • Non-­English language studies • Miscarriage, neonatal death, termination of pregnancy • Note: an inclusive approach was adopted –­ studies were still included if they also included stillbirth and another type of pregnancy loss in their population of interest, e.g. perinatal death (stillbirth and neonatal death). Only stillbirth-­ relevant outcomes were extracted. • No restriction by country worldwide (including high-­, middle-­, lower-­income countries according to World Bank Lending Group definition271) • Pregnancy loss <20 weeks' gestation • Studies including healthcare professionals only as research and outcome measurement population • Any study evaluating an intervention (or type of care) following the identification of stillbirth • Interventions prior to stillbirth being identified • Interventions for prevention of stillbirth (with the exception of interventions to prevent recurrence of stillbirth in a subsequent pregnancy after stillbirth) • Immediate hospital interventions, e.g. induction of birth, mode of birth, standard hospital/bereavement care • Interventions for understanding the causes of stillbirth, e.g. clinical investigations, postmortem, parental engagement in the perinatal mortality review process • Detailed histopathological or mechanistic molecular studies e.g. investigations of specific lesions in placentas, specific genetic abnormality or where main aim was not to identify cause of death • Interventions in the follow up period in the community, e.g. bereavement support, social support • Psychosocial interventions, e.g. counselling, psychotherapy, social support • Interventions in the inter-­pregnancy interval to improve health optimization • Interventions in the subsequent pregnancy after stillbirth, e.g. medical. Quality assessment psychosocial, support • Clinical/medical, care experience, psychological, social, economic, resource outcomes • Labour & birth, postpartum (within the first 6 weeks), within the first year, within the first 5 years (medium term), 5 years or more (longer-­term outcomes) g • Subsequent pregnancy after stillbirth outcomes, e.g. clinical or psychological outcomes specifically related to a subsequent pregnancy measurement tools for stillbirth care research, not to syn- thesise any measured effect. Therefore, we do not report on risk of bias. verbatim from the published abstract, methods or results including tables. Data extraction from all publications was conducted by the primary author (DB) and team members conducted independent data extraction on 50% of these to ensure reliability of extraction. All disagreements were re- solved through a third senior reviewer (CB). • Studies that do not report an outcome following an intervention after stillbirth 3  |  RESULTS Our initial searches identified 21 893 records (Appendix S1). After excluding 6398 duplicate records, 15 495 titles and ab- stracts were screened. An additional 217 articles were identi- fied from searching the reference lists of identified articles and relevant systematic reviews. A total of 1492 studies were included for full text review. Of these, 240 studies met the inclusion criteria, representing approximately 298 762 participants.17–­256 Similar interventions were grouped into the following categories: labour and birth care, postpartum bereavement care, investigations into causes of stillbirth, psychosocial support, multiple pregnancy and interventions in a subse- quent pregnancy. Heterogeneity in outcome reporting was assessed in randomised controlled trials according to in- tervention category. We calculated the number of different definitions and outcome measurement tools described for an individual outcome. The frequency of outcomes assessed at specific time intervals post-­stillbirth is reported. An info- graphic was produced to illustrate the types and timings of interventions after stillbirth (Figure 1). See Table S1 for detailed characteristics of included stud- ies and Appendix S3 for PRISMA flow diagram. Studies from 64 different countries were included. A total of 183 studies conducted research in high-­income, 24 from upper/middle income, 28 from lower-­middle and five from low-­income countries. The majority of studies were con- ducted in Europe (111 studies), followed by North America (52 studies) and Asia (42 studies). Only 23 studies included fathers in their interventions. Lastly, of 240 studies, only 10 involved patients and members of the public in the study 2.7  | 2.6 Following data extraction, true duplicate outcomes were re- moved. Subsequently, to ensure methodological transparency, a further process was conducted whereby two reviewers (a cli- nician, DB and an experienced researcher, AD) organised and classified the outcomes into outcome domains independently using the Cochrane reviews and COMET core outcome set database taxonomy.16 This organisation process allowed for BAKHBAKHI et al. the results and review of the manuscript. The parent in- volvement panel included 11 bereaved parents and had global representation (including Africa, Australasia, Europe, North America) through the iCHOOSE collabora- tive group. outcomes described using the same terminology to be iden- tified and grouped together to enable identification of truly unique outcomes. The Cochrane reviews and COMET taxon- omy had more clinical domains than required and therefore the outcomes were further grouped into an adapted stillbirth care research outcome taxonomy (Table  S2).16 The adapted taxonomy was created to better reflect the needs of stillbirth care research and was developed from ongoing qualitative re- search and bereaved parent input. 2.7 Parents who experienced a stillbirth were involved in the design of the research question through to the analysis of F IG U R E 1  Types and timing of interventions for stillbirth care research. *Number illustrates number of studies. Infographic by Anni King, Senior Research Associate in Medical Imaging, Bristol, UK. F IG U R E 1  Types and timing of interventions for stillbirth care research. *Number illustrates number of studies. Infographic by Anni King, Senior Research Associate in Medical Imaging, Bristol, UK. SYSTEMATIC REVIEW OF STILLBIRTH CARE OUTCOMES TA B L E 2  Study characteristics for included studies in the systematic review. Types of intervention Number of studies (n = 240) Labour and birth care Induction of labour 46 (19.2%) General labour and birth 2 (0.8%) Mode of birth 3 (1.3%) Neural axial analgesia 1 (0.4%) General hospital/bereavement care Multi-­component bereavement carea 15 (6.3%) Seeing, holding and making memories with baby 12 (5%) Bereavement photography 1 (0.4%) Investigations to understand cause of stillbirth Multi-­component postmortem investigationsb 41 (17.1%) Postmortem 28 (11.7%) Postmortem & additional imaging 9 (3.8%) Genetic testing 7 (2.9%) Placental examination 7 (2.9%) Verbal autopsy 6 (2.5%) Postmortem imaging 4 (1.7%) Minimally invasive autopsy and biopsy 3 (1.3%) Testing for thrombophilia 3 (1.3%) Antinuclear antibody test 1 (0.4%) Educational programme for professionals and multi-­component investigations 1 (0.4%) Genetic counselling 1 (0.4%) Kleihauer–­Betke testing 1 (0.4%) Parental engagement in the perinatal mortality review 1 (0.4%) Perinatal death clinical investigation tool 1 (0.4%) Perinatal Death Surveillance and Response (PDSR) system 1 (0.4%) Perinatal mortality review 1 (0.4%) Stillbirth in a multiple pregnancy Bereavement care for stillbirth in a multiple pregnancy 1 (0.4%) Intrauterine rescue transfusion 1 (0.4%) Psychosocial support Bereavement support intervention 5 (2.1%) Cognitive behavioural therapy 4 (1.7%) Counselling 4 (1.7%) Online yoga 3 (1.3%) Social supportd 3 (1.3%) Internet peer support group 2 (0.8%) Support groups 2 (0.8%) Intergenerational bereavement programme 1 (0.4%) Interpersonal psychotherapy 1 (0.4%) Massage 1 (0.4%) Mindfulness 1 (0.4%) Occupation-­based retreat 1 (0.4%) Care in a subsequent pregnancy Thromboprophylaxis in a subsequent pregnancy 6 (2.5%) General care in a subsequent pregnancy 3 (1.3%) Intravenous immunoglobulin in a subsequent pregnancy 1 (0.4%) (Continues) TA B L E 2  Study characteristics for included studies in the systematic review. design and selection of their outcomes and/or outcome measurement tools. A summary of included study details is shown in Table 2. 2.7 Fifty-­eight different types of interventions were identified (Figure 1 and Table 2). A total of 817 outcomes were reported; after de-­ duplication and classification of outcomes, 391 unique out- comes remained. The 391 unique outcomes were organised into 14 outcome domains (Table 3). See Table S3 for a comprehensive list of outcomes reported across all studies, by outcome domain and study design. No outcome was reported in all studies of a specific intervention type. A further analysis of outcome reporting in randomised controlled trials (RCTs) only (Table S4) indicated variability in outcomes reported and no outcome was reported by every RCT of a specific type. 3.1  |  Labour and birth care: Interventions and outcomes Interventions included in this category were induction of labour (46 studies), mode of birth (3 studies) and neural axial analgesia (1 study). The five most commonly reported outcomes in studies reporting on labour and birth inter- ventions were induction to birth interval, reported by 65% of studies (34 of 52 studies), complications or side effects of treatment, reported by 39% of studies (20 of 52 studies), successful induction, reported by 31% of studies (16 of 52 studies), use of analgesia during labour and birth, reported by 25% of studies (13 of 52 studies) and dose of misopros- tol required, reported by 15% (8 of 52 studies). Only one study reported maternal death as an outcome of interest, and only two studies (4% of labour and birth interventions) reported satisfaction with intervention or care. No studies reported psychological (e.g. grief, anxiety) outcomes. 3.3  |  Investigations to understand cause of stillbirth: Interventions and outcomes Interventions included 41 studies evaluating multiple component investigation protocols (e.g. at least two of re- view of the medical history, postmortem pathological ex- amination, placental examination, postmortem imaging, laboratory blood testing for mother or baby). Outcomes were most frequently reported in the investigation do- main (127 outcomes). The six most frequently reported outcomes were identification of cause of death, reported in 41% (47 of 116 studies), proportion consenting to post- mortem, reported by 16% (18 of 116 studies), uptake of postmortem, reported by 12% (14 of 116 studies), identi- fication of fetal congenital abnormality, reported by 10% (11 of 116 studies), identification of a placental cause of death and identification of acquired or inherited throm- bophilia, reported by 6% (7 of 116 studies). Only one study measured parents' experience of an intervention to understand why a baby died and only one study reported on parents' perceived understanding of the cause of their baby's death. 3.4  |  Psychosocial support: Interventions and outcomes Psychosocial support interventions evaluated included bereavement support interventions (5 studies), cognitive behavioural therapy (4 studies), counselling (4 studies) and yoga (3 studies). Outcomes were most frequently re- ported in the mental health domain (10 outcomes). The most commonly reported outcomes were experience of intervention/care, reported by 43% (12 of 28 studies), de- pression, reported by 29% studies (8 of 28 studies), grief, reported by 29% studies (8 of 28), PTSD, reported in 25% of studies (7 of 28 studies), and anxiety, reported in 14% (4 of 28 studies). Only two studies within this category re- ported on relationship outcomes and no studies assessed the effect of a psychosocial intervention on existing chil- dren or family. aMulti-­component bereavement care –­ including at least two of the following intervention or care variables: sensitive care during labour and delivery, mode of birth, time spent with baby, seeing and holding baby, hand/footprints, photos and mementos, including children or family members in care, care or support from healthcare professionals and services, e.g. doctor, bereavement midwife, chaplain, anaesthetist interactions, postmortem investigations, grief support, care after birth, having a funeral, post-­natal appointments, hospital-­based counselling, family support. bMulti-­component postmortem investigations –­ including at least two of the following investigations or care variables. Review of the medical and obstetrics history, postmortem pathological examination, placental examination, postmortem radiographs, postmortem MRI, laboratory blood testing for mother or baby (e.g. congenital infections, diabetes, auto-­antibody testing, thrombophilia testing, biochemistry), microbiological testing, virology, genetic testing, counselling, perinatal mortality review. aMulti-­component bereavement care –­ including at least two of the following intervention or care variables: sensitive care during labour and delivery, mode of birth, time spent with baby, seeing and holding baby, hand/footprints, photos and mementos, including children or family members in care, care or support from healthcare professionals and services, e.g. doctor, bereavement midwife, chaplain, anaesthetist interactions, postmortem investigations, grief support, care after birth, having a funeral, post-­natal appointments, hospital-­based counselling, family support. bMulti-­component postmortem investigations –­ including at least two of the following investigations or care variables. Review of the medical and obstetrics history, postmortem pathological examination, placental examination, postmortem radiographs, postmortem MRI, laboratory blood testing for mother or baby (e.g. congenital infections, diabetes, auto-­antibody testing, thrombophilia testing, biochemistry), microbiological testing, virology, genetic testing, counselling, perinatal mortality review. 3.2  |  Bereavement care: Interventions and outcomes Fifteen studies were identified evaluating multiple compo- nents of bereavement care (e.g. at least two seeing and hold- ing baby, making hand or footprints, photos and mementos, including children or family members in care, care or sup- port from healthcare professionals). The greatest number of outcomes was reported within the delivery of care out- come domain (15 outcomes), followed by the emotional functioning domain (15 outcomes). The most frequently reported outcomes included experience of intervention or care reported by 32% (9 of 28 studies), depression reported by 29% (8 of 28 studies), anxiety reported by 21% (6 of 28 studies), post-­traumatic stress disorder reported by 17% (post-­traumatic stress disorder [PTSD], 5 of 28 studies) and grief reported by 18% (5 of 28 studies). No studies measured the impact of postnatal hospital care on parents, role, e.g. returning to work or parenting, or impact of care on existing older children. BAKHBAKHI et al. 6  |      Types of intervention Number of studies (n = 240) Maternity waiting homec 1 (0.4%) Muscle relaxation exercises 1 (0.4%) Psychoeducation 1 (0.4%) Support intervention in a subsequent pregnancy 1 (0.4%) Total number of participants ~298 762 Study characteristic Number of studies (n = 240) Number of randomised control trials 40 (16.7%) Number of observational studies 200 (83.3%) Number of unique countries 64 (26.7%) Studies by region Europe 111 (46.3%) North America 52 (21.7%) Asia 42 (17.5%) Oceania 16 (6.7%) Africa 13 (5.4%) International 5 (2.1%) South America 1 (0.4%) World Bank Lending Groupe High-­income 183 (76.3%) Lower-­middle-­income 28 (11.7%) Upper/middle-­income 24 (10%) Low-­income 5 (2.1%) Number of fathers 23 (9.6%) Number of patient & public involvement 10 (4.2%) Year published 1998–­2001 27 (11.3%) 2002–­2005 35 (14.7%) 2006–­2009 41 (16%) 2010–­2013 48 (20.2%) 2014–­2017 53 (21.8%) 2018–­2021 38 (16%) TA B L E 2  (Continued) 3.5  |  Multiple pregnancy: Interventions and outcomes Only two interventions and two studies were included in this category. One study assessed the impact of intrauter- ine rescue transfusion and the other on bereavement care for a stillbirth in a multiple pregnancy. The study related to intrauterine rescue transfusion reported solely on medical outcomes related to the surviving twin, e.g. abnormalities on cranial ultrasound, fetal acidaemia or neurodevelopment outcome of the surviving twin. No psychosocial, experien- tial or grief outcomes were reported. cMaternity waiting home –­ A maternity waiting home is a residential facility located near a medical facility, where ‘high risk’ women can await their delivery to ‘bridge the geographical gap’ in obstetric care between rural areas with poor access to services.15 dSocial support –­ including at least two of the following support from hospital, doctor, partner, family, friends, work, parent support groups. 271 cMaternity waiting home –­ A maternity waiting home is a residential facility located near a medical facility, where ‘high risk’ women can await their delivery to ‘bridge the geographical gap’ in obstetric care between rural areas with poor access to services.15 dSocial support –­ including at least two of the following support from hospital, doctor, partner, family, friends, work, parent support groups. eRegion –­ World Bank Lending Group.271 |  7 SYSTEMATIC REVIEW OF STILLBIRTH CARE OUTCOMES TA B L E 3  Summary table of outcomes and domains from systematic review. Domain Definition No. of outcomes No. 3.5  |  Multiple pregnancy: Interventions and outcomes of studies Labour & Birth Medical outcomes related labour and birth, for example, time from induction to birth, adverse events or complications during birth, mode of birth, use of analgesia 52 55 Postpartum Medical outcomes immediately following birth and up to 6 weeks afterwards, postpartum complications, for example, postpartum haemorrhage, retained placenta 38 32 Delivery of care Care related outcomes, for example, experience of satisfaction with care or healthcare professionals, support from healthcare professionals, adherence to intervention, hospital use outcomes, length of hospital stay following diagnosis of stillbirth 29 45 Investigations Outcomes related to the investigation of stillbirth, for example, identification of cause of death or medical diagnosis following investigation, proportion consenting to postmortem or investigations 127 120 Multiple pregnancy outcomes Outcomes specifically related to cases where a stillbirth occurs in a multiple pregnancy, for example, clinical outcomes of surviving twin, attachment to survivor 8 2 Mental health Outcomes related to mental health, for example, depression, anxiety, post-­traumatic stress disorder 18 35 Emotional functioning Outcomes related to emotional health, for example, emotional regulation, feelings, self-­compassion 27 20 Grief and bereavement outcomes Outcomes related to grief and bereavement, for example, grief, complicated grief, coping with grief 9 22 Social functioning Outcomes related to social functioning, for example, social support, support from family, friends, social role impairment 6 6 Relationship outcomes Outcomes related to relationships with partner, friends, family, for example, relationship difficulties, quality 6 6 Whole person outcomes Outcomes related to physical functioning, for example, poor physical health, physical mobility, health-­related quality of life, outcomes affecting the whole body and not attributed to a particular system, self-­reported health, sleep 7 7 Subsequent pregnancy Outcomes related to a subsequent pregnancy after stillbirth, for example, live birth, complications in pregnancy, preterm birth, pregnancy anxiety 47 12 Subsequent children and siblings Outcomes related to subsequent children and siblings after stillbirth, for example, attachment to infant, parental concerns 2 2 Economic Outcomes related to the financial cost of stillbirth intervention or care, for example, costs of hospital care and treatment 15 5 SYSTEMATIC REVIEW OF STILLBIRTH CARE OUTCOMES TA B L E 3  Summary table of outcomes and domains from systematic review. 3.6  |  Care in subsequent pregnancy: Interventions and outcomes attachment in a subsequent pregnancy. No studies reported on the frequency of post-­traumatic stress disorder (PTSD) or grief in a subsequent pregnancy. Interventions in this category primarily focused on the medical treatment of women in a subsequent pregnancy, in- cluding six studies on thromboprophylaxis in a subsequent pregnancy. Only three studies evaluated care and one study reported on psychological support interventions in a subse- quent pregnancy. The most frequently reported outcomes were live birth in a subsequent pregnancy, reported in 29% of studies (4 of 14 studies), complications during a subsequent pregnancy, reported in 21% (3 of 14 studies), birthweight in a subsequent pregnancy, reported in 21% (3 of 14 studies), and anxiety, reported in 21% (3 of 14 studies). Only two stud- ies reported on experience of care and one study on prenatal Interpretation This systematic review highlights the wide variation in re- search studies relating to stillbirth care, by identifying the heterogeneity of interventions and outcomes measured and reported. The lack of standardisation and the frequent fail- ure to report on important outcomes such as maternal mor- tality and psychosocial outcomes, and to assess long-­term effects, in many studies hampers progress towards provid- ing optimal care after stillbirth. The problems for stillbirth care evidence are not unique; previous systematic reviews conducted in obstetrics and gynaecology and other special- ties, have found similar heterogeneity in outcome reporting, definitions and outcome measurement tools.260–­268 The out- comes identified in this systematic review have contributed to the development of an outcome long-­list and are being used in an international Delphi consensus process to define a minimal core outcome set for stillbirth care research.13 3.7  |  Outcome measurement Table S5 lists all outcomes, their definitions and measure- ment instruments used (if applicable). There was variation in the definition of reported outcomes (range of definitions 0–­ 35). For example, for postpartum complications there were five different definitions. No definition was provided for 247 outcomes. In all, 242 outcome measurement tools were iden- tified. There was variation in the type of outcome measure- ment tools used to measure the same outcomes, with a range BAKHBAKHI et al. 8 limited the number studies identified from low-­ and middle-­income countries. We found that very few stud- ies have been conducted in low-­income countries (which have the highest burden of stillbirth). Therefore, the out- come list generated from this review may omit outcomes most relevant to these settings. Engaging low-­ and middle-­ income countries in future core outcome set development will be vital to ensure a globally representative core out- come set is created. of 0–­22 tools used for a single outcome. Outcomes were measured at different timepoints relative to the stillbirth and were dependent on the type of intervention (Appendix S4). A total of 190 outcomes were measured during labour and birth, 76 outcomes in the postpartum period (up to 6 weeks postpartum), 246 outcomes following investigations, 66 out- comes within the first year, 101 outcomes in the first 5 years and 24 at 5 years or more. Only studies published over the last 24 years were in- cluded. Older publications may describe different inter- ventions or outcomes; however, they might not have been as relevant for informing a contemporary outcome inven- tory, as stillbirth bereavement care has advanced in recent times.258 Case studies, conference abstracts, protocols and dissertations were excluded. This could have led to the omission of newer interventions and novel outcomes eval- uated in research yet to be published in full manuscript form. Furthermore, this review found that only 23 studies included fathers or non-­birthing partners in the assessment of their outcomes, even though the impact of stillbirth has a dyadic (couple) context for many.259 We identified only 10 studies that included parents or members of the public in their study design. This underlines the need for a future core outcome set to incorporate the viewpoints of patients and members of the public in the selection of the most im- portant outcomes. 4  |  DISCUSSION AND CONCLUSION | The objective of this systematic review was to generate a comprehensive long-­list of outcomes to inform the develop- ment of a core outcome set for stillbirth care research; in all, we identified 391 unique outcomes. We demonstrated the wide variation of interventions implemented and assessed, and outcomes reported. Where studies reported the same outcome, there was considerable variation in the report- ing of the outcome definition and measurement tool used. Outcomes were measured at different timepoints relative to the stillbirth, with few studies measuring long-­term out- comes, i.e. within the first year or beyond 5 years. We identified a diverse range of interventions after still- birth. However, there is a paucity of evidence on a number of specific types of intervention, for example, counselling, specific psychological therapy or targeted interventions in a subsequent pregnancy. Interventions after stillbirth address different aspects of care, including medical, psychological, social and long-­term health. We found that the majority of studies did not measure the effect of interventions or care on parents, perceived experience, grief or psychosocial outcomes. 4.2 A strength of this study is its comprehensive inclusion of both non-­randomised, non-­comparative and RCTs, allowing for a wide range of interventions and outcomes to be identified. Previous systematic reviews on stillbirth care have only fo- cused on RCTs or interventions targeting physical or mental health of parents, rather than broader outcomes, e.g. social, economic or experiential outcomes.8–­10,257 Robust methods A strength of this study is its comprehensive inclusion of both non-­randomised, non-­comparative and RCTs, allowing for a wide range of interventions and outcomes to be identified. Previous systematic reviews on stillbirth care have only fo- cused on RCTs or interventions targeting physical or mental health of parents, rather than broader outcomes, e.g. social, economic or experiential outcomes.8–­10,257 Robust methods have been utilised in the review, including independent du- plicate screening, double extraction and extensive reference searching. An inclusive approach was adopted and high-­, middle-­ and low-­income countries have been included in the systematic review, increasing the global relevance of the review. An international steering group, including parents with lived experience of stillbirth, have informed the scope, study design and development of the outcome domains and long-­list. have been utilised in the review, including independent du- plicate screening, double extraction and extensive reference searching. An inclusive approach was adopted and high-­, middle-­ and low-­income countries have been included in the systematic review, increasing the global relevance of the review. An international steering group, including parents with lived experience of stillbirth, have informed the scope, study design and development of the outcome domains and long-­list. More studies with robust methodology are needed to improve the clinical evidence for care after stillbirth. For example, there were no RCTs identified for interventions to improve hospital or follow-­up bereavement care. This could be due in part to the ethical challenges of performing trials in this field, such as the perceived fear of causing harm to bereaved parents and the appropriateness of RCT method- ology to evaluate psychosocial support interventions after stillbirth.12 Studies have found bereaved parents are positive about participating in research and good recruitment rates A limitation is that for resource reasons, non-­English language articles were excluded, which in turn may have SYSTEMATIC REVIEW OF STILLBIRTH CARE OUTCOMES have been demonstrated when the approach has been guided by patient and public involvement.225,248,269 have been demonstrated when the approach has been guided by patient and public involvement.225,248,269 for Health Research (NIHR DRF-­2017-­10-­130). ACKNO​WLE​DGE​MENTS We would like to thank all members of the iCHOOSE parent and public involvement group with their assistance in the research. 5. Siassakos D, Jackson S, Gleeson K, Chebsey C, Ellis A, Storey C, et al. All bereaved parents are entitled to good care after still- birth: a mixed-­methods multicentre study (INSIGHT). BJOG. 2018;125(2):160–­70. 6. Peters MDJ, Lisy K, Riitano D, Jordan Z, Aromataris E. Providing meaningful care for families experiencing stillbirth: a meta-­ synthesis of qualitative evidence. J Perinatol. 2016;36(1):3–­9. 6. Peters MDJ, Lisy K, Riitano D, Jordan Z, Aromataris E. Providing meaningful care for families experiencing stillbirth: a meta-­ synthesis of qualitative evidence. J Perinatol. 2016;36(1):3–­9. R EFER ENCES Study concept: DB, CB, AF, AD, DS, LH, JMND. Study design: DB, CB, AF, AD, DS, LH, JMND, AM, KB & iCHOOSE Collaborative Group. Drafting of the article: DB. Development of search strategy and electronic searches of the medical literature databases: DB & KB. Screening of titles, abstracts and full texts: DB, AM, AD, CS, KB. Data extraction: DB, AM, AD, CS, KD, KB, ES, AL, CB. Data analysis: DB, AD, CB & AF. Critical revision of the article for important intellectual content and approval of final paper: DB, CB, AF, AD, DS, LH, JMND, AM, KB, ES, CS, KD, AL & iCHOOSE collaborative group. Study supervision: CB, AF, DS, LH & AD. 1. Hug L, You D, Blencowe H, Mishra A, Wang Z, Fix MJ, et al. Global, regional, and national estimates and trends in stillbirths from 2000 to 2019: a systematic assessment. Lancet. 2021;398(10302):772–­85. 2. Burden C, Bradley S, Storey C, Ellis A, Heazell AEP, Downe S, et al. From grief, guilt pain and stigma to hope and pride –­ a systematic review and meta-­analysis of mixed-­method research of the psycho- social impact of stillbirth. BMC Pregnancy Childbirth. 2016;16(1):9. https://doi.org/10.1186/s1288​4-­016-­0800-­8 p g 3. Heazell AEP, Siassakos D, Blencowe H, Burden C, Bhutta ZA, Cacciatore J, et al. Stillbirths: economic and psychosocial conse- quences. Lancet. 2016;387(10018):604. 4. Ellis A, Chebsey C, Storey C, Bradley S, Jackson S, Flenady V, et al. Systematic review to understand and improve care after stillbirth: a review of parents, and healthcare professionals, experiences. BMC Pregnancy Childbirth. 2016;16(1):16. https://doi.org/10.1186/s1288​ 4-­016-­0806-­2 CONFLICT OF INTEREST STATEMENT Dr Aleena Wojcieszek has received consulting fees from the Stillbirth Centre for Research Excellence. Dr Lisa Hinton is based in The Healthcare Improvement Studies Institute (THIS Institute), University of Cambridge. THIS Institute is supported by the Health Foundation, an independent charity committed to bringing about better health and healthcare for people in the UK. Dr Lisa Hinton is funded by the National Institute for Heatlh Research (NIHR) Programme Grant for applied research (RP-­PG-­1209-­10051) MRC/ESRC/Wellcome Trust/DFID Health Systems Research Initiative, NIHR Health Technology Assessment and NIHR Health Services Research and Delivery. Dr Abigail Fraser is funded by the British Heart Foundation, Wellcome Trust, Medical Research Council and Templeton Foundation. Dr Christy Burden is funded by NIHR Research for Patient Benefit, Health Data Research UK and Tommy's charity. There are no other com- peting interests to declare. Completed disclosure of interest forms are available to view online as supporting information. 4.2 The views ex- pressed in this publication are those of the authors and not necessarily those of the National Health Service, the National Institute for Health Research or the Department of Health. There appears to be several significant evidence-­practice gaps into specific interventions after stillbirth. Surprisingly, no interventions were identified on lactation care (e.g. breast milk suppression or milk donation) and personalisation of care at any stage. Several interventions related to subsequent pregnancy have not been studied, including continuity of care, pre-­pregnancy counselling, targeted antenatal inter- ventions for women with modifiable risk factors (e.g. dia- betes or smoking) and additional antepartum ultrasound surveillance.12 Moreover, no interventions were identified to support parents from minority ethnic and socio-­economic backgrounds following stillbirth, which could be intensi- fying health inequalities.270 Interestingly, we identified no studies on interventions to support the LBTQ+ (lesbian, gay, bisexual, transgender, queer/questioning, asexual and others) community. Future research should focus on an ex- ploration of potential interventions in these contexts and populations. ORCID Anna Davies  https://orcid.org/0000-0003-0743-6547 Abi Merriel  https://orcid.org/0000-0003-0352-2106 g Katie Barnard  https://orcid.org/0000-0001-7084-4055 Katie Barnard  https://orcid.org/0000-0001-7084-4055 ETHICS APPROVAL None required. None required. 5 This systematic review has highlighted the large variation in outcomes assessed, and outcome definitions and out- come measurement instruments used. These inconsisten- cies limit the utility of primary research and of evidence synthesis, and impact adversely on quality of decision making in the field of stillbirth aftercare. Considerable re- search gaps on specific intervention types in stillbirth care were also identified. The findings of this systematic review strongly support the need to develop a core outcome set for stillbirth care research. DATA AVAILABILITY STATEMENT Data sharing not applicable as no new data generated. ETHICS APPROVAL None required. FUNDING INFORMATION This report is an independent research arising from a doc- toral fellowship (DRF) supported by the National Institute BAKHBAKHI et al. 26. Vujanić GM, Cartlidge PHT, Stewart JH. Improving the quality of perinatal and infant necropsy examinations: a follow up study. J Clin Pathol. 1998;51(11):850–­3. 7. Lind J. The stillbirth priority setting partnership [Internet]. [cited 2022 Mar 6]. Available from: https://www.jla.nihr.ac.uk/prior​ity-­setti​ ng-­partn​ershi​ps/still​birth/​downl​oads/Still​birth​-­PSP-­final​-­report.pdf 27. Larsen LG, Græm N. Morphological findings and value of placental examination at fetal and perinatal autopsy. Apmis. 1999;107(3):337–­ 45. https://doi.org/10.1111/j.1699-­0463.1999.tb015​62.x 8. Wojcieszek AM, Shepherd E, Middleton P, Gardener G, Ellwood DA, McClure EM, et al. Interventions for investigating and iden- tifying the causes of stillbirth. Cochrane Database Syst Rev. 2018;4(4):CD012504. 28. Kupferminc MJ, Eldor A, Steinman N, Many A, Bar-­Am A, Jaffa A, et al. Increased frequency of genetic thrombophilia in women with complications of pregnancy. N Engl J Med. 1999;340(1):9–­13. https://doi.org/10.1056/NEJM1​99901​07340​0102 9. Koopmans L, Wilson T, Cacciatore J, Flenady V. Support for moth- ers, fathers and families after perinatal death. Cochrane Database Syst Rev. 2013;6:CD000452. https://doi.org/10.1002/14651​858.CD000​452. pub3 29. Owen J, Hauth JC. Vaginal misoprostol vs. concentrated oxytocin plus low-­dose prostaglandin E2 for second trimester pregnancy ter- mination. J Matern Neonatal Med. 1999;8(2):48–­50. 10. Wojcieszek AM, Shepherd E, Middleton P, Lassi ZS, Wilson T, Murphy MM, et al. Care prior to and during subsequent preg- nancies following stillbirth for improving outcomes. Cochrane Database Syst Rev. 2018;12:CD012203. Available from: https://doi. org/10.1002/14651​858.CD012​203.pub2 30. Jain J. A comparison of two dosing regimens of intravaginal misoprostol for second-­trimester pregnancy termination. Obstet Gynecol. 1999;93(4):571–­5. 31. Faye-­Petersen OM, Guinn DA, Wenstrom KD. Value of perinatal autopsy. Obstet Gynecol. 1999;94(6):915–­20. 11. Williamson PR, Altman DG, Bagley H, Barnes KL, Blazeby JM, Brookes ST, et al. The COMET handbook: version 1.0. Trials. 2017;18(3):280. https://doi.org/10.1186/s1306​3-­017-­1978-­4 32. Benara SK, Singh P. Validity of causes of infant death by verbal au- topsy. Indian J Pediatr. 1999;66(5):647–­50. 12. Wojcieszek AM, Heazell AEP, Middleton P, Ellwood D, Silver RM, Flenady V. Research priorities and potential methodologies to in- form care in subsequent pregnancies following stillbirth: a web-­ based survey of healthcare professionals, researchers and advocates. BMJ Open. 2019;9(6):e028735. 33. Murray JA, Terry DJ, Vance JC, Battistutta D, Connolly Y. Effects of a program of intervention on parental distress following infant death. Death Stud. 2000;24(4):275–­305. https://doi.org/10.1080/07481​ 18002​00469 34. Martinelli I, Taioli E, Cetin I, Marinoni A, Gerosa S, Villa MV, et al. doi.org/10.1177/10541​37300​00800303 16. Dodd S, Clarke M, Becker L, Mavergames C, Fish R, Williamson PR. A taxonomy has been developed for outcomes in medical re- search to help improve knowledge discovery. J Clin Epidemiol. 2018;96:84–­92. 36. Nakintu N. A comparative study of vaginal misoprostol and in- travenous oxytocin for induction of labour in women with intra uterine fetal death in Mulago hospital, Uganda. Afr Health Sci. 2001;1(2):55–­9. 17. De Galan-­Roosen AEM, Kuijpers JC, Meershoek APJ, Van Velzen D. Contribution of congenital malformations to perinatal mor- tality. A 10 years prospective regional study in The Netherlands. Eur J Obstet Gynecol Reprod Biol. 1998;80(1):55–­61. https://doi. org/10.1016/S0301​-­2115(98)00085​-­2 37. Rdestad I. Stillbirth: care and long-­term psychological effects. Br J Midwifery. 2001;9(8):474–­80. https://doi.org/10.12968/​bjom.2001.​ 9.8.7931 38. De Boer MA, Van Gemund N, Scherjon SA, Kanhai HHH. Low dose sulprostone for termination of second and third trimester pregnan- cies. Eur J Obstet Gynecol Reprod Biol. 2001;99(2):244–­8. https:// doi.org/10.1016/S0301​-­2115(01)00406​-­7 18. Hayati AR, Khong TY, Zainul R. The usefulness of limited placental sampling in stillbirths. Malays J Pathol. 1998;20(2):99–­102. 39. Tanawattanacharoen S, Taylor MJO, Letsky EA, Cox PM, Cowan FM, Fisk NM. Intrauterine rescue transfusion in monochorionic multiple pregnancies with recent single intrauterine death. Prenat Diagn. 2001;21(4):274–­8. 19. Incerpi MH, Banks EH, Goodwein SN, Samadi R, Goodwin TM. Significance of antinuclear antibody testing in unexplained sec- ond and third trimester fetal deaths. J Matern Neonatal Med. 1998;7(2):61–­4. 40. Munthali J, Moodley J. The use of misoprostol for mid-­trimester therapeutic termination of pregnancy. Trop Doct. 2001;31(3):157–­ 61. https://doi.org/10.1177/00494​75501​03100315 20. Srisomboon J, Pongpisuttinun S. Efficacy of intracervicovaginal misoprostol in second-­trimester pregnancy termination: a com- parison between live and dead fetuses. J Obstet Gynaecol Res. 1998;24(1):1–­5. https://doi.org/10.1111/j.1447-­0756.1998.tb000​44.x 41. DiMarco MA, Menke EM, McNamara T. Evaluating a sup- port group for perinatal loss. MCN Am J Matern Child Nurs. 2001;26(3):135–­40. 21. Dickinson JE, Godfrey M, Evans SF. Efficacy of intravaginal miso- prostol in second-­trimester pregnancy termination: a randomized controlled trial. J Matern Neonatal Med. 1998;7(3):115–­9. 42. Elsheikh A, Antsaklis A, Mesogitis S, Papantoniou N, Rodolakis A, Vogas E, et al. Use of misoprostol for the termination of second tri- mester pregnancies. Arch Gynecol Obstet. 2001;265(4):204–­6. 22. Ghorab MNM, El Helw BA. Second-­trimester termination of pregnancy by extra-­amniotic prostaglandin F2α or endocervical misoprostol. A comparative study. Acta Obstet Gynecol Scand. 1998;77(4):429–­32. 43. Salamat SM, Landy HJ, O'Sullivan MJ. Labor induction after fetal death: a retrospective analysis. J Reprod Med Obstet Gynecol. 2002;47(1):23–­6. 23. FUNDING INFORMATION Mutations in coagulation factors in women with unexplained late Fetal loss. N Engl J Med. 2000;343(14):1015–­8. https://doi. org/10.1056/NEJM2​00010​05343​1405 13. Bakhbakhi D, Fraser A, Siasakos D, Hinton L, Davies A, Merriel A, et al. Protocol for the development of a core outcome set for stillbirth care research (iCHOOSE Study). BMJ Open. 2022;12(2):e056629. 35. Rich DE. The impact of postpregnancy loss services on grief out- come: integrating research and practice in the Design of Perinatal Bereavement Programs. Illn Crises Loss. 2000;8(3):244–­64. https:// doi.org/10.1177/10541​37300​00800303 14. Satement P. Preferred reporting items for systematic reviews and meta-­analyses (PRISMA). 15. Covidence Innovation VH. Covidence systematic review software. Melbourne: Covidence; 2022. Med Channel. 2012;18(1):74–­6. 71. Gris JC, Mercier E, Quéré I, Lavigne-­Lissalde G, Cochery-­Nouvellon E, Hoffet M, et al. Low-­molecular-­weight heparin versus low-­dose aspirin in women with one fetal loss and a constitutional thrombo- philic disorder. Blood. 2004;103(10):3695–­9. https://doi.org/10.1182/ blood​-­2003-­12-­4250 53. Wagaarachchi PT, Ashok PW, Narvekar NN, Smith NC, Templeton A. Medical management of late intrauterine death using a combi- nation of mifepristone and misoprostol. BJOG. 2002;109(4):443–­7. https://doi.org/10.1111/j.1471-­0528.2002.01238.x 72. Lim TLW, Tan KH, Tee CS, Yeo GSH. Investigating stillbirths using a simplified obstetric events-­based protocol. Singapore Med J. 2005;46(2):63–­8. 54. Olsen E, Espeland A, Maartmann-­Moe H, Lachman RS, Rosendahl K. Diagnostic value of radiography in cases of perinatal death: a population based study. Arch Dis Child Fetal Neonatal Ed. 2003;88(6):F521–­4. 73. Yilmaz B, Kelekci S, Ertas IE, Kahyaoglu S, Ozel M, Sut N, et al. Misoprostol moistened with acetic acid or saline for second trimes- ter pregnancy termination: a randomized prospective double-­blind trial. Hum Reprod. 2005;20(11):3067–­71. https://doi.org/10.1093/ humre​p/dei204 55. Griffiths PD, Variend D, Evans M, Jones A, Wilkinson ID, Paley MNJ, et al. Postmortem MR imaging of the fetal and stillborn cen- tral nervous system. Am J Neuroradiol. 2003;24(1):22–­7. 56. Bourlière-­Najean B, Russel AS, Panuel M, Piercecchi-­Marti MD, Sigaudy S, Fredouille C, et al. Value of fetal skeletal radiographs in the diagnosis of fetal death. Eur Radiol. 2003;13(5):1046–­9. https:// doi.org/10.1007/s0033​0-­002-­1474-­3 74. Daskalakis GJ, Mesogitis SA, Papantoniou NE, Moulopoulos GG, Papapanagiotou AA, Antsaklis AJ. Misoprostol for second trimes- ter pregnancy termination in women with prior caesarean section. BJOG. 2005;112(1):97–­9. 57. Debby A, Golan A, Sagiv R, Sadan O, Glezerman M. Midtrimester abortion in patients with a previous uterine scar. Eur J Obstet Gynecol Reprod Biol. 2003;109(2):177–­80. https://doi.org/10.1016/ S0301​-­2115(03)00121​-­0 75. Khare M, Howarth E, Sadler J, Healey K, Konje JC. A comparison of prenatal versus postnatal karyotyping for the investigation of in- trauterine fetal death after the first trimester of pregnancy. Prenat Diagn. 2005;25(13):1192–­5. https://doi.org/10.1002/pd.1295 58. Ramsey PS, Savage K, Lincoln T, Owen J. Vaginal misoprostol ver- sus concentrated oxytocin and vaginal PGE 2 for second-­trimester labor induction. Obstet Gynecol. 2004;104(1):138–­45. 76. Fairley TE, Mackenzie M, Owen P, Mackenzie F. Management of late intrauterine death using a combination of mifepristone and misoprostol –­ experience of two regimens. Eur J Obstet Gynecol Reprod Biol. 2005;118(1):28–­31. https://doi.org/10.1016/j. ejogrb.2004.04.001 59. Feldman DM, Borgida AF, Rodis JF, Leo MV, Campbell WA. A randomized comparison of two regimens of misoprostol for second-­trimester pregnancy termination. Am J Obstet Gynecol. Funen County, Denmark, 1986–­96. J Matern Neonatal Med. 2003;13(6):403–­7. https://doi.org/10.1080/jmf.13.6.403.407 46. Michalski ST, Porter J, Pauli RM. Costs and consequences of comprehensive stillbirth assessment. Am J Obstet Gynecol. 2002;186(5):1027–­34. https://doi.org/10.1067/mob.2002.122450 64. 64. Johns N, Al-­Salti W, Cox P, Kilby MD. A comparative study of pre- natal ultrasound findings and post-­mortem examination in a ter- tiary referral center. Prenat Diagn. 2004;24(5):339–­46. https://doi. org/10.1002/pd.871 47. Dickinson JE, Evans SF. The optimization of intravaginal misopros- tol dosing schedules in second-­trimester pregnancy termination. Am J Obstet Gynecol. 2002;186(3):470–­4. 65. Pector EA. How bereaved multiple-­birth parents cope with hospi- talization, homecoming, disposition for deceased, and attachment to survivors. J Perinatol. 2004;24(11):714–­22. 48. Bebbington MW, Kent N, Lim K, Gagnon A, Delisle MF, Tessier F, et al. A randomized controlled trial comparing two protocols for the use of misoprostol in midtrimester pregnancy termination. Am J Obstet Gynecol. 2002;187(4):853–­7. https://doi.org/10.1067/ mob.2002.127461 66. Hickey L, Murphy A, Devaney D, Gillan J, Clarke T. The value of neonatal autopsy. Neonatology. 2012;101(1):68–­73. 49. Mendilcioglu I, Simsek M, Seker PE, Erbay O, Zorlu CG, Trak B. Misoprostol in second and early third trimester for termina- tion of pregnancies with fetal anomalies. Int J Gynecol Obstet. 2002;79(2):131–­5. https://doi.org/10.1016/S0020​-­7292(02)00224​-­2 67. Horn LC, Langner A, Stiehl P, Wittekind C, Faber R. Identification of the causes of intrauterine death during 310 consecutive autopsies. Eur J Obstet Gynecol Reprod Biol. 2004;113(2):134–­8. https://doi. org/10.1016/S0301​-­2115(03)00371​-­3 68. De Heus R, Graziosi GCM, Christiaens GCML, Bruinse HW, Mol BWJ. Medical management for termination of second and third trimester pregnancies: a comparison of strategies. Eur J Obstet Gynecol Reprod Biol. 2004;116(1):16–­21. https://doi.org/10.1016/j. ejogrb.2003.12.012 50. Hughes P, Turton P, Hopper E, Evans CDH. Assessment of guide- lines for good practice in psychosocial care of mothers after still- birth: a cohort study. Lancet. 2002;360(9327):114–­8. https://doi. org/10.1016/S0140​-­6736(02)09410​-­2 51. Rankin J, Wright C, Lind T. Cross sectional survey of parents, experience and views of the postmortem examination. Br Med J. 2002;324(7341):816–­8. 69. Ezechi OC, Kalu BKE, Njokanma FO, Nwokoro CA, Okeke GCE. Vaginal misoprostol induction of labour: a Nigerian hospital experience. J Obstet Gynaecol. 2004;24(3):239–­42. https://doi. org/10.1080/01443​61041​00016​60698 52. Christiansen OB, Pedersen B, Rosgaard A, Husth M. A randomized, double-­blind, placebo-­controlled trial of intravenous immuno- globulin in the prevention of recurrent miscarriage: evidence for a therapeutic effect in women with secondary recurrent miscarriage. Hum Reprod. 2002;17(3):809–­16. https://doi.org/10.1093/humre​ p/17.3.809 70. Bhatti K. Comparison of vaginal and oral misoprostol for in- duction of labour with intrauterine foetal death. doi.org/10.1177/10541​37300​00800303 Rådestad I, Nordin C, Steineck G, Sjögren B. A comparison of women s memories of care during pregnancy, labour and delivery after stillbirth or live birth. Midwifery. 1998;14(2):111–­7. 44. De Galan-­Roosen AEM, Kuijpers JC, Van Der Straaten PJC, Merkus JMWM. Evaluation of 239 cases of perinatal death using a funda- mental classification system. Eur J Obstet Gynecol Reprod Biol. 2002;103(1):37–­42. https://doi.org/10.1016/S0301​-­2115(02)00024​-­6 24. Incerpi MH, Miller DA, Samadi R, Settlage RH, Goodwin TM. Stillbirth evaluation: what tests are needed? Am J Obstet Gynecol. 1998;178(6):1121–­5. https://doi.org/10.1016/S0002​-­9378(98)70311​-­4 45. Karin P, Katarina B, Roger B, Alexandra H, Ingela HV, Marius K, et al. Diagnostic evaluation of intrauterine fetal deaths in Stockholm 1998–­99. Acta Obstet Gynecol Scand. 2002;81(4):284–­ 92. 10.1034/j.1600-­0412.2002.810402.x 25. Thornton CM, O'Hara MD. A regional audit of perinatal and infant autopsies in Northern Ireland. BJOG. 1998;105(1):18–­23. https://doi. org/10.1111/j.1471-­0528.1998.tb093​44.x SYSTEMATIC REVIEW OF STILLBIRTH CARE OUTCOMES |  11 11 2003;189(3):710–­3. https://doi.org/10.1067/S0002​-­9378(03)00659​-­8 77. Hidar S, Bouddebous M, Chaïeb A, Jerbi M, Bibi M, Khaïri H. Randomized controlled trial of vaginal misoprostol versus vaginal misoprostol and isosorbide dinitrate for termination of pregnancy at 13-­29 weeks. Arch Gynecol Obstet. 2005;273(3):157–­60. https:// doi.org/10.1007/s0040​4-­005-­0053-­7 60. Alderliesten ME, Peringa J, Van Der Hulst VPM, Blaauwgeers HLG, Van Lith JMM. Perinatal mortality: clinical value of post- mortem magnetic resonance imaging compared with autopsy in routine obstetric practice. BJOG. 2003;110(4):378–­82. https://doi. org/10.1046/j.1471-­0528.2003.02076.x 78. Sankar VH, Phadke SR. Clinical utility of fetal autopsy and compar- ison with prenatal ultrasound findings. J Perinatol. 2006;26(4):224–­ 9. https://doi.org/10.1038/sj.jp.7211482 61. Chittacharoen A, Herabutya Y, Punyavachira P. A randomized trial of oral and vaginal misoprostol to manage delivery in cases of fetal death. Obstet Gynecol. 2003;101(1):70–­3. 79. Widjaja E, Whitby EH, Cohen M, Paley MNJ, Griffiths PD. Post-­ mortem MRI of the foetal spine and spinal cord. Clin Radiol. 2006;61(8):679–­85. https://doi.org/10.1016/j.crad.2006.01.016 62. Makhlouf AM, Al-­Hussaini TK, Habib DM, Makarem MH. Second-­trimester pregnancy termination: comparison of three dif- ferent methods. J Obstet Gynaecol. 2003;23(4):407–­11. https://doi. org/10.1080/01443​61031​00012​0923 80. Khong TY, Tanner AR. Foetal and neonatal autopsy rates and use of tissue for research: the influence of “organ retention” controversy and new consent process. J Paediatr Child Health. 2006;42(6):366–­ 9. https://doi.org/10.1111/j.1440-­1754.2006.00874.x 63. Kock KF, Vestergaard V, Hardt-­Madsen M, Garne E. Declining autopsy rates in stillbirths and infant deaths: results from 12 BAKHBAKHI et al. 101. Bennett SM, Litz BT, Maguen S, Ehrenreich JT. An exploratory study of the psychological impact and clinical care of perinatal loss. J Loss Trauma. 2008;13(6):485–­510. https://doi.org/10.1080/15325​ 02080​2171268 81. Nor Azlin MI, Abdullah HSNA, Zainul Rashid MR, Jamil MA. Misoprostol (alone) in second trimester terminations of pregnancy: as effective as Gemeprost? J Obstet Gynaecol. 2006;26(6):546–­9. https://doi.org/10.1080/01443​61060​0811383 82. Säflund K, Wredling R. Differences within couples, experience of their hospital care and well-­being three months after experiencing a stillbirth. Acta Obstet Gynecol Scand. 2006;85(10):1193–­9. 102. Korteweg FJ, Bouman K, Erwich JJHM, Timmer A, Veeger NJGM, Ravisé JM, et al. Cytogenetic analysis after evaluation of 750 fetal deaths: proposal for diagnostic workup. Obstet Gynecol. 2008;111(4):865–­74. 83. Elklit A, Björk GD. Assessment of guidelines for good psychosocial practice for parents who have lost an infant through perinatal or postnatal death. Vol. 58, Nordic psychology. Elklit, Ask: Institute of Psychology, University of Aarhus, Nobelparken: Dansk psykologisk Forlag; 2006. p. 315–­30. 103. Cohen MC, Paley MN, Griffiths PD, Whitby EH. A study of 534 fetal pathology cases from prenatal diagnosis referrals analyzed from 1989 through 2000. Am J Med Genet Part A. 2007;143(24):3107–­20. https://doi.org/10.1002/ajmg.a.32094 111. Caliskan E, Doger E, Cakiroglu Y, Corakci A, Yucesoy I. Sublingual misoprostol 100 microgram versus 200 microgram for second tri- mester abortion: a randomised trial. Eur J Contracept Reprod Health Care. 2009;14(1):55–­60. https://doi.org/10.1080/13625180802360865 91. Adappa R, Paranjothy S, Roberts Z, Cartlidge PHT. Perinatal and in- fant autopsy. Arch Dis Child Fetal Neonatal Ed. 2007;92(1):F49–­50. 92. Zanconato G, Piazzola E, Caloi E, Iacovella C, Ruffo R, Franchi M. Clinicopathological evaluation of 59 cases of fetal death. Arch Gynecol Obstet. 2007;276(6):619–­23. 112. Rådestad I, Säflund K, Wredling R, Onelöv E, Steineck G. Holding a stillborn baby: mothers, feelings of tenderness and grief. Br J Midwifery. 2009;17(3):178–­80. 93. Vergani P, Cozzolino S, Pozzi E, Cuttin MS, Greco M, Ornaghi S, et al. Identifying the causes of stillbirth: a comparison of four classification systems. Am J Obstet Gynecol. 2008;199(3):319.e1–­4. https://doi.org/10.1016/j.ajog.2008.06.098 113. Surkan PJ, Rådestad I, Cnattingius S, Steineck G, Dickman PW. Social support after stillbirth for prevention of maternal depression. Acta Obstet Gynecol Scand. 2009;88(12):1358–­64. 94. Walsh CA, Vallerie AM, Baxi LV. Etiology of stillbirth at term: a 10-­year cohort study. J Matern Neonatal Med. 2008;21(7):493–­501. https://doi.org/10.1080/14767​05080​2086669 114. Rey E, Garneau P, David M, Gauthier R, Leduc L, Michon N, et al. Dalteparin for the prevention of recurrence of placental-­mediated complications of pregnancy in women without thrombophilia: a pilot randomized controlled trial. J Thromb Haemost. 2009;7(1):58–­ 64. https://doi.org/10.1111/j.1538-­7836.2008.03230.x 95. Varli IH, Petersson K, Bottinga R, Bremme K, Hofsjö A, Holm M, et al. The Stockholm classification of stillbirth. Acta Obstet Gynecol Scand. 2008;87(11):1202–­12. https://doi.org/10.1080/00016​34080​2460271 115. Rådestad I, Surkan PJ, Steineck G, Cnattingius S, Onelöv E, Dickman PW. Long-­term outcomes for mothers who have or have not held their stillborn baby. Midwifery. 2009;25(4):422–­9. https:// doi.org/10.1016/j.midw.2007.03.005 96. Behrashi M, Mahdian M. Vaginal versus oral misoprostol for second-­trimester pregnancy termination: a randomized trial. Pak J Biol Sci. 2008;11(21):2505–­8. 116. Simchen MJ, Ofir K, Moran O, Kedem A, Sivan E, Schiff E. Thrombophilic risk factors for placental stillbirth. Eur J Obstet Gynecol Reprod Biol. 2010;153(2):160–­4. https://doi.org/10.1016/j. ejogrb.2010.07.031 97. Edmond KM, Quigley MA, Zandoh C, Danso S, Hurt C, Agyei SO, et al. Diagnostic accuracy of verbal autopsies in ascertain- ing the causes of stillbirths and neonatal deaths in rural Ghana. Paediatr Perinat Epidemiol. 2008;22(5):417–­29. https://doi. org/10.1111/j.1365-­3016.2008.00962.x 117. Less invasive autopsy: benefits and limitations of the use of magnetic reso- nance imaging in the perinatal postmortem. Pediatr Dev Pathol. 2008;11(1):1–­9. 84. Cacciatore J. Effects of support groups on post traumatic stress re- sponses in women experiencing stillbirth. Omega J Death Dying. 2007;55(1):71–­90. https://doi.org/10.2190/M447-­1X11-­6566-­8042 104. Cacciatore J, Schnebly S, Froen JF. The effects of social support on maternal anxiety and depression after stillbirth. Health Soc Care Community. 2009;17(2):167–­76. 105. Kidron D, Bernheim J, Aviram R. Placental findings contributing to Fetal death, a study of 120 stillbirths between 23 and 40 weeks gestation. Placenta. 2009;30(8):700–­4. 85. Väyrynen W, Heikinheimo O, Nuutila M. Misoprostol-­only versus mifepristone plus misoprostol in induction of labor following intra- uterine fetal death. Acta Obstet Gynecol Scand. 2007;86(6):701–­5. https://doi.org/10.1080/00016​34070​1379853 106. Korteweg FJ, Erwich JJHM, Holm JP, Ravisé JM, Van Der Meer J, Veeger NJGM, et al. Diverse placental pathologies as the main causes of fetal death. Obstet Gynecol. 2009;114(4):809–­17. 86. Yilmaz B, Kelekci S, Ertas IE, Ozel M, Sut N, Mollamahmutoglu L, et al. Randomized comparison of second trimester pregnancy termi- nation utilizing saline moistened or dry misoprostol. Arch Gynecol Obstet. 2007;276(5):511–­6. https://doi.org/10.1007/s0040​4-­007-­0374-­9 107. Amir H, Weintraub A, Aricha-­Tamir B, Apel-­Sarid L, Holcberg G, Sheiner E. A piece in the puzzle of intrauterine fetal death: patho- logical findings in placentas from term and preterm intrauterine fetal death pregnancies. J Matern Neonatal Med. 2009;22(9):759–­64. https://doi.org/10.3109/14767​05090​2929396 87. Bhattacharjee N, Ganguly RP, Saha SP. Misoprostol for termination of mid-­trimester post-­caesarean pregnancy. Aust N Z J Obstet Gynaecol. 2007;47(1):23–­5. https://doi.org/10.1111/j.1479-­828X.2006.00673.x 108. Glynn A, Collins V, Halliday J. Utilization of genetic counseling after diagnosis of a birth defect-­trends over time and variables asso- ciated with utilization. Genet Med. 2009;11(4):287–­93. 88. Kleebkaow P, Ratanasiri T, Komwilaisak R. Autopsy findings of fetal death. J Med Assoc Thai. 2007;90(1):21–­5. 89. Measey MA, Charles A, D'Espaignet ET, Harrison C, de Klerk N, Douglass C. Aetiology of stillbirth: unexplored is not unex- plained. Aust N Z J Public Health. 2007;31(5):444–­9. https://doi. org/10.1111/j.1753-­6405.2007.00116.x 109. Headley E, Gordon A, Jeffery H. Reclassification of unexplained still- births using clinical practice guidelines. Aust N Z J Obstet Gynaecol. 2009;49(3):285–­9. https://doi.org/10.1111/j.1479-­828X.2009.00989.x 110. Van Mensel K, Claerhout F, Debois P, Keirse MJNC, Hanssens M. A randomized controlled trial of misoprostol and Sulprostone to end pregnancy after Fetal death. Obstet Gynecol Int. 2009;2009:1–­8. 90. Laury A, Sanchez-­Lara PA, Pepkowitz S, Graham JM. Ramirez MM, Gilbert S, Landon MB, Rouse DJ, Spong CY, Varner MW, et al. Mode of delivery in women with antepartum fetal death and prior cesarean delivery. Am J Perinatol. 2010;27(10):825–­9. 98. Cacciatore J, Rådestad I, Frøen JF. Effects of contact with stillborn ba- bies on maternal anxiety and depression. Birth. 2008;35(4):313–­20. 118. Stock SJ, Goldsmith L, Evans MJ, Laing IA. Interventions to im- prove rates of post-­mortem examination after stillbirth. Eur J Obstet Gynecol Reprod Biol. 2010;153(2):148–­50. https://doi.org/10.1016/j. ejogrb.2010.07.022 99. Korteweg FJ, Gordijn SJ, Timmer A, Holm JP, Ravisé JM, Erwich JJHM. A placental cause of intra-­uterine fetal death depends on the perinatal mortality classification system used. Placenta. 2008;29(1):71–­80. 100. Surkan PJ, Rådestad I, Cnattingius S, Steineck G, Dickman PW. Events after stillbirth in relation to maternal depressive symptoms: a brief report. Birth. 2008;35(2):153–­7. 119. Dudley DJ, Goldenberg R, Conway D, Silver RM, Saade GR, Varner MW, et al. A new system for determining the causes of stillbirth. Obstet Gynecol. 2010;116(2):254–­60. |  13 13 SYSTEMATIC REVIEW OF STILLBIRTH CARE OUTCOMES 120. Korteweg FJ, Erwich JJHM, Folkeringa N, Timmer A, Veeger NJGM, Ravisé JM, et al. Prevalence of parental thrombophilic defects after fetal death and relation to cause. Obstet Gynecol. 2010;116(2):355–­64. 138. Pinar H, Koch MA, Hawkins H, Heim-­Hall J, Shehata B, Thorsten VR, et al. The stillbirth collaborative research network (SCRN) pla- cental and umbilical cord examination protocol. Am J Perinatol. 2011;28(10):781–­92. 121. Breeze ACG, Jessop FA, Set PAK, Whitehead AL, Cross JJ, Lomas DJ, et al. Minimally-­invasive fetal autopsy using magnetic reso- nance imaging and percutaneous organ biopsies: clinical value and comparison to conventional autopsy. Ultrasound Obstet Gynecol. 2011;37(3):317–­23. https://doi.org/10.1002/uog.8844 139. Valayatham V, Hiu J. Perinatal postmortem: factors influencing uptake and subsequent outcomes in an Asian population. Med J Malaysia. 2012;67(1):87–­90. 140. Bennett SM, Ehrenreich-­May J, Litz BT, Boisseau CL, Barlow DH. Development and preliminary evaluation of a cognitive-­ behavioral intervention for perinatal grief. Cogn Behav Pract. 2012;19(1):161–­73. 122. Pinar H, Koch M, Hawkins H, Heim-­Hall J, Abramowsky C, Thorsten V, et al. The stillbirth collaborative research network post- mortem examination protocol. Am J Perinatol. 2012;29(3):187–­202. 141. Reddy UM, Page GP, Saade GR, Silver RM, Thorsten VR, Parker CB, et al. Karyotype versus microarray testing for genetic abnormalities after stillbirth. N Engl J Med. 2012;367(23):2185–­93. 123. Sharma D, Singhal SR, Poonam, Kunika PA. 2012;28(2):154–­61. 129. El-­Gharib MN, Elebyary MT. Low-­dose vaginal misoprostol in the management of intrauterine fetal death. J Matern Neonatal Med. 2011;24(10):1239–­42. https://doi.org/10.3109/14767​058.2011.561386 130. Lin CJ, Chien SC, Chen CP. The use of misoprostol in termina- tion of second-­trimester pregnancy. Taiwan J Obstet Gynecol. 2011;50(3):275–­82. 148. O'Donoghue K, O'Regan KN, Sheridan CP, O'Connor OJ, Benson J, McWilliams S, et al. Investigation of the role of computed tomog- raphy as an adjunct to autopsy in the evaluation of stillbirth. Eur J Radiol. 2012;81(7):1667–­75. 131. Kersting A, Kroker K, Schlicht S, Baust K, Wagner B. Efficacy of cognitive behavioral internet-­based therapy in parents after the loss of a child during pregnancy: pilot data from a randomized con- trolled trial. Arch Womens Ment Health. 2011;14(6):465–­77. 149. Martinelli I, Ruggenenti P, Cetin I, Pardi G, Perna A, Vergani P, et al. Heparin in pregnant women with previous placenta-­mediated pregnancy complications: a prospective, randomized, multicenter, controlled clinical trial. Blood. 2012;119(14):3269–­75. https://doi. org/10.1182/blood​-­2011-­11-­391383 132. Rådestad I, Westerberg A, Ekholm A, Davidsson-­Bremborg A, Erlandsson K. Evaluation of care after stillbirth in Sweden based on mothers, gratitude. Br J Midwifery. 2011;19(10):646–­52. https://doi. org/10.12968/​bjom.2011.19.10.646 150. Cannie M, Votino C, Moerman PH, Vanheste R, Segers V, Van Berkel K, et al. Acceptance, reliability and confidence of di- agnosis of fetal and neonatal virtuopsy compared with con- ventional autopsy: a prospective study. Obstet Gynecol Surv. 2012;67(10):615–­7. 133. Hutti MH, Armstrong DS, Myers J. Healthcare utilization in the pregnancy following a perinatal loss. MCN Am J Matern Nurs. 2011;36(2):104–­11. 151. Vogt C, Blaas HGK, Salvesen KÅ, Eik-­Nes SH. Comparison be- tween prenatal ultrasound and postmortem findings in fetuses and infants with developmental anomalies. Ultrasound Obstet Gynecol. 2012;39(6):666–­72. https://doi.org/10.1002/uog.10106 134. Aho AL, Tarkka MT, Åstedt-­Kurki P, Sorvari L, Kaunonen M. Evaluating a bereavement follow-­up intervention for grieving fa- thers and their experiences of support after the death of a child-­a pilot study. Death Stud. 2011;35(10):879–­904. 135. Roose RE, Blanford CR. Perinatal grief and support spans the gen- erations: Parents, and grandparents, evaluations of an intergener- ational perinatal bereavement program. J Perinat Neonatal Nurs. 2011;25(1):77–­85. 152. Pinar H, Koch M, Hawkins H, Heim-­Hall J, Abramowsky C, Thorsten V, et al. The stillbirth collaborative research network post- mortem examination protocol. Am J Perinatol. 2011;29(3):187–­202. 153. Thayyil S, Sebire NJ, Chitty LS, Wade A, Chong W, Olsen O, et al. Post-­mortem MRI versus conventional autopsy in fetuses and chil- dren: a prospective validation study. Lancet. 2013;382(9888):223–­ 33. Comparison of mife- pristone combination with misoprostol and misoprostol alone in the management of intrauterine death: condensation -­ misoprostol and mifepristone combination is more effective than misoprostol alone in the management of intrauterine death. Taiwan J Obstet Gynecol. 2011;50(3):322–­5. 142. Heazell AEP, McLaughlin MJ, Schmidt EB, Cox P, Flenady V, Khong TY, et al. A difficult conversation? The views and experiences of parents and professionals on the consent process for perinatal postmortem after stillbirth. BJOG. 2012;119(8):987–­97. https://doi. org/10.1111/j.1471-­0528.2012.03357.x 124. Cayrac M, Faillie JL, Flandrin A, Boulot P. Second-­ and third-­ trimester management of medical termination of pregnancy and fetal death in utero after prior caesarean section. Eur J Obstet Gynecol Reprod Biol. 2011;157(2):145–­9. https://doi.org/10.1016/j. ejogrb.2011.03.013 143. Korteweg FJ, Erwich JJHM, Timmer A, Van Der Meer J, Ravisé JM, Veeger NJGM, et al. Evaluation of 1025 fetal deaths: proposed diag- nostic workup. Am J Obstet Gynecol. 2012;206(1):53.e1–­12. https:// doi.org/10.1016/j.ajog.2011.10.026 125. Erlandsson K, SäFlund K, Wredling R, Rådestad I. Support after stillbirth and its effect on parental grief over time. J Soc Work End Life Palliat Care. 2011;7(2–­3):139–­52. https://doi.org/10.1080/15524​ 256.2011.593152 144. Engmann C, Garces A, Jehan I, Ditekemena J, Phin M, Thorsten V, et al. Birth attendants as perinatal verbal autopsy respondents in low-­ and middle-­income countries: a viable alternative? Bull World Health Organ. 2012;90(3):200–­8. 126. Bonetti LR, Ferrari P, Trani N, MacCio L, Schirosi L, Giuliana S, et al. The role of fetal autopsy and placental examination in the causes of fetal death: a retrospective study of 132 cases of stillbirths. Arch Gynecol Obstet. 2011;283(2):231–­41. 145. Bapat U, Alcock G, More NS, Das S, Joshi W, Osrin D. Stillbirths and newborn deaths in slum settlements in Mumbai, India: a prospec- tive verbal autopsy study. BMC Pregnancy Childbirth. 2012;12:39. https://doi.org/10.1186/1471-­2393-­12-­39 127. Bukowski R, Carpenter M, Conway D, Coustan D, Dudley DJ, Goldenberg RL, et al. Causes of death among stillbirths. Obstet Gynecol Surv. 2012;67(4):223–­5. 146. Monari F, Alberico S, Avagliano L, Cetin I, Cozzolino S, Gargano G, et al. Relation between maternal thrombophilia and stillbirth ac- cording to causes/associated conditions of death. Early Hum Dev. 2012;88(4):251–­4. 128. Zhang L, Hong ZX, Liu WJ, Hong RM, Yan PQ, Wei J. Cytogenetic analysis of 355 cases of fetal loss in different trimesters. Prenat Diagn. 2011;31(2):152–­8. 147. Hakverdi S, Güzelmansur I, Güngören A, Toprak S, Yaldiz M, Hakverdi AU. Evaluation of fetal autopsy findings in the Hatay region: 274 cases. Turk Patoloji Dergisi/Turkish J Pathol. https://doi.org/10.1016/S0140​-­6736(13)60134​-­8 136. Vanderwielen B, Zaleski C, Cold C, Mcpherson E. Wisconsin still- birth services program: a multifocal approach to stillbirth anal- ysis. Am J Med Genet Part A. 2011;155(5):1073–­80. https://doi. org/10.1002/ajmg.a.34016 154. Helgadõttir LB, Turowski G, Skjeldestad FE, Jacobsen AF, Sandset PM, Roald B, et al. Classification of stillbirths and risk factors by cause of death -­ a case-­control study. Acta Obstet Gynecol Scand. 2013;92(3):325–­33. https://doi.org/10.1111/aogs.12044 137. Tellefsen CH, Vogt C. How important is placental examination in cases of perinatal deaths? Pediatr Dev Pathol. 2011;14(2):99–­104. 10.2350/10-­07-­0870-­OA.1 14 BAKHBAKHI et al. 175. Kumar M, Singh A, Gupta U, Anand R, Thakur S. Relevance of labor room fetal autopsy in increasing its acceptance. J Matern Neonatal Med. 2015;28(3):344–­9. 155. Panda S, Jha V, Singh S. Role of combination of mifepristone and misoprostol verses misoprostol alone in induction of labour in late intrauterin fetal death: a prospective study. J Fam Plann Reprod Health. 2013;7(4):177–­9. 176. Warland J, O'Brien LM, Heazell AEP, Mitchell EA, Collins JH, Huberty JL, et al. An international internet survey of the experi- ences of 1,714 mothers with a late stillbirth: the STARS cohort study. BMC Pregnancy Childbirth. 2015;15(1):172. 156. Gawron LM, Kiley JW. Labor induction outcomes in third-­trimester stillbirths. Int J Gynecol Obstet. 2013;123(3):203–­6. 157. Crawley R, Lomax S, Ayers S. Recovering from stillbirth: the effects of making and sharing memories on maternal mental health. J Reprod Infant Psychol. 2013;31(2):195–­207. https://doi. org/10.1080/02646​838.2013.795216 177. Rosenfeld JA, Tucker ME, Escobar LF, Neill NJ, Torchia BS, McDaniel LD, et al. Diagnostic utility of microarray testing in preg- nancy loss. Ultrasound Obstet Gynecol. 2015;46(4):478–­86. https:// doi.org/10.1002/uog.14866 158. Kalyani R, Bindra MS, Mahansetty H. Congenital malformations in perinatal autopsy: a twoyear prospective study. J Indian Med Assoc. 2013;111(2):89–­93. 178. Rogers J, Spink M, Magrill A, Burgess K, Agius M. Evaluation of a specialised counselling service for perinatal bereavement. Psychiatr Danub. 2015;27:S482–­5. 159. Nausheen S, Soofi SB, Sadiq K, Habib A, Turab A, Memon Z, et al. Validation of verbal autopsy tool for ascertaining the causes of still- birth. PLoS One. 2013;8(10):e76933. https://doi.org/10.1371/journ​ al.pone.0076933 179. Simpson C, Lee P, Lionel J. The effect of bereavement Counseling on women with psychological problems associated with late pregnancy loss. J Asian Midwives. 2015;2(2):5–­21. 180. Raitio K, Kaunonen M, Aho AL. Evaluating a bereavement follow-­up intervention for grieving mothers after the death of a child. Scand J Caring Sci. 2015;29(3):510–­20. https://doi.org/10.1111/scs.12183 160. Kersting A, Dölemeyer R, Steinig J, Walter F, Kroker K, Baust K, et al. Brief internet-­based intervention reduces posttraumatic stress and pro- longed grief in parents after the loss of a child during pregnancy: a ran- domized controlled trial. Psychother Psychosom. 2013;82(6):372–­81. 181. O'Leary BD, Walsh CA, Fitzgerald JM, Downey P, McAuliffe FM. The contribution of massive fetomaternal hemorrhage to antepar- tum stillbirth: a 25-­year cross-­sectional study. Acta Obstet Gynecol Scand. 2015;94(12):1354–­8. 161. Gold KJ, Sen A, Xu X. Hospital costs associated with stillbirth deliv- ery. Matern Child Health J. 2013;17(10):1835–­41. 162. Erlandsson K, Warland J, Cacciatore J, Rådestad I. Seeing and hold- ing a stillborn baby: mothers, feelings in relation to how their babies were presented to them after birth-­findings from an online ques- tionnaire. Midwifery. 2013;29(3):246–­50. https://doi.org/10.1016/j. midw.2012.01.007 182. Mills TA, Ricklesford C, Heazell AEP, Cooke A, Lavender T. Marvellous to mediocre: findings of national survey of UK prac- tice and provision of care in pregnancies after stillbirth or neonatal death. BMC Pregnancy Childbirth. 2016;16(1):101. 163. Kapoor K, Singh K, Sharma A, Singh B, Huria A, Kochhar S. Congenital anomalies in North Western Indian population –­ a fetal autopsy study. Eur J Anat. 2013;17(3):166–­75. 183. Man J, Hutchinson JC, Ashworth M, Judge-­Kronis L, Levine S, Sebire NJ. Stillbirth and intrauterine fetal death: role of routine histologi- cal organ sampling to determine cause of death. Ultrasound Obstet Gynecol. 2016;48(5):596–­601. https://doi.org/10.1002/uog.16020 164. Arthurs OJ, Calder AD, Kiho L, Taylor AM, Sebire NJ. Routine peri- natal and paediatric post-­mortem radiography: detection rates and implications for practice. Pediatr Radiol. 2014;44(3):252–­7. https:// doi.org/10.1007/s0024​7-­013-­2804-­0 184. Gold KJ, Mozurkewich EL, Puder KS, Treadwell MC. Maternal complications associated with stillbirth delivery: a cross-­sectional analysis. J Obstet Gynaecol. 2016;36(2):208–­12. 185. Redshaw M, Hennegan JM, Henderson J. Impact of holding the baby following stillbirth on maternal mental health and well-­being: findings from a national survey. BMJ Open. 2016;6(8):e010996. 165. Bracken H, Ngoc NTN, Banks E, Blumenthal PD, Derman RJ, Patel A, et al. Buccal misoprostol for treatment of fetal death at 14-­ 28 weeks of pregnancy: a double-­blind randomized controlled trial. Contraception. 2014;89(3):187–­92. 186. Vullo A, Panebianco V, Cannavale G, Aromatario M, Cipolloni L, Frati P, et al. Post-­mortem magnetic resonance foetal imaging: a study of morphological correlation with conventional autopsy and histopathological findings. Radiol Med. 2016;121(11):847–­56. https://doi.org/10.1007/s1154​7-­016-­0672-­z 166. Basu M, Mukerji S, Doumouchtsis SK. Perineal trauma in women undergoing vaginal delivery following intra-­uterine fetal demise: a case-­control analysis. Int Urogynecol J Pelvic Floor Dysfunct. 2014;25(1):61–­4. https://doi.org/10.1007/s0019​2-­013-­2148-­1 167. Jorgensen M, Mcpherson E, Zaleski C, Shivaram P, Cold C. Stillbirth: the heart of the matter. Am J Med Genet Part A. 2014;164(3):691–­9. 187. Moond S, Banerjee KP, Arya R. A comparative study of mifepri- stone and misoprostol versus misoprostol alone in induction of labour in late intrauterine fetal death. Int J Med Biomed Stud. 2021;5(2):348–­51. 168. Blood C, Cacciatore J. Parental grief and memento Mori pho- tography: narrative, meaning, culture, and context. Death Stud. 2014;38(4):224–­33. 188. Puri RD, Kotecha U, Lall M, Dash P, Bijarnia-­Mahay S, Verma IC. Is the diagnostic yield influenced by the indication for fetal autopsy? Am J Med Genet Part A. 2016;170(8):2119–­26. 169. Agrawal A, Basnet P, Thakur A, Rizal P, Rai R. Induction of labor using misoprostol with or without mifepristone in intrauterine death. J Nepal Med Assoc. 2014;52(194):781–­6. 189. Auger N, Tiandrazana RC, Healy-­Profitos J, Costopoulos A. Inequality in fetal autopsy in Canada. J Health Care Poor Underserved. 2016;27(3):1384–­96. 170. Pásztor N, Keresztúri A, Kozinszky Z, Pál A. Identification of causes of stillbirth through autopsy and placental examination reports. Fetal Pediatr Pathol. 2014;33(1):49–­54. https://doi.org/10.3109/15513​ 815.2013.850132 190. Abediasl Z, Sheikh M, Pooransari P, Farahani Z, Kalani F. Vaginal misoprostol versus intravenous oxytocin for the management of second-­trimester pregnancies with intrauterine fetal death: a ran- domized clinical trial. J Obstet Gynaecol Res. 2016;42(3):246–­51. 171. Côté-­Arsenault D, Schwartz K, Krowchuk H, McCoy TP. Evidence-­ based intervention with women pregnant after perinatal loss. MCN Am J Matern Nurs. 2014;39(3):177–­86. 191. Man J, Hutchinson JC, Heazell AE, Ashworth M, Jeffrey I, Sebire NJ. Stillbirth and intrauterine fetal death: role of routine histopatho- logical placental findings to determine cause of death. Ultrasound Obstet Gynecol. 2016;48(5):579–­84. 172. do Nascimento MI, Cunha Ade A, Oliveira SR. Clinical manage- ment of the induction of labor in intrauterine fetal death: evaluation of incidence of cesarean section and related conditions. Rev Bras Epidemiol. 2014;17(1):203–­16. 192. Gold KJ, Normandin MM, Boggs ME. Are participants in face-­ to-­face and internet support groups the same? Comparison of demographics and depression levels among women bereaved by stillbirth. Arch Womens Ment Health. 2016;19(6):1073–­8. https:// doi.org/10.1007/s0073​7-­016-­0657-­x 173. Chaudhuri P, Datta S. Mifepristone and misoprostol compared with misoprostol alone for induction of labor in intrauterine fetal death: a randomized trial. J Obstet Gynaecol Res. 2015;41(12):1884–­90. https://doi.org/10.1111/jog.12815 193. 194. Miller ES, Minturn L, Linn R, Weese-­Mayer DE, Ernst LM. Stillbirth evaluation: a stepwise assessment of placental pathology and autopsy. Am J Obstet Gynecol. 2016;214(1):115.e1–­6. (perinatal) deaths: insights from the Wisconsin stillbirth service program. Birth Defects Res. 2017;109(18):1430–­41. 214. Petrou S, Kim SW, McParland P, Boyle EM. Mode of delivery and long-­term health-­related quality-­of-­life outcomes: a prospective population-­based study. Birth. 2017;44(2):110. 195. Waterman CA, Batstone P, Bown N, Cresswell L, Delmege C, English CJ, et al. The clinical utility of genetic testing of tissues from pregnancy losses. BJOG. 2018;125(7):867–­73. 215. Sahoo T, Dzidic N, Strecker MN, Commander S, Travis MK, Doherty C, et al. Comprehensive genetic analysis of pregnancy loss by chromosomal microarrays: outcomes, benefits, and challenges. Obstet Gynecol Surv. 2017;72(5):268–­70. 196. Roberts L, Montgomery S. Mindfulness-­based intervention for perina- tal grief education and reduction among poor women in Chhattisgarh, India: a pilot study. Interdiscip J Best Pract Glob Dev. 2016;2(1):1. 216. Cacciatore J. ‘She used his name’: provider trait mindfulness in peri- natal death counselling. Estud Psicol. 2017;38(3):639–­66. 197. Silver RM, Saade GR, Thorsten V, Parker CB, Reddy UM, Drews-­ Botsch C, et al. Factor V Leiden, prothrombin G20210A, and methylene tetrahydrofolate reductase mutations and stillbirth: the stillbirth Collaborative Research Network. Am J Obstet Gynecol. 2016;215(4):468.e1–­17. 217. Cronin RS, Li M, Wise M, Bradford B, Culling V, Zuccollo J, et al. Late stillbirth post mortem examination in New Zealand: maternal decision-­making. Aust N Z J Obstet Gynaecol. 2018;58(6):667–­73. https://doi.org/10.1111/ajo.12790 198. Salim R, Nachum Z, Gavish I, Romano S, Braverman M, Garmi G. Adjusting enoxaparin dosage according to anti-­fxa levels and preg- nancy outcome in thrombophilic women: a randomised controlled trial. Thromb Haemost. 2016;116(4):687–­95. 218. Wojcieszek AM, Boyle FM, Belizán JM, Cassidy J, Cassidy P, Erwich JJHM, et al. Care in subsequent pregnancies following stillbirth: an international survey of parents. BJOG. 2018;125(2):193–­201. 199. Man J, Hutchinson JC, Heazell AE, Ashworth M, Levine S, Sebire NJ. Stillbirth and intrauterine fetal death: factors affecting deter- mination of cause of death at autopsy. Ultrasound Obstet Gynecol. 2016;48(5):566–­73. 219. Inati V, Matic M, Phillips C, Maconachie N, Vanderhook F, Kent AL. A survey of the experiences of families with bereavement sup- port services following a perinatal loss. Aust N Z J Obstet Gynaecol. 2018;58(1):54–­63. 200. Opsjøn BE, Vogt C. Explaining fetal death-­what are the contribu- tions of fetal autopsy and placenta examination? Pediatr Dev Pathol. 2016;19(1):24–­30. https://doi.org/10.2350/15-­03-­1614-­OA.1 220. Shruthi M, Gupta N, Jana M, Mridha AR, Kumar A, Agarwal R, et al. Conventional vs virtual autopsy with postmortem MRI in phenotypic characterization of stillbirths and fetal malforma- tions. Ultrasound Obstet Gynecol. 2018;51(2):236–­45. https://doi. org/10.1002/uog.17468 201. Human M, Goldstein RD, Groenewald CA, Kinney HC, Odendaal HJ. Bereaved mothers, attitudes regarding autopsy of their stillborn baby. S Afr J Obstet Gynaecol. 2017;23(3):93–­6. 221. Bond D, Raynes-­Greenow C, Gordon A. Bereaved parents, experi- ence of care and follow-­up after stillbirth in Sydney hospitals. Aust N Z J Obstet Gynaecol. 2018;58(2):185–­91. https://doi.org/10.1111/ ajo.12684 202. Navidian A, Saravani Z. Impact of cognitive behavioral-­based counseling on grief symptoms severity in mothers after stillbirth. Iran J Psychiatry Behav Sci. 2018;12(1):650–­4. 203. Ibiebele I, Boyle FM, Horey D, Lourie R, Wilson P, Coory M, et al. Predictors of autopsy following stillbirth in Queensland, Australia: a population-­based study. Aust N Z J Obstet Gynaecol. 2017;57(1):33–­9. 222. Redshaw M, Henderson J. Care associated with stillbirth for the most disadvantaged women: a multi-­method study of care in England. Birth. 2018;45(3):275–­85. https://doi.org/10.1111/birt.12335 223. Cassidy PR. Care quality following intrauterine death in Spanish hospitals: results from an online survey. BMC Pregnancy Childbirth. 2018;18(1):22. 204. Jones F, Thibon P, Guyot M, Molin A, Jeanne-­Pasquier C, Guillois B, et al. Practice of pathological examinations in stillbirths: a 10-­year retrospective study. J Gynecol Obstet Hum Reprod. 2017;46(1):61–­7. 224. Moond S, Banerjee KP, Arya R. A comparative study of mifepristone and misoprostol versus misoprostol alone in induction of labour in late intrauterine Fetal death. Int J Med Biomed Stud. 2021;5(2):987. 205. Campbell J, Armstrong K, Palaniappan N, Maher E, Glancy M, Porteous M, et al. In a genomic era, placental pathology still holds the key in the nondysmorphic stillbirth. Pediatr Dev Pathol. 2018;21(3):308–­18. 225. Siassakos D, Jackson S, Gleeson K, Chebsey C, Ellis A, Storey C, et al. All bereaved parents are entitled to good care after still- birth: a mixed-­methods multicentre study (INSIGHT). BJOG. 2018;125(2):160–­70. 206. Aiyelaagbe E, Scott RE, Holmes V, Lane E, Heazell AEP. Assessing the quality of bereavement care after perinatal death: development and piloting of a questionnaire to assess parents, experiences. J Obstet Gynaecol. 2017;37(7):931–­6. 226. Navidian A, Saravani Z. Impact of cognitive behavioral-­based counseling on grief symptoms severity in mothers after stillbirth. Iran J Psychiatry Behav Sci. 2018;12(1):e9275. 207. Singh K, Speizer I, Kim ET, Lemani C, Phoya A. Reaching vul- nerable women through maternity waiting homes in Malawi. Johnson JE, Price AB, Kao JC, Fernandes K, Stout R, Gobin RL, et al. Interpersonal psychotherapy (IPT) for major depression following perinatal loss: a pilot randomized controlled trial. Arch Womens Ment Health. 2016;19(5):845–­59. 174. Wilson PA, Boyle FM, Ware RS. Holding a stillborn baby: the view from a specialist perinatal bereavement service. Aust N Z J Obstet Gynaecol. 2015;55(4):337–­43. SYSTEMATIC REVIEW OF STILLBIRTH CARE OUTCOMES 15 doi.org/10.1111/ajo.13334 Contact with the baby fol- lowing stillbirth and parental mental health and well-­being: a sys- tematic review. BMJ Open. 2015;5(11):e008616. 240. Manocha A, Ravikumar G, Crasta J. Placenta in intrauterine fetal demise (IUFD): a comprehensive study from a tertiary care hos- pital. J Matern Neonatal Med. 2019;32(23):3939–­47. https://doi. org/10.1080/14767​058.2018.1479390 259. Cacciatore J, Defrain J, Jones KLC, Jones H. Stillbirth and the cou- ple: a gender-­based exploration. J Fam Soc Work. 2008;11(4):351–­70. 260. Duffy JMN, Hirsch M, Kawsar A, Gale C, Pealing L, Plana MN, et al. Outcome reporting across randomised controlled trials evaluating therapeutic interventions for pre-­eclampsia. BJOG. 2017;124(12):1829–­39. 241. Panaitescu AM, Ceaușelu L, Gică N, Ciobanu AM, Gheoca G, Dumitru A, et al. Fetal death in utero. Ten years retrospective anal- ysis of a tertiary maternity. Rom. J Leg Med. 2020;28(3):236–­41. 242. Evans MJ, Draper ES, Smith LK. Impact of sociodemographic and clinical factors on offer and parental consent to postmortem fol- lowing stillbirth or neonatal death: a UK population-­based cohort study. Arch Dis Child Fetal Neonatal Ed. 2020;105(5):532–­7. 261. Koot MH, Boelig RC, van't Hooft J, Limpens J, Roseboom TJ, Painter RC, et al. Variation in hyperemesis gravidarum defi- nition and outcome reporting in randomised clinical trials: a systematic review. BJOG. 2018;125(12):1514–­21. https://doi. org/10.1111/1471-­0528.15272 243. Masereka EM, Naturinda A, Tumusiime A, Munguiko C. Implementation of the perinatal death surveillance and response guidelines: lessons from annual health system strengthening inter- ventions in the Rwenzori sub-­region, Western Uganda. Nurs Open. 2020;7(5):1497–­505. 262. Kim BV, Aromataris EC, de Lint W, Middleton P, Townsent R, Khalil A, et al. Developing a core outcome set in interventions to prevent stillbirth: a systematic review on variations of outcome re- porting. Eur J Obstet Gynecol Reprod Biol. 2021;259:196–­206. 244. Shelmerdine SC, Hutchinson JC, Ward L, Sekar T, Ashworth MT, Levine S, et al. Feasibility of INTACT (INcisionless TArgeted Core tissue) biopsy procedure for perinatal autopsy. Ultrasound Obstet Gynecol. 2020;55(5):667–­75. https://doi.org/10.1002/uog.20387 263. Hirsch M, Duffy JMN, Kusznir JO, Davis CJ, Plana MN, Khan KS, et al. Variation in outcome reporting in endometriosis trials: a sys- tematic review. Am J Obstet Gynecol. 2016;214(4):452–­64. https:// doi.org/10.1016/j.ajog.2015.12.039 245. Patil NJ, Tele JS, Kadam RS, Pawar SJ, Kumbar SM. Placental pa- thology in intrauterine fetal death. Int J Res Pharm Sci. 2020;11(SPL 4):2376–­80. 264. Ghai V, Subramanian V, Jan H, Pergialiotis V, Thakar R, Doumouchtsis SK, et al. doi.org/10.1111/ajo.13334 234. Steen SE. Raising the bar: development of a perinatal bereavement programme. Int J Palliat Nurs. 2019;25(12):578–­86. https://doi. org/10.12968/​ijpn.2019.25.12.578 252. Arocha PR, Range LM. Events surrounding stillbirth and their effect on symptoms of depression among mothers. Death Stud. 2021;45(7):573–­7. https://doi.org/10.1080/07481​187.2019.1679911 235. Lehner C, Harry A, Pelecanos A, Wilson L, Pink K, Sekar R. The feasibility of a clinical audit tool to investigate stillbirth in Australia –­ a single Centre experience. Aust N Z J Obstet Gynaecol. 2019;59(1):59–­65. https://doi.org/10.1111/ajo.12799 253. Horey D, Boyle FM, Cassidy J, Cassidy PR, Erwich JJHM, Gold KJ, et al. Parents, experiences of care offered after stillbirth: an inter- national online survey of high and middle-­income countries. Birth. 2021;48(3):366–­74. https://doi.org/10.1111/birt.12546 236. Po G, Monari F, Zanni F, Grandi G, Lupi C, Facchinetti F, et al. A regional audit system for stillbirth: a way to better understand the phenomenon. BMC Pregnancy Childbirth. 2019;19(1):276. https:// doi.org/10.1186/s1288​4-­019-­2432-­2 254. Cullen S, Mooney E, Downey P. A review of findings from pla- cental histology in cases of stillbirth following the amendment to the Coroner,s act. Ir J Med Sci. 2021;190(4):1435–­7. https://doi. org/10.1007/s1184​5-­020-­02446​-­6 237. Hutchinson JC, Shelmerdine SC, Lewis C, Parmenter J, Simcock IC, Ward L, et al. Minimally invasive perinatal and pediatric autopsy with laparoscopically assisted tissue sampling: feasibility and ex- perience of the MinImAL procedure. Ultrasound Obstet Gynecol. 2019;54(5):661–­9. https://doi.org/10.1002/uog.20211 255. Jørgensen ML, Prinds C, Mørk S, Hvidtjørn D. Stillbirth –­ transi- tions and rituals when birth brings death: data from a danish na- tional cohort seen through an anthropological lens. Scand J Caring Sci. 2022;36(1):100–­8. https://doi.org/10.1111/scs.12967 256. Duman M, Durgun Ozan Y, Aksoy Derya Y, Timur TS. The ef- fect of relaxation exercises training on pregnancy-­related anxiety after perinatal loss: a pilot randomized control trial. Explorer. 2022;18(1):44–­50. 238. Blythe C, Vazquez REZ, Cabrera MS, Zekic Tomas S, Oc Anumba D, Cohen MC. Results of full postmortem examination in a co- hort of clinically unexplained stillbirths: undetected fetal growth restriction and placental insufficiency are prevalent findings. J Perinatol. 2019;39(9):1196–­203. https://doi.org/10.1038/s4137​ 2-­019-­0412-­z 257. Huberty JL, Matthews J, Leiferman J, Hermer J, Cacciatore J. When a baby dies: a systematic review of experimental interventions for women after stillbirth. Reprod Sci. 2017;24(7):967–­75. 239. Jawad AK, Alalaf SK, Ali MS, Bawadikji AKA. Bemiparin as a prophy- laxis after an unexplained stillbirth: open-­label interventional prospec- tive study. Clin Appl Thromb Hemost. 2019;25:1076029619896629. 258. Hennegan JM, Henderson J, Redshaw M. 16  | 250. Fogarty S. A role for massage after antenatal or neonatal loss: evalua- tions from a community program. Adv Integr Med. 2021;8(2):129–­35. 233. Huberty J, Green J, Gold KJ, Leiferman J, Cacciatore J. An itera- tive design process to develop a randomized feasibility study and inform recruitment of minority women after stillbirth. Pilot Feasibility Stud. 2019;5(1):1–­15. https://doi.org/10.1186/s4081​ 4-­019-­0526-­2 251. Sexton JK, Mahomed K, Marsden T, Coory M, Gardener G, Ellwood D, et al. Prospective cohort study: causes of stillbirth in Australia 2013–­2018. Aust N Z J Obstet Gynaecol. 2021;61(5):667–­74. https:// doi.org/10.1111/ajo.13334 Int J Gynecol Obstet. 2016;136(1):91–­7. 227. Campbell HE, Kurinczuk JJ, Heazell AEP, Leal J, Rivero-­Arias O. Healthcare and wider societal implications of stillbirth: a population-­based cost-­of-­illness study. BJOG. 2018;125(2):108–­17. 208. Page JM, Christiansen-­Lindquist L, Thorsten V, Parker CB, Reddy UM, Dudley DJ, et al. Diagnostic tests for evaluation of stillbirth: results from the stillbirth collaborative research network. Obstet Gynecol. 2017;129(4):699–­706. 228. Hennegan JM, Henderson J, Redshaw M. Is partners, mental health and well-­being affected by holding the baby after stillbirth? Mothers, accounts from a national survey. J Reprod Infant Psychol. 2018;36(2):120–­31. https://doi.org/10.1080/02646​838.2018.1424325 209. Lee JH, Peralta FM, Palatnik A, Gaupp CL, McCarthy RJ. Neuraxial labor analgesia is not an independent predictor of perineal lacer- ations after vaginal delivery of patients with intrauterine fetal de- mise. Int J Obstet Anesth. 2017;32:21–­7. https://doi.org/10.1016/j. ijoa.2017.05.008 229. Akinshina S, Makatsariya A, Bitsadze V, Khizroeva J, Khamani N. Thromboprophylaxis in pregnant women with thrombophilia and a history of thrombosis. J Perinat Med. 2018;46(8):893–­9. https://doi. org/10.1515/jpm-­2017-­0329 210. Huberty JL, Matthews J, Leiferman J, Cacciatore J. Experiences of women who participated in a beta-­test for an online-­streamed yoga intervention after a stillbirth. Int J Yoga Therap. 2017;27(1):59–­68. 230. Azogh M, Shakiba M, Navidian A. The effect of psychoeducation on anxiety in subsequent pregnancy following stillbirth: a quasi-­ experimental study. J Fam Plann Reprod Health. 2018;12(1):42–­50. 211. Singh K, Speizer I, Kim ET, Lemani C, Phoya A. Reaching vul- nerable women through maternity waiting homes in Malawi. Int J Gynecol Obstet. 2016;136(1):91–­7. 231. Gold KJ, Boggs ME, Kavanaugh KL. MOMSonLINE: lessons learned from a feasibility RCT of online support for mothers be- reaved by perinatal loss. Omega. 2021;83(4):656–­72. https://doi. org/10.1177/00302​22819​861558 212. Henderson J, Redshaw M. Parents, experience of perinatal post-­ mortem following stillbirth: a mixed methods study. PLoS One. 2017;12(6):e0178475. https://doi.org/10.1371/journ​al.pone.0178475 232. Hanish KK, Margulies I, Cogan AM. Evaluation of an occupation-­ based retreat for women after pregnancy or infant loss. Am J Occup Ther. 2019;73(5):7305345030p1–­6. https://doi.org/10.5014/ ajot.2019.034025 g j 213. McPherson E, Nestoridi E, Heinke D, Roberts DJ, Fretts R, Yazdy MM, et al. Alternatives to autopsy for Fetal and early neonatal 16 BAKHBAKHI et al. APPENDIX 1 iCHOOSE Collaborative Group 270. Kingdon C, Roberts D, Turner MA, Storey C, Crossland N, Finlayson KW, et al. Inequalities and stillbirth in the UK: a meta-­ narrative review. BMJ Open. 2019;9(9):e029672. Maggie Redshaw, University of Oxford; Vicki Flenady, The University of Queensland; Alexander Heazell, Maternal and Fetal Health Research Centre, University of Manchester; Laura Timlin, North Bristol NHS Trust, UK; Mary Lynch, University of Bristol, UK; Soo Downe, University of Central Lancashire; Pauline Slade, University of Liverpool; Lisa Thorne, NHS Devon; Heather-­Jane Coombs, Sands, UK; Aleena Wojcieszek, Mater Research Institute -­ The University of Queensland (MRI-­UQ); Margaret Murphy, University College Cork; Heloisa de Oliveira Salgado, University of Sao Paulo; Lindsey Wimmer, Star Legacy Foundation; Danielle Pollock, JBI, University of Adelaide; Neelam Aggarwal, Post Graduate Institute of Medical Education and Research, Chandigarh, India; Susannah Hopkins Leisher, International Stillbirth Alliance; Kate Mulley, Sands Charity, United Kingdom; Irene Attachie, University of Health and Allied Sciences, Ghana; Bethany Atkins, University College London, UK. 271. The World Bank. World Bank country and lending groups [Internet]. [cited 2023 Mar 14]. Available from: https://datah​elpde​ sk.world​bank.org/knowl​edgeb​ase/artic​les/906519-world-bank- count​ry-and-lendi​ng-groups doi.org/10.1111/ajo.13334 A systematic review on reported outcomes and outcome measures in female idiopathic chronic pelvic pain for the development of a core outcome set. BJOG. 2021;128(4):628–­34. https://doi.org/10.1111/1471-­0528.16412 246. Pekkola M, Tikkanen M, Loukovaara M, Lohi J, Paavonen J, Stefanovica V. Postmortem examination protocol and system- atic re-­evaluation reduce the proportion of unexplained still- births. J Perinat Med. 2020;48(8):771–­7. https://doi.org/10.1515/ jpm-­2019-­0426 265. Perry H, Duffy JMN, Umadia O, Khalil A. Outcome reporting across randomized trials and observational studies evaluating treatments for twin–­twin transfusion syndrome: systematic review. Ultrasound Obstet Gynecol. 2018;52(5):577–­85. 247. Huberty J, Sullivan M, Green J, Kurka J, Leiferman J, Gold K, et al. Online yoga to reduce post traumatic stress in women who have experienced stillbirth: a randomized control feasibility trial. BMC Complement Med Ther. 2020;20(1):173. 266. Young AE, Davies A, Bland S, Brookes S, Blazeby JM. Systematic re- view of clinical outcome reporting in randomised controlled trials of burn care. BMJ Open. 2019;9(2):e025135. 267. Alkhaffaf B, Blazeby JM, Williamson PR, Bruce IA, Glenny A-­M. Reporting of outcomes in gastric cancer surgery trials: a systematic review. BMJ Open. 2018;8(10):e021796. 248. Burden C, Bakhbakhi D, Heazell AE, Lynch M, Timlin L, Bevan C, et al. Parents, active role and ENgagement in the review of their stillbirth/perinatal death 2 (PARENTS 2) study: a mixed-­methods study of implementation. BMJ Open. 2021;11(3):e044563. 268. Potter S, Brigic A, Whiting PF, Cawthorn SJ, Avery KNL, Donovan JL, et al. Reporting clinical outcomes of breast reconstruction: a systematic review. J Natl Cancer Inst. 2011;103(1):31–­46. https://doi. org/10.1093/jnci/djq438 249. Wong KY, Ng NC. Views of Chinese women with perinatal loss on seeing and holding the baby. Hong Kong J Gynaecol Obstet Midwifery. 2021;21(1):23–­8. SYSTEMATIC REVIEW OF STILLBIRTH CARE OUTCOMES 17 269. Breeze ACG, Statham H, Hackett GA, Jessop FA, Lees CC. Attitudes to perinatal postmortem: parental views about research participa- tion. J Med Ethics. 2011;37(6):364–­7. SUPPORTING INFORMATION Additional supporting information can be found online in the Supporting Information section at the end of this article. How to cite this article: Bakhbakhi D, Siassakos D, Davies A, Merriel A, Barnard K, Stead E, et al. Interventions, outcomes and outcome measurement instruments in stillbirth care research: A systematic review to inform the development of a core outcome set. BJOG. 2023;00:1–­17. https://doi.org/10.1111/1471- 0528.17390 How to cite this article: Bakhbakhi D, Siassakos D, Davies A, Merriel A, Barnard K, Stead E, et al. Interventions, outcomes and outcome measurement instruments in stillbirth care research: A systematic review to inform the development of a core outcome set. BJOG. 2023;00:1–­17. https://doi.org/10.1111/1471- 0528.17390 How to cite this article: Bakhbakhi D, Siassakos D, Davies A, Merriel A, Barnard K, Stead E, et al. Interventions, outcomes and outcome measurement instruments in stillbirth care research: A systematic review to inform the development of a core outcome set. BJOG. 2023;00:1–­17. https://doi.org/10.1111/1471- 0528.17390
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Well-Posedness of Triequilibrium-Like Problems
International journal of analysis and applications
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∗Corresponding author: noormaslam@gmail.com Abstract. This work emphasizes in presenting new class of equilibrium-like problems, termed as equilibrium- like problems with trifunction. We establish some metric characterizations for the well-posed triequilibrium- like problems. We give some conditions under which the equilibrium-like problems are strongly well- posed. Our results, which give essential and adequate conditions to the well-posedness of triequilibrium- like problems, are acquired by utilizing the assumption of pseudomonotonicity. Technique and ideas of this paper inspire further research in this dynamic field. Department of Mathematics, COMSATS University Islamabad, Islamabad, Pakistan Department of Mathematics, COMSATS University Islamabad, Islamabad, Pakistan Key words and phrases. variational-like inequalities; preinvex functions; equilibrium problems; well-posed; pseudomonotonicity. https://doi.org/10.28924/2291-8639-20-2022-3 ISSN: 2291-8639 2010 Mathematics Subject Classification. 49J40, 90C33. 2010 Mathematics Subject Classification. 49J40, 90C33. Received: Sep. 08, 2021. Int. J. Anal. Appl. (2022), 20:3 Int. J. Anal. Appl. (2022), 20:3 Received: Sep. 08, 2021. Received: Sep. 08, 2021. Received: Sep. 08, 2021. Received: Sep. 08, 2021. Received: Sep. 08, 2021. 2010 Mathematics Subject Classification. 49J40, 90C33. Key words and phrases. variational-like inequalities; preinvex functions; equilibrium problems; well-posed; pseudomonotonicity. 1. Introduction The theory of equilibrium problems is an engrossing and significant offshoot of variational inequali- ties in practice with a broad variety of industrial, physical, geographical and social applications. Across various areas of pure, applied and engineering sciences, equilibrium problem theory has shown incred- ible potential and great impact. In nearly all disciplines, of mathematics and engineering, this theory has registered its exceptional ever-expanding mark. A new and incisive treatment of a broad list of problems, that occur in ecology, finance, economics, elasticity, network, image reconstruction, opti- mization and transport, are exhaustively approached by the equilibrium problem theory. In 1994, Blum and Oettli [3] and Noor and Oettli [23] rendered equilibrium problems their existing form. The classi- cal equilibrium problems theory revolves around the assumption of convexity of the set and objective function. Equilibrium problems cover a diverse set of applications including hemivariational inequali- ties, variational inequalities, game theory, Nash equilibrium, variational-like inequalities and fixed point https://doi.org/10.28924/2291-8639-20-2022-3 ISSN: 2291-8639 © 2022 the author(s). Int. J. Anal. Appl. (2022), 20:3 2 point theory, see [1–7,12–19,21,22,24–29]. Recently, the notion of convexity has started expanding to numerous fields showing the capacity for various useful applications. Hanson [8] derived invex functions as a special extension of convex functions. Different results were presented to make this fact noticeable that what holds for convex functions in mathematical programming also holds for a generalized class of functions known as invex functions. Ben-Israel and Mond [1] and Weir and Jeyakumar [31] works led to preinvex functions as another generalized class of convex functions. Weir and Mond [30] has shown in their work the inter- changeability of preinvex functions with convex functions in optimization problems. In [15], it is made evident that the minimum of preinvex on the invex set can be disciplined into variational inequalities, widely known as variational-like inequalities. Variational-like inequalities and equilibrium-like problems, owing to their specialized nature, cannot allow traditional resolvent method, projection method and their prevalent variant forms to propound any iterative methods. To bridge this gap, we resort to a technique named as auxiliary principle, proposed by Glowinski et al. [4]. To solve numerous variational inequalities and equilibrium problems, Noor [15, 19, 20] and Noor et al. [22, 24, 25, 27] employed the technique of auxiliary principle to propose various iterative methods. Research of our paper is devoted to present a new class of equilibrium problems, termed as equilibrium-like problems with trifunction. 1. Introduction The notion of well-posedness of variational ineaqualities and equilibrium problems was introduced by Lucchetti and Patrone [9,10]. We expand the notion of well-posedness to contemplate and establish the well-posedness of triequilibrium-like problems. Several interesting and important cases are discussed as applications of the obtained results. 2. Basic concepts and formulations Let ˜H be a real Hilbert space. The inner product and norm on ˜H are denoted by ⟨., .⟩and ∥. ∥ respectively. Let Kℏbe a nonempty invex set in ˜H. Let ℑ: Kℏ→ℜand ℏ(., .) : ˜H × ˜H →˜H are continuous functions. First we recall the following well-known results and concepts, before discussing our main results. Definition 2.1. ( [1]). A nonempty set Kℏin ˜H is said to be an invex set, if there exists a bifunction ℏ(., .), such that Definition 2.1. ( [1]). A nonempty set Kℏin ˜H is said to be an invex set, if there exists a bifunction ℏ(., .), such that ℏ(., .), such that ξ + τℏ(ζ, ξ) ∈Kℏ, ∀ξ, ζ ∈Kℏ, τ ∈[0, 1]. f the set Kℏis invex at each ξ ∈Kℏ, then Kℏis also called ℏ−connected set. Definition 2.2. ( [1]). A function ℑ: Kℏ→ℜis said to be a preinvex function, if there exists a bifunction ℏ(., .), such that ℑ(ξ + τℏ(ζ, ξ)) ≤(1 −τ)ℑ(ξ) + τℑ(ζ), ∀ξ, ζ ∈Kℏ, τ ∈[0, 1]. 3 The function ℑ: Kℏ→ℜis said to be preconcave if and only if −ℑis preinvex. Kℏ→ℜis said to be preconcave if and only if −ℑis preinvex. Definition 2.3. ( [8]). A differentiable function ℑ: Kℏ→ℜis said to be an invex function, if there exists a bifunction ℏ(., .), such that Definition 2.3. ( [8]). A differentiable function ℑ: Kℏ→ℜis said to be an invex function, if there exists a bifunction ℏ(., .), such that ℑ(ζ) −ℑ(ξ) ≥⟨ℑ′(ξ) , ℏ(ζ, ξ)⟩, ∀ξ, ζ ∈Kℏ, τ ∈[0, 1], where ℑ′(ξ) is the differential of ℑat ξ. From above definitions, it is clear that the differentiable preinvex functions are the invex functions but the converse is not true, see [21]. We note that, if ℏ(ζ, ξ) = ζ −ξ, the invex set Kℏreduces to the convex set K and preinvex functions reduce to convex functions. There are some functions which are preinvex but not convex. where ℑ′(ξ) is the differential of ℑat ξ. 1. Introduction From above definitions, it is clear that the differentiable preinvex functions are the invex functions but the converse is not true, see [21]. We note that, if ℏ(ζ, ξ) = ζ −ξ, the invex set Kℏreduces to the convex set K and preinvex functions reduce to convex functions. There are some functions which are preinvex but not convex. Definition 2.4. . The bifunction ℏ(., .) : ˜H × ˜H →ℜsatisfies the following condition ℏ(ξ + τ1(ζ −ξ), ξ + τ2(ζ −ξ)) = (τ1 −τ2)ℏ(ζ, ξ) , ∀ξ ζ ∈˜H Definition 2.4. . The bifunction ℏ(., .) : ˜H × ˜H →ℜsatisfies the following condition ℏ(ξ + τ (ζ ξ) ξ + τ (ζ ξ)) (τ τ )ℏ(ζ ξ) finition 2.4. . The bifunction ℏ(., .) : ˜H × ˜H →ℜsatisfies the following condition ℏ(ξ + τ1(ζ −ξ), ξ + τ2(ζ −ξ)) = (τ1 −τ2)ℏ(ζ, ξ) , ∀ξ, ζ ∈˜H. For τ1 = 0, 1 and τ2 = τ, we get Condition C of Mohan and Neogy [11], For τ1 = 0, 1 and τ2 = τ, we get Condition C of Mohan and Neogy [11], (i) ℏ(ξ, ξ + τ(ζ −ξ)) = −τℏ(ζ, ξ) , (ii) ℏ(ζ, ξ + τ(ζ −ξ)) = (1 −τ)ℏ(ζ, ξ) , ∀ξ, ζ ∈˜H. (i) ℏ(ξ, ξ + τ(ζ −ξ)) = −τℏ(ζ, ξ) , (ii) ℏ(ζ, ξ + τ(ζ −ξ)) = (1 −τ)ℏ(ζ, ξ) , Mohan and Neogy [11] used definition 2.4 to show that an invex function on an invex set Kℏ, is also a preinvex function and the converse also hold. Given an operator Υ : ˜H →ℜand a continuous trifunction Ψ(., ., .) : ˜H × ˜H × ˜H →ℜ, consider the problem of finding ξ ∈Kℏ, such that Mohan and Neogy [11] used definition 2.4 to show that an invex function on an invex set Kℏ, is also a preinvex function and the converse also hold. Given an operator Υ : ˜H →ℜand a continuous trifunction Ψ(., ., .) : ˜H × ˜H × ˜H →ℜ, consider the problem of finding ξ ∈Kℏ, such that Ψ(ξ, Υ(ξ), ℏ(ζ, ξ)) ≥0 , ∀ζ ∈Kℏ. (2.1) (2.1) The problem (2.1) is called an equilibrium-like problem with trifunction. For Ψ(ξ, Υ(ξ), ℏ(ζ, ξ)) = ⟨ξ, Υ(ξ), ℏ(ζ, ξ)⟩, problem (2.1) is called variational-like inequality with trifunction of finding ξ ∈Kℏ, such that m (2.1) is called an equilibrium-like problem with trifunction. 1. Introduction (ii) partially relaxed jointly strong ℏ−monotone, if there exists a constant α > 0 such that (ii) partially relaxed jointly strong ℏ−monotone, if there exists a constant α > 0 such that Ψ(ξ, Υ(ξ), ℏ(ζ, z)) + Ψ(ζ, Υ(ζ), ℏ(z, ζ)) ≤α ∥ℏ(z, ξ) ∥2 , rtially relaxed jointly strong ℏ−monotone, if there exists a constant α > 0 such that Ψ(ξ, Υ(ξ), ℏ(ζ, z)) + Ψ(ζ, Υ(ζ), ℏ(z, ζ)) ≤α ∥ℏ(z, ξ) ∥2 , ∀ξ, ζ, z ∈Kℏ. ∀ξ, ζ, z ∈Kℏ. (iii) jointly ℏ−monotone, if Ψ(ξ, Υ(ξ), ℏ(ζ, ξ)) + Ψ(ζ, Υ(ζ), ℏ(ξ, ζ)) ≤0 , ∀ξ, ζ ∈Kℏ. Ψ(ξ, Υ(ξ), ℏ(ζ, ξ)) + Ψ(ζ, Υ(ζ), ℏ(ξ, ζ)) ≤0 , ∀ξ, ζ ∈Kℏ. (iv) jointly ℏ−hemicontinuous, if the mapping 1. Introduction For Ψ(ξ, Υ(ξ), ℏ(ζ, ξ)) = ⟨ξ, Υ(ξ), ℏ(ζ, ξ)⟩, problem (2.1) is called variational-like inequality with trifunction of finding ξ ∈Kℏ, such that ⟨ξ, Υ(ξ), ℏ(ζ, ξ)⟩≥0 , ∀ζ ∈Kℏ. (2.2) (2.2) For ⟨ξ, Υ(ξ), ℏ(ζ, ξ)⟩= ⟨Υ(ξ), ℏ(ζ, ξ)⟩, problem (2.2) is called variational-like inequality of finding ξ ∈˜H such that For ⟨ξ, Υ(ξ), ℏ(ζ, ξ)⟩= ⟨Υ(ξ), ℏ(ζ, ξ)⟩, problem (2.2) is called variational-like inequality of finding ξ ∈˜H such that ⟨Υ(ξ), ℏ(ζ, ξ)⟩≥0 , ∀ζ ∈Kℏ (2.3) (2.3) If ℏ(ζ, ξ) = ζ −ξ, then an invex set reduces to a convex set and problem (2.1) is equivalent to finding ξ ∈K, such that Ψ(ξ, Υ(ξ), ζ −ξ) ≥0 , ∀ζ ∈K, (2.4) (2.4) Int. J. Anal. Appl. (2022), 20:3 4 which is called an equilibrium problem with trifunction and gives offan impression of being new. Variational-like inequality with trifunction (2.2) reduces to variational inequality with trifunction of finding ξ ∈K, such that which is called an equilibrium problem with trifunction and gives offan impression of being new. Variational-like inequality with trifunction (2.2) reduces to variational inequality with trifunction of finding ξ ∈K, such that ⟨ξ, Υ(ξ), ζ −ξ⟩≥0 , ∀ζ ∈K. (2.5) ⟨ξ, Υ(ξ), ζ −ξ⟩≥0 , ∀ζ ∈K. (2.5) Also variational-like inequality (2.3) is equivalent to finding ξ ∈K, such that ⟨Υ(ξ), ζ −ξ⟩≥0 , ∀ζ ∈Kℏ, (2.6) (2.6) ⟨Υ(ξ), ζ −ξ⟩≥0 , ∀ζ ∈Kℏ, which is known as variational inequality, proposed and cosidered by Stampacchia [20]. In brief, for suitable and appropriate choice of the functions Ψ(., ., .), ℏ(., .) and the spaces, one can obtain a number of new and known problems as special cases of the problem (2.1). This shows that problem (2.1) is quite general and unifying. Definition 2.5. The operator Υ : ˜H →ℜand the function Ψ(., ., .) are said to be: (i) jointly ℏ−pseudomonotone, if Ψ(ξ, Υ(ξ), ℏ(ζ, ξ)) ≥0, Ψ(ξ, Υ(ξ), ℏ(ζ, ξ)) ≥0, =⇒Ψ(ζ, Υ(ζ), ℏ(ξ, ζ)) ≤0 , ∀ξ, ζ ∈Kℏ. =⇒Ψ(ζ, Υ(ζ), ℏ(ξ, ζ)) ≤0 , ∀ξ, ζ ∈Kℏ. (iv) jointly ℏ−hemicontinuous, if the mapping Ψ(ξ + τℏ(ζ, ξ), Υ(ξ + τℏ(ζ, ξ)), ℏ(ζ, ξ)) ∀ξ, ζ ∈Kℏ, τ ∈[0, 1], is continuous. We note that, for z = ξ, partially relaxed jointly strong ℏ−monotonicity reverts to jointly ℏ−monotonicity. Lemma 2.1. Let the trifunction Ψ(., ., .) and operator Υ be jointly ℏ−pseudomonotone and jointly ℏ−hemicontinuous. If Assumption (2.4) holds, then problem (2.1) is equivalent to finding ξ ∈Kℏ, such that Lemma 2.1. Let the trifunction Ψ(., ., .) and operator Υ be jointly ℏ−pseudomonotone and jointly ℏ−hemicontinuous. If Assumption (2.4) holds, then problem (2.1) is equivalent to finding ξ ∈Kℏ, such that Ψ(ζ, Υ(ζ), ℏ(ξ, ζ)) ≤0 , ∀ξ, ζ ∈Kℏ. Ψ(ζ, Υ(ζ), ℏ(ξ, ζ)) ≤0 , ∀ξ, ζ ∈Kℏ. 5 Int. J. Anal. Appl. (2022), 20:3 Proof: Let ξ ∈Kℏbe a solution of equilibrium-like problem (2.1), then Ψ(ξ, Υ(ξ), ℏ(ζ, ξ)) ≥0, Ψ(ξ, Υ(ξ), ℏ(ζ, ξ)) ≥0, implies Ψ(ζ, Υ(ζ), ℏ(ξ, ζ)) ≤0 , ∀ξ, ζ ∈Kℏ, (2.7) (2.7) since Ψ(., ., .) and Υ are jointly ℏ−pseudomonotone. since Ψ(., ., .) and Υ are jointly ℏ−pseudomonotone. Conversely, let ∀ξ, ζ ∈Kℏ, we define ζτ = ξ + τℏ(ζ, ξ) ∈˜H. Replacing ζ by ζτ in (2.7), we have Ψ(ζτ, Υ(ζτ), ℏ(ξ, ζτ)) ≤0 , ∀ξ, ζ ∈Kℏ. ) et ∀ξ, ζ ∈Kℏ, we define ζτ = ξ + τℏ(ζ, ξ) ∈˜H. Replacing ζ by ζτ in (2.7), we have Ψ(ζτ, Υ(ζτ), ℏ(ξ, ζτ)) ≤0 , ∀ξ, ζ ∈Kℏ. Now by using Assumption (2.4) , we have Now by using Assumption (2.4) , we have −τΨ(ζτ, Υ(ζτ), ℏ(ζ, ξ)) ≤0. (2.8) −τΨ(ζτ, Υ(ζτ), ℏ(ζ, ξ)) ≤0. (2.8) (2.8) Now dividing (2.8) by τ and letting τ −→0 and using jointly ℏ−hemicontinuity of Ψ(., ., .) and Υ, we get Now dividing (2.8) by τ and letting τ −→0 and using jointly ℏ−hemicontinuity of Ψ(., ., .) and Υ, we get Ψ(ξ, Υ(ξ), ℏ(ζ, ξ)) ≥0, which shows that ξ ∈Kℏis a solution of problem (2.1), the required result. □ □ which shows that ξ ∈Kℏis a solution of problem (2.1), the required result. □ Lemma (2.1) can be considered as the generalized form of Minty’s Lemma for triequilibrium-like problems. Result obtained in above Lemma is termed as the dual triequilibrium -like problem. 3. Well-Posedness 3. Well-Posedness We generalize the notion of well-posedness to triequilibrium-like problems. By using the assumption of pseudomonotonicity we obtain some results for well-posed equilibrium-like problems with trifunction. since Ψ(., ., .) and Υ are jointly ℏ−pseudomonotone. Thus M(ε) ⊂N(ε). (3.4) M(ε) ⊂N(ε). (3.4) M(ε) ⊂N(ε). (3.4) M(ε) ⊂N(ε). M(ε) ⊂N(ε). (3.4) rsely, for any ξ ∈Kℏ, (3.3) holds. Conversely, for any ξ ∈Kℏ, (3.3) holds. Conversely, for any ξ ∈Kℏ, (3.3) holds. Now, let ∀ξ, ζ ∈Kℏwe define ζτ = ξ + τℏ(ζ, ξ) ∈Kℏ. Replacing ζ by ζτ in (3.3), we have Ψ(ζτ, Υ(ζτ), ℏ(ξ, ζτ)) ≤ε ∥ℏ(ζτ, ξ) ∥, ∀ξ, ζ ∈Kℏ. y y ξ ℏ( ) Now, let ∀ξ, ζ ∈Kℏwe define ζτ = ξ + τℏ(ζ, ξ) ∈Kℏ. Replacing ζ by ζτ in (3.3), we have Ψ(ζτ, Υ(ζτ), ℏ(ξ, ζτ)) ≤ε ∥ℏ(ζτ, ξ) ∥, ∀ξ, ζ ∈Kℏ. Now, let ∀ξ, ζ ∈Kℏwe define ζτ = ξ + τℏ(ζ, ξ) ∈Kℏ. Replacing ζ by ζτ in (3.3), w Now by using Assumption (2.4), we have Now by using Assumption (2.4), we have −τΨ(ζτ, Υ(ζτ), ℏ(ζ, ξ)) ≤τε ∥ℏ(ζ, ξ) ∥. (3.5) (3.5) Now dividing (3.5) by τ and letting τ −→0 and using jointly ℏ−hemicontinuity of Ψ(., ., .) and T, we get Ψ(ξ, Υ(ξ), ℏ(ζ, ξ)) ≥−ε ∥ℏ(ζ, ξ) ∥, which implies that which implies that N(ε) ⊂M(ε). (3.6) N(ε) ⊂M(ε). (iv) jointly ℏ−hemicontinuous, if the mapping Our obtained results could be considered, an extension of the results which were obtained and studied in [6,8,9,16–18] onsider two sets Given ε > 0, consider two sets M(ε) = {ξ ∈˜ H : Ψ(ξ , Υ(ξ) , ℏ(ζ, ξ)) ≥−ε ∥ℏ(ζ, ξ) ∥, ∀ζ ∈Kℏ}, (3.1) (3.1) and and N(ε) = {ξ ∈˜ H : Ψ(ζ , Υ(ζ) , ℏ(ξ, ζ)) ≤ε ∥ℏ(ζ, ξ) ∥, ∀ζ ∈Kℏ. (3.2) For a non-empty set S ⊂˜H, define the diameter of S, denoted by D(S), as: N(ε) = {ξ ∈˜ H : Ψ(ζ , Υ(ζ) , ℏ(ξ, ζ)) ≤ε ∥ℏ(ζ, ξ) ∥, ∀ζ ∈Kℏ. (3.2) (3.2) For a non-empty set S ⊂˜H, define the diameter of S, denoted by D(S), as: For a non-empty set S ⊂˜H, define the diameter of S, denoted by D(S), as: D(S) = sup[∥ζ −ξ ∥; ∀ξ, ζ ∈S]. D(S) = sup[∥ζ −ξ ∥; ∀ξ, ζ ∈S]. Definition 3.1. [18]. The triequilibrium-like problem (2.1) is well-posed, if (i) For any ε > 0, M(ε) ̸= ∅, (ii) D(M(ε)) −→0 as ε −→0. (ii) D(M(ε)) −→0 as ε −→0. Int. J. Anal. Appl. (2022), 20:3 6 Theorem 3.1. Let the trifunction Ψ(., ., .) and operator Υ be jointly ℏ−pseudomonotone and jointly ℏ−hemicontinuous. If Assumption (2.4) holds, then M(ε) = N(ε). Proof: Let ξ ∈Kℏbe such that implies Ψ(ζ , Υ(ζ) , ℏ(ξ, ζ)) ≤ε ∥ℏ(ζ, ξ) ∥, ∀ζ ∈Kℏ, (3.3) Ψ(ζ , Υ(ζ) , ℏ(ξ, ζ)) ≤ε ∥ℏ(ζ, ξ) ∥, ∀ζ ∈Kℏ, (3.3) Ψ(ζ , Υ(ζ) , ℏ(ξ, ζ)) ≤ε ∥ℏ(ζ, ξ) ∥, ∀ζ ∈Kℏ, (3.3) since Ψ(., ., .) and Υ are jointly ℏ−pseudomonotone. Thus since Ψ(., ., .) and Υ are jointly ℏ−pseudomonotone. Thus since Ψ(., ., .) and Υ are jointly ℏ−pseudomonotone. Thus N(ε) ⊂M(ε). (3.6) By combining (3.4) and (3.6), we get our required result By combining (3.4) and (3.6), we get our required result N(ε) = M(ε). N(ε) = M(ε). Theorem 3.2. Let the trifunction Ψ(., ., .) and operator Υ be jointly ℏ−pseudomonotone and jointly ℏ−hemicontinuous. Then for all ε > 0, N(ε) is closed in ˜H. Theorem 3.2. Let the trifunction Ψ(., ., .) and operator Υ be jointly ℏ−pseudomonotone and jointly ℏ−hemicontinuous. Then for all ε > 0, N(ε) is closed in ˜H. Proof: Let {ξn : n ∈N} ⊂N(ε) be a sequence, such that ξn −→ξ in Kℏas n −→∞. Then ξn ∈Kℏand Proof: Let {ξn : n ∈N} ⊂N(ε) be a sequence, such that ξn −→ξ in Kℏas n −→∞. Then ξn ∈Kℏand Ψ(ζ , Υ(ζ) , ℏ(ξn, ζ)) ≤ε ∥ℏ(ζ, ξn) ∥, ∀ζ ∈Kℏ. (3.7) (3.7) By taking limit n −→∞in (3.7), we get ∞in (3.7), we get By taking limit n −→∞in (3.7), we get Ψ(ζ , Υ(ζ) , ℏ(ξ, ζ)) ≤ε ∥ℏ(ζ, ξ) ∥, ∀ζ ∈Kℏ. Ψ(ζ , Υ(ζ) , ℏ(ξ, ζ)) ≤ε ∥ℏ(ζ, ξ) ∥, ∀ζ ∈Kℏ. Ψ(ζ , Υ(ζ) , ℏ(ξ, ζ)) ≤ε ∥ℏ(ζ, ξ) ∥, ∀ζ ∈Kℏ. 7 □ Theorem 3.3. Let the trifunction Ψ(., ., .) and operator Υ be jointly ℏ−pseudomonotone and jointly ℏ−hemicontinuous. If triequilibrium-like problem (2.1) is well-posed and Assumption (2.4) holds, then there exists a unique solution of problem (2.1). Proof: Let the sequence {ξn : n ∈N}, defined by ξn ∈M( 1 n). Let ε > 0 be very small and let p, q ∈N, such that p ≥q ≥1 ε. Then M(1 p) ⊂M(1 q ) ⊂M(ε). So ∥ξp −ξq ∥≤D(M(1 p)). ∥ξp −ξq ∥≤D(M(1 p)). Thus, the sequence {ξn} is a Cauchy sequence and ξn −→ξ in Kℏ. By using results of Theorem (3.1) and Theorem (3.2), we get M(ε) is a closed set. Thus ξ ∈ \ ε>0 M(ε), ξ ∈ \ ε>0 M(ε), so, ξ is solution of problem (2.1). Uniqueness of solution ξ follows from second condition of well- posedness. □ so, ξ is solution of problem (2.1). Uniqueness of solution ξ follows from second condition of well- posedness. □ Theorem 3.4. Let the trifunction Ψ(., ., .) and operator Υ be jointly ℏ−pseudomonotone and jointly ℏ−hemicontinuous. N(ε) ⊂M(ε). If M(ε) ̸= 0, for all ε > 0 and M(ε) is bounded for some ε0, then there exists at least one solution of problem (2.1). Proof: Let ξk ∈M( 1 k ), then for large enough k, we have Proof: Let ξk ∈M( 1 k ), then for large enough k, we have Proof: Let ξk ∈M( 1 k ), then for large enough k, we have Proof: Let ξk ∈M( 1 k ), then for large enough k, we have M(1 k ) ⊂M(ε). Thus for some subsequence ξk −→ξ ∈Kℏ, we get Thus for some subsequence ξk −→ξ ∈Kℏ, we get Ψ(ζ , Υ(ζ) , ℏ(ξk, ζ)) ≤ 1 k ∥ℏ(ζ, ξk) ∥ ≤ 1 k {∥ζ ∥+c} ∀∈˜H. Now by taking limit k −→∞, we get Now by taking limit k −→∞, we get Now by taking limit k −→∞, we get Now by taking limit k −→∞, we get Now by taking limit k −→∞, we get Ψ(ζ , Υ(ζ) , ℏ(ξ, ζ)) ≤0, Ψ(ζ , Υ(ζ) , ℏ(ξ, ζ)) ≤0, 4. Perspective In this section, we discuss some research perspective of the equilibrium-like problem with trifunction. We show that the results derived in this paper can also be extended for a class of nonconvex equilibrium problem with trifunction. For the given operators Υ, g : ˜H →ℜand a nonlinear continuous trifunction Ψ(., ., .) : ˜H× ˜H× ˜H →ℜ, consider the problem of finding ξ ∈Kℏ, such that For the given operators Υ, g : ˜H →ℜand a nonlinear continuous trifunction Ψ(., ., .) : ˜H× ˜H× ˜H →ℜ, consider the problem of finding ξ ∈Kℏ, such that Ψ(g(ξ), Υ(g(ξ)), (g(ζ)) ≥0 , ∀ζ ∈Kℏ, (4.1) (4.1) Ψ(g(ξ), Υ(g(ξ)), (g(ζ)) ≥0 , ∀ζ ∈Kℏ, (4 which is called nonconvex triequilibrium problem. For the formulation and applications of problem (4.1) see, [12,15,18] and references therein. For g ≡I, where I is the identity operator, then the g- convex set becomes becomes the convex set and the problem (4.1) is called the triequilibrium problem of finding ξ ∈Kℏ, such that which is called nonconvex triequilibrium problem. For the formulation and applications of problem (4.1) see, [12,15,18] and references therein. For g ≡I, where I is the identity operator, then the g- convex set becomes becomes the convex set and the problem (4.1) is called the triequilibrium problem of finding ξ ∈Kℏ, such that Ψ(ξ, Υ(ξ), ζ) ≥0 , ∀ζ ∈Kℏ, (4.2) (4.2) which was introduced and investigated by Noor and Oettli [14]. For ℏ(ζ, ξ) = ζ −ξ, the invex set reduces to convex set. Thus from (4.1) and (4.2), we obtain that the triequilibrium-like problem is equivalent to the nonconvex equilibrium problem with trifunction (4.1). Hence all the above discussed results continue to hold for nonconvex triequilibrium problem (4.1). 5. Conclusion 5. Conclusion 5. Conclusion In our work we focused on introducing another class of equilibrium-like problems terming it as triequilibrium-like problems. We studied and established the well-posedness of triequilibrium-like prob- lems by using the assumption of pseudomonotonicity. The demonstrated results in this endeavour can rightly be considered as an enhancement and sophistication of already existing work. Ψ(ζ , Υ(ζ) , ℏ(ξ, ζ)) ≤0, which implies that ξ ∈N(0). By Theorem (3.1), we get ξ ∈N(0) = M(0), which implies ξ ∈M(0). which implies that ξ ∈N(0). By Theorem (3.1), we get ξ ∈N(0) = M(0), which implies ξ ∈M(0). Hence triequilibrium-like problem (2.1) has at least one solution. □ Hence triequilibrium-like problem (2.1) has at least one solution. □ Int. J. Anal. Appl. (2022), 20:3 8 Remark 3.1. (i) If triequilibrium-like problem has a unique solution, then M(ε) ̸= 0, ∀ε > 0 and T ε>0 = {ξ0}. Remark 3.1. (i) If triequilibrium-like problem has a unique solution, then M(ε) ̸= 0, ∀ε > 0 and T ε>0 = {ξ0}. Remark 3.1. (i) If triequilibrium-like problem has a unique solution, then M(ε) ̸= 0, ∀ε > 0 and T ε>0 = {ξ0}. ε>0 (ii) It is well-known, that if there is a unique solution to variational inequality (2.6), then it is not well-posed,see [9]. (ii) It is well-known, that if there is a unique solution to variational inequality (2.6), then it is not well-posed,see [9]. (iii) Theorem (3.3) concludes that, the unique solution of problem (2.1) could be calc (iii) Theorem (3.3) concludes that, the unique solution of problem (2.1) could be calculated by utilizing ε−equilibrium-like problem with trifunction, that is, find ξε ∈˜H, such that (iii) Theorem (3.3) concludes that, the unique solution of problem (2.1) could be calculated by utilizing ε−equilibrium-like problem with trifunction, that is, find ξε ∈˜H, such that ε−equilibrium-like problem with trifunction, that is, find ξε ∈˜H, such that Ψ(ξε , Υ(ξε) , ℏ(ζ, ξε)) ≥−ε ∥ℏ(ζ, ξε) ∥, ∀ζ ∈Kℏ. 4. Perspective T ε>0 = {ξ0}. Acknowledgements We wish to express our deepest gratitude to our colleagues, collaborators and friends, who have direct or indirect contributions in the process of this paper. We are also grateful to Rector, COMSATS University Islamabad, Pakistan for the research facilities and support in our research endeavors. Int. J. Anal. Appl. (2022), 20:3 9 Conflicts of Interest: The author(s) declare that there are no conflicts of interest regarding the publication of this paper. References [1] A. Ben-Israel and B. Mond, What is invexity?, J. Austral. Math. Soc. Ser. B. 28 (1986), 1-9. https://doi.org/ 10.1017/S0334270000005142. [2] M. I. Bloach and M. A. Noor, Perturbed mixed variational-like inequalities, AIMS Math. 5(3) (2019), 2153-2162. https://doi.org/10.3934/math.2020143. [3] E. Blum and W. Oettli, From optimization and variational inequalities to equilibrium problems, Math. Student. 63 (1994), 123-145. [4] R. Glowinski, J. L. Lions and R. Tremolieres, Numerical analysis of variational inequalities, North-Holland, Amsterdam, 1981. [5] F. Giannessi and A. Maugeri, Variational Inequalities and Network Equilibrium Problems. Plenum Press, New York, 1995. [6] F. Giannessi, A. Maugeri and P. M. Pardalos, Equilibrium Problems: Nonsmooth Optimization and Variational inequality Models, Kluwer Academic Publishers, Dordrecht, Holland, 2001. [7] D. Goeleven and D. Mantaque, Well-posed hemivariational inequalities. Numer. Funct. Anal. Optim. 16 (1995), 909-921. https://doi.org/10.1080/01630569508816652. [8] M. A. Hanson, On sufficiency of the Kuhn-Tucker conditions, J. Math. Anal. Appl. 80 (1981), 545-550. https: //doi.org/10.1016/0022-247X(81)90123-2. [9] R. Lucchetti and F. Patrone, A characterization of Tykhonov well-posedness for minimum problems with appli- cations to variational inequalities. Numer. Funct. Anal. Optim. 3 (1981), 461-476. https://doi.org/10.1080/ 01630568108816100. 10] R. Lucchetti and F. Patrone, Some properties of well-posed variational inequalities governed by [10] R. Lucchetti and F. Patrone, Some properties of well-posed variational inequalities governed by linear operators. Numer Funct Anal Optim 5 (1983) 349 361 https://doi org/10 1080/01630568308816145 Numer. Funct. Anal. Optim. 5 (1983), 349-361. https://doi.org/10.1080/01630568308816145. [11] S. R. Mohan and S. K. Neogy, On invex set and preinvex functions. J. Math. Anal. Appl. 189 (1995), 901-908. https://doi.org/10.1006/jmaa.1995.1057. 11] S. R. Mohan and S. K. Neogy, On invex set and preinvex functions. J. Math. Anal. Appl. 189 [11] S. R. Mohan and S. K. Neogy, On invex set and preinvex functions. J. Math. Anal. Appl. 189 (1995), 901 908. https://doi.org/10.1006/jmaa.1995.1057. T. V. Nghi1 and N. N. Tam, General variational inequalities: existence of solutions, Tikhonov-Type [12] T. V. Nghi1 and N. N. Tam, General variational inequalities: existence of solutions, Tikhonov-Type regularization, and well-posedness, Acta Math. Vietnam. (2021). Acknowledgements https://doi.org/10.1007/s40306-021-00435-0. [12] T. V. Nghi1 and N. N. Tam, General variational inequalities: existence of solutions, Tikhonov-Type regularizat and well-posedness, Acta Math. Vietnam. (2021). https://doi.org/10.1007/s40306-021-00435-0. and well-posedness, Acta Math. Vietnam. (2021). https://doi.org/10.1007/s40306-021-00435-0. [13] B. B. Mohsen, M. A. Noor, K. I. Noor and M. Postolache, Strongly convex functions of higher order involving bifunction, Mathematics, 7(11) (2019), 1028. https://doi.org/10.3390/math7111028. [14] M. A. Noor, General variational inequalities. Appl. Math. Lett. 1 (1988), 119-121. https://doi.org/10.1016/ 0893-9659(88)90054-7. [15] M. A. Noor, Variational-like inequalities. Optimization, 30 (1994), 323-330. https://doi.org/10.1080/ 02331939408843995. [16] M. A. Noor, New approximation schemes for general variational inequalities. J. Math. Anal. Appl. 251 (2000), 217-229. https://doi.org/10.1006/jmaa.2000.7042. [17] M. A. Noor, Merit function for variational–like inequalitiets, Math. Inequal. Appl. 1 (2000), 117-128. [18] M. A. Noor, Well-posed variational inequalities. J. Appl. Math. Comput. 11 (2003), 165-172. https://doi.org/ 10.1007/BF02935729. 19] M. A. Noor, Fundamentals of mixed quasi variational inequalities. Int. J. Pure. Appl. Math. 15 (2 [19] M. A. Noor, Fundamentals of mixed quasi variational inequalities. Int. J. Pure. Appl. Math. 15 (2004), 137-250. [20] M. A. Noor, Fundamentals of equilibrium problems. Math. Inequal. Appl. 9 (2006), 529-566. https://doi.org/ 10.7153/mia-09-51. [20] M. A. Noor, Fundamentals of equilibrium problems. Math. Inequal. Appl. 9 (2006), 529-566. https://doi.org/ 10.7153/mia-09-51. Int. J. Anal. Appl. (2022), 20:3 10 [21] M. A. Noor, Extended general variational inequalities. Appl. Math. Lett. 22(2) (2009), 182-186. https://doi. org/10.1016/j.aml.2008.03.007. oor and K. I. Noor, Some new trends in mixed variational inequalities, J. Adv. Math. Stud. in press. [22] M. A. Noor and K. I. Noor, Some new trends in mixed variational inequalities, J. Adv. Math. [23] M. A. Noor and W. Oettli, On general nonlinear complementarity problems and quasi-equilibria. Le Mathematiche, 49 (1994), 313-331. [24] M. A. Noor, K. I. Noor and H. M. Y. Al-Bayatti, Higher order variational inequalities, Inf. Sci. Lett. 11 (2022), 1-5. [24] M. A. Noor, K. I. Noor and H. M. Y. Al-Bayatti, Higher order variational inequalities, Inf. Sci. Lett. 11 (2022), 1-5. [25] M. A. Noor, K. I. Noor and M. I. Baloch, Auxiliary principle technique for strongly mixed variational-like inequalities. U.P.B. Sci. Bull. Ser. A, 80 (2018), 93-100. [25] M. A. Noor, K. I. Noor and M. I. Baloch, Auxiliary principle technique for strongly mixed variational-like inequalities. U.P.B. Sci. Bull. Ser. A, 80 (2018), 93-100. [26] M. A. Noor, K. I. Noor, A. Hamdi and E. H. El-shemas, On difference of two monotone operators, Optim. Lett. Acknowledgements 3 (2009), 329. https://doi.org/10.1007/s11590-008-0112-7. [27] M.A. Noor, K.I. Noor, M.Th. Rassias, New trends in general variational inequalities, Acta Appl. Math. 170 (2020), 981–1064. https://doi.org/10.1007/s10440-020-00366-2. [28] M. A. Noor, K. I. Noor, M. U. Awan and A. G. Khan, Quasi variational inclusions involving three operators, Inform. Sci. Lett. in press. [29] G. Stampacchia, Formes bilineaires coercitives sur les ensembles convexes. C. R. Acad. Sci. Paris, 258 (1964), 4413-4416. [30] T. Weir and B. Mond, Preinvex functions in multiple objective optimization. J. Math. Anal. Appl. 136 (1988), 29-38. https://doi.org/10.1016/0022-247X(88)90113-8. [30] T. Weir and B. Mond, Preinvex functions in multiple objective optimization. J. Math. Anal. Appl. 136 (1988), 29-38. https://doi.org/10.1016/0022-247X(88)90113-8. [31] T. Weir and V. Jeyakumar, A class of nonconvex functions and mathematical programming. Bull. Austral. Math. Soc. 38 (1988), 177-189. https://doi.org/10.1017/S0004972700027441. [31] T. Weir and V. Jeyakumar, A class of nonconvex functions and mathematical programming. Bull. Austral. Math. Soc. 38 (1988), 177-189. https://doi.org/10.1017/S0004972700027441.
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N-SLEEVE GASTRECTOMY: AN OPTION FOR OBESITY AND GERD
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HEADINGS - Sleeve gastrectomy. GERD. Obesity. Bariatric surgery. HEADINGS - Sleeve gastrectomy. GERD. Obesity. Bariatric surgery. HEADINGS - Sleeve gastrectomy. GERD. Obesity. Bariatric surgery. RESUMO - Racional: A obesidade representa ameaça crescente à saúde da população em todo o mundo. A gastrectomia por laparoscopia induz alteração do ângulo esofagogástrico devido à própria técnica, hipotonia do esfíncter esofágico inferior após secção de fibras musculares da junção, diminuição do volume gástrico e, consequentemente, aumento da pressão intragástrica; é por isso que alguns pacientes têm refluxo após a gastrectomia vertical. Objetivo: Descrever uma técnica e resultados preliminares da gastrectomia vertical com fundoplicatura a Nissen, a fim de diminuir o refluxo após ela. Método: No artigo atual, descrevemos a técnica passo a passo, principalmente focada na criação da válvula e seu cuidado. Resultados: Este procedimento foi aplicado em um caso de mulher com IMC 45 de 53 anos com DRGE. Foi realizada endoscopia demonstrando hérnia hiatal e cinco pólipos benignos. A gastrectomia vertical com Nissen foi realizada devido à DRGE, à hérnia hiatal e aos múltiplos pólipos no estômago. Ela tolerou bem o procedimento e recebeu alta sem intercorrências 48 h depois. Conclusão: A N-gastrectomia vertical (N-sleeve) é alternativa viável e segura em pacientes obesos com refluxo e hérnia hiatal quando não é indicado o desvio gástrico em Y-de-Roux. Received for publication: 12/08/2019 Accepted for publication: 01/10/2019 Received for publication: 12/08/2019 Accepted for publication: 01/10/2019 DESCRITORES - Gastrectomia vertical. Doença do refluxo gastroesofágico. Cirurgia bariátrica INTRODUCTION O besity represents a growing threat to population health all over the world. According to data from the National Health and Nutrition Examination Survey, in 2015/2016, the prevalence of obesity was 39.8% in adults and 18.5% in youth in United States1,2. Obesity, one of the main factors, is reported to increase the intra-gastric pressure with impaired gastric emptying, the frequency of transient lower esophageal sphincter (LES) relaxation episode and the gastroesophageal pressure gradient, potentially leading to GERD3,4,5,17,18,19. Laparoscopic sleeve gastrectomy induces alteration of the esophagogastric angle due to surgery itself, hypotony of the LES after division of muscular sling fibers, decrease of the gastric volume and, consequently, increase of intragastric pressure, that’s why some patients have reflux after sleeve. O A The objective of this paper was to describe a technique of sleeve gastrectomy with a Nissen fundoplication (described by Prof. Nocca), in order to decrease reflux after sleeve1,2,6,7,8,10,23,24. Original Article – Technique Original Article – Technique Original Article – Technique ABCD Arq Bras Cir Dig 2019;32(4):e1482 DOI: /10.1590/0102-672020190001e1482 ABCD Arq Bras Cir Dig 2019;32(4):e1482 N-gastrectomia vertical: uma opção para obesidade associada à doença do refluxo gastroesofágico Mariano PALERMO1, Edgardo SERRA1, Guillermo DUZA1 How to cite this article: Palermo M, Serra E, Duza G. N-sleeve gastrectomy: an option for obesity and GERD. ABCD Arq Bras Cir Dig. 2019;32(4):e1482. DOI: /10.1590/0102-672020190001e1482 From the 1Division of Bariatric Surgery, Centro CIEN - DIAGNOMED, Affiliated to the University of Buenos Aires, Buenos Aires, Argentina. ABSTRACT - Background: Obesity represents a growing threat to population health all over the world. Laparoscopic sleeve gastrectomy induces alteration of the esophagogastric angle due to surgery itself, hypotony of the lower esophageal sphincter after division of muscular sling fibers, decrease of the gastric volume and, consequently, increase of intragastric pressure; that’s why some patients have reflux after sleeve. Aim: To describe a technique and preliminary results of sleeve gastrectomy with a Nissen fundoplication, in order to decrease reflux after sleeve. Method: In the current article we describe the technique step by step mostly focused on the creation of the wrap and it care. Results: This procedure was applied in a case of 45 BMI female of 53 years old, with GERD. An endoscopy was done demonstrating a hiatal hernia, and five benign polyps. A Nissen sleeve was performed due to its GERD, hiatal hernia and multiple polyps on the stomach. She tolerated well the procedure and was discharged home uneventfully 48 h after. Conclusion: N-sleeve is a feasible and safe alternative in obese patients with reflux and hiatal hernia when Roux-en-Y gastric bypass it is not indicated. HEADINGS - Sleeve gastrectomy. GERD. Obesity. Bariatric surgery. Surgical technique l i By laparoscopic approach with the surgeon standing between the patient’s legs, five trocars are placed (Figure 1). Pneumoperitoneum is insuflated up to to 15 mmHg. The trocar placement is the same as in standard laparoscopic sleeve gastrectomy (LSG) or Roux-en-Y gastric bypass (RYGBP). 1/4 1/4 ABCD Arq Bras Cir Dig 2019;32(4):e1482 Original Article – Technique The first step of the N-sleeve is the dissection and reduction of a hiatal hernia. An extension of at least 5 to 6 cm of abdominal esophagus is mobilized and all the anterior and posterior esophageal hiatal space is dissected (Figure 2A). The greater curvature of the stomach is then dissected from the short gastric vessels and gastrocolic ligament, starting 5 cm from the pylorus. Two non-absorbable sutures are used to close the hiatal hernia and a 36 Fr calibration boggie is inserted as a regular LSG (Figures 2B and C). After that step a short 360º valve of 3 cm is created using silk. The wrap valve is fixed to the anterior part of the esophagus (Figure 3A and B). Then the rest of the greater curvature is dissected. A laparoscopic 60 mm linear stapler is used to perform the first division of the antrum. Then the rest of the sleeve gastrectomy is performed as usual with special care in the last fire in order not to cut the “4” layers (Figures 4A and B). All the staple lines are reinforced as we do in the regular LSG (Figure 5). Blue test is performed. We routinely place a JP drain. The postoperative care is the same than the regular LSG. FIGURE 5 - Staple line reinforcement with absorbable sutures FIGURE 5 - Staple line reinforcement with absorbable sutures FIGURE 1 - Placement of the trocars FIGURE 2 – A) Hiatal hernia; B) closure of the hiatal hernia with silk; C) final aspect of the hernia closure calibrating it with a 36 Fr tube Contrary to standard LSG, for the N–sleeve some technical details are very important: 1) avoid ischemia of the gastric wall during short gastric vessels dissection; 2) delicate handling of the gastric fundus during fundoplication; 3) avoid double stapling of the gastric fundus10,32,36,37. RESULTS This procedure was applied in a female of 53 years; she was admitted to our multidisciplinary group for obesity treatment. She had a BMI of 45. All the preoperative exams were done (laboratory, endoscopy, gastrointestinal series, functional lung test, HPB ultrasound). In the endoscopy a hiatal hernia was demonstrated, and five benign polyps were resected by endoscopy. The patient had GERD. We performed a N-sleeve due to its GERD, hiatal hernia and multiple polyps on the stomach. She tolerated well the procedure, was discharged home uneventfully 48 h after the procedure and in the medium term follow up she did well, with adequate weight loss and non recurrence of her GERD symptoms. We will still follow up her in order to have more long-term data. FIGURE 1 - Placement of the trocars FIGURE 2 – A) Hiatal hernia; B) closure of the hiatal hernia with silk; C) final aspect of the hernia closure calibrating it with a 36 Fr tube A CT scan was performed for another reason not related with the surgery and we could see the wrap with no complications and an adequate sleeve (Figure 6). FIGURE 2 – A) Hiatal hernia; B) closure of the hiatal hernia with silk; C) final aspect of the hernia closure calibrating it with a 36 Fr tube FIGURE 2 – A) Hiatal hernia; B) closure of the hiatal hernia with silk; C) final aspect of the hernia closure calibrating it with a 36 Fr tube FIGURE 6 – CT demonstrating and adequate Nissen wrap with no complications and a normal sleeve size. FIGURE 3 - A and B) The wrap is being performed FIGURE 4 – A and B) The last stapling and the final aspect of the N-sleeve FIGURE 6 – CT demonstrating and adequate Nissen wrap with no complications and a normal sleeve size. FIGURE 6 – CT demonstrating and adequate Nissen wrap with no complications and a normal sleeve size. REFERENCES Effect of sleeve gastrectomy on gastroesophageal reflux disease: a systematic review. SurgObesRelat Dis. 20117:510-15. 6. Craig M. Hales, Margaret D. Carroll, Cheryl D. Fryar, Cynthia L. Ogden, Prevalence of Obesity Among Adults and Youth: United States, 2015–2016. NCHS Data Brief. 2017 Oct;(288):1-8.) 6. Craig M. Hales, Margaret D. Carroll, Cheryl D. Fryar, Cynthia L. Ogden, Prevalence of Obesity Among Adults and Youth: United States, 2015–2016. NCHS Data Brief. 2017 Oct;(288):1-8.) However, reflux control (by medical treatment or anti-reflux surgery) is associated with regression of Barrett’s mucosa10,12,25,27,28, an important reason to combine an anti-reflux mechanism to a bariatric procedure. 7. David MB, Abu-Gazala S, Sadot E, Wasserberg N, Kashtan H, Keidar A. Laparoscopic conversion of failed vertical banded gastroplasty to Roux-en-Y gastric bypass or biliopancreatic diversion. SurgObesRelat Dis. 2015 Sep-Oct;11(5):1085-91. 8. Disse E, A. Pasquer, P. Espalieu, G. Poncet, C. Gouillat, M. Robert. Greater weight loss with the omega loop bypass compared to the Roux-en-Y gastric bypass: a comparative study ObesSurg, 2014 Jun;24(6):841-6 LSG has evolved into a primary surgical procedure for morbid obesity. It has gained popularity worldwide as a primary bariatric procedure, now established as the most frequent bariatric procedure worldwide12,23,34,37. This growth can be explained by several advantages that LSG carries over more complex bariatric procedures, such as RYGBP or duodenal switch, including the absence of most side effects of bypass procedures like dumping syndrome, marginal ulcers, malabsorption, small bowel obstruction and internal hernia, and a better quality of life over gastric banding17,23,24,32. 9. El-Serag HB, Sweet S, Winchester CC, Dent J. Update on the epidemiology of gastro-oesophageal reflux disease: a systematic review. Gut. jun 2014;63(6):871-80. 10. Fezzi M, Kolotkin RL, Nedelcu M et al. Improvement in quality of life after laparoscopic sleeve gastrectomy. Obes Surg. 2011 Aug;21(8):1161-7. f 11. Gagner M, Hutchinson C, Rosenthal R. Fifth International Consensus Conference: current status of sleeve gastrectomy. SurgObesRelat Dis Off J Am SocBariatr Surg. mai 2016;12(4):750‑6. 12. Gagner M, Ramos A, Palermo M, Noel P, Nocca D. The perfect Sleeve gastrectomy. SPRINGER. In Press. Besides prior described alterations, LSG decreases ghrelin, hence dismotility10,24,25,27. All these factors contribute to expose the patient to the risk of increasing GERD and proton pump inhibitors dependency or developing new GERD onset. On the other hand, weight loss after surgery together with accelerated gastric emptying, decreases acid production and restores esophagogastric angle over time supposing to improve reflux symptoms. Mariano Palermo: 0000-0001-7366-3321 Edgardo Serra: 0000-0001-8346-3702 Mariano Palermo: 0000-0001-7366-3321 Edgardo Serra: 0000-0001-8346-3702 REFERENCES However, the presence of preoperative GERD should be considered a relative contraindication to LSG12,24,31. 13. Genco A, Soricelli E, Casella G, Maselli R, Castagneto-Gissey L, Di Lorenzo N, Basso N. Gastroesophageal reflux disease and Barrett’s esophagus after laparoscopic sleeve gastrectomy: a possible, underestimated long-term complication. SurgObesRelat Dis. 2017 Apr;13(4):568-574. 14. Hales CM, Fryar CD, Carroll MD, Freedman DS, Ogden CL. Trends in Obesity and Severe Obesity Prevalence in US Youth and Adults by Sex and Age, 2007-2008 to 2015-2016. JAMA. 2018 Apr 24;319(16):1723-1725. 15. Higa K, Ho T, Tercero F, Yunus T, Boone KB. Laparoscopic Roux-en-Y gastricbypass: 10-year follow-up. SurgObesRelat Dis. 2011 Jul-Aug;7(4):516-25. 16. Himpens J, Dapri G, Cadière GB. A prospective randomized study between laparoscopic gastric banding and laparoscopic isolated sleeve gastrectomy: results after 1 and 3 years. Obes Surg. nov 2006;16(11):1450-6. Here we introduced the concept of N-sleeve as an option to prevent GERD. Although the laparoscopic RYGB was considered the gold standard procedure for obese patients with reflux disease, more than one third of patients who underwent this operation had at least one complication within the 10-year follow-up period33. Himpens et al. reported new gastro- esophageal reflux complaints in 21% of patients. Considering all these findings and encouraged by the good results of LSG and concomitant hiatal hernia repair10,12,21,34, David Nocca and his team have developed a modification to the usual surgical technique by adding a Nissen fundoplication in order to minimize both leaks and GERD32,37. 17. Kirkil C, Aygen E, Korkmaz MF, Bozan MB. Quality of life after laparoscopic sleeve gastrectomy usi̇ng baros system. Arq Bras Cir Dig. 2018 Aug 16;31(3):e1385. doi: 10.1590/0102-672020180001e1385 18. Lasnibat JP, Braghetto I, Gutierrez L, Sanchez F. Sleeve gastrectomy and fundoplication as a single procedure in patients with obesity and gastroesophageal reflux. Arq Bras Cir Dig. 2017 Jul-Sep;30(3):216-221. doi: 10.1590/0102-6720201700030012. 19. Lazzati A, Guy-Lachuer R, Delaunay V, Szwarcensztein K, Azoulay D Bariatric surgery trends in France: 2005-2011.Surg ObesRelat Dis. 2014 Mar-Apr;10(2):328-34 20. Lundell L, Dent J, Bennett J, Blum A, Armstrong D, Galmiche J, et al. Endoscopic assessment of oesophagitis: clinical and functional correlates and further validation of the Los Angeles classification. Gut. août 1999;45(2):172‑80. The aim of this article was to describe our N-sleeve technique performed in Buenos Aires as an option for patients who have hiatal hernia with reflux and are not candidates to perform a RYGBP. 21. RESULTS FIGURE 3 - A and B) The wrap is being performed FIGURE 3 - A and B) The wrap is being performed FIGURE 3 - A and B) The wrap is being performed FIGURE 4 – A and B) The last stapling and the final aspect of the N-sleeve FIGURE 4 – A and B) The last stapling and the final aspect of the N-sleeve FIGURE 6 – CT demonstrating and adequate Nissen wrap with no complications and a normal sleeve size. FIGURE 6 – CT demonstrating and adequate Nissen wrap with no complications and a normal sleeve size. FIGURE 4 – A and B) The last stapling and the final aspect of the N-sleeve ABCD Arq Bras Cir Dig 2019;32(4):e1482 ABCD Arq Bras Cir Dig 2019;32(4):e1482 2/4 N-SLEEVE GASTRECTOMY: AN OPTION FOR OBESITY AND GERD CONCLUSION N-sleeve is a feasible and safe alternative in obese patients with reflux and hiatal hernia when RYGBP it is not indicated. Nocca et al.23 by 2016 published the first 25 patients all with esophageal syndromes. Ninety-two had typical symptoms of GERD and two asymptomatic but with esophageal injury. Three months after N-sleeve, 76% of the patients remained asymptomatic without proton pump inhibitor use. At six months and one year, three (12%) patients were still experiencing reflux. Excess weight loss at one year was 58±23%, total weight loss was 27±10%, and body mass index change was -11±4 kg/m². They concluded that N-sleeve seems to be a safe procedure that provides an adequate reflux control with no clear interference on the expected bariatric results of a standard LSG10,12,24.i REFERENCES Regarding GERD, the Montreal conference defines it as a disorder related to reflux of stomach contents leading to discomfort or complications affecting the patient´s quality of life. Typical symptoms are: heartburn (upstream esophageal burning) and regurgitation, and atypical are: epigastric burns, chest pain, respiratory symptoms (chronic cough and asthma), dental erosions2,4,20,22,23,26. 1. Angrisani L, Santonicola A, Iovino P, Vitiello A, Higa K, Himpens J, Buchwald H, Scopinaro N. IFSO Worldwide Survey 2016: Primary, Endoluminal, and Revisional Procedures. Obes Surg. 2018 Dec;28(12):3783-3794 1. Angrisani L, Santonicola A, Iovino P, Vitiello A, Higa K, Himpens J, Buchwald H, Scopinaro N. IFSO Worldwide Survey 2016: Primary, Endoluminal, and Revisional Procedures. Obes Surg. 2018 Dec;28(12):3783-3794 1. Angrisani L, Santonicola A, Iovino P, Vitiello A, Higa K, Himpens J, Buchwald H, Scopinaro N. IFSO Worldwide Survey 2016: Primary, Endoluminal, and Revisional Procedures. Obes Surg. 2018 Dec;28(12):3783-3794 g 2. Braghetto I, Lanzarini E, Korn O, Valladares H, Molina JC, Henriquez A. Manometricchanges of the lower esophageal sphincter after sleeve gastrectomy in obese patients.Obes Surg. mars 2010;20(3):357-62. g y p g 3. Brown CS, Lapin B, Goldstein JL, Linn JG, Talamonti MS, Carbray J, et al. Predicting Progression in Barrett’s Esophagus: Development and Validation of the Barrett’s Esophagus Assessment of Risk Score (BEAR Score). Ann Surg. 22 févr 2017 g y p g 3. Brown CS, Lapin B, Goldstein JL, Linn JG, Talamonti MS, Carbray J, et al. Predicting Progression in Barrett’s Esophagus: Development and Validation of the Barrett’s Esophagus Assessment of Risk Score (BEAR Score). Ann Surg. 22 févr 2017 GERD is complex, especially in the era of bariatric surgery35. A chronic inflammation can induce more serious lesions, since up to 10-15% of patients develop dysplasia, as Barrett’s esophagus, that can lead to esophageal cancer9,10,11,13. 4. Brown CS, Lapin B, Wang C, Goldstein JL, Linn JG, Denham W, et al. Reflux control is important in the management of Barrett’s Esophagus: results from a retrospective 1,830 patient cohort. SurgEndosc. déc 2015;29(12):3528‑34. f p g Variables associated with an increased risk of progression of Barrett’s esophagus in dysplasia or adenocarcinoma are: age >70 years, male, absence of treatment with proton pump inhibitor, Barrett’s esophagus longer than 3 cm and esophageal candidiasis14,15,16,17.ll 5. Chiu S, Birch DW, Shi X, et al. Effect of sleeve gastrectomy on gastroesophageal reflux disease: a systematic review. SurgObesRelat Dis. 20117:510-15. 5. Chiu S, Birch DW, Shi X, et al. REFERENCES Melissas J, Daskalakis M, Koukouraki S, Askoxylakis I, Metaxari M, Dimitriadis E, et al. Sleeve gastrectomy-a « food limiting » operation. Obes Surg. oct 2008;18(10):1251-6. 22. Mognol P, Chosidow D, Marmuse JP Roux-en-Y gastric bypass after failed vertical banded gastroplasty. Obes Surg. 2007 Nov;17(11):1431-4. 22. Mognol P, Chosidow D, Marmuse JP Roux-en-Y gastric bypass after failed vertical banded gastroplasty. Obes Surg. 2007 Nov;17(11):1431-4. 3/4 ABCD Arq Bras Cir Dig 2019;32(4):e1482 Original Article – Technique 23. Nocca D, Skalli EM, Boulay E, Nedelcu M, Michel Fabre J, Loureiro M. Nissen Sleeve (N-Sleeve) operation: preliminary results of a pilot study. Surg Obes Relat Dis. 2016 Dec;12(10):1832-1837. doi: 10.1016/j. soard.2016.02.010. Epub 2016 Feb 22. 31. Sebastianelli L, Benois M, Vanbiervliet G, Bailly L, Robert M, Turrin N, Gizard E, Foletto M, Bisello M, Albanese A, Santonicola A, Iovino P, Piche T, Angrisani L, Turchi L, Schiavo L, Iannelli A. Systematic Endoscopy 5 Years After Sleeve Gastrectomy Results in a High Rate of Barrett’s Esophagus: Results of a Multicenter Study. Obes Surg. 2019 Jan 21. doi: 10.1007/ s11695-019-03704. p 24. Oh DS, Demeester SR. Pathophysiology and treatment of Barrett’s esophagus. World J Gastroenterol. 14 août 2010;16(30):3762‑72. p g 25. Ponce J, DeMaria EJ, Nguyen NT, Hutter M, Sudan R, Morton JM. American Society for Metabolic and Bariatric Surgery estimation of bariatric surgery procedures in 2015 and surgeon workforce in the United States. SurgObesRelat Dis. 2016 Aug. 26 32. Sohn S, Fischer J, Booth M.Adenocarcinoma of the gastro-oesophageal junction aftersleeve gastrectomy: a case report.ANZ J Surg. 2017 Oct;87(10):E163-E164. 33. Soricelli E, Iossa A, Casella G, Abbatini F, Calì B, Basso N. Sleeve gastrectomy and crural repair in obese patients with gastroesophageal reflux disease and/or hiatal hernia. SurgObesRelat Dis Off J Am SocBariatr Surg. juin 2013;9(3):356‑61. g g 26. Porcelli ICS, Corsi NM, Fracasso MLC, Pascotto RC, Cardelli AAM, Poli- Frederico RC, Nasser D, Maciel SM. Oral health promotion in patients with morbid obesity after gastroplasty: a randomized clinical trial. Arq Bras Cir Dig. 2019 Aug 26;32(2):e1437. doi: 10.1590/0102-672020190001e1437. 34. Tolonen P, Victorzon M, Niemi R, Mäkelä J. Does gastric banding for morbid obesity reduce or increase gastroesophageal reflux? Obes Surg. 2006 Nov;16(11):1469-74. g g 27. Rosenthal RJ, International Sleeve Gastrectomy Expert Panel, Diaz AA, Arvidsson D, Baker RS, Basso N, et al. International Sleeve Gastrectomy Expert Panel Consensus Statement: best practice guidelines based on experience of >12,000 cases. SurgObesRelat Dis Off J Am SocBariatr Surg. REFERENCES févr 2012;8(1):819. 35. Wada AM, Hashiba K, Otoch JP, Brasil H, Marson FP, Cassab J, Abdalla R, Artifon ELA. Full-thickness endoscopic gastric resection using a stapler and gastrostomy: a feasibility study. Arq Bras Cir Dig. 2018 Aug 16;31(3):e1386. doi: 10.1590/0102-672020180001e1386 g 28. Saarinen T, Räsänen J, Salo J, Loimaala A, Pitkonen M, Leivonen M, Juuti A. Bile Reflux Scintigraphy After Mini-Gastric Bypass. ObesSurg. 2017 Aug;27(8):2083-2089 36. Weiss AC, Parina R, Horgan S, Talamini M, Chang DC, Sandler B. Quality and safety in obesity surgery-15 years of Roux-en-Y gastric bypass outcomes from a longitudinal database. SurgObesRelat Dis. 2016 Jan;12(1):33-40 g 29. Samakar K, McKenzie TJ, Tavakkoli A, Vernon AH, Robinson MK, Shikora SA. The Effect of Laparoscopic Sleeve Gastrectomy with Concomitant Hiatal Hernia Repair on Gastroesophageal Reflux Disease in the Morbidly Obese. Obes Surg. janv 2016;26(1):61‑6. g g 37. Woodman G, Cywes R, Billy H, Montgomery K, Cornell C, Okerson T; Effect of adjustable gastric banding on changes in gastroesophageal reflux disease (GERD) and quality of life. APEX Study Group. Curr Med Res Opin. 2012 Apr;28(4):581-9. g j 30. Sanchez-Pernaute, M.A. Rubio, M. Conde, E. Arrue, E. Perez-Aguirre, A. Torres Single-anastomosis duodenoileal bypass as a second step after sleeve gastrectomy. SurgObesRelat Dis 2015 Mar-Apr;11(2):351-5 4/4 ABCD Arq Bras Cir Dig 2019;32(4):e1482 4/4
https://openalex.org/W3080143764
https://iris.unimore.it/bitstream/11380/1208250/1/Recent%20advances%20on%20chitosan-based%20films.pdf
English
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Recent advances on chitosan-based films for sustainable food packaging applications
Food packaging and shelf life
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ERROR: type should be string, got "https://doi.org/10.1016/j.fpsl.2020.100551 \nReceived 23 March 2020; Received in revised form 26 July 2020; Accepted 31 July 2020 \n2214-2894/ ©\n 2020 Published by Elsevier Ltd. Hossein Haghighia, Fabio Licciardelloa,b,*, Patrizia Favaa,b, Heinz Wilhelm Sieslerc, \nAndrea Pulvirentia,b Hossein Haghighia, Fabio Licciardelloa,b,*, Patrizia Favaa,b, Heinz Wilhelm Sieslerc, \nAndrea Pulvirentia,b a Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy \nb Interdepartmental Research Centre BIOGEST-SITEIA, University of Modena and Reggio Emilia, Reggio Emilia, Italy \nc Department of Physical Chemistry, University of Duisburg-Essen, Essen, Germany ⁎ Corresponding author. \nE-mail address: fabio.licciardello@unimore.it (F. Licciardello). A B S T R A C T Keywords: \nBiopolymer \nBlend \nFilm \nFood packaging \nMechanical properties \nPermeability The recent sharp increase of sensitivity towards environmental issues arising from plastic packaging has boosted \ninterest towards alternative sustainable packaging materials. This new trend promotes the industrial exploitation \nof knowledge on chitosan-based films. Chitosan has been extensively investigated and used due to its unique \nbiological and functional properties. However, inherent drawbacks including low mechanical properties and \nhigh sensitivity to humidity represent major limitations to its industrial applications, including food packaging. In the present study, the scientific literature of the last five years has been extensively reviewed (source: Web of \nScience) addressing chitosan-based films for their potential application in the food packaging industry. The \ncontribution summarizes the various strategies adopted to overcome inherent drawbacks and improve the \nproperties of chitosan-based films, with special regards for blending with natural and synthetic biopolymers. biodegradable materials are produced from renewable resources \n(Rujnić-Sokele & Pilipović, 2017). A schematic classification of biode­\ngradable polymers according to their source is presented in Fig. 1. Food Packaging and Shelf Life 26 (2020) 100551 Food Packaging and Shelf Life 26 (2020) 100551 1. Introduction Fig. 1. Schematic classification of biodegradable polymers. Fig. 1. Schematic classification of biodegradable polymers. Bioplastics, whether biobased, biodegradable, or both, have unique \nadvantages over conventional plastics to reduce reliance on fossil re­\nsources and to mitigate carbon footprint and greenhouse gas emissions. Besides, they promote resource efficiency and offer extra waste man­\nagement options such as organic recovery (Arikan & Ozsoy, 2015; \nKumar & Thakur, 2017). interrogation of the Web of Science database was performed searching \n“chitosan, film, blend, food packaging” within title, abstract and key­\nwords in the timeframe 2015–2020. Nevertheless, among the very large \nnumber of papers available dealing with a wide range of characteristics \nand functionalities, only the most significant studies and achievements \nwill be analyzed and discussed. ,\n)\nRecently, biodegradable polymers derived from renewable re­\nsources have been proposed as the future generation of packaging \nmaterials (Lei et al., 2014). The basic material employed to form bio­\nbased films are polysaccharides, proteins, lipids, and their derivatives \n(De Leo et al., 2018; Ramos, Valdés, Beltrán, & Garrigós, 2016). Pro­\nteins and polysaccharides have acceptable mechanical and gas barrier \nproperties, but they show high moisture sensitivity (Rhim & Ng, 2007). On the contrary, lipid films exhibit acceptable water vapor barrier \nproperty and high oxygen permeability, but they have poor mechanical \nproperties (Vodnar, Pop, Dulf, & Socaciu, 2015). Among poly­\nsaccharides, chitosan has received considerable attention from aca­\ndemics and industry for food packaging applications due to its parti­\ncular \nphysicochemical \nfeatures, \nbiodegradability, \nnon-toxicity, \nbiocompatibility, good film-forming properties, chemical stability, high \nreactivity (Dutta, Tripathi, & Dutta, 2012; Lago et al., 2014; Mujtaba \net al., 2019). General values for the parameters of interest for food \npackaging applications are reported in Table 1. The reader should \nconsider these values as merely representative since they could dar­\namatically change upon addition of additives such as plasticizers or \ncrosslinker. Chitoasan has also intrinsic antioxidant and antimicrobial \nactivities against fungi, molds, yeasts, and bacteria (Aider, 2010; \nLeceta, Guerrero, & de la Caba, 2013). However, inherent drawbacks of \nchitosan including low mechanical and thermal stability and high \nsensitivity to humidity are causing a major restriction for its industrial \napplications (Elsabee & Abdou, 2013). One strategy to overcome these \ndrawbacks is blending chitosan with other biopolymers to combine \ntheir advantages as well as minimize their disadvantages. 1. Introduction Annually, more than 350 million tons of plastics are produced in the \nworld (Ritchie & Roser, 2018). It is expected that plastics will account \nfor 20 % of total oil consumption by 2050 (Newell, Qian, & Raimi, \n2016; Cui, Borgemenke, Qin, Liu, & Li, 2019). Packaging, particularly \nfood packaging, is one of the largest application fields for plastics (Cui, \nSurendhiran, Li, & Lin, 2020). Food packaging is represented as a co­\nordinated system for processing, transporting, distributing, retailing, \nprotecting and preserving food to satisfy the industry demands and \nconsumer desires, to retain food safety and to protect food from ex­\nternal contamination with optimal cost (Marsh & Bugusu, 2007; Shin & \nSelke, 2014; Yam & Lee, 2012). However, accumulation of huge \namounts of plastic waste in the environment, and also rapid depletion \nof fossil reserves and increases in the cost of petroleum, are pushing the \nfood packaging industry toward the development and application of \neco-friendly materials, such as bioplastics (Arikan & Ozsoy, 2015; Philp, \nBartsev, Ritchie, Baucher, & Guy, 2013). The term “biobased” refers to the derivation of material from bio­\nmass (Soroudi & Jakubowicz, 2013). The term “biodegradable” in­\ndicates materials that can disintegrate or break down naturally into \nCO2, CH4, H2O, and inorganic compounds, or biomass in which the \nprevalent process is the enzymatic function of microorganisms \n(Peelman et al., 2013), that can be measured by standardized tests \n(ASTM Standard D-5488-94d). Some of these polymers can also be \ncompostable, which means disintegration occurs in a compost site at a \nrate consistent with known compostable materials and without re­\nleasing toxic substances (Siracusa, Rocculi, Romani, & Dalla Rosa, \n2008). As stated by the European Bioplastic Organization, bioplastics \nconstitute approximately 1 % of the total global plastics production \nannually (Rujnić-Sokele & Pilipović, 2017). Packaging, as one of the \nlargest application fields for bioplastics, shares almost 65 % of the total \nbioplastics market. This number is predicted to rise continuously in the \nupcoming years mainly due to the increasing consumer requirements \nfor sustainable products and growing awareness over environmental \nissues (van den Oever, Molenveld, van der Zee, & Bos, 2017). Bioplastics can be referred to as plastics obtained from renewable \nresources (biobased), plastics that are biodegradable and/or compo­\nstable, or materials that feature both properties (Kumar & Thakur, \n2017). Hence, not all biobased materials are biodegradable and not all Food Packaging and Shelf Life 26 (2020) 100551 H. Haghighi, et al. 1. Introduction Therefore, \nthe objective of the present paper is to provide a comprehensive lit­\nerature review of the last five years addressing chitosan-based films and \nstrategies adopted for the improvement of their performances for po­\ntential food packaging applications. To get an idea of the complexity of \nthe theme and of the work that has been done in the last years, an 2. History, features, and potential of chitosan Molecular weight \nMoisture content (%) \nTransparency value (A600/T) \nL* \na* \nb* \nΔE* \nWVP \n(× 10-13 g cm-1 s-1 Pa-1) \nOP \n(cm3 μm m-2 day-1 KPa-1) \nTS \n(MPa) \nE \n(%) \nHigh molecular weight chitosan \n15.70 \n0.754 \n96.39 \n−0.23 \n3.15 \n1.68 \n8.07 \n6.65 \n61.82 \n4.59 \nLow molecular weight chitosan \n19.43 \n0.760 \n96.54 \n−0.57 \n4.74 \n5.29 \n9.21 \n7.70 \n55.83 \n4.58 \n. Haghighi, et al. hydrolyzed chitin in several ways and extracted chitosan from marine \narthropods (e.g., crab, shrimp, and lobster). In the 1940s, both chitin \nand chitosan attracted considerable attention as evidenced by about 50 \npatents. In 1950, the structure of chitosan was discovered using X-ray \n(Darmon & Rudall, 1950). The first book about chitosan was published \nby Albert Glenn Richards in 1951 (Richards, 1951). Nowadays, chitin and chitosan are simply described as copolymers \nof N-acetyl-D-glucosamine and D-glucosamine units linked with β-(1–4)- \nglycosidic bonds (Hosseinnejad & Jafari, 2016). They attract consider­\nable attention and are employed worldwide for a broad range of ap­\nplications. In the food industry, they are applied as antimicrobial agents \n(bactericidal and fungicidal), edible films and coating (e.g., post-har­\nvest deterioration control in fruits), additives (e.g., natural flavor ex­\ntender, emulsifying agents, thickeners, stabilizing agents, and color \nstabilizers), integrators (e.g., dietary fiber), enzyme immobilization, \nencapsulation of nutraceuticals, and purification of water (e.g. removal \nof dyes) (Ahmed & Ikram, 2017; Dutta, Tripathi, Mehrotra, & Dutta, \n2009; López-Caballero, Gómez-Guillén, Pérez-Mateos, & Montero, \n2005; Zargar et al., 2015; Zhang, Li, & Liu, 2011). g\ng\nChitosan exhibits antioxidant (Ngo & Kim, 2014; Ojagh, Rezaei, \nRazavi, & Hosseini, 2010) and antimicrobial activity against a broad \nrange of pathogenic and spoilage microorganisms, including fungi \n(yeasts and molds), Gram-positive and Gram-negative bacteria \n(Friedman & Juneja, 2010; Kong, Chen, Xing, & Park, 2010; van den \nBroek, Knoop, Kappen, & Boeriu, 2015). The antimicrobial activity of \nchitosan has drawn attention as a potential natural food preservative \n(Del Nobile et al., 2009; No, Meyers, Prinyawiwatkul, & Xu, 2007). Several hypotheses have been suggested to elucidate the mechanism of \nantimicrobial activity of chitosan: the most reasonable hypothesis is \nelectro statistic interaction between protonated amino groups (NH3\n+) \nof glucosamine in the chitosan backbone and microbial negative cell \nmembrane constituents such as phosphoryl groups of the phospholipid \ncomponents, proteins, amino acids, and various lipopolysaccharides \n(Elsabee & Abdou, 2013; Mousavi Khaneghah, Hashemi, & Limbo, \n2018). 2. History, features, and potential of chitosan This interaction affects the membrane integrity and perme­\nability, interfering with energy metabolism, nutrient transport, pro­\nvoking the permeation of proteinaceous and other intracellular com­\nponents, and causing disruptions that lead to cell death of \nmicroorganisms (Goy, de Britto, & Assis, 2009). Another possible me­\nchanism is the interaction of chitosan with cellular DNA of micro­\norganisms, thus preventing DNA transcription, RNA translation, and \nprotein synthesis (Raafat & Sahl, 2009; Sharif et al., 2018; Verlee et al., \n2017). Moreover, chitosan acts as a chelating agent that selectively \nbinds essential trace metals, spores, prevents the production of toxins \nand microbial growth (Hosseinnejad & Jafari, 2016; Vodnar et al., \n2015). Several researchers also suggested that microbial growth in­\nhibition occurs by blocking the supply of essential nutrients into the cell \n(No et al., 2007; Raafat & Sahl, 2009). Chitosan exhibits antioxidant (Ngo & Kim, 2014; Ojagh, Rezaei, \nRazavi, & Hosseini, 2010) and antimicrobial activity against a broad \nrange of pathogenic and spoilage microorganisms, including fungi \n(yeasts and molds), Gram-positive and Gram-negative bacteria \n(Friedman & Juneja, 2010; Kong, Chen, Xing, & Park, 2010; van den \nBroek, Knoop, Kappen, & Boeriu, 2015). The antimicrobial activity of \nchitosan has drawn attention as a potential natural food preservative \n(Del Nobile et al., 2009; No, Meyers, Prinyawiwatkul, & Xu, 2007). l h\nh\nh\nb\nd\nl\nd\nh\nh\nf 2. History, features, and potential of chitosan Chitosan is a unique natural biopolymer, commercially originated \nfrom the deacetylation (to varying degrees) of chitin (Verlee, Mincke, & \nStevens, 2017). It is the second most abundant natural polysaccharide \nbehind \ncellulose \n(Salari, \nSowti \nKhiabani, \nRezaei \nMokarram, \nGhanbarzadeh, & Samadi Kafil, 2018) and the most abundant biopo­\nlymer of animal origin (Priyadarshi & Rhim, 2020). Chitin can be ob­\ntained from terrestrial arthropods (e.g., spiders, scorpions, beetles, \ncockroaches, and brachiopods), marine crustaceans (e.g., crab, lobster, \nprawn, and krill), Mollusca (e.g., squid) and microorganisms (e.g., fungi \ncell walls) (Zargar, Asghari, & Dashti, 2015). The waste of marine food \nproduction (particularly exoskeleton of crabs, lobsters, and shrimps) is \ncurrently the main industrial source of biomass for chitin production \n(Gutiérrez, 2017). i The first report on chitin traces back to 1811 by French Professor of \nnatural history Henri Braconnot. He found out the alkaline-insoluble \nfraction from mushrooms and named it “fungine”. In 1823, Antoine \nOdier extracted this alkaline-insoluble fraction from the cuticle of in­\nsects and named it “chitine”, originated from the Greek word “khiton” \nmeaning “tunic” or “envelope”. Twenty years later, Jean Louis \nLassaigne proved the presence of nitrogen in chitin. In 1859, Prof. C. Rouget discovered the deacylated form of chitin. He treated chitin with \nconcentrated potassium hydroxide solution and heat to become soluble \nin dilute organic acids and named it “modified chitin” (Rouget, 1859). In 1878, Ledderhose identified that chitin was made of glucosamine and \nacetic acid. In 1894, Hoppe-Seyler treated the shells of crabs, scorpions, \nand spiders with potassium hydroxide solution at 180 °C and dissolved \nthe product in dilute acid solution and named it “chitosan”. In 1894, \nGilson proved the presence of glucosamine in chitin. In 1930, Ram­\nmelberg found more chitin sources apart from insects and fungi. He 2 Food Packaging and Shelf Life 26 (2020) 100551 H. Haghighi, et al. Table 1 \nMoisture content, transparency value, color parameters including L* (lightness), a* (redness/greenness) and b*(yellowness/blueness), ΔE* (total color difference), water vapor permeability (WVP), oxygen permeability \n(OP), tensile strength (TS) and elongation at break (E) of low and high molecular weight chitosan films. Adapted from Leceta, Guerrero, & de la Caba (2013). 3. Strategies for the improvement of properties of chitosan-based \nfilms Inherent drawbacks of chitosan such as high sensitivity to water, \nlow mechanical and thermal stability lead to a shorter food shelf life \ncompared to the conventional food packaging material and conse­\nquently limited its applications in food packaging (Al-Tayyar, Youssef, \n& Al-hindi, 2020; Elsabee & Abdou, 2013). Therefore, different strate­\ngies have been proposed to tackle these issues and to improve the \nproperties of chitosan-based materials, such as cross-linking (Jahan, \nMathad, & Farheen, 2016; Khouri, Penlidis, & Moresoli, 2019; Liang, \nWang, & Chen, 2019; Yeamsuksawat & Liang, 2019), enzyme treatment \n(Águila-Almanza, Salgado-Delgado, Vargas-Galarza, García-Hernández, \n& Hernández-Cocoletzi, 2019), graft copolymerization (Argüelles- \nMonal, Lizardi-Mendoza, Fernández-Quiroz, Recillas-Mota, & Montiel- \nHerrera, 2018; Wang, Yu et al., 2016; Wang et al., 2019), complexation \n(Wang, Wang, & Heuzey, 2016), surface coating (Khwaldia, Basta, 3 Food Packaging and Shelf Life 26 (2020) 100551 H. Haghighi, et al. plications. Improvement of the parameters investigated in each contribution is reported as \nantimicrobial activity\nHaghig (continued on next page) Table 2 \nSynopsis of research published between 2015 – 2020 addressing chitosan-polysaccharide blend films for food packaging applications. Improvement of the parameters investigated in each contribution is reported as\nfollows. M: mechanical properties, WB: water barrier properties, GB: gas barrier permeability, AO: antioxidant activity, AM: antimicrobial activity. Biopolymer \nAdditives \nKey findings \nM \nWB \nGB \nAO \nAM \nReference \n• Pectin (2 % w/v) \n• Nano chitosan (2 % w/v) \n• Films with different ratios of pectin/nano chitosan (100:0, 75:25, \n50:50, 25:75, and 0:100 w/w) were developed. • Blending pectin with nano chitosan at proportions of 50:50 \nincreased the tensile strength while water solubility, water vapor \npermeability, and oxygen permeability decreased. • Developed films showed antimicrobial activity against C. gloeosporioides, S. cerevisiae, A. niger, and E. coli. ✓ \n✓ \n✓ \n✓ \nNgo, Nguyen, Dang, Tran, and \nRachtanapun (2020) \n• Cassava starch (2 % w/w) \n• Chitosan (1 % w/w) \n• Pitanga leaf extract (2.25 % w/w of film forming \nsolution) \n• Natamycin (1 % w/w of film forming solution) \n• Pitanga leaf extract /Natamycin mixture \n• Addition of natamycin into the biopolymers blend caused an \nincrease in tensile strength while water vapor permeability \ndecreased. • Films containing additive showed excellent barrier to UV light. • Addition of pitanga leaf extract caused an increase in antioxidant \nactivity while a combination of pitanga leaf extract and natamycin \nled to the reduction of antioxidant activity. 3. Strategies for the improvement of properties of chitosan-based \nfilms • Addition of natamycin showed positive anti-fungal activity against \nAspergillus flavus and Aspergillus parasiticus. ✓ \n✓ \n✓ \n✓ \nSirisha Nallan Chakravartula et al. (2020) \n• Purple yam starch (2 % w/v) \n• Chitosan (0.5 and 1 % w/v) \n• Increasing concentration of chitosan in the biopolymers blend \ncaused an increase in water vapor permeability while moisture \ncontent was reduced. • Application of a purple yam starch/chitosan blend film on apple \nfruits for 4 weeks preserved the fruit quality compared to \nuntreated apple samples. Martins da Costa, Lima Miki, da \nSilva Ramos, and Teixeira-Costa \n(2020) \n• Bacterial cellulose (0.5 % w/v) \n• Chitosan (2 % w/v) \n• Borate (4 %) \n• Tripolyphosphate (4 %) \n• Borate/Tripolyphosphate mixture \n• Films with different proportion of bacterial cellulose/chitosan 0, \n1/64, 1/32, 1/16, 1/8, and 1/4 were developed. • Addition of borate and tripolyphosphate into the biopolymers \nblend (1/32) showed an improvement in tensile strength and \nelasticity values mainly. • Antimicrobial activity of composite film against E. coli, B. cinerea, \nand S. cerevisiae reduced by addition of cross-linking agent. ✓ \n✓ \nLiang et al. (2019) \n• Potato starch (4 % w/v) \n• Chitosan (1.5 % w/v) \n• Citric acid (5, 10, 15, and 20 % w/w based on a dry \nbiopolymer basis) \n• Addition of citric acid into the biopolymers blend improved tensile \nstrength and elasticity. • Active films containing citric acid showed a homogenous and \ncompact structure. • Moisture content and water solubility reduced while water vapor \npermeability, mechanical and antimicrobial properties improved \nby addition of citric acid to the biopolymers blend. • Both control and films containing citric acid showed antibacterial \nactivity against E. coli and S. aureus. ✓ \n✓ \n✓ \nWu et al. (2019) \n• Hemicellulose (2 % w/v) \n• Chitosan (2 % w/v) \n• Cellulose nanofiber (5, 10, 15, and 20 % w/w based on \nbiopolymers \n• Glycerol, xylitol, sorbitol (10, 20, 30, and 40 % v/w on a \ndry biopolymer basis) \n• Adding 5 % cellulose nanofiber to the biopolymers blend \nincreased tensile strength. Films containing glycerol showed \nbetter mechanical properties than films containing xylitol and \nsorbitol. • Films containing glycerol, xylitol and sorbitol showed higher \nwater solubility, barrier properties to water vapor and oxygen, \nlower contact angle and opacity. 3. Strategies for the improvement of properties of chitosan-based \nfilms ✓ \nXu, Xia, Zheng, Yuan, and Sun \n(2019) \n• Xylan (20, 30, and 40 % w/w \nbased on chitosan) \n• Chitosan (1 % w/v) \n• Carvacrol (10 % w/w based on dry chitosan weight) \n• Addition of xylan into the biopolymers blend caused an increase in \nelasticity and samples with 20 and 25 wt.% xylan showed higher \ntensile strength and elastic modulus. • Thermal analysis showed that addition of xylan to chitosan moved \nthe degradation peak to a lower temperature with a lower rate of \ndegradation. • Addition of carvacrol into the biopolymer blend did not show \nantibacterial activity against E. coli and L. innocua. ✓ \nKamdem, Shen, Nabinejad, and \nShu (2019) \n(continued on next page\n4 Food Packaging and Shelf Life 26 (2020) 100551 H. Haghighi, et al. H. Haghighi, et al. (continued on next page) Biopolymer \nAdditives \nKey findings \nM \nWB \nGB \nAO \nAM \nReference \n• Carboxy methyl chitosan (1 % w/ \nv) \n• Chitosan (2 % w/v) \n• Nisin (1000 and 6000 IU/mL of film forming solution) \n• Blending carboxymethyl chitosan with chitosan increased \nelasticity while it reduced thermal stability. • Incorporation of nisin into the biopolymers blend showed \nantibacterial activity against L. monocytogenes. ✓ \n✓ \nZimet et al. (2019) \n• Starch (1.5 % w/v) \n• Chitosan (1.5 % w/v) \n• Clove essential oil (3, 6, 9, and 12 % w/w) \n• Nano titanium dioxide (1, 3, 5, and 7 % w/w) \n• Addition of nano titanium dioxide into the biopolymers blend \ncaused an increase in tensile strength and antioxidant activity \nwhile water vapor permeability and elasticity decreased. • Addition of clove essential oil into the biopolymers blend reduced \ntensile strength, water content, and water vapor permeability \nwhile antioxidant and antibacterial activity against E. coli and S. aureus improved. ✓ \n✓ \n✓ \n✓ \nLi et al. (2019) \n• Carboxymethyl cellulose (2 % w/ \nv) \n• Chitosan (1 % w/v) \n• Cinnamon essential oil (1.5 % v/v) \n• Oleic acid (1 % w/v) \n• Glutaraldehyde (0.01 % w/v) \n• Addition of glutaraldehyde into the biopolymers blend caused an \nimprovement in mechanical property, water solubility, and water \nvapor permeability. • Addition of cinnamon essential oil into the biopolymers blend \nshowed antioxidant and antimicrobial activities against L. monocytogenes and P. aeruginosa. • Addition of cinnamon essential oil and glutaraldehyde at the same \ntime into the biopolymers blend increased the antioxidant and \nantibacterial activities. 3. Strategies for the improvement of properties of chitosan-based \nfilms • Addition of oleic acid into the biopolymers blend reduced water \nsolubility, tensile strength, antioxidant and antimicrobial \nactivities while elasticity, and water vapor permeability increased. ✓ \n✓ \n✓ \n✓ \nValizadeh et al. (2019) \n• Gum arabic (1.5 % w/v) \n• Chitosan (1.5 %w/v) \n• Cinnamon essential oil (8 % w/w of total solid) \n• Increasing gum arabic proportion into the biopolymers blend (1:0, \n1:0.25, 1:0.5, 1:1, 1:2, 1:4) reduced thickness, water content, \ntensile strength, elasticity, and water vapor permeability. • Addition of cinnamon essential oil into the biopolymers blend \nshowed antioxidant activity. Antioxidant activity enhanced when \nthe ratio of chitosan/gum arabic changed from 1:0 to 1:2. Antioxidant activity quickly reduced by further increasing of gum \narabic proportions in biopolymers blend to 1:4. ✓ \n✓ \nXu, Gao, Feng, Yang, Shen and\nTang et al. (2019) \n• Gum arabic (1.5 % w/v) \n• Chitosan (1.5 %w/v) \n• Cinnamon essential oil (5, 10, and 15 % w/w based on \ngum arabic) \n• Clove essential oil (10 % w/w based on gum arabic) \n• cinnamon and clove essential oil combination (5 % w/w \nbased on gum arabic) \n• Addition of essential oils into the biopolymers blend decreased the \nζ-potential and viscosity, while particle size increased. • Addition of essential oils (in particular cinnamon essential oil) \ncaused an increase in elasticity while tensile strength and water \nbarrier properties were reduced \n• Films containing cinnamon essential oils or a combination of \ncinnamon and clove showed better water barrier properties \ncompared to films containing clove. • Films containing cinnamon and clove essential oils combinations \nexhibited better antimicrobial activity against E. coli and S. aureus. Besides, films containing cinnamon essential oil showed better \nantibacterial activity compared to the clove essential oil. ✓ \n✓ \n✓ \nXu, Gao, Feng, Huang, Yang et \n(2019) \n• Corn starch (3 % w/v) \n• Cassava starch (3 % w/v) \n• Chitosan (0.5 % w/v) \n• Glutaraldehyde(10 % w/v based on a dry biopolymer \nbasis) \n• Composite films showed antibacterial activity against aerobic \nmesophilic bacteria. ✓ \nLuchese et al. (2018) \n• Hardleaf oatchestnut starch (0.5, 2, \nand 8 % w/v) \n• Chitosan (2 % w/v) \n• Litsea cubeba oil (4, 8, 12, and 16 % w/w, based on \nbiopolymers total weight) \n• Blending chitosan and hardleaf oatchestnut (ratio 1:1) caused an \nincrease in tensile strength and an improvement in water vapor \npermeability. 3. Strategies for the improvement of properties of chitosan-based \nfilms • The incorporation of Litsea cubeba oil into the biopolymers blend \n(ratio 1:1) decreased tensile strength, elasticity, water vapor \npermeability, water content, and water solubility while contact \nangle values increased. • Addition of Litsea cubeba oil into the biopolymers blend showed \nantimicrobial activity against E. coli and S. aureus. ✓ \n✓ \n✓ \nZheng et al. (2018) \n(continued on next p\n5 5 Food Packaging and Shelf Life 26 (2020) 100551 H. Haghighi, et al. H. Haghighi, et al. (\n)\nBiopolymer \nAdditives \nKey findings \nM \nWB \nGB \nAO \nAM \nReference \n• Cassava starch \n• Chitosan (0, 25, 50, 75, 100, and \n150 mg chitosan/g starch ratios) \n• Gallic acid \n• Increasing chitosan proportion in biopolymers blend decreased \nmoisture content, water activity, water vapor permeability, total \nphenolic contents, and antioxidant activities. • Blending chitosan and cassava starch reduced the growth of \nspoilage microorganisms and prolonged the shelf life of cooked \nham. ✓ \n✓ \nZhao, Teixeira, Gänzle, and \nSaldaña (2018) \n• Burdock root inulin (4 % w/v) \n• Chitosan (2.5 % w/v) \n• Water vapor permeability, water solubility, water content, tensile \nstrength, and lightness value of inulin-chitosan films were reduced \nwith increasing oregano-thyme essential oils blend. • Addition of oregano-thyme essential oils blend into the \nbiopolymers blend increased elasticity, opacity, a*, and b* values. • Active films containing oregano-thyme essential oils blend showed \nantioxidant and antibacterial activity against E. coli, L. monocytogenes, S. aureus, and S. typhimurium. ✓ \n✓ \n✓ \nCao, Yang, and Song (2018) \n• TEMPO cellulose nanofiber (0, 15, \n25 and 100 wt.%) \n• Chitosan (0, 75, 85 and 100 wt.%) \n• Increasing proportion of chitosan in biopolymers blend showed a \nsignificant reduction in the growth of S. enterica, E. coli O157:H7, \nand L. monocytogenes and also had a significant increase in the \nantioxidant activity. ✓ \n✓ \nSoni, Mahmoud, Chang, El-Giar, \nand Hassan (2018) \n• Corn starch (5 % w/v) \n• Chitosan (1, 2, 3 and 4 % w/v) \n• Blending chitosan and corn starch showed an increase in water \nsolubility, total color differences, tensile strength and elasticity, \nand a reduction in crystallinity, elastic modulus, and water vapor \npermeability. • Increasing concentration of chitosan in biopolymers blend caused \nan increase in water vapor permeability and water content values. ✓ \n✓ \nRen et al. 3. Strategies for the improvement of properties of chitosan-based \nfilms (2017) \n• Rice starch (2 % w/v) \n• Chitosan (2 % w/v) \n• Cranberry, blueberry, beetroot, pomegranate, oregano, \npitaya, and resveratrol extract (0.5, 2, and 5 % w/w \nbased on dry biopolymers weight) \n• Addition of plant extracts into the biopolymers blend improved \nUV-Vis light barrier properties. • Active films containing beetroot, cranberry, and blueberry \nextracts showed higher antibacterial activity against E. coli, \naerobic mesophilic bacteria, and fungi (P. notatum, A. niger, and A. fumigatus). ✓ \nLozano-Navarro et al. (2017) \n• Pectin (2 % w/v) \n• Chitosan (2 % w/v) \n• Increasing pectin proportion in biopolymers blend caused an \nincrease in water solubility, water content, and swelling index. • Increasing chitosan proportion in biopolymers blend increased \ntensile strength and reduced elasticity values. ✓ \nBaron et al. (2017) \n• Xanthan gum (1.5 % w/v) \n• Chitosan (1.5 % w/v) \n• Addition of xanthan gum into the biopolymers blend did not affect \nthe water vapor permeability, solubility, and moisture content. • Increasing xanthan gum proportion in biopolymers blend caused \nan increase in tensile strength while it reduced elasticity values. ✓ \nde Morais Lima et al. (2017) \n• Tapioca starch (3 % w/w) \n• Chitosan (20, 40, 60, 80 % w/w of \ndry starch solid weight) \n• Increasing chitosan proportion in biopolymers blend up to 60 % \n(w/w) caused an increase in tensile strength and elastic modulus \nwhile elasticity values reduced. ✓ \nShapi’i and Othman (2016) \n• Carboxymethyl cellulose (1 % w/ \nv) \n• Chitosan (2 % w/v) \n• Zinc oxide nanoparticles (2, 4, and 8 % w/w) \n• Incorporation of zinc oxide nanoparticles into the biopolymers \nblend showed antimicrobial activity against S. aureus, P. aeruginosa, E. coli, C. albicans and prolonged the shelf life of white \nsoft cheese. ✓ \nYoussef, El-Sayed, El-Sayed, \nSalama, and Dufresne (2016) \n(continued on next page\n6 (\n)\nBiopolymer \nAdditives \nKey findings \nM \nWB \nGB \nAO \nAM \nReference \n• Cassava starch \n• Chitosan (0, 25, 50, 75, 100, and \n150 mg chitosan/g starch ratios) \n• Gallic acid \n• Increasing chitosan proportion in biopolymers blend decreased \nmoisture content, water activity, water vapor permeability, total \nphenolic contents, and antioxidant activities. • Blending chitosan and cassava starch reduced the growth of \nspoilage microorganisms and prolonged the shelf life of cooked \nham. 3. Strategies for the improvement of properties of chitosan-based \nfilms ✓ \n✓ \nZhao, Teixeira, Gänzle, and \nSaldaña (2018) \n• Burdock root inulin (4 % w/v) \n• Chitosan (2.5 % w/v) \n• Water vapor permeability, water solubility, water content, tensile \nstrength, and lightness value of inulin-chitosan films were reduced \nwith increasing oregano-thyme essential oils blend. • Addition of oregano-thyme essential oils blend into the \nbiopolymers blend increased elasticity, opacity, a*, and b* values. • Active films containing oregano-thyme essential oils blend showed \nantioxidant and antibacterial activity against E. coli, L. monocytogenes, S. aureus, and S. typhimurium. ✓ \n✓ \n✓ \nCao, Yang, and Song (2018) \n• TEMPO cellulose nanofiber (0, 15, \n25 and 100 wt.%) \n• Chitosan (0, 75, 85 and 100 wt.%) \n• Increasing proportion of chitosan in biopolymers blend showed a \nsignificant reduction in the growth of S. enterica, E. coli O157:H7, \nand L. monocytogenes and also had a significant increase in the \nantioxidant activity. ✓ \n✓ \nSoni, Mahmoud, Chang, El-G\nand Hassan (2018) \n• Corn starch (5 % w/v) \n• Chitosan (1, 2, 3 and 4 % w/v) \n• Blending chitosan and corn starch showed an increase in water \nsolubility, total color differences, tensile strength and elasticity, \nand a reduction in crystallinity, elastic modulus, and water vapor \npermeability. • Increasing concentration of chitosan in biopolymers blend caused \nan increase in water vapor permeability and water content values. ✓ \n✓ \nRen et al. (2017) \n• Rice starch (2 % w/v) \n• Chitosan (2 % w/v) \n• Cranberry, blueberry, beetroot, pomegranate, oregano, \npitaya, and resveratrol extract (0.5, 2, and 5 % w/w \nbased on dry biopolymers weight) \n• Addition of plant extracts into the biopolymers blend improved \nUV-Vis light barrier properties. • Active films containing beetroot, cranberry, and blueberry \nextracts showed higher antibacterial activity against E. coli, \naerobic mesophilic bacteria, and fungi (P. notatum, A. niger, and A. fumigatus). ✓ \nLozano-Navarro et al. (2017)\n• Pectin (2 % w/v) \n• Chitosan (2 % w/v) \n• Increasing pectin proportion in biopolymers blend caused an \nincrease in water solubility, water content, and swelling index. • Increasing chitosan proportion in biopolymers blend increased \ntensile strength and reduced elasticity values. ✓ \nBaron et al. (2017) \n• Xanthan gum (1.5 % w/v) \n• Chitosan (1.5 % w/v) \n• Addition of xanthan gum into the biopolymers blend did not affect \nthe water vapor permeability, solubility, and moisture content. • Increasing xanthan gum proportion in biopolymers blend caused \nan increase in tensile strength while it reduced elasticity values. 3. Strategies for the improvement of properties of chitosan-based \nfilms ✓ \nde Morais Lima et al. (2017)\n• Tapioca starch (3 % w/w) \n• Chitosan (20, 40, 60, 80 % w/w of \ndry starch solid weight) \n• Increasing chitosan proportion in biopolymers blend up to 60 % \n(w/w) caused an increase in tensile strength and elastic modulus \nwhile elasticity values reduced. ✓ \nShapi’i and Othman (2016) \n• Carboxymethyl cellulose (1 % w/ \nv) \n• Chitosan (2 % w/v) \n• Zinc oxide nanoparticles (2, 4, and 8 % w/w) \n• Incorporation of zinc oxide nanoparticles into the biopolymers \nblend showed antimicrobial activity against S. aureus, P. aeruginosa, E. coli, C. albicans and prolonged the shelf life of white \nsoft cheese. ✓ \nYoussef, El-Sayed, El-Sayed, \nSalama, and Dufresne (2016)\n(continued on nex\n6 6 Food Packaging and Shelf Life 26 (2020) 100551 H. Haghighi, et al. H. Haghighi, et al. Table 2 (continued) \nBiopolymer \nAdditives \nKey findings \nM \nWB \nGB \nAO \nAM \nReference \n• Carboxymethyl cellulose (2 % w/ \nv) \n• Qaternized chitosan (5 % w/v) \n• Increasing carboxymethyl cellulose proportion in biopolymers \nblend caused an improvement in tensile strength, thermostability, \nand water vapor permeability values while oxygen permeability \nand opacity values increased. • Increasing carboxymethyl cellulose proportion in biopolymers \nblend caused a reduction in antibacterial activity against E. coli \nand S. aureus. • Higher proportion of quaternized chitosan in biopolymers blend \ndelayed the deterioration of banana fruit. • Quaternary ammonium chitosan was water soluble over a wide \nrange of pH values. The antibacterial activity of quaternized \nchitosan films was better than that of chitosan itself, but these \nfilms showed poor mechanical properties. ✓ \n✓ \n✓ \n✓ \nHu, Wang, and Wang (2016) \ng g , Aloui, & El-Saied, 2014), fillers incorporation (Abdelrazek, Elashmawi, \n& Labeeb, 2010), high-energy irradiation (Shahbazi, Rajabzadeh, & \nAhmadi, 2017) and blending with other biopolymers (Muxika, \nEtxabide, Uranga, Guerrero, & de la Caba, 2017; Wang, Qian, & Ding, \n2018). Blending chitosan with other polymers to form a composite film \ncould combine the advantages of the base polymers into a film with \nhigher performances compared with those of each constituent. A series \nof natural and synthetic polymers have been reported to blend with \nchitosan, such as pectin (Baron, Pérez, Salcedo, Córdoba, & do A. 3. Strategies for the improvement of properties of chitosan-based \nfilms Sobral, 2017; Younis & Zhao, 2019), cellulose and its derivatives \n(Noshirvani et al., 2017; Valizadeh, Naseri, Babaei, Hosseini, & Imani, \n2019), starch (Ren, Yan, Zhou, Tong, & Su, 2017; Suriyatem, Auras, & \nRachtanapun, 2018), gelatin (Bonilla, Poloni, Lourenço, & Sobral, \n2018; Guo et al., 2019), soy protein isolate (Li et al., 2017), polyvinyl \nalcohol (Do Yoon, Kim, Kim, & Je, 2017), polylactic acid (Liu, Wang, \nZhang, Lan, & Qin, 2017), etc. 4. Chitosan blends A polymer blend is a compatible or phase-separated mixture of at \nleast two polymers or copolymers, that is produced to enhance the \nphysical properties of each component (Cazón & Vázquez, 2020; Khan, \nMansha, & Mazumder, 2018). The objective of polymer blending is to \ndevelop composite materials in a simple and cost-effective route which \nwould combine the features of components, possibly enhancing their \nuseful attributes, and minimizing their drawbacks (Parameswaranpillai, \nThomas, & Grohens, 2015; Unger, Sedlmair, Siesler, & Hirschmugl, \n2014). The success of polymer blending as a strategy to improve packaging \nmaterials relies on the wide range of resulting physical, thermal, me­\nchanical, barrier, and optical properties. Therefore, studying these \nproperties plays a key factor in the suitable formulation of blends ad­\ndressed to specific applications. i\nThe growing interest towards chitosan for packaging applications \nhas resulted in many published studies focusing on the production and \ninvestigation of properties of films obtained from chitosan blended with \nother natural and synthetic polymers (Kumar, Mukherjee, & Dutta, \n2020). In this study, chitosan blends have been classified into two main \ngroups, respectively chitosan-natural biopolymers blends and chitosan- \nsynthetic polymers blends. A synopsis of the literature published in the \nlast five years is presented in each subsection considering: type of \npolymer and its concentration, active compounds, and other additives \nincorporated in the blend and the main properties of the blend films \naddressed for food packaging applications. 4.1. Chitosan-natural biopolymer blends The functional properties of chitosan-based films can be improved \nby blending with other natural biopolymers such as polysaccharides, \nproteins, and their derivatives (Aider, 2010; Cazón & Vázquez, 2020; \nElsabee & Abdou, 2013). Compatibility between chitosan and these \npolymers depends on the ability to associate through electrostatic in­\nteraction due to chitosan cationic character at appropriate pH condi­\ntions and the availability of high-polarity groups, such as NH/NH2, OH, \nC]O, C−O−Cee, in its backbone to form intermolecular hydrogen \nbonds or dipole association with the corresponding functional groups of \nother biopolymers (Bonilla et al., 2018). It has been reported that \npolysaccharides such as pectin, starch (from rice, corn, potato, cassava, \netc.), alginate, carrageenan, xanthan gum, xylan, glucose, kefiran, cel­\nlulose, and its derivatives can be blended with chitosan (Wang et al., \n2018). A synopsis of recent advances in chitosan-polysaccharide blend \nfilms for packaging applications is presented in Table 2. i i\nProtein-based films from animal sources (gelatin, collagen, casein, \nwhey protein, etc.) and plant source (soy protein isolate, corn zein, \nkidney bean protein isolate, quinoa protein, wheat gluten, etc.) have \nbeen studied for the development of biodegradable films due to their 7 Food Packaging and Shelf Life 26 (2020) 100551 H. Haghighi, et al. . Improvement of the parameters investigated in each contribution is reported as follows. M: \nal activity\nHaghig (continued on next page) Table 3 \nSynopsis of research published between 2015 – 2020 addressing chitosan-protein blend films for food packaging applications. Improvement of the parameters investigated in each contribution is reported as follows\nmechanical properties, WB: water barrier property, GB: gas barrier permeability, AO: antioxidant activity, AM: antimicrobial activity. Biopolymer \nAdditives \nKey findings \nM \nWB \nGB \nAO \nAM \nReference \n• Sheep bone collagen (1.5 % w/v) \n• Skin gelatin (1.5 % w/v) \n• Chitosan (1.5 % w/v) \n• Addition of chitosan into bone collagen improved transparency and \ntensile strength of bone collagen film. • Increasing proportion of chitosan over 50 % in the biopolymers blend \nimproved the elasticity value. • Blending chitosan and bone collagen led to an improvement in UV barrier \nproperty, water solubility, and thermal stability while water vapor \npermeability increased. ✓ \nHou et al. 4.1. Chitosan-natural biopolymer blends (2020) \n• Hordein nanofiber (11 % w/v) \n• Chitosan (0.4 % w/v) \n• Quercetin (5 % w/w based on hordein) \n• Addition of quercetin into the nano biopolymers blend showed \nantioxidant activity and treating films with different temperatures (90, \n120, 150, and 180 °C) did not influence the antioxidant activity. • Heat treatment enhanced the water resistance of nano biopolymers blend. • Covering apple and potato samples with heat treated nano fiber films \ndelayed the rate of enzymatic browning and preserved their fresh color \nafter 6 and 12 h, respectively. ✓ \n✓ \nLi, Yan, Guan, and Huang (2020\n• Zein (2 % w/v) \n• Chitosan (2 % w/v) \n• α-tocopherol (50 % w/w based on the content \nof dry materials) \n• Active zein-chitosan films containing α-tocopherol reduced the \npostharvest deterioration of mushroom (Agaricus bisporus) at 4 °C for 12 \ndays. This was mainly due to the excellent gas barrier property and \nantioxidant activity of films. ✓ \n✓ \nZhang, Liu, Sun, Wang, and Li \n(2020) \n• Gelatin (2 % w/v) \n• Chitosan (2 % w/v) \n• Polyphenols from the fruits of Chinese \nhawthorn (2, 4, and 6 % w/w on the total \nbiopolymer weight) \n• Addition of the polyphenol extract into the biopolymers blend increased \nthickness, tensile strength, elasticity, opacity, and total color difference, \nwhile water content and water vapor permeability reduced. • Antioxidant activity of films significantly improved by increasing the \nconcentration of polyphenol extract. ✓ \n✓ \n✓ \nKan et al. (2019) \n• Gelatin (5 % w/v) \n• Chitosan (3, 6 and 9 % w/w based on \ngelatin) \n• Citric acid (10 and 20 % w/w based on gelatin \nweight) \n• Incorporation of citric acid into the biopolymer blend improved elasticity \nvalues. • Higher concentration of chitosan and citric acid in biopolymers blend led \nto better antibacterial activity against E. coli. ✓ \n✓ \nUranga et al. (2019) \n• Fish myofibrillar protein (0.45, 0.8, \n1.3, 1.8, and 2.14 % w/v) \n• Chitosan (13.18, 20, 30, 40, and \n46.81 % w/w) \n• The optimum formulation to produce biodegradable film contained 1.3 % \n(w/v) fish myofibrillar proteins, 30 % (w/w) chitosan, and 40 % (w/w) \nglycerol. • Adding chitosan in the biopolymers blend increased elasticity, thermal \nstability, UV barrier properties while solubility, swelling degree, and \nwater vapor permeability decreased. 4.1. Chitosan-natural biopolymer blends ✓ \n✓ \nBatista, Araújo, Peixoto Joele, Sil\nJúnior, and Lourenço (2019) \n• Porcine plasma protein (3 % w/w) \n• Chitosan (1 % w/w) \n• The porcine plasma protein/chitosan blend film had lower transparency \nthan neat porcine plasma protein and chitosan film. • Blending porcine plasma protein and chitosan increased thermal stability. • Blend films (ratio 1:1) showed improvement in water resistance and \nwater vapor permeability, solubility, and mechanical properties \ncompared to the neat porcine plasma protein film. ✓ \n✓ \nSamsalee and Sothornvit (2019) \n• Gelatin (2 % w/v) \n• Chitosan (2 % w/v) \n• Cinnamon, citronella, pink clove, nutmeg and \nthyme essential oils (1 % w/w based on \nweight) \n• Addition of essential oils into the biopolymers blend improved UV barrier \nproperties and increased thickness, water content, water vapor \npermeability, opacity, and total color difference values. • Incorporation of essential oils into biopolymers blend showed \nantibacterial activity against C. jejuni, E. coli, L. monocytogenes, and S. typhimurium. ✓ \n✓ \nHaghighi, Biard et al. (2019) \n• Gelatin (1 % w/v) \n• Chitosan (1 % w/v) \n• Cinnamon essential oil (0.4 % w/w based on a \ndry biopolymer weight) \n• Addition of cinnamon essential oil into the biopolymer blend improved \nelasticity, thermal stability, water vapor permeability, UV barrier, and \ncontact angle values. • Active films containing cinnamon essential oils showed antibacterial \nactivity against E. coli and S. aureus. ✓ \n✓ \n✓ \nGuo et al. (2019) \n• Collagen (3.5 % w/v) \n• Chitosan (1 % w/v) \n• Pomegranate peel extract (1, 3, and 5 % v/v) • Addition of 5 % pomegranate peel extract into the biopolymers blend \ncaused a reduction in water solubility and enhanced antibacterial activity \nagainst B. saprophyticus, B. subtilis, S. typhi, and E. coli. ✓ \nBhuimbar, Bhagwat, and Dandge\n(2019) \n(continued on next p 8 Food Packaging and Shelf Life 26 (2020) 100551 H. Haghighi, et al. H. Haghighi, et al. Table 3 (continued) \nBiopolymer \nAdditives \nKey findings \nM \nWB \nGB \nAO \nAM \nReference \n• Zein (10 % w/v) \n• Chitosan (6 wt%) \n• TiO2 nanoparticles (0.05, 0.1, 0.15, 0.2, and \n0.25 % w/w) \n• Addition of TiO2 nanoparticles up to 0.2 % into the biopolymers blend \nenhanced water absorption and water vapor permeability. • Biopolymers blend containing TiO2 nanoparticles showed antibacterial \nactivity against S. aureus, E. coli, and S. enteritidis. ✓ \n✓ \nQu et al. 4.1. Chitosan-natural biopolymer blends (2019) \n• Gelatin (2 % w/v) \n• Chitosan (2 % w/v) \n• Ethyl lauroyl arginate (0.1 % v/v) \n• Blending chitosan and gelatin caused an improvement in mechanical and \nwater barrier properties. • Incorporation of ethyl lauroyl arginate into the biopolymer blend \nconferred antibacterial activity against C. jejuni, E. coli, L. monocytogenes, \nand S. typhimurium. ✓ \n✓ \n✓ \nHaghighi, De Leo et al. (2019) \n• Gelatin (2 % w/v) \n• Chitosan (2 % w/v) \n• Silver nanoparticle (0.05 and 0.1 % w/w) \n• Addition of silver nanoparticles into the biopolymers blend enhanced \nelasticity values while tensile strength and light transmittance in the \nvisible light region were reduced. • Incorporation of silver nanoparticles into the biopolymers blend showed \nantimicrobial activity. • Shelf life of red grapes fruits wrapped with gelatin-chitosan blend \nenriched with silver nanoparticles was extended for additional two weeks. ✓ \n✓ \nKumar, Shukla, Baul, Mitra, and \nHalder (2018) \n• Gelatin (1 % w/v) \n• Chitosan (2 % w/v) \n• β-Carotene loaded starch nanocrystals (1mg/ \n1 mL) \n• Addition of β-carotene loaded starch nanocrystals into the biopolymers \nblend caused a significant reduction in water solubility while antioxidant \nactivity increased. ✓ \nHari, Francis, Rajendran Nair, and \nNair (2018) \n• Gelatin (3 % w/v) \n• Chitosan (1 % w/v) \n• Gallic acid (1 % w/w total dry weight of film) \n• Tween 80 (50 and 100 % w/w based on the \nweight of the gallic acid \n• β-cyclodextrin \n• Ethanol \n• Addition of gallic acid into the biopolymers blend increased opacity and \nelasticity. • Incorporation of β-cyclodextrin and gallic acid into the biopolymers blend \nreduced water barrier properties. ✓ \n✓ \nRezaee, Askari, EmamDjomeh, and\nSalami (2018) \n• Gelatin (4 % w/v) \n• Chitosan (1 % w/v) \n• Eugenol and ginger essential oils (0.5 % w/w \nbased on dry biopolymers weight) \n• Addition of essential oils into the biopolymers blend improved elasticity \nand UV barrier properties. • Incorporation of essential oils into biopolymers blend showed significant \nantioxidant activity. ✓ \n✓ \nBonilla et al. (2018) \n• Gelatin (3 % w/v) \n• Chitosan (1 % w/v) \n• Procyanidin (0.25, 0.5, 0.75, and 1 mg/mL) • Addition of procyanidin into the biopolymers blend improved elasticity, \nwater vapor permeability, water solubility, swelling index, and UV barrier \nproperties while tensile strength was reduced. • Incorporation of procyanidin into the biopolymers blend showed \nantioxidant activity and antibacterial activity against S. aureus and E. coli \nstrains. 4.1. Chitosan-natural biopolymer blends ✓ \n✓ \n✓ \n✓ \nRamziia, Ma, Yao, Wei, and Huang\n(2018) \n• Soy protein isolate (2 % w/w) \n• Chitosan (2 % w/w) \n• Elasticity, thermal stability, and homogeneity of chitosan film increased \nby blending with soy protein isolate. ✓ \nXing, Zhang, Li, Li, and Shi (2018)\n• Soy protein isolate \n• Chitosan (1 % w/w) \n• Cu nanoclusters (20 mmol/L) \n• Incorporation of copper nanoclusters into the biopolymers blend \nimproved tensile strength, elasticity, water vapor permeability, contact \nangle, and thermal stability. ✓ \n✓ \nLi et al. (2017) \n• Eggshell membrane gelatin (3 % w/v) \n• Chitosan (1.5 % w/v) \n• Blending chitosan and gelatin showed an improvement in elasticity, water \nsolubility, and water barrier property. ✓ \n✓ \nMohammadi et al. (2018) \n• Gelatin (4 %w/v) \n• Chitosan (1 % w/w) \n• Cinnamon, guarana, rosemary and boldo-do- \nchile ethanolic extract (1 % v/v) \n• Increasing chitosan proportion in biopolymers blend improved the \nmechanical properties and water vapor permeability. • Addition of ethanolic extracts into the biopolymers blend enhanced \nantioxidant and antibacterial activity against S. aureus and E. coli. ✓ \n✓ \n✓ \n✓ \nBonilla and Sobral (2016) \n• Gelatin (10 % w/v) \n• Chitosan (2 % w/v) \n• Boric acid (2, 3, 4 and 5 % w/w) \n• Polyethylene glycol (5, 10 and 20 % v/v) \n• Blending chitosan and gelatin showed UV barrier property. • Addition of boric acid into the biopolymer blend improved tensile \nstrength and water solubility, moisture content, and water vapor \npermeability. • Addition of polyethylene glycol into the biopolymers blend caused an \nincrease in elasticity, water content, and water solubility. ✓ \n✓ \nAhmed and Ikram (2016) \n• Corn starch (2 and 5 % w/v) \n• Gelatin (2 and 5 % w/v) \n• Chitosan (2 % w/v) \n• Glycerol and sorbitol (1, 2, 5, and 10 % w/w) • Addition of sorbitol into the chitosan-starch or chitosan-gelatin blend \nfilms enhanced water vapor permeability compared with films containing \nglycerol. ✓ \n✓ \nBadawy, Rabea, and El-Nouby \n(2016) 9 Food Packaging and Shelf Life 26 (2020) 100551 H. Haghighi, et al. H. Haghighi, et al. high abundance, acceptable mechanical properties, excellent gas bar­\nrier properties to non-condensable gases (oxygen, carbon dioxide, and \nnitrogen) and aromas (Arfat, Ahmed, Hiremath, Auras, & Joseph, \n2017). 4.1. Chitosan-natural biopolymer blends The chitosan-protein blend film could render better functional \nproperties than single proteins and chitosan film, thus promoting their \napplication in food packaging (Basta, Khwaldia, Aloui, & El-Saied, \n2015; Ma et al., 2012; Wang et al., 2018). A synopsis of recent advances \nin chitosan-protein blend films for packaging applications is presented \nin Table 3. Biopolymer \nAdditives \nKey findings \nM \nWB \nGB \nAO \nAM \nReference \n• Addition of glycerol and sorbitol into the biopolymers blend showed \nantioxidant activity. • Quinoa protein (6.7 % w/v) \n• Chitosan (1.5 and 2 % w/v) \n• Chitosan-tripolyphosphate nano \nparticles (0.3 w/v) \n• Thymol nanoparticles (0.1 % w/v) \n• Addition of chitosan-tripolyphosphate nanoparticles into the biopolymers \nblend improved water vapor permeability. • Incorporation of chitosan-tripolyphosphate-thymol nanoparticles into the \nbiopolymers blend enhanced antibacterial activity against L. innocua, S. aureus, S. typhimurium, E. aerogenes, P. aeruginosa, and E. coli. ✓ \n✓ \nCaro et al. (2016) \n• Gelatin (3 % w/v) \n• Chitosan (2 % w/v) \n• Red grape seed extract (1 and 2 % w/w) \n• Ziziphora clinopodioides essential oil (1 and 2 \n% w/w) \n• Addition of red grape seed extract and Ziziphora clinopodioides into the \nbiopolymers blend showed antibacterial activity against L. monocytogenes, \ntotal mesophilic and psychrotrophic bacteria, Pseudomonas spp., P. fluorescens, S. putrefaciens, lactic acid bacteria and Enterobacteriaceae \nfamily. • Packing minced rainbow trout fillets with chitosan-gelatin blend enriched \nwith red grape seed extract and Ziziphora clinopodioides essential oil \nextended the shelf life at refrigerated condition due to the delay of lipid \noxidation and inhibition of bacterial growth. ✓ \n✓ \nKakaei and Shahbazi (2016) \n• Brewer’s spent grain protein (3 % w/ \nv) \n• Chitosan (2 % w/v) \n• Blending brewer’s spent grain protein with chitosan caused an \nimprovement in water vapor permeability and mechanical properties. • Blend films showed antioxidant and antibacterial activity against S. aureus, E. coli, L. monocytogenes, and S. typhimurium. ✓ \n✓ \n✓ \n✓ \nLee, Lee, Yang, and Song (2015) 4.2. Chitosan-synthetic polymers blends Blending chitosan with synthetic polymers (polyvinyl alcohol - PVA, \npolyvinyl pyrrolidone - PVP, polylactic acid - PLA, etc.) has been ex­\ntensively studied for the positive effects on the physical, mechanical, \nand biological features of composite films. The success of synthetic \npolymers as biodegradable materials depends on their diverse range of \nmechanical properties, chemical resistance, and low production costs \ncompared to natural polymers (Bourakadi et al., 2019). Chitosan is \npotentially miscible with some synthetic polymers mainly due to the \nformation of intermolecular hydrogen bonds between hydroxyl groups \nof synthetic polymer and hydroxyl and amine groups of chitosan \n(Bonilla, Fortunati, Atarés, Chiralt, & Kenny, 2014). Depending on the \ninteractions between polymer components, blending chitosan with \nsynthetic biopolymers can enhance the mechanical and water barrier \nproperties of films in some cases. A synopsis of recent advances in \nchitosan-synthetic polymer blend films for packaging applications is \npresented in Table 4. 5. Conclusions and future perspectives Packaging is an essential item responsible for the protection of the \nproduct and provides food safety assurance during marketing. Conventional plastic packaging material due to non-biodegradability \nand insufficient waste management system has labeled the food in­\ndustry as a source of pollution and social concerns. Therefore, bio- \nbased, and biodegradable materials have received considerable atten­\ntion to address these issues in recent years. The adoption of chitosan as \npackaging material could contribute to mitigating the environmental \nconcern, despite some drawbacks in terms of thermal stability, barrier \nand mechanical properties, and production costs. Blending chitosan \nwith other natural and synthetic polymers is an effective way to over­\ncome these limitations, making the films suitable for specific uses. This \napproach appears to have a bright future for innovative food packaging \ndesign since it will allow the partial replacement of the existing syn­\nthetic plastic packaging materials presently available in the market. Potential applications of chitosan blend-based films are for fresh pro­\nducts (vegetable, meat and fish) and foods with short to medium shelf \nlife. Such films may represent an interesting alternative to conventional \nplastic films especially when recycling is not possible or is compromised \ndue to presence of food residues: in these cases, the feature of biode­\ngradability/compostability offers a valid end-of-life alternative. Nanotechnologies certainly represent a promising complementary tool \nfor further improvement of mechanical and barrier properties of chit­\nosan-based films and for the addition of other functionalities (anti­\nmicrobial and antioxidant capacity), but their development and appli­\ncation faces resistance due to toxicological issues. In particular, \nnanocomposite materials based on the incorporation of biobased na­\nnomaterials such as nano-cellulose, emerge for their potential to pro­\nvide a barrier and mechanical strength maintaining the full biode­\ngradability of the material. Finally, despite contributions retrieved in \nliterature in the considered timeframe, the aspect of biodegradability \nremains mostly disregarded. This omission has two reasons: the first is \nlinked to the difficulty of applying a real holistic and multidisciplinary \napproach, necessary for the development of food packaging; the second \narises from the consideration that making a new material from 10 Food Packaging and Shelf Life 26 (2020) 100551 applications. Improvement of the parameters investigated in each contribution is reported as \n: antimicrobial activity\nHaghig H. Haghighi, et al. Table 4 \nSynopsis of research published between 2015 – 2020 addressing chitosan-synthetic biopolymer blend films for food packaging applications. 5. Conclusions and future perspectives Improvement of the parameters investigated in each contribution is reported as \nfollows. M: mechanical properties, WB: water barrier properties, GB: gas barrier permeability, AO: antioxidant activity, AM: antimicrobial activity. Biopolymer \nAdditives \nKey findings \nM \nWB \nGB \nAO \nAM \nReference \n• PVA (0.5, 1, 1.5, and 2 % w/v) \n• Chitosan (0.5, 1, 1.5, and 2 % w/ \nv) \n• Ethyl vanillin (2 % w/v) \n• Addition of ethyl vanillin into the biopolymers blend caused an \nimprovement in the tensile strength, surface hydrophobicity, and UV barrier \nproperties while water vapor transmission rate and oxygen transmission rate \nwere reduced. • Blend films containing ethyl vanillin showed antimicrobial activity against \nS. aureus and E. coli. ✓ \n✓ \n✓ \n✓ \nNarasagoudr, Hegde, Vanjeri, \nChougale, and Masti (2020) \n• PVA (4 % w/w) \n• Chitosan (2 % w/w) \n• Glycerol \n• Polyethylene glycol \n• Glycerol/ Polyethylene glycol \n• Addition of glycerol showed an enhancement in the crystallinity of PVA/ \nchitosan blends while polyethylene glycol reduced the extent of \ncrystallization. • Combination of glycerol and polyethylene glycol led to the highest level of \ncompatibility. Flexibility of the blend plasticized with the combination of \npolyethylene glycol and glycerol was improved five-times of the blend \nplasticized with glycerol. However, the antibacterial activity of the \nchitosan/PVA blend plasticized with polyethylene glycol /glycerol was \nsignificantly reduced compared to that of glycerol or polyethylene glycol. ✓ \n✓ \nShojaee Kang Sofla, Mortazavi, \nand Seyfi (2020) \n• PVA (4 % w/w) \n• Liquefied chitin (1 % w/w) \n• Silica (0.1, 0.2, 0.4, 0.8, and 1.6 wt.%) \n• Addition of silica into the biopolymers blend up to 0.2 % (wt.) improved the \ntensile strength and elasticity values. • Addition of silica into the biopolymers blend up to 0.2 % (wt.) improved the \nbrowning index of fresh cherries. • Compared with synthetic food packaging materials, the blend films \ndegraded quickly in the soil while addition of silica slightly reduced the \nbiodegradability. ✓ \nZhang, Xu et al. (2020) \n• PVA (5 % w/v) \n• Chitosan (1 % w/v) \n• Ethyl lauroyl arginate (1, 2.5, 5, and 10 % w/w) • Addition of ethyl lauroyl arginate into the biopolymers blend negatively \ninfluenced elasticity, tensile strength, and water barrier properties while \nbarrier properties to UV light improved. • Chitosan-gelatin blend enriched with ethyl lauroyl arginate exhibited \nantibacterial activity against C. jejuni, E. coli, L. monocytogenes and S. typhimurium. ✓ \nHaghighi et al. 5. Conclusions and future perspectives ✓ \nCazón, Vázquez, and Velazquez \n(2018) \n• PVA (3 % w/v) \n• Chitosan (1.5 % w/v) \n• Cellulose nanocrystals from rice straw (1, 3, and 5 \n% w/w base on polyvinyl alcohol-chitosan blend) • Addition of cellulose nanocrystals into PVA-chitosan blend improved tensile \nstrength and thermal properties. • PVA-chitosan blend films enriched with cellulose nanocrystal from rice \nstraw showed antifungal activity against C. gloeosporioides and antibacterial \nactivity against S. mutans, S.aureus, E.coli, and P.aeruginosa. ✓ \n✓ \nPerumal, Sellamuthu, Nambiar, \nand Sadiku (2018) \n• PVA (1 % w/v) \n• Chitosan (2 % w/v) \n• SiO2 (0.3, 0.6, and 0.9 %w/w) \n• Addition of silicon dioxide into the biopolymers blend caused an \nenhancement in mechanical, water and oxygen barrier properties. ✓ \n✓ \nYu, Li, Chu, and Zhang (2018) \n• PVA (10 %w/v) \n• Chitosan (2, 2.5, 3, and 3.5 % w/ \nv) \n• In comparison to neat PVA film, blending PVA and chitosan caused an \nimprovement in elasticity and oxygen barrier properties while water barrier \npropertied decreased. Increasing proportion of chitosan in biopolymers \nblend showed better antibacterial activity against S. aureus and E. coli. ✓ \n✓ \n✓ \nLiu, Wang, and Lan (2018) \n• PVA (2 % w/v) \n• Chitosan (2 % w/v) \n• Sulfosuccinic acid \n• (5, 10, 15, 20, and 30 wt%) \n• Glycerol (0−60 wt%) \n• Xylitol (0−60 wt%)\n• Addition of sulfosuccinic acid into the biopolymers blend caused an \nenhancement in tensile strength, elasticity, swelling degree, water solubility, \nthermal stability, and optical properties. ✓ \nYun, Lee, Kim, and Yoon (2017) \naghighi, et al. Biopolymer \nAdditives \nKey findings \nM \nWB \nGB \nAO \nAM \nReference \n• Microcrystalline cellulose (3, 4 \nand 5 % w/w) \n• PVA (2 and 4 % w/w) \n• Chitosan (0.5 and 1 % w/w) \n• Addition of chitosan-PVA blend into the cellulose based films caused an \nimprovement in mechanical properties. • Blending chitosan and cellulose improved barrier properties to the UV light. • Addition of PVA into the biopolymers blend caused an improvement in light \ntransmittance values. ✓ \nCazón, Vázquez, and Velaz\n(2018) \n• PVA (3 % w/v) \n• Chitosan (1.5 % w/v) \n• Cellulose nanocrystals from rice straw (1, 3, and 5 \n% w/w base on polyvinyl alcohol-chitosan blend) • Addition of cellulose nanocrystals into PVA-chitosan blend improved tensile \nstrength and thermal properties. • PVA-chitosan blend films enriched with cellulose nanocrystal from rice \nstraw showed antifungal activity against C. gloeosporioides and antibacterial \nactivity against S. 5. Conclusions and future perspectives mutans, S.aureus, E.coli, and P.aeruginosa. ✓ \n✓ \nPerumal, Sellamuthu, Nam\nand Sadiku (2018) \n• PVA (1 % w/v) \n• Chitosan (2 % w/v) \n• SiO2 (0.3, 0.6, and 0.9 %w/w) \n• Addition of silicon dioxide into the biopolymers blend caused an \nenhancement in mechanical, water and oxygen barrier properties. ✓ \n✓ \nYu, Li, Chu, and Zhang (20\n• PVA (10 %w/v) \n• Chitosan (2, 2.5, 3, and 3.5 % w/ \nv) \n• In comparison to neat PVA film, blending PVA and chitosan caused an \nimprovement in elasticity and oxygen barrier properties while water barrier \npropertied decreased. Increasing proportion of chitosan in biopolymers \nblend showed better antibacterial activity against S. aureus and E. coli. ✓ \n✓ \n✓ \nLiu, Wang, and Lan (2018)\n• PVA (2 % w/v) \n• Chitosan (2 % w/v) \n• Sulfosuccinic acid \n• (5, 10, 15, 20, and 30 wt%) \n• Glycerol (0−60 wt%) \n• Xylitol (0−60 wt%) \n• Sorbitol (0−60 wt%) \n• Addition of sulfosuccinic acid into the biopolymers blend caused an \nenhancement in tensile strength, elasticity, swelling degree, water solubility, \nthermal stability, and optical properties. ✓ \nYun, Lee, Kim, and Yoon (2\n• PVA (1 % w/v) \n• Chitosan-gallic acid (0.1, 0.5, and \n1 % w/v) \n• Increasing chitosan-gallic acid concentration into the biopolymers blend and \ntreating with UV caused an increase in tensile strength while elasticity \nvalues were reduced. • Films containing chitosan-galic acid (1 % w/v) showed antibacterial activity \nagainst E. coli, S. typhimurium, S. aureus, and B. cereus. ✓ \n✓ \nDo Yoon et al. (2017) \n• PVA (5 % w/v) \n• Sodium lactate loaded chitosan \n(2 % w/v) \n• Montmorillonite (0, 5, 10, 15, and 20 % w/w, \nbased on the dry weight of CS/PVA) \n• Montmorillonite concentration up to 15 % in biopolymers blend improved \ntensile strength and elastic modulus while elasticity values decreased. • Addition of montmorillonite into the biopolymers blend enhanced barrier \nproperties to water vapor, oxygen, and carbon dioxide. Blend films showed \nantibacterial activity against E. coli. ✓ \n✓ \n✓ \n✓ \nZhang et al. (2017) \n• PVA (5 % w/v) \n• Chitosan (0.15 % w/w) \n• Carvacrol (5 % w/v) \n• Cellulose nanocrystals (3 % w/w) \n• Addition of carvacrol and cellulose nanocrystal into the biopolymer blend \ncaused an improvement in mechanical properties while color and \ntransparency were not affected. • Blend films showed antioxidant activity and antimicrobial activity against P. carotovorum subsp. Odoriferum, and X. axonopodis. 5. Conclusions and future perspectives (2020) \n• PVA (0.5 % w/v) \n• Xylan (0.5 % w/v) \n• Chitosan (1 % w/v) \n• Nano hydroxyapatite \n• (0.01 w/v) \n• Curcumin (0.01 w/v) \n• PVA-xylan-chitosan-nano hydroxyapatite-curcumin films were developed as \nintelligent packaging to assess the freshness of Indian oil sardine fish at \nroom temperature. • In vitro biodegradation test showed that incorporation of curcumin into the \nbiopolymers blend increased resistance to biodegradation and improved \nlongevity of these scaffolds for longer last. ✓ \nVadivel et al. (2019) \n• Poly(ε-capro-lactone) (6 % w/v) \n• Chitosan (1 % w/v) \n• Oregano essential oil (1, 3, and 5 % w/w) \n• Addition of oregano essential oil into the biopolymers blend caused a \nreduction in tensile strength and elastic modulus while water vapor \npermeability and elasticity values increased. • Poly(ε-caprlactone)-chitosan blend mats containing 5 % oregano essential \noil showed antibacterial activity against S. aureus, L. monocytogenes, S. enteritidis, and E. coli. ✓ \nHasanpour Ardekani-Zadeh and \nHosseini (2019) \n• PVA (2 % w/v) \n• Fish gelatin (2 % w/v) \n• Chitosan (1.5 % w/v) \n• Increasing fish gelatin proportion in biopolymers blend caused an increase \nin water vapor permeability, water absorption, and opacity values while \nwater solubility, tensile strength, and elasticity values reduced. Ghaderi, Hosseini, Keyvani, and \nGómez-Guillén (2019) \n• PVA (4% w/v) \n• Chitosan (1.25 % w/v) \n• Thiabendazol-ium-montmorillonite (5 % w/w) \n• Addition of thiabendazolium into the biopolymers blend caused an increase \nin tensile strength and elastic modulus values. Chitosan-PVA blend films \ncontaining thiabendazolium showed antibacterial activity against P, \naeruginosa, S. aureus, and E. coli. ✓ \n✓ \nBourakadi et al. (2019) \n• PVA (2 % w/v) \n• Chitosan (2 % w/v) \n• Increasing chitosan proportion in the biopolymer blend caused a reduction \nin tensile strength and elasticity values while UV barrier properties \nimproved. Wu, Ying, Liu, Zhang, and Huang \n(2018) \n(\nd\n)\n11 11 Food Packaging and Shelf Life 26 (2020) 100551 H. Haghighi, et al. Biopolymer \nAdditives \nKey findings \nM \nWB \nGB \nAO \nAM \nReference \n• Microcrystalline cellulose (3, 4 \nand 5 % w/w) \n• PVA (2 and 4 % w/w) \n• Chitosan (0.5 and 1 % w/w) \n• Addition of chitosan-PVA blend into the cellulose based films caused an \nimprovement in mechanical properties. • Blending chitosan and cellulose improved barrier properties to the UV light. • Addition of PVA into the biopolymers blend caused an improvement in light \ntransmittance values. References Abdelrazek, E. M., Elashmawi, I. S., & Labeeb, S. (2010). Chitosan filler effects on the \nexperimental characterization, spectroscopic investigation and thermal studies of \nPVA / PVP blend films. Physica B: Physics of Condensed Matter, 405(8), 2021–2027. https://doi.org/10.1016/j.physb.2010.01.095. Águila-Almanza, E., Salgado-Delgado, R., Vargas-Galarza, Z., García-Hernández, E., & \nHernández-Cocoletzi, H. (2019). Enzymatic depolymerization of chitosan for the \npreparation of functional membranes. Journal of Chemistry, 2019, 1–8. https://doi. org/10.1155/2019/5416297. i Ahmed, S., & Ikram, S. (2016). Chitosan and gelatin based biodegradable packaging films \nwith UV-light protection. Journal of Photochemistry and Photobiology B, Biology, 163, \n115–124. https://doi.org/10.1016/j.jphotobiol.2016.08.023. Ahmed, S., & Ikram, S. (2017). Chitin and chitosan: History, composition and properties. In S. Ahmed, & S. Ikram (Eds.). Chitosan: Derivatives, composites and applications (pp. 1–24). Scrivener Publishing LLC. i g\nAider, M. (2010). Chitosan application for active bio-based films production and potential \nin the food industry: Review. LWT - Food Science and Technology, 43(6), 837–842. https://doi.org/10.1016/j.lwt.2010.01.021. g\nj\nAl-Tayyar, N. A., Youssef, A. M., & Al-hindi, R. (2020). Antimicrobial food packaging \nbased on sustainable bio-based materials for reducing foodborne pathogens: A re­\nview. Food Chemistry, 310, Article 125915. https://doi.org/10.1016/j.foodchem. 2019.125915. Arfat, Y. A., Ahmed, J., Hiremath, N., Auras, R., & Joseph, A. (2017). Thermo-mechanical, \nrheological, structural and antimicrobial properties of bionanocomposite films based \non fish skin gelatin and silver-copper nanoparticles. Food Hydrocolloids, 62, 191–202. https://doi.org/10.1016/j.foodhyd.2016.08.009. Argüelles-Monal, W. M., Lizardi-Mendoza, J., Fernández-Quiroz, D., Recillas-Mota, M. T., \n& Montiel-Herrera, M. (2018). Chitosan derivatives: Introducing new functionalities \nwith a controlled molecular architecture for innovative materials. Polymers, 10(3), \n342. https://doi.org/10.3390/polym10030342. g\ny\nArikan, E. B., & Ozsoy, H. D. (2015). A review: Investigation of bioplastics. Journal of Civil \nEngineering and Architecture, 9(2), 188–192. https://doi.org/10.17265/1934-7359/ \n2015.02.007. Badawy, M. E. I., Rabea, E. I., & El-Nouby, M. A. M. (2016). Preparation, physicochemical \ncharacterizations, and the antioxidant activity of the biopolymer films based on \nmodified chitosan with starch, gelatin, and plasticizers. Journal of Polymer Materials, \n33(1), 17–32. https://doi.org/10.1007/s10924-013-0621-z. Baron, R. D., Pérez, L. L., Salcedo, J. M., Córdoba, L. P., & do A. Sobral, P. J. (2017). Production and characterization of films based on blends of chitosan from blue crab \n(Callinectes sapidus) waste and pectin from Orange (Citrus sinensis Osbeck) peel. International Journal of Biological Macromolecules, 98, 676–683. https://doi.org/10. 1016/j.ijbiomac.2017.02.004. j j\nBasta, A. H., Khwaldia, K., Aloui, H., & El-Saied, H. (2015). Enhancing the performance of \ncarboxymethyl cellulose by chitosan in producing barrier coated paper sheets. 5. Conclusions and future perspectives (2016) \n• PLA (1 % w/v) \n• Chitosan (1 % w/v) \n• Methyldiphenyl diisocyanate (0.2,1, 2, and 3 % w/ \nw of the final PLA/chitosan solution) \n• Increasing concentration of methyldiphenyl diisocyanate in biopolymers \nblend improved tensile strength and contact angle values. ✓ \nGartner, Li, and Almenar (2015) Biopolymer \nAdditives \nKey findings \nM \nWB \nGB \nAO \nAM \nReference \n• PVA \n• Chitosan (1 % w/v) \n• Potassium nitrate \n• (0.1, 0.2, 0.3, 0.4, and 0.5 % w/w) \n• Addition of potassium nitrate into the biopolymers blend caused an \nimprovement in tensile strength and elasticity due to its crosslinking effect. • The degradation behavior can be improved with addition of potassium \nnitrate. ✓ \nJahan et al. (2016) \n• PLA (1 % w/v) \n• Chitosan (1 % w/v) \n• Methyldiphenyl diisocyanate (0.2,1, 2, and 3 % w/ \nw of the final PLA/chitosan solution) \n• Increasing concentration of methyldiphenyl diisocyanate in biopolymers \nblend improved tensile strength and contact angle values. ✓ \nGartner, Li, and Almenar (2015) biodegradable components would result in a new biodegradable ma­\nterial. This should not be taken for granted and requires verification \nespecially in the case of film incorporation of antimicrobial compounds. Indeed, compounds which inhibit microbial food spoilage might also \ncause negative effects in the composting process. Hence, future research \non chitosan-based films and sustainable materials, in general, should \ninclude biodegradability among the targeted parameters. 5. Conclusions and future perspectives ✓ \n✓ \n✓ \nLuzi et al. (2017) \n• PVA (2 % w/v) \n• Chitosan (2 % w/v) \n• Increasing proportion of PVA in biopolymers blend caused an increase in \ntensile strength and elasticity. • Increasing proportion of chitosan in the blend improved antioxidant activity \nand antibacterial activity against S. aureus, B. cereus M. luteus, S. enterica, E. coli, and S. typhimurium. ✓ \n✓ \n✓ \nHajji et al. (2016) \n• PVA (10, 20, and 30 % w/w) \n• Montmorillonite (5 %w/v) \n• Chitosan (2 % w/v) \n• Addition of PVA into the biopolymers blend caused a plasticizing effect \nwhile tensile strength decreased. Also, barrier properties to water and \noxygen improved. • Incorporation of montmorillonite into the biopolymer blend enhanced the \nmechanical and antimicrobial activities while barrier properties to water \nand oxygen reduced. ✓ \n✓ \n✓ \n✓ \nGiannakas et al. (2016) \n• EVOH (4 % w/v) \n• Chitosan \n• Nano zinc oxide (1 and 2 %w/w) \n• Addition of nano zinc oxide into the biopolymers blend caused an \nimprovement in barrier properties against water vapor and oxygen. • Presence of chitosan and nano zinc oxide caused excellent antimicrobial \nactivity against A. niger and E.coli. Adding nano zinc oxide improved barrier, \nmechanical, and antimicrobial properties. ✓ \n✓ \n✓ \n✓ \nSadeghi and Shahedi (2016\n(continued on nex 12 Additives \nKey findings \nM \nWB \nGB \nAO \nAM \nReference \n• Potassium nitrate \n• (0.1, 0.2, 0.3, 0.4, and 0.5 % w/w) \n• Addition of potassium nitrate into the biopolymers blend caused an \nimprovement in tensile strength and elasticity due to its crosslinking effect. • The degradation behavior can be improved with addition of potassium \nnitrate. ✓ \nJahan et al. (2016) \n• Methyldiphenyl diisocyanate (0.2,1, 2, and 3 % w/ \nw of the final PLA/chitosan solution) \n• Increasing concentration of methyldiphenyl diisocyanate in biopolymers \nblend improved tensile strength and contact angle values. ✓ \nGartner, Li, and Almenar (2015) \nHaghighi, et al. Food Packaging and Shelf Life 26 (2020) 100551 H. Haghighi, et al. H. Haghighi, et al. Biopolymer \nAdditives \nKey findings \nM \nWB \nGB \nAO \nAM \nReference \n• PVA \n• Chitosan (1 % w/v) \n• Potassium nitrate \n• (0.1, 0.2, 0.3, 0.4, and 0.5 % w/w) \n• Addition of potassium nitrate into the biopolymers blend caused an \nimprovement in tensile strength and elasticity due to its crosslinking effect. • The degradation behavior can be improved with addition of potassium \nnitrate. ✓ \nJahan et al. References Nordic \nPulp and Paper Research Journal, 30(4), 617–625. https://doi.org/10.3183/npprj- \n2015-30-04-p617-625. p\nBatista, J. T. S., Araújo, C. S., Peixoto Joele, M. R. S., Silva Júnior, J. O. C., & Lourenço, L. F. H. (2019). Study of the effect of the chitosan use on the properties of biodegradable \nfilms of myofibrillar proteins of fish residues using response surface methodology. Food Packaging and Shelf Life, 20, Article 100306. https://doi.org/10.1016/j.fpsl. 2019.100306. Bhuimbar, M. V., Bhagwat, P. K., & Dandge, P. B. (2019). Extraction and characterization \nof acid soluble collagen from fish waste: Development of collagen-chitosan blend as \nfood packaging film. Journal of Environmental Chemical Engineering, 7(2), Article \n102983. https://doi.org/10.1016/j.jece.2019.102983. Bonilla, J., & Sobral, P. J. A. (2016). Investigation of the physicochemical, antimicrobial \nand antioxidant properties of gelatin-chitosan edible film mixed with plant ethanolic \nextracts. Food Bioscience, 16, 17–25. https://doi.org/10.1016/j.fbio.2016.07.003. Bonilla, J., Poloni, T., Lourenço, R. V., & Sobral, P. J. A. (2018). Antioxidant potential of \neugenol and ginger essential oils with gelatin/chitosan films. Food Bioscience, 23, \n107–114. https://doi.org/10.1016/j.fbio.2018.03.007. Bonilla, J., Fortunati, E., Atarés, L., Chiralt, A., & Kenny, J. M. (2014). Physical, structural \nand antimicrobial properties of poly vinyl alcohol-chitosan biodegradable films. Food \nHydrocolloids, 35, 463–470. https://doi.org/10.1016/j.foodhyd.2013.07.002. El Bourakadi, K., Merghoub, N., Fardioui, M., Mekhzoum, M. E. M., Kadmiri, I. M., \nEssassi, E. M., et al. (2019). Chitosan/polyvinyl alcohol/thiabendazoluim-montmor­\nillonite bio-nanocomposite films: Mechanical, morphological and antimicrobial \nproperties. Composites Part B Engineering, 172, 103–110. https://doi.org/10.1016/j. 13 H. Haghighi, et al. Food Packaging and Shelf Life 26 (2020) 100551 packaging applications. Food Packaging and Shelf Life, 19, 31–39. https://doi.org/10. 1016/j.fpsl.2018.11.015. i packaging applications. Food Packaging and Shelf Life, 19, 31–39. https://doi.org/10. 1016/j.fpsl.2018.11.015. i Cao, T. L., Yang, S. Y., & Song, K. B. (2018). Development of burdock root inulin/chitosan \nblend films containing oregano and thyme essential oils. International Journal of \nMolecular Sciences, 19(1), 1–12. https://doi.org/10.3390/ijms19010131. Hajji, S., Chaker, A., Jridi, M., Maalej, H., Jellouli, K., Boufi, S., et al. (2016). Structural \nanalysis, and antioxidant and antibacterial properties of chitosan-poly (vinyl alcohol) \nbiodegradable films. Environmental Science and Pollution Research, 23(15), \n15310–15320. https://doi.org/10.1007/s11356-016-6699-9. Caro, N., Medina, E., Díaz-Dosque, M., López, L., Abugoch, L., & Tapia, C. (2016). Novel \nactive packaging based on films of chitosan and chitosan/quinoa protein printed with \nchitosan-tripolyphosphate-thymol nanoparticles via thermal ink-jet printing. Food \nHydrocolloids, 52, 520–532. https://doi.org/10.1016/j.foodhyd.2015.07.028. Hari, N., Francis, S., Rajendran Nair, A. G., & Nair, A. J. (2018). References Synthesis, character­\nization and biological evaluation of chitosan film incorporated with β-Carotene \nloaded starch nanocrystals. Food Packaging and Shelf Life, 16, 69–76. https://doi.org/ \n10.1016/j.fpsl.2018.02.003. Cazón, P., & Vázquez, M. (2020). Mechanical and barrier properties of chitosan combined \nwith other components as food packaging film. Environmental Chemistry Letters, 18, \n257–267. https://doi.org/10.1007/s10311-019-00936-3. i Hasanpour Ardekani-Zadeh, A., & Hosseini, S. F. (2019). Electrospun essential oil-doped \nchitosan/poly(ε-caprolactone) hybrid nanofibrous mats for antimicrobial food bio­\npackaging exploits. Carbohydrate Polymers, 223, Article 115108. https://doi.org/10. 1016/j.carbpol.2019.115108. ff Cazón, P., Vázquez, M., & Velazquez, G. (2018). Composite films of regenerate cellulose \nwith chitosan and polyvinyl alcohol: Evaluation of water adsorption, mechanical and \noptical properties. International Journal of Biological Macromolecules, 117, 235–246. https://doi.org/10.1016/j.ijbiomac.2018.05.148. i Hosseinnejad, M., & Jafari, S. M. (2016). Evaluation of different factors affecting anti­\nmicrobial properties of chitosan. International Journal of Biological Macromolecules, \n85, 467–475. https://doi.org/10.1016/j.ijbiomac.2016.01.022. p\ng\nj j\nCui, H., Surendhiran, D., Li, C., & Lin, L. (2020). Biodegradable zein active film containing \nchitosan nanoparticle encapsulated with pomegranate peel extract for food packa­\nging. Food Packaging and Shelf Life, 24, Article 100511. https://doi.org/10.1016/j. fpsl.2020.100511. Hou, C., Gao, L., Wang, Z., Rao, W., Du, M., & Zhang, D. (2020). Mechanical properties, \nthermal stability, and solubility of sheep bone collagen–chitosan films. Journal of \nFood Process Engineering, 43(1), Article e13086. https://doi.org/10.1111/jfpe.13086. p\nCui, S., Borgemenke, J., Qin, Y., Liu, Z., & Li, Y. (2019). Bio-based polycarbonates from \nrenewable feedstocks and carbon dioxide. In Y. Li, & X. Ge (Eds.). Advances in bioe­\nnergy (pp. 183–208). Elsevier Inc.. https://doi.org/10.1016/bs.aibe.2019.04.001. Hu, D., Wang, H., & Wang, L. (2016). Physical properties and antibacterial activity of \nquaternized chitosan/carboxymethyl cellulose blend films. LWT - Food Science and \nTechnology, 65, 398–405. https://doi.org/10.1016/j.lwt.2015.08.033. f Darmon, S. E., & Rudall, K. M. (1950). Infra-red and X-ray studies on chitin. Discussions of \nthe Faraday Society, 9, 251–260. Jahan, F., Mathad, R. D., & Farheen, S. (2016). Effect of mechanical strength on chitosan- \nPVA blend through ionic crosslinking for food packaging application. Materials Today \nProceedings, 3(10), 3689–3696. https://doi.org/10.1016/j.matpr.2016.11.014. fi De Leo, R., Quartieri, A., Haghighi, H., Gigliano, S., Bedin, E., & Pulvirenti, A. (2018). Application of pectin-alginate and pectin-alginate-laurolyl arginate ethyl coatings to \neliminate Salmonella enteritidis cross contamination in egg shells. Journal of Food \nSafety, 38(6), Article e12567. https://doi.org/10.1111/jfs.12567. Kakaei, S., & Shahbazi, Y. (2016). References Materials Science and Engineering C, 33(4), 1819–1841. https://doi.org/10.1016/j. msec.2013.01.010. g\nj\np\nKong, M., Chen, X. G., Xing, K., & Park, H. J. (2010). Antimicrobial properties of chitosan \nand mode of action: A state of the art review. International Journal of Food \nMicrobiology, 144(1), 51–63. https://doi.org/10.1016/j.ijfoodmicro.2010.09.012. i Friedman, M., & Juneja, V. K. (2010). Review of antimicrobial and antioxidative activities \nof chitosans in food. Journal of Food Protection, 73(9), 1737–1761. https://doi.org/ \n10.4315/0362-028X-73.9.1737. gy\np\ng\nj j\nKumar, S., & Thakur, K. (2017). Bioplastics - classification, production and their potential \nfood applications. Journal of Hill Agriculture, 8(2), 118. https://doi.org/10.5958/ \n2230-7338.2017.00024.6. i Gartner, H., Li, Y., & Almenar, E. (2015). Improved wettability and adhesion of polylactic \nacid/chitosan coating for bio-based multilayer film development. Applied Surface \nScience, 332, 488–493. https://doi.org/10.1016/j.apsusc.2015.01.157. Kumar, S., Mukherjee, A., & Dutta, J. (2020). Chitosan based nanocomposite films and \ncoatings: Emerging antimicrobial food packaging alternatives. Trends in Food Science \n& Technology, 97, 196–209. https://doi.org/10.1016/j.tifs.2020.01.002. Ghaderi, J., Hosseini, S. F., Keyvani, N., & Gómez-Guillén, M. C. (2019). Polymer \nblending effects on the physicochemical and structural features of the chitosan/poly \n(vinyl alcohol)/fish gelatin ternary biodegradable films. Food Hydrocolloids, 95, \n122–132. https://doi.org/10.1016/j.foodhyd.2019.04.021. Kumar, S., Shukla, A., Baul, P. P., Mitra, A., & Halder, D. (2018). Biodegradable hybrid \nnanocomposites of chitosan/gelatin and silver nanoparticles for active food packa­\nging applications. Food Packaging and Shelf Life, 16, 178–184. https://doi.org/10. 1016/j.fpsl.2018.03.008. Giannakas, A., Vlacha, M., Salmas, C., Leontiou, A., Katapodis, P., Stamatis, H., et al. (2016). Preparation, characterization, mechanical, barrier and antimicrobial prop­\nerties of chitosan/PVOH/clay nanocomposites. Carbohydrate Polymers, 140, 408–415. https://doi.org/10.1016/j.carbpol.2015.12.072. Lago, M. A., Sendón, R., de Quirós, A. R. B., Sanches-Silva, A., Costa, H. S., Sánchez- \nMachado, D. I., et al. (2014). Preparation and characterization of antimicrobial films \nbased on chitosan for active food packaging applications. Food and Bioprocess \nTechnology, 7(10), 2932–2941. https://doi.org/10.1007/s11947-014-1276-z. p\ng\nj\np\nGoy, R. C., de Britto, D., & Assis, O. B. G. (2009). A review of the antimicrobial activity of \nchitosan. Polimeros: Ciência e Tecnologia, 19(3), 241–247. https://doi.org/10.1590/ \nS0104-14282009000300013. Leceta, I., Guerrero, P., & de la Caba, K. (2013). Functional properties of chitosan-based \nfilms. Carbohydrate Polymers, 93(1), 339–346. https://doi.org/10.1016/j.carbpol. 2012.04.031. Guo, Y., Chen, X., Yang, F., Wang, T., Ni, M., Chen, Y., et al. (2019). Preparation and \ncharacterization of chitosan-based ternary blend edible films with efficient anti­\nmicrobial activities for food packaging applications. Journal of Food Science, 84(6), \n1411–1419. https://doi.org/10.1111/1750-3841.14650. References Effect of chitosan-gelatin film incorporated with \nethanolic red grape seed extract and Ziziphora clinopodioides essential oil on survival \nof Listeria monocytogenes and chemical, microbial and sensory properties of minced \ntrout fillet. LWT - Food Science and Technology, 72, 432–438. https://doi.org/10. 1016/j.lwt.2016.05.021. de Morais Lima, M., Carneiro, L. C., Bianchini, D., Dias, A. R. G., da R. Zavareze, E., \nPrentice, C., et al. (2017). Structural, thermal, physical, mechanical, and barrier \nproperties of chitosan films with the addition of xanthan gum. Journal of Food Science, \n82(3), 698–705. https://doi.org/10.1111/1750-3841.13653. Kamdem, D. P., Shen, Z., Nabinejad, O., & Shu, Z. (2019). Development of biodegradable \ncomposite chitosan-based films incorporated with xylan and carvacrol for food \npackaging application. Food Packaging and Shelf Life, 21, Article 100344. https://doi. org/10.1016/j.fpsl.2019.100344. Del Nobile, M. A., Di Benedetto, N., Suriano, N., Conte, A., Corbo, M. R., & Sinigaglia, M. (2009). Combined effects of chitosan and MAP to improve the microbial quality of \namaranth homemade fresh pasta. Food Microbiology, 26(6), 587–591. https://doi.org/ \n10.1016/j.fm.2009.03.012. Kan, J., Liu, J., Yong, H., Liu, Y., Qin, Y., & Liu, J. (2019). Development of active \npackaging based on chitosan-gelatin blend films functionalized with Chinese haw­\nthorn (Crataegus pinnatifida) fruit extract. International Journal of Biological \nMacromolecules, 140, 384–392. https://doi.org/10.1016/j.ijbiomac.2019.08.155. Do Yoon, S., Kim, Y. M., Kim, B. I. L., & Je, J. Y. (2017). Preparation and antibacterial \nactivities of chitosan-gallic acid/polyvinyl alcohol blend film by LED-UV irradiation. Journal of Photochemistry and Photobiology B, Biology, 176, 145–149. https://doi.org/ \n10.1016/j.jphotobiol.2017.09.024. Khan, I., Mansha, M., & Mazumder, M. A. J. (2018). Polymer blends. In M. J. Mazumder, \nH. Sheardown, & A. Al-Ahmed (Eds.). Polymers and polymeric composite: A reference \nseries (pp. 1–38). Cham, Switzerland: Springer. https://doi.org/10.1007/978-3-319- \n92067-2_16-1. Dutta, J., Tripathi, S., & Dutta, P. K. (2012). Progress in antimicrobial activities of chitin, \nchitosan and its oligosaccharides: A systematic study needs for food applications. Food Science and Technology International, 18(1), 3–34. https://doi.org/10.1177/ \n1082013211399195. Khouri, J., Penlidis, A., & Moresoli, C. (2019). Viscoelastic properties of crosslinked \nchitosan Films. Processes, 7(3), 157. https://doi.org/10.3390/pr7030157. Dutta, P. K., Tripathi, S., Mehrotra, G. K., & Dutta, J. (2009). Perspectives for chitosan \nbased antimicrobial films in food applications. Food Chemistry, 114(4), 1173–1182. https://doi.org/10.1016/j.foodchem.2008.11.047. i Khwaldia, K., Basta, A. H., Aloui, H., & El-Saied, H. (2014). Chitosan-caseinate bilayer \ncoatings for paper packaging materials. Carbohydrate Polymers, 99, 508–516. https:// \ndoi.org/10.1016/j.carbpol.2013.08.086. Elsabee, M. Z., & Abdou, E. S. (2013). Chitosan based edible films and coatings: A review. References Applied Surface Science, 449, 591–602. https:// \ndoi.org/10.1016/j.apsusc.2018.01.022. Liu, Y., Wang, S., & Lan, W. (2018). Fabrication of antibacterial chitosan-PVA blended \nfilm using electrospray technique for food packaging applications. International \nJournal of Biological Macromolecules, 107(PartA), 848–854. https://doi.org/10.1016/ \nj.ijbiomac.2017.09.044. Philp, J. C., Bartsev, A., Ritchie, R. J., Baucher, M. A., & Guy, K. (2013). Bioplastics \nscience from a policy vantage point. New Biotechnology, 30(6), 635–646. https://doi. org/10.1016/j.nbt.2012.11.021. i g\nj\nPriyadarshi, R., & Rhim, J.-W. (2020). Chitosan-based biodegradable functional films for \nfood packaging applications. Innovative Food Science & Emerging Technologies, 62, \nArticle 102346. https://doi.org/10.1016/j.ifset.2020.102346. Liu, Y., Wang, S., Zhang, R., Lan, W., & Qin, W. (2017). Development of poly(lactic acid)/ \nchitosan fibers loaded with essential oil for antimicrobial applications. Nanomaterials, \n7(7), 194. https://doi.org/10.3390/nano7070194. Qu, L., Chen, G., Dong, S., Huo, Y., Yin, Z., Li, S., et al. (2019). Improved mechanical and \nantimicrobial properties of zein/chitosan films by adding highly dispersed nano-TiO2. Industrial Crops and Products, 130, 450–458. https://doi.org/10.1016/j.indcrop.2018. 12.093. López-Caballero, M. E., Gómez-Guillén, M. C., Pérez-Mateos, M., & Montero, P. (2005). A \nchitosan-gelatin blend as a coating for fish patties. Food Hydrocolloids, 19(2), \n303–311. https://doi.org/10.1016/j.foodhyd.2004.06.006. Raafat, D., & Sahl, H. G. (2009). Chitosan and its antimicrobial potential - A critical \nliterature survey. Microbial Biotechnology, 2(2), 186–201. https://doi.org/10.1111/j. 1751-7915.2008.00080.x. i Lozano-Navarro, J. I., Díaz-Zavala, N. P., Velasco-Santos, C., Martínez-Hernández, A. L., \nTijerina-Ramos, B. I., García-Hernández, M., et al. (2017). Antimicrobial, optical and \nmechanical properties of chitosan–starch films with natural extracts. International \nJournal of Molecular Sciences, 18(5), 1–18. https://doi.org/10.3390/ijms18050997. Ramos, M., Valdés, A., Beltrán, A., & Garrigós, M. (2016). Gelatin-based films and coat­\nings for food packaging applications. Coatings, 6(4), 41. https://doi.org/10.3390/ \ncoatings6040041. Luchese, C. L., Pavoni, J. M. F., dos Santos, N. Z., Quines, L. K., Pollo, L. D., Spada, J. C., \net al. (2018). Effect of chitosan addition on the properties of films prepared with corn \nand cassava starches. Journal of Food Science and Technology, 55(8), 2963–2973. https://doi.org/10.1007/s13197-018-3214-y. Ramziia, S., Ma, H., Yao, Y., Wei, K., & Huang, Y. (2018). Enhanced antioxidant activity \nof fish gelatin–chitosan edible films incorporated with procyanidin. Journal of Applied \nPolymer Science, 135(10), 1–10. https://doi.org/10.1002/app.45781. l Luzi, F., Fortunati, E., Giovanale, G., Mazzaglia, A., Torre, L., & Balestra, G. M. (2017). Cellulose nanocrystals from Actinidia deliciosa pruning residues combined with \ncarvacrol in PVA_CH films with antioxidant/antimicrobial properties for packaging \napplications. International Journal of Biological Macromolecules, 104, 43–55. https:// \ndoi.org/10.1016/j.ijbiomac.2017.05.176. References Ren, L., Yan, X., Zhou, J., Tong, J., & Su, X. (2017). Influence of chitosan concentration on \nmechanical and barrier properties of corn starch/chitosan films. International Journal \nof Biological Macromolecules, 105, 1636–1643. https://doi.org/10.1016/j.ijbiomac. 2017.02.008. f Ma, W., Tang, C. H., Yin, S. W., Yang, X. Q., Wang, Q., Liu, F., et al. (2012). Characterization of gelatin-based edible films incorporated with olive oil. Food \nResearch International, 49(1), 572–579. https://doi.org/10.1016/j.foodres.2012.07. 037. Rezaee, M., Askari, G., EmamDjomeh, Z., & Salami, M. (2018). Effect of organic additives \non physiochemical properties and anti-oxidant release from chitosan-gelatin com­\nposite films to fatty food simulant. International Journal of Biological Macromolecules, \n114, 844–850. https://doi.org/10.1016/j.ijbiomac.2018.03.122. i Marsh, K., & Bugusu, B. (2007). Food packaging - Roles, materials, and environmental \nissues: Scientific status summary. Journal of Food Science, 72(3), https://doi.org/10. 1111/j.1750-3841.2007.00301.x. Rhim, J.-W., & Ng, P. K. W. (2007). Natural biopolymer-based nanocomposite films for \npackaging applications. Critical Reviews in Food Science and Nutrition, 47(4), 411–433. https://doi.org/10.1080/10408390600846366. j\nMartins da Costa, J. C., Lima Miki, K. S., da Silva Ramos, A., & Teixeira-Costa, B. E. (2020). Development of biodegradable films based on purple yam starch/chitosan for \nfood application. Heliyon, 6(4), Article e03718. https://doi.org/10.1016/j.heliyon. 2020.e03718. Richards, A. G. (1951). The integument of arthropods: The chemical components and their \nproperties, the anatomy and development, and the permeability. Minneapolis: University \nof Minnesota Press. Ritchie, H., & Roser, M. (2018). Plastic pollution. Our world in data. https:// \nourworldindata.org/plastic-pollution. Mohammadi, R., Amin, M., Rouhi, M., Kariminejad, M., Mohammad, A., & Sadeghi, E. (2018). Physico-mechanical and structural properties of eggshell membrane gelatin- \nchitosan blend edible films. International Journal of Biological Macromolecules, 107, \n406–412. https://doi.org/10.1016/j.ijbiomac.2017.09.003. Rouget, C. (1859). Des substances amylacees dans Ie tissue des animaux, specialement les \nAtricules (Chitine). Comptes rendus hebdomadaires des seances de l’Academie des sci­\nences, 48, 792–795. Rujnić-Sokele, M., & Pilipović, A. (2017). Challenges and opportunities of biodegradable \nplastics: A mini review. Waste Management Research, 35(2), 132–140. https://doi. org/10.1177/0734242X16683272. Mousavi Khaneghah, A., Hashemi, S. M. B., & Limbo, S. (2018). Antimicrobial agents and \npackaging systems in antimicrobial active food packaging : An overview of ap­\nproaches and interactions. Food and Bioproducts Processing, 111, 1–19. https://doi. org/10.1016/j.fbp.2018.05.001. Sadeghi, K., & Shahedi, M. (2016). Physical, mechanical, and antimicrobial properties of \nethylene vinyl alcohol copolymer/chitosan/nano-ZnO (ECNZn) nanocomposite films \nincorporating glycerol plasticizer. Journal of Food Measurement & Characterization, \n10(1), 137–147. https://doi.org/10.1007/s11694-015-9287-7. i Mujtaba, M., Morsi, R. E., Kerch, G., Elsabee, M. References Z., Kaya, M., Labidi, J., et al. (2019). Current advancements in chitosan-based film production for food technology; A re­\nview. International Journal of Biological Macromolecules, 121, 889–904. https://doi. org/10.1016/j.ijbiomac.2018.10.109. Salari, M., Sowti Khiabani, M., Rezaei Mokarram, R., Ghanbarzadeh, B., & Samadi Kafil, \nH. (2018). Development and evaluation of chitosan based active nanocomposite films \ncontaining bacterial cellulose nanocrystals and silver nanoparticles. Food \nHydrocolloids, 84, 414–423. https://doi.org/10.1016/j.foodhyd.2018.05.037. Muxika, A., Etxabide, A., Uranga, J., Guerrero, P., & de la Caba, K. (2017). Chitosan as a \nbioactive polymer: Processing, properties and applications. International Journal of \nBiological Macromolecules, 105, 1358–1368. https://doi.org/10.1016/j.ijbiomac. 2017.07.087. Samsalee, N., & Sothornvit, R. (2019). Development and characterization of porcine \nplasma protein-chitosan blended films. Food Packaging and Shelf Life, 22, Article \n100406. https://doi.org/10.1016/j.fpsl.2019.100406. Narasagoudr, S. S., Hegde, V. G., Vanjeri, V. N., Chougale, R. B., & Masti, S. P. (2020). Ethyl vanillin incorporated chitosan/poly(vinyl alcohol) active films for food \npackaging applications. Carbohydrate Polymers, 236, Article 116049. https://doi.org/ \n10.1016/j.carbpol.2020.116049. Shahbazi, M., Rajabzadeh, G., & Ahmadi, S. J. (2017). Characterization of nanocomposite \nfilm based on chitosan intercalated in clay platelets by electron beam irradiation. Carbohydrate Polymers, 157, 226–235. https://doi.org/10.1016/j.carbpol.2016.09. 018. f Newell, R., Qian, Y., & Raimi, D. (2016). Global energy outlook 2015. Cambridge, MA: \nNational Bureau of Economic Researchhttps://doi.org/10.3386/w22075 Working \nPaper No. 22075. f Shapi’i, R. A., & Othman, S. H. (2016). Effect of concentration of chitosan on the me­\nchanical, morphological and optical properties of tapioca starch film. International \nFood Research Journal, 23, S187–S193. http://www.ifrj.upm.edu.my/23%20(06)% \n202016%20supplementary/(27)%20IFRJ-16271%20Othman.pdf. Ngo, D. H., & Kim, S. K. (2014). Antioxidant effects of chitin, chitosan, and their deri­\nvatives. Advances in Food and Nutrition Research, 73, 15–31. https://doi.org/10.1016/ \nB978-0-12-800268-1.00002-0. Ngo, T. M. P., Nguyen, T. H., Dang, T. M. Q., Tran, T. X., & Rachtanapun, P. (2020). Characteristics and antimicrobial properties of active edible films based on pectin and \nnanochitosan. International Journal of Molecular Sciences, 21(6), 2224. https://doi. org/10.3390/ijms21062224. Sharif, R., Mujtaba, M., Rahman, M. U., Shalmani, A., Ahmad, H., Anwar, T., et al. (2018). The multifunctional role of chitosan in horticultural crops; a review. Molecules, 23(4), \n1–20. https://doi.org/10.3390/molecules23040872. p\ng\nShin, J., & Selke, S. E. M. (2014). Food packaging. In S. Clark, S. Jung, & B. Lamsal (Eds.). Food processing: Principles and applications (pp. 249–273). Chichester, UK: John Wiley \n& Sons, Ltd. https://doi.org/10.1002/9781118846315.ch11. li No, H. K., Meyers, S. P., Prinyawiwatkul, W., & Xu, Z. (2007). Soroudi, A., & Jakubowicz, I. (2013). Recycling of bioplastics, their blends and bio­\ncomposites: A review. European Polymer Journal, 49(10), 2839–2858. https://doi.org/ References Lee, J.-H., Lee, J.-H., Yang, H.-J., & Song, K. (2015). Preparation and characterization of \nbrewer’s spent grain protein-chitosan composite films. Journal of Food Science and \nTechnology, 52(11), 7549–7555. https://doi.org/10.1007/s13197-015-1941-x. Lei, J., Yang, L., Zhan, Y., Wang, Y., Ye, T., Li, Y., et al. (2014). Plasma treated poly­\nethylene terephthalate/polypropylene films assembled with chitosan and various \npreservatives for antimicrobial food packaging. Colloids and Surfaces B: Biointerfaces, \n114, 60–66. https://doi.org/10.1016/j.colsurfb.2013.09.052. Gutiérrez, T. J. (2017). Chitosan applications for the food industry. In S. Ahmed, & S. Ikram (Eds.). Chitosan: Derivatives, composites and applications (pp. 183–232). Scrivener Publishing LLC, Wiley. https://doi.org/10.1002/9781119364849 ch8. Haghighi, H., Leugoue, S. K., Pfeifer, F., Siesler, H. W., Licciardello, F., Fava, P., et al. (2020). Development of antimicrobial films based on chitosan-polyvinyl alcohol \nblend enriched with ethyl lauroyl arginate (LAE) for food packaging applications. Food Hydrocolloids, 100, Article 105419. https://doi.org/10.1016/j.foodhyd.2019. 105419. Li, K., Jin, S., Liu, X., Chen, H., He, J., & Li, J. (2017). Preparation and characterization of \nchitosan/soy protein isolate nanocomposite film reinforced by Cu nanoclusters. Polymers, 9(7), 247. https://doi.org/10.3390/polym9070247. Li, S., Yan, Y., Guan, X., & Huang, K. (2020). Preparation of a hordein-quercetin-chitosan \nantioxidant electrospun nanofibre film for food packaging and improvement of the \nfilm hydrophobic properties by heat treatment. Food Packaging and Shelf Life, 23, \nArticle 100466. https://doi.org/10.1016/j.fpsl.2020.100466. l Haghighi, H., Biard, S., Bigi, F., De Leo, R., Bedin, E., Pfeifer, F., et al. (2019). Comprehensive characterization of active chitosan-gelatin blend films enriched with \ndifferent essential oils. Food Hydrocolloids, 95, 33–42. https://doi.org/10.1016/j. foodhyd.2019.04.019. g\nj\nLi, W., Zheng, K., Chen, H., Feng, S., Wang, W., & Qin, C. (2019). Influence of nano \ntitanium dioxide and clove oil on chitosan–starch film characteristics. Polymers, \n11(9), 1418. https://doi.org/10.3390/polym11091418. y\nHaghighi, H., De Leo, R., Bedin, E., Pfeifer, F., Siesler, H. W., & Pulvirenti, A. (2019). Comparative analysis of blend and bilayer films based on chitosan and gelatin en­\nriched with LAE (lauroyl arginate ethyl) with antimicrobial activity for food ( ),\np\ng\np\ny\nLiang, J., Wang, R., & Chen, R. (2019). The impact of cross-linking mode on the physical 14 H. Haghighi, et al. Food Packaging and Shelf Life 26 (2020) 100551 and antimicrobial properties of a chitosan/bacterial cellulose composite. Polymers, \n11(3), 491. https://doi.org/10.3390/polym11030491. and antimicrobial properties of a chitosan/bacterial cellulose composite. Polymers, \n11(3), 491. https://doi.org/10.3390/polym11030491. nanocrystals isolated from rice straw. Applied Surface Science, 449, 591–602. https:// \ndoi.org/10.1016/j.apsusc.2018.01.022. nanocrystals isolated from rice straw. References Applications of chitosan for \nimprovement of quality and shelf life of foods: A review. Journal of Food Science, \n72(5), 87–100. https://doi.org/10.1111/j.1750-3841.2007.00383.x. Shojaee Kang Sofla, M., Mortazavi, S., & Seyfi, J. (2020). Preparation and characterization \nof polyvinyl alcohol/chitosan blends plasticized and compatibilized by glycerol/ \npolyethylene glycol. Carbohydrate Polymers, 232, Article 115784. https://doi.org/10. 1016/j.carbpol.2019.115784. Noshirvani, N., Ghanbarzadeh, B., Gardrat, C., Rezaei, M. R., Hashemi, M., Le Coz, C., \net al. (2017). Cinnamon and ginger essential oils to improve antifungal, physical and \nmechanical properties of chitosan-carboxymethyl cellulose films. Food Hydrocolloids, \n70, 36–45. https://doi.org/10.1016/j.foodhyd.2017.03.015. f Siracusa, V., Rocculi, P., Romani, S., & Dalla Rosa, M. (2008). Biodegradable polymers for \nfood packaging: A review. Trends in Food Science & Technology, 19(12), 634–643. https://doi.org/10.1016/j.tifs.2008.07.003. i\n70, 36–45. https://doi.org/10.1016/j.foodhyd.2017.03.015. p\ng\nj\ny\nOjagh, S. M., Rezaei, M., Razavi, S. H., & Hosseini, S. M. H. (2010). Effect of chitosan \ncoatings enriched with cinnamon oil on the quality of refrigerated rainbow trout. Food Chemistry, 120(1), 193–198. https://doi.org/10.1016/j.foodchem.2009.10.006. Sirisha Nallan Chakravartula, S., Lourenço, R. V., Balestra, F., Quinta Barbosa Bittante, A. M., do A. Sobral, P. J., & Dalla Rosa, M. (2020). Influence of pitanga (Eugenia uniflora \nL.) leaf extract and/or natamycin on properties of cassava starch/chitosan active \nfilms. Food Packaging and Shelf Life, 24, Article 100498. https://doi.org/10.1016/j. fpsl.2020.100498. Parameswaranpillai, J., Thomas, S., & Grohens, Y. (2015). Polymer blends: State of the \nart, new challenges, and opportunities. In S. Thomas, Y. Grohens, & P. Jyotishkumar \n(Eds.). Characterization of polymer blends: Miscibility, morphology and interfaces (pp. 1– \n6). Wiley-VCH Verlag GmbH & Co. KGaA. https://doi.org/10.1002/9783527645602 \nch01. Soni, B., Mahmoud, B., Chang, S., El-Giar, E. M., & Hassan, E. B. (2018). Physicochemical, \nantimicrobial and antioxidant properties of chitosan/TEMPO biocomposite packa­\nging films. Food Packaging and Shelf Life, 17, 73–79. https://doi.org/10.1016/j.fpsl. 2018.06.001. Peelman, N., Ragaert, P., De Meulenaer, B., Adons, D., Peeters, R., Cardon, L., et al. (2013). Application of bioplastics for food packaging. Trends in Food Science & \nTechnology, 32(2), 128–141. https://doi.org/10.1016/j.tifs.2013.06.003. Soroudi, A., & Jakubowicz, I. (2013). Recycling of bioplastics, their blends and bio­\ncomposites: A review. European Polymer Journal, 49(10), 2839–2858. https://doi.org/ Perumal, A. B., Sellamuthu, P. S., Nambiar, R. B., & Sadiku, E. R. (2018). Development of \npolyvinyl alcohol/chitosan bio-nanocomposite films reinforced with cellulose 15 H. Haghighi, et al. Food Packaging and Shelf Life 26 (2020) 100551 gum arabic polyelectrolyte complexed films. Carbohydrate Polymers, 217, 116–125. https://doi.org/10.1016/j.carbpol.2019.03.084. Suriyatem, R., Auras, R. A., & Rachtanapun, P. (2018). References Carbohydrate Polymers, 116, 237–242. https://doi.org/10.1016/j.carbpol.2014.07.039. Yu, Z., Li, B., Chu, J., & Zhang, P. (2018). Silica in situ enhanced PVA/chitosan biode­\ngradable films for food packages. Carbohydrate Polymers, 184, 214–220. https://doi. org/10.1016/j.carbpol.2017.12.043. van den Oever, M., Molenveld, K., van der Zee, M., & Bos, H. (2017). Bio-based and \nbiodegradable plastics - facts and figures: Focus on food packaging in the Netherlands. (Wageningen Food & Biobased Research; No. 1722). Wageningen: Wageningen Food & \nBiobased Researchhttps://doi.org/10.18174/408350. Yun, Y. H., Lee, C. M., Kim, Y. S., & Do Yoon, S. (2017). Preparation of chitosan/polyvinyl \nalcohol blended films containing sulfosuccinic acid as the crosslinking agent using UV \ncuring process. Food Research International, 100(part 1), 377–386. https://doi.org/10. 1016/j.foodres.2017.07.030. Verlee, A., Mincke, S., & Stevens, C. V. (2017). Recent developments in antibacterial and \nantifungal chitosan and its derivatives. Carbohydrate Polymers, 164, 268–283. https:// \ndoi.org/10.1016/j.carbpol.2017.02.001. fi g\nj\np\nVodnar, D. C., Pop, O. L., Dulf, F. V., & Socaciu, C. (2015). Antimicrobial efficiency of \nedible films in food industry. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 43(2), \n302–312. https://doi.org/10.15835/nbha43210048. i Zargar, V., Asghari, M., & Dashti, A. (2015). A review on chitin and chitosan polymers: \nStructure, chemistry, solubility, derivatives, and applications. ChemBioEng Reviews, \n2(3), 204–226. https://doi.org/10.1002/cben.201400025. f p\ng\nWang, H., Qian, J., & Ding, F. (2018). Emerging chitosan-based films for food packaging \napplications. Journal of Agricultural and Food Chemistry, 66, 395–413. https://doi.org/ \n10.1021/acs.jafc.7b04528. p\ng\nZhang, H., Li, R., & Liu, W. (2011). Effects of chitin and its derivative chitosan on post­\nharvest decay of fruits: A review. International Journal of Molecular Sciences, 12(2), \n917–934. https://doi.org/10.3390/ijms12020917. j\nWang, Y., Du, H., Xie, M., Ma, G., Yang, W., Hu, Q., et al. (2019). Characterization of the \nphysical properties and biological activity of chitosan films grafted with gallic acid \nand caffeic acid: A comparison study. Food Packaging and Shelf Life, 22, Article \n100401. https://doi.org/10.1016/j.fpsl.2019.100401. g\nj\nZhang, L., Wang, H., Jin, C., Zhang, R., Li, L., Li, X., et al. (2017). Sodium lactate loaded \nchitosan-polyvinyl alcohol/montmorillonite composite film towards active food \npackaging. Innovative Food Science and Emerging Technologies, 42, 101–108. https:// \ndoi.org/10.1016/j.ifset.2017.06.007. f\n100401. https://doi.org/10.1016/j.fpsl.2019.100401. Zhang, L., Liu, Z., Sun, Y., Wang, X., & Li, L. (2020). Combined antioxidant and sensory \neffects of active chitosan/zein film containing α-tocopherol on Agaricus bisporus. Food \nPackaging and Shelf Life, 24, Article 100470. https://doi.org/10.1016/j.fpsl.2020. 100470. Wang, X. Y., Wang, C. S., & Heuzey, M. C. (2016). References Improvement of mechanical \nproperties and thermal stability of biodegradable rice starch–based films blended \nwith carboxymethyl chitosan. Industrial Crops and Products, 122, 37–48. https://doi. org/10.1016/j.indcrop.2018.05.047. Xu, T., Gao, C. C., Feng, X., Yang, Y., Shen, X., & Tang, X. (2019). Structure, physical and \nantioxidant properties of chitosan-gum arabic edible films incorporated with cin­\nnamon essential oil. International Journal of Biological Macromolecules, 134, 230–236. https://doi.org/10.1016/j.ijbiomac.2019.04.189. g\nj\np\nUnger, M., Sedlmair, J., Siesler, H. W., & Hirschmugl, C. (2014). 3D FT-IR imaging \nspectroscopy of phase-separation in a poly(3-hydroxybutyrate)/poly(L-lactic acid) \nblend. Vibrational Spectroscopy, 75, 169–172. https://doi.org/10.1016/j.vibspec. 2014.07.007. Xu, J., Xia, R., Zheng, L., Yuan, T., & Sun, R. (2019). Plasticized hemicelluloses/chitosan- \nbased edible films reinforced by cellulose nanofiber with enhanced mechanical \nproperties. Carbohydrate Polymers, 224, Article 115164. https://doi.org/10.1016/j. carbpol.2019.115164. Uranga, J., Puertas, A. I., Etxabide, A., Dueñas, M. T., Guerrero, P., & de la Caba, K. (2019). Citric acid-incorporated fish gelatin/chitosan composite films. Food \nHydrocolloids, 86, 95–103. https://doi.org/10.1016/j.foodhyd.2018.02.018. Yam, K. L., & Lee, D. S. (2012). Emerging food packaging technologies: An overview. In K. Yam, & D. S. Lee (Eds.). Emerging food packaging technologies principle and practice (pp. 1–9). Woodhead Publishing Limited. https://doi.org/10.1533/9780857095664.1. Vadivel, M., Sankarganesh, M., Raja, J. D., Rajesh, J., Mohanasundaram, D., & Alagar, M. (2019). Bioactive constituents and bio-waste derived chitosan / xylan based biode­\ngradable hybrid nanocomposite for sensitive detection of fish freshness. Food \nPackaging and Shelf Life, 22, Article 100384. https://doi.org/10.1016/j.fpsl.2019. 100384 Yeamsuksawat, T., & Liang, J. (2019). Characterization and release kinetic of crosslinked \nchitosan film incorporated with α-tocopherol. Food Packaging and Shelf Life, 22, \nArticle 100415. https://doi.org/10.1016/j.fpsl.2019.100415. i Younis, H. G. R., & Zhao, G. (2019). Physicochemical properties of the edible films from \nthe blends of high methoxyl apple pectin and chitosan. International Journal of \nBiological Macromolecules, 131, 1057–1066. https://doi.org/10.1016/j.ijbiomac. 2019.03.096. Valizadeh, S., Naseri, M., Babaei, S., Hosseini, S. M. H., & Imani, A. (2019). Development \nof bioactive composite films from chitosan and carboxymethyl cellulose using glu­\ntaraldehyde, cinnamon essential oil and oleic acid. International Journal of Biological \nMacromolecules, 134, 604–612. https://doi.org/10.1016/j.ijbiomac.2019.05.071. Youssef, A. M., El-Sayed, S. M., El-Sayed, H. S., Salama, H. H., & Dufresne, A. (2016). Enhancement of Egyptian soft white cheese shelf life using a novel chitosan/car­\nboxymethyl cellulose/zinc oxide bionanocomposite film. Carbohydrate Polymers, 151, \n9–19. https://doi.org/10.1016/j.carbpol.2016.05.023. van den Broek, L. A. M., Knoop, R. J. I., Kappen, F. H. J., & Boeriu, C. G. (2015). Chitosan \nfilms and blends for packaging material. References Complexation of chitosan and gelatin: \nFrom soluble complexes to colloidal gel. International Journal of Polymeric Materials \nand Polymeric Biomaterials, 65(2), 96–104. https://doi.org/10.1080/00914037.2015. 1074908. Wang, J., Wang, L., Yu, H., Zain-ul-Abdin, Chen, Y., Chen, Q., et al. (2016). Recent \nprogress on synthesis, property and application of modified chitosan: An overview. International Journal of Biological Macromolecules, 88, 333–344. https://doi.org/10. 1016/j.ijbiomac.2016.04.002. f Zhang, J., Xu, W.-R., Zhang, Y.-C., Han, X.-D., Chen, C., & Chen, A. (2020). In situ gen­\nerated silica reinforced polyvinyl alcohol/liquefied chitin biodegradable films for \nfood packaging. Carbohydrate Polymers, 238, Article 116182. https://doi.org/10. 1016/j.carbpol.2020.116182. j\np\nZhao, Y., Teixeira, J. S., Gänzle, M. M., & Saldaña, M. D. A. (2018). Development of \nantimicrobial films based on cassava starch, chitosan and gallic acid using subcritical \nwater technology. The Journal of Supercritical Fluids, 137, 101–110. https://doi.org/ \n10.1016/j.supflu.2018.03.010. j j\nWu, H., Lei, Y., Lu, J., Zhu, R., Xiao, D., Jiao, C., et al. (2019). Effect of citric acid induced \ncrosslinking on the structure and properties of potato starch/chitosan composite \nfilms. Food Hydrocolloids, 97, Article 105208. https://doi.org/10.1016/j.foodhyd. 2019.105208. Wu, Y., Ying, Y., Liu, Y., Zhang, H., & Huang, J. (2018). Preparation of chitosan/poly \nvinyl alcohol films and their inhibition of biofilm formation against Pseudomonas \naeruginosa PAO1. International Journal of Biological Macromolecules, 118, 2131–2137. https://doi.org/10.1016/j.ijbiomac.2018.07.061. l\nZheng, K., Li, W., Fu, B., Fu, M., Ren, Q., Yang, F., et al. (2018). Physical, antibacterial \nand antioxidant properties of chitosan films containing hardleaf oatchestnut starch \nand Litsea cubeba oil. International Journal of Biological Macromolecules, 118, 707–715. https://doi.org/10.1016/j.ijbiomac.2018.06.126. g\nj j\nXing, F., Zhang, S., Li, J., Li, L., & Shi, J. (2018). Crosslinked chitosan-based biocomposite \nfilms modified with soy protein isolate. Polymer Composites, 39(3), 942–949. https:// \ndoi.org/10.1002/pc.24024. Zimet, P., Mombrú, Á., Mombrú, D., Castro, A., Villanueva, J., Pardo, H., et al. (2019). Physico-chemical and antilisterial properties of nisin-incorporated chitosan/carbox­\nymethyl chitosan films. Carbohydrate Polymers, 219, 334–343. https://doi.org/10. 1016/j.carbpol.2019.05.013. Xu, T., Gao, C., Feng, X., Huang, M., Yang, Y., Shen, X., et al. (2019). Cinnamon and clove \nessential oils to improve physical, thermal and antimicrobial properties of chitosan- 16"
https://openalex.org/W2049659810
https://europepmc.org/articles/pmc2363838?pdf=render
English
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Effect of pravastatin on survival in patients with advanced hepatocellular carcinoma. A randomized controlled trial
British journal of cancer
2,001
cc-by
5,393
Effect of pravastatin on survival in patients with advanced hepatocellular carcinoma. A randomized controlled trial Yamasaki1, T Nagase1, Y Inui1, N Ito1, Y Matsuda1, M Inada1, S Tamura1, S Noda1, Y Imai1 and S Kawata1, 2, E Yamasaki1, T Nagase1, Y Inui1, N Ito1, Y Matsuda1, M Inada1, S Tamura1, S No Y Matsuzawa1 S Kawata1, 2, E Yamasaki1, T Nagase1, Y Inui1, N Ito1, Y Matsuda1, M Inada1, S Tamura1, S Noda1, Y Imai1 and Y Matsuzawa1 1Department of Internal Medicine and Molecular Science, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan, and 2Department of Internal Medicine, Yamagata University School of Medicine, Yamagata 990-9585, Japan Summary Chemotherapy is not effective for hepatocellular carcinoma (HCC). HMG-CoA redutase inhibitors have cytostatic activity for cancer cells, but their clinical usefulness is unknown. To investigate whether pravastatin, a potent HMG-CoA reductase inhibitor, prolongs survival in patients with advanced HCC, this randomized controlled trial was conducted between February 1990 and February 1998 at Osaka University Hospital. 91 consecutive patients <71 years old (mean age 62) with unresectable HCC were enroled in this study. 8 patients were withdrawn because of progressive liver dysfunction; 83 patients were randomized to standard treatment with or without pravastatin. All patients underwent transcatheter arterial embolization (TAE) followed by oral 5-FU 200 mg–1 d for 2 months. Patients were then randomly assigned to control (n = 42) and pravastatin (n = 41) groups. Pravastatin was administered at a daily dose of 40 mg. The effect of pravastatin on tumour growth was assessed by ultrasonography. Primary endpoint was death due to progression of HCC. The duration of pravastatin administration was 16.5 ± 9.8 months (mean ± SD). No patients in either group were lost to follow-up. Median survival was 18 months in the pravastatin group versus 9 months in controls (P = 0.006). The Cox proportional hazards model showed that pravastatin was a significant factor contributing to survival. Pravastatin prolonged the survival of patients with advanced HCC, suggesting its value for adjuvant treatment. © 2001 Cancer Research Campaign http://www.bjcancer.com Keywords: hepatocellular carcinoma; pravastatin; HMG-CoA reductase inhibitor; survival these inhibitors could lead to suppression of tumour growth by interfering with the function of Ras p21. However, there are no report on whether such inhibitors have potential in cancer patients. In this study, we tested whether administration of HMG-CoA reductase inhibitor would contribute to the survival of patients with advanced HCC. Received 22 February 2000 Revised 28 December 2000 Accepted 19 January 2001 Correspondence to: S Kawata Effect of pravastatin on survival in patients with advanced hepatocellular carcinoma. A randomized controlled trial We administered pravastatin (40 mg day–1), for which the liver has a high affinity, to HCC patients in a randomized controlled trial after transcatheter arterial emboliza- tion (TAE) (Charnsagavej et al, 1983; Yamada et al, 1983; Stefanini et al, 1995) and oral 5-fluorouracil (5-FU) as standard treatment. Hepatocellular carcinoma (HCC) causes death in patients with cirrhosis and is one of the most prevalent malignant tumours worldwide (Simonetti et al, 1991; Okuda, 1992; Di Bisceglie, 1995). Its incidence has substantially increased in Japan (Okuda et al, 1987) and in the United States (El-Serag and Mason, 1999). HCC has a dismal 5-year survival rate, and there is no effective chemotherapy. these inhibitors could lead to suppression of tumour growth by interfering with the function of Ras p21. However, there are no report on whether such inhibitors have potential in cancer patients. In this study, we tested whether administration of HMG-CoA reductase inhibitor would contribute to the survival of patients with advanced HCC. We administered pravastatin (40 mg day–1), for which the liver has a high affinity, to HCC patients in a randomized controlled trial after transcatheter arterial emboliza- tion (TAE) (Charnsagavej et al, 1983; Yamada et al, 1983; Stefanini et al, 1995) and oral 5-fluorouracil (5-FU) as standard treatment. Signal transduction inhibitors, including farnesyl transferase inhibitors and mitogen-activated protein kinase (MAPK) kinase inhibitors, have been developed as anti-cancer agents (Gibbs et al, 1993; James et al, 1993; Kohl et al, 1993; Stebolt- Leopold et al, 1999). The activity of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, the rate-limiting enzyme of cholesterol biosynthesis, has been positively correlated with mammalian cell growth (Kandutsch and Chen, 1979). Mevalonic acid, produced by HMG-CoA reductase, regulates cell growth independent of cholesterogenesis: Ras p21 and lamins A and B undergo covalent modification at the carboxyl terminus by meval- onate-derived farnesyl isoprenoid (Goldstein and Brown, 1990). HMG-CoA reductase inhibitors exhibit cytostatic activity possibly as signal transduction inhibitors, when added to proliferating cells in culture or in vivo (Goldstein et al, 1979; Habenicht et al, 1980; Maltese et al, 1985). Decreased farnesyl isoprenoid formation by British Journal of Cancer (2001) 84(7), 886–891 © 2001 Cancer Research Campaign British Journal of Cancer (2001) 84(7), 886–891 © 2001 Cancer Research Campaign http://www.bjcancer.com © 2001 Cancer Research Campaign doi: 10.1054/ bjoc.2001.1716, available online at http://www.idealibrary.com on Assessment Death was the primary endpoint. Clinical status and laboratory data, including hepatic and renal function tests and haematologic examinations, were followed at least once a month in the outpa- tient clinics of Osaka University Hospital and during hospitaliza- tion. Duing the first 2 months, serum transaminases, bilirubin, prothrombin time, cholesterol and albumin, were checked weekly to detect any liver damage due to pravastatin. Serum creatine kinase activity was also checked every month. Tumour status was followed by US or computed tomography at least 4 times each year and tumour marker (AFP, alfa-fetoprotein) monthly. Maximal diameters of the main tumours in each group were sequentially measured with US at 2, 6 and 12 months after starting pravastatin to evaluate its effect on tumour growth. Pravastatin was stopped when patients had satisfied exclusion criteria Follow-up till death; lost to follow-up (n = 0) Patients The cohort comprised 91 consecutive patients with unresectable advanced HCC who were younger than 70 years old (Figure 1); 71 patients were male and 20 were female. The mean age was 62 (ranging from 39 to 70). The diagnosis of cirrhosis was confined by biochemical data and ultrasonography (US). The histologic diagnosis of underlying liver disease was carried out in 47 patients by US-guided liver biopsy. The diagnosis of HCC was based on clinical features and findings from US, computed tomography, and hepatic arteriography. Tumour stage (I–IV) was determined according to the criteria of the Primary Liver Cancer Study Group of Japan: stage I, a single tumour ≤2 cm in its greatest dimension without vascular invasion; stage II, a single tumour <2 cm in its greatest dimension with vascular invasion, or multiple tumours 886 Effect of pravastatin on human hepatoma Eligible patients (n = 91) Randomization (n = 83) Pravastatin group (n = 41) Standard Treatment: TAE and oral 5-FU (n = 91) Control group (n = 42) Withdrawal due to advanced liver dysfunction during or after standard treatment (n = 8) Pravastatin was stopped when patients had satisfied exclusion criteria Follow-up till death; lost to follow-up (n = 0) Follow-up till death; lost to follow-up (n = 0) Completed trial (n = 41) Completed trial (n = 42) Figure 1 Protocol for enrolment, randomization and follow-up. TAE; transcatheter arterial embolization drugs. Pravastatin was discontinued when patients showed any of the exclusion criteria, or signs and symptoms ascribed to adverse effects of the drug. The control group was not treated with any anti-cancer drugs. Written informed consent was obtained from all subjects prior to entry. The protocol in this study was approved by the local scientific ethical committee. Measurement of urinary pravastatin Compliance with pravastatin treatment was assessed by detecting pravastatin in urine according to the method described previously (Koga et al, 1995). Urine was obtained every 2 months after entry. Figure 1 Protocol for enrolment, randomization and follow-up. TAE; transcatheter arterial embolization with a maximum diameter ≤2 cm confined to one lobe, or a single tumour with a diameter >2 cm, without vascular invasion; stage III, a single tumour with a diameter >2 cm, with vascular invasion, or multiple tumours >2 cm confined to one lobe; stage IV, multiple tumours in more than one lobe or associated vascular invasion in the first branch of the portal or hepatic veins (The Liver Cancer Study Group of Japan, 1989). The histologic diagnosis of HCC was confirmed in the 47 patients with US-guided biopsy. All patients had died by the end of February 1998, and the histologic diagnosis of HCC was confirmed by autopsy or needle necropsy in all patients. Statistical analysis Fisher’s exact (two-tailed) test was used to compare the baseline characteristics of both groups. Survival curves were generated by the Kaplan–Meier method. The log-rank test was used to compare survival. Factors contributing to survival were selected using the Cox proportional-hazards regression analysis. Changes in lab- oratory profiles between the 2 groups were compared using Mann–Whitney test. As standard treatment, all patients underwent transcatheter arterial embolization (TAE). For the TAE procedure, patients were treated with gelatin-sponge particles and ethyl ester of poppyseed oil fatty acids containing 38% iodine by weight (Lipiodol; Andre- Gelbe Laboratories, Paris, France) after intraarterial infusion of doxorubicin (30 mg) (Matsuda et al, 1994). Oral 5-FU at a daily dose of 200 mg was started 2 weeks after the TAE procedure and continued for 2 months. © 2001 Cancer Research Campaign RESULTS 91 patients with advanced HCC were enroled between February 1990 and January 1993. All patients underwent TAE and oral administration of 5-FU. 8 patients were withdrawn because of progressive liver dysfunction. The control (n = 42) and pravastatin (n = 41) groups were similar in terms of age, sex, liver function, renal function, stage of disease (The Liver Cancer Study Group of Japan, 1989), and presence of vascular invasion in portal veins, extra-hepatic spread or past history of encephalopathy (Table 1) at the start of pravastatin treatment. Both groups were not different in TAE-related complications. 33 patients in the pravastatin group had cirrhosis versus 34 controls. In the pravastatin group, the Child–Pugh classification in the cirrhotic patients was class A for 5 patients and class B for 28, compared with 4 and 30 in the control group, respectively. The Karnofsky performance scale was 80 to 90 for 34 patients and 60 to 70 for 7 patients in the pravas- tatin group versus 80 to 90 for 36 patients and 60 to 70 for 6 patients in the control group. HBs Ag was positive in 5 pravastatin patients and 4 controls. Anti-HCV antibody by second or third generation ELISA (Ortho Diagnostics, Tokyo) was positive in 33 8 of 91 patients were withdrawn during standard treatment for any of the following exclusion criteria: hyperbilirubinaemia >51 micro mol l–1; hyperammonaemia >70 micro mol l–1; prothrombin time >14 seconds; hypoalbuminaemia <25 g l–1; serum alanine aminotransferase (ALT) level >150 U l–1; or massive ascites. The remaining 83 patients were randomly divided into control (n = 42) and pravastatin (n = 41) groups after standard treatment; randomization was generated by a computer program. Survival analysis in both groups began on the 15th day after 5-FU was completed. The pravastatin group received oral drug at a dose of 20 mg beginning on the 15th day after the end of 5-FU administra- tion. 2 weeks later, pravastatin was increased to 40 mg per day. RESULTS The pravastatin group was not treated with any other anti-cancer British Journal of Cancer (2001) 84(7), 886–891 © 2001 Cancer Research Campaign 888 S Kawata et al 888 S Kawata et al Table 1 Baseline demographics for pravastatin and control groups Table 1 Baseline demographics for pravastatin and control groups Table 1 Baseline demographics for pravastatin and control groups Variable Pravastatin group (n = 41) Control group (n = 42) P value* n (%) n (%) Age (y) <60 15 (37) 19 (45) >0.2 ≥60 26 (63) 23 (55) Sex Female 10 (24) 8 (20) >0.2 Male 31 (76) 34 (80) Tumour stage IV 11 (27) 13 (31) >0.2 II or III 30 (73) 29 (69) Vascular invasion in portal veins Yes 5 (12) 6 (14) >0.2 No 36 (88) 36 (86) Extra-hepatic spread Yes 2 (5) 1 (2) >0.2 No 39 (95) 41 (98) Serum ALT** level <60 U l–1 25 (61) 23 (55) >0.2 ≥60 U l–1 16 (39) 19 (45) Serum alkaline phosphatase level <200 IU l–1 26 (63) 24 (57) >0.2 ≥200 IU l–1 15 (37) 18 (43) Serum albumin level ≥35 g l–1 21 (51) 20 (47) >0.2 <35 g l–1 20 (49) 22 (53) Serum total bilirubin level <22 micro mol l–1 17 (41) 19 (45) >0.2 ≥22 micro mol l–1 24 (59) 23 (55) Serum creatinine level <1.2 mg dl-1 21 (51) 20 (47) >0.2 ≥1.2 mg dl-1 20 (49) 22 (53) Past history of encephalopathy Yes 2 (5) 2 (5) >0.2 No 39 (95) 40 (95) Tumour stage was according to the criteria of the Liver Cancer Study Group of Japan (The Liver Cancer Study Group of Japan, 1989). *Fisher’s exact test; **alanine aminotransferase. Tumour stage was according to the criteria of the Liver Cancer Study Group of Japan (The Liver Cancer Study Group of Japan, 1989). *Fisher’s exact test; **alanine aminotransferase. By the end of February 1998, all patients in both groups had died due to HCC progression and/or hepatic failure. The median survival was 18 months in the pravastatin group and 9 months in controls. Survival in the pravastatin group was significantly longer (P = 0.006 by the log-rank test) (Figure 2). Using the Cox proportional-hazards model, pravastatin was a significant factor contributing to prolonged survival (P = 0.02 for univariate analysis and P = 0.005 for multivariate analysis) (Table 3). RESULTS Absence of the vascular invasion in portal veins was also a significant factor contributing to prolonged survival (P = 0.03 for multivariate analysis). of the pravastatin group and 35 of the control group. Patients were unresectable because of extensive tumour in 28 pravastatin patients and 30 controls and because of advanced liver disease in 13 and 12, respectively. The median follow-up was 11 months (range 2 to 66 months) by the end of February 1998. No patients were lost to follow-up. The duration of pravastatin administration was 16.5 ± 9.8 months (mean ± SD). Pravastatin was discontinued in all patients because of advancing disease and not because of any adverse effects of the medicine. The reasons for discontinuation were hyperbilirubinaemia in 7 patients, prolonged prothrombin time in 5, massive ascites in 8, hyperammonaemia in 9, and hypoalbu- minaemia in 12. No patient had an elevation of ALT levels to >150 U l–1. During the administration period, pravastation was detected in all urine samples. Serum AFP level was lower in the pravastatin group compared with controls 6 months and 1 year after the entry (P = 0.04 and P = 0.03, respectively; Mann–Whitney test) (Table 2). Regression of tumour was not observed in the pravastatin group at 2, 6 or 12 months. However, increase in maximal diameter was significantly less in the pravastatin group at 6 and 12 months compared with controls (P = 0.03 and P = 0.01, respectively; Mann–Whitney test), suggesting that tumour growth was suppressed by pravastatin. Serum ALT and total bilirubin did not differ between the 2 groups at 2 and 6 months after the start of pravastatin (Table 2). However, the serum cholesterol concentration was lower in the pravastatin group at 2 and 6 months (P < 0.001 for both). The median of total bilirubin level 1 year after entry was 28 micro mol l–1 (n = 25) in the pravastatin group and 43 (n = 11) in controls (P = 0.04, Mann–Whitney test). In addition, the median of serum albumin level 1 year after entry was 31 g l–1 in the pravastatin and 26 in the control group (P = 0.02). These results suggested that liver function deteriorated more rapidly in the control group. In the control group, 35 patients died of tumour progression and 7 died of hepatic failure. In the pravastatin group, 36 died of tumour progression and 5 died of hepatic failure. RESULTS Of the 36 patients who died of tumour progression in the pravastatin group, 1 had severe cholestasis due to tumour invasion into the bile ducts, 3 had massive pleural effusion due to lung metastasis, and 28 had © 2001 Cancer Research Campaign British Journal of Cancer (2001) 84(7), 886–891 Effect of pravastatin on human hepatoma 889 Table 2 Changes in liver function test and tumour markers after start of pravastatin administration Variable Pravastatin group (n = 41) Control group (n = 42) P value Serum ALT* level (U l–1) Baseline 58# (42–85)## 63 (45–97) > 0.2 2M 57 (39–90) (n = 41) 65 (42–92) (n = 42) > 0.2 6M 60 (40–86) (n = 35) 59 (43–108) (n = 22) > 0.2 1Y 52 (36–74) (n = 25) 68 (48–93) (n = 11) > 0.2 Serum total bilirubin level (micro mol l–1) Baseline 24 (18–37) 25 (18–40) > 0.2 2M 25 (19–35) (n = 41) 28 (19–44) (n = 42) > 0.2 6M 28 (21–38) (n = 35) 36 (25–55) (n = 22) > 0.2 1Y 28 (22–40) (n = 25) 43 (24–58) (n = 11) 0.04 Serum albumin level (g l–1) Baseline 35 (29–40) 36 (26–38) > 0.2 2M 36 (28–41) (n = 41) 34 (25–36) (n = 42) > 0.2 6M 33 (26–37) (n = 35) 29 (24–34) (n = 22) 0.06 1Y 31 (24–35) (n = 25) 26 (23–32) (n = 11) 0.02 Serum AFP level (ng dl–1) Baseline 130 (25–5140) 120 (5–3450) > 0.2 2M 108 (21–4270) (n = 41) 172 (45–6710) (n = 42) > 0.2 6M 218 (60–6540) (n = 35) 292 (85–9573) (n = 22) 0.04 1Y 261 (78–7940) (n = 25) 4140 (140–17300) (n = 11) 0.03 Serum total cholesterol level (mmol l–1) Baseline 4.30 (3.67–5.03) 4.20 (3.58–4.96) > 0.2 2M 3.56 (3.25–3.94) (n = 41) 3.93 (3.42–4.75) (n = 42) < 0.001 6M 3.24 (2.80–3.82) (n = 35) 3.78 (3.52–4.63) (n = 22) < 0.001 1Y 3.10 (2.63–3.55) (n = 25) 3.40 (2.86–4.07) (n = 11) 0.03 Diameter of main tumour (mm) Baseline 38 (22–48) 36 (24–52) > 0.2 2M 40 (24–52) (n = 41) 43 (25–62) (n = 42) > 0.2 6M 45 (30–67) (n = 35) 60 (34–83) (n = 22) 0.03 1Y 52 (42–78) (n = 25) 73 (45–106) (n = 11) 0.01 2M, 2 months after pravastatin; 6M, 6 months after pravastatin; 1Y, 1 year after pravastatin. RESULTS # Median of values, ## range of values. Table 2 Changes in liver function test and tumour markers after start of pravastatin administration 2M, 2 months after pravastatin; 6M, 6 months after pravastatin; 1Y, 1 year after pravastatin. # Median of values, ## range of values 2M, 2 months after pravastatin; 6M, 6 months after pravastatin; 1Y, 1 year after pravastatin. # Median of values, ## range of values. 1.0 0.8 0.6 0.4 0.2 0 0 1 2 3 4 5 pravastatin group control group Years of follow-up Cumulative survival Figure 2 Kaplan–Meier survival curves in pravastatin (n = 41) and control (n = 42) groups. The median survival was 18 months in the pravastatin group and 9 months in the control group (P = 0.006 by the log-rank test) 1.0 0.8 0.6 0.4 0.2 0 0 1 2 3 4 5 pravastatin group control group Years of follow-up Cumulative survival massive ascites due to the obstruction of the portal vein by tumour. Of the 5 patients who died of hepatic failure in the pravastatin group, 3 patients developed hepatic coma with progressive cirrhosis, and 2 had rupture of gastric varices. © 2001 Cancer Research Campaign DISCUSSION Chemotherapy that prolongs survival is not available for advanced HCC. To test whether pravastatin, a potent HMG-CoA reductase inhibitor, might increase the survival of patients with advanced HCC, we designed a randomized clinical trial with death as the primary endpoint. We chose TAE and 5-FU as standard treatment before introducing pravastatin administration. TAE prevents tumour progression (Charnsagavej et al, 1983; Yamada et al, 1983; Stefanini et al, 1995) and is one of the standard treatments for unresectable HCC in Japan. 5-FU also has activity against HCC (Cavalli et al, 1981; Coi et al, 1984; Falkson et al, 1984). To avoid any bias based on pretreatment, all 91 patients underwent a single TAE followed by oral 5-FU at a uniform dose for 2 months. 83 patients completed the standard treatment and were randomly assigned to pravastatin or control groups. Years of follow-up Figure 2 Kaplan–Meier survival curves in pravastatin (n = 41) and control (n = 42) groups. The median survival was 18 months in the pravastatin group and 9 months in the control group (P = 0.006 by the log-rank test) The biochemical data after randomization suggested that liver function deteriorated more rapid in patients who were not taking pravastatin (Table 2). This may represent more rapid progression of either tumour or underlying liver disease in the control groups. Serum AFP concentrations more rapidly increased in controls (Table 2). Regression of the main tumour was not observed in the pravastatin group. Yet, growth of the main tumours was signifi- cantly slowed at 6 and 12 months after pravastatin administration, suggesting that pravastatin suppressed tumour growth. Pravastatin effects on survival may therefore have resulted from stabilization Patients in the pravastatin group survived significantly longer than those in the control group (Figure 2). Analysis using the Cox proportional-hazards model showed that treatment with pravas- tatin was the significant factor contributing to prolonged survival (P = 0.02 for univariate analysis and P = 0.005 for multivariate analysis). This result suggests that HMG-CoA reductase inhibitors offer a survival advantage in the treatment of advanced HCC. DISCUSSION © 2001 Cancer Research Campaign British Journal of Cancer (2001) 84(7), 886–891 890 S Kawata et al 890 S Kawata et al 890 Table 3 Factors contributing to survival in HCC patients g p Univariate analysis Multivariate analysis Variable Risk ratio 95% CI* P value# Risk ratio 95% CI P value Age < 60 1 1 ≥60 1.72 0.58–4.84 >0.2 1.30 0.67–2.65 >0.2 Sex Female 1 1 Male 0.62 0.22–1.72 >0.2 0.82 0.38–1.70 >0.2 Tumour stage IV 1 1 II or III 0.67 0.22–2.06 >0.2 0.72 0.34–1.63 >0.2 Vascular invasion in portal veins Yes 1 1 No 0.38 0.12–1.25 0.10 0.18 0.04–0.81 0.03 Extra-hepatic spread Yes 1 1 No 0.65 0.22–1.98 >0.2 0.57 0.25–1.62 >0.2 Serum ALT## level <60 U l–1 1 1 ≥60 U l–1 1.46 0.45–4.64 >0.2 1.80 0.85–4.16 >0.2 Serum alkaline phosphatase level <200 IU l–1 1 1 ≥200 IU l–1 2.05 0.66–6.35 >0.2 1.47 0.64–3.67 >0.2 Serum albumin level ≥35 g l–1 1 1 <35 g l–1 1.33 0.43–4.35 >0.2 1.58 0.68–3.15 >0.2 Serum total bilirubin level <22 micro mol l–1 1 1 >22 micro mol l–1 2.3 0.71–7.46 >0.2 1.35 0.62–3.05 >0.2 Serum creatinine level <1.2 mg dl–1 1 1 ≥1.2 mg dl–1 1.84 0.56–6.13 >0.2 1.63 0.55–4.65 >0.2 Past history of encephalopathy Yes 1 1 No 0.67 0.21–2.08 >0.2 0.52 0.18–1.50 >0.2 Pravastatin administration No 1 1 Yes 0.42 0.20–0.83 0.02 0.35 0.17–0.61 0.005 *CI denotes confidence interval. # Cox proportional-hazards regression analysis. ## analine aminotransferase. values. In general, patients with advanced HCC tolerated long- term administration of a daily dose of 40 mg of pravastatin. of the tumour. Signal transduction inhibitors are generally cyto- static in their activity against malignant cells, and our results are consistent with other in vivo studies (Stebolt-Leopold et al, 1999). HMG-CoA reductase inhibitors have been reported to have cyto- static activity, possibly due to suppression of protein isoprenylation (Sinensky et al, 1990). Cholesterol is a primary source for membrane formation and thus is in great demand in rapid-growth tissues such as cancers. Previously, we reported that HMG-CoA reductase activity and protein content, as well as cholesterol bio- synthesis, were increased in human HCC tissues (Kawata et al, 1990). The liver has a high affinity for pravastatin (Tsujita et al, 1986). © 2001 Cancer Research Campaign DISCUSSION Prior to this study, we observed that pravastatin at a daily dose of 40 mg led to a significant decrease in serum concentrations of cholesterol and AFP in 3 patients with hypercholesterolaemia associated with HCC as a paraneoplastic syndrome (data not shown). This agent might have been effectively taken up to hepatoma cells in vivo. In future studies, to clarify the mechanism(s) whereby pravastatin may prolong survival in advanced HCC, liver biopsy should be done before and after therapy to monitor changes in protein isoprenylation and cholesterol content in tumour cells. ( p , ) Long-term administration of a daily dosage of 40 mg of pravas- tatin has been reported to prevent cardiovascular events (Byington et al, 1995; Shepherd et al, 1995). This dosage was well-tolerated without severe adverse effects. Because our patients had advanced HCC with chronic hepatitis and/or cirrhosis, we administered a daily dose of 20 mg of pravastatin during the first 2 weeks to check adverse effects. No significant problems were noted, and all patients subsequently received 40 mg of pravastatin. During the first 2 months, we found no elevations of serum bilirubin or transaminase values which could be attributed to pravastatin. Throughout the observation period, there were no significant differences in liver function tests or haematologic data between the 2 groups. After 2 months, pravastatin was continued until exclu- sion criteria were satisfied. All patients in the pravastatin group appeared to die of progressive disease. Patients with chronic liver disease often have muscle cramps. In this study, the frequency of muscle cramps did not differ between the 2 groups (data not shown). None of the patients in either group showed more than a 10-fold elevation in serum creatine kinase This study was not blinded, although it was randomized. The study also included treatment with TAE and oral 5-FU, although randomization was done after completion of those treatments. © 2001 Cancer Research Campaign British Journal of Cancer (2001) 84(7), 886–891 Effect of pravastatin on human hepatoma 891 These factors may have introduced bias in assessing the effect of pravastatin on survival. In the future, a randomized, placebo- controlled, double-blind study will be needed to clarify whether HMG-CoA reductase inhibitors are useful as adjuvant anti-cancer therapy. Kohl NE, Mosser SD, deSolms SJ, Giuliani EA, Pompliano DL, Graham SL, Smith RL, Scolnick EM, Oliff A and Gibbs JB (1993) Selective inhibition of ras-dependent transformation by a farnesyltransferase inhibitor. REFERENCES Sinensky M, Beck LA, Leonard S and Evans R (1990) Differential inhibitory effects of lovastatin on protein isoprenylation and sterol synthesis. J Biol Chem 265: 19937–19941 Byington KP, Jukema JW, Salonen JT, Bertram P, Bruscheke AV, Hoen H, Furberg CD and Mancini GBJ (1995) Reduction in cardiovascular events during pravastatin therapy. Pooled analysis of clinical events of the pravastatin atherosclerosis intervention program. Circulation 92: 2419–2425 Stebolt-Leopold JS, Dudley DT, Herrera R, Becelaere KV, Wiland A, Gowan RC, Tecle H, Barrett SD, Bridges A, Przybranowski S, Leopold WR and Saltiel AR (1999) Blockade of the MAP kinase pathway suppresses growth of colon tumors in vivo. Nature Med 5: 810–816 Cavalli F, Rozencweig M, Goldhirsch A and Hansen HH (1981) Phase II study of oral VP-16-213 in hepatocellular carcinoma. Eur J Cancer Clin Oncol 17: 1079–1082 Stefanini GF, Amorati P, Beselli M, Mucci F, Celi A, Arienti V, Roversi R, Rossi C, Re G and Gasbarrini G (1995) Efficacy of transarterial targeted treatment on survival of patients with hepatocellular carcinoma. Cancer 75: 2427–2434 Charnsagavej S, Chuang VP, Wallace S, Soo CS and Bowers T (1983) Transcatheter management of promary carcinoma of the liver. Radiology 147: 51–55 The Liver Cancer Study Group of Japan (1989) The general rules of the clinical and pathological study of primary liver cancer. Jpn J Sur 19: 98–129 Coi TK, Lee NW and Wong J (1984) Chemotherapy for advanced hepatocellular carcinoma. Adriamycin versus quadruple chemotherapy. Cancer 53: 401 Tsujita Y, Kuroda M, Shimada Y, Tanzawa K, Arai M, Kaneko I, Tanaka M, Matsuda H, Tarumi C, Watanabe Y and Fujii S (1986) CS-514, a competitive inhibitor of 3-hydroxy-3-methylglutaryl coenzyme A reductase: tissue- selective inhibiton of sterol synthesis and hypolipidemic effect on various animal species. Biophys Biochem Acta 877: 50–60 Di Bisceglie AM (1995) Hepatitis C and hepatoecllular carcinoma. Seminar Liver Dis 15: 64–69 El-Serag HB and Mason AC (1999) Rising incidence of heptocellular carcinoma in the United States. N Engl J Med 340: 745–750 Falkson G, MacIntyre JM, Moertel CG, Johnson LA and Scherman RC (1984) Primary liver cancer: An Eastern JM Cooperative Oncology Group Trial. Cancer 54: 970–977 Yamada R, Sato M, Kawabata M, Nakatsuka H, Nakamura K and Takashima S (1983) Hepatic artery embolization in 120 patients with unresectable hepatoma. DISCUSSION Science 260: 1934–1937 Maltese WA, Defendini R, Green RA, Sheridan KM and Donley DK (1985) Suppression of murine neuroblastoma growth in vivo by mevinolin, a competitive inhibitor of 3-hydroxy-3-methylglutaryl coenzyme A reductase. J Clin Invest 76: 1748–1754 In conclusion, pravastatin prolonged the survival of patients with advanced HCC. This result should encourage the develop- ment of HMG-CoA reductase inhibitors as adjuvant therapy against HCC. Matsuda Y, Kawata S, Nagase T, Maeda Y, Yamasaki E, Kiso S, Ishiguro H and Matsuzawa Y (1994) Interleukin-6 in transcatheter arterial embolization for patients with hepatocellular carcinoma. Cancer 73: 53–57 Okuda K (1992) Hepatocellular carcinoma: recent progress. Hepatology 15: 948–963 REFERENCES Radiology 148: 397–401 Gibbs JB, Pompliano DL, Mosser SD, Rands E, Lingham RB, Singh SB, Scolnick EM, Kohl NE and Oliff A (1993) Selective inhibition of farnesyl: transferase blocks ras processing in vivo. J Biol Chem 268: 7617–7620 Goldstein JL and Brown MS (1990) Regulation of the mevalonate pathway. Nature 343: 425–430 ACKNOWLEDGEMENTS Okuda K, Fujimoto I, Hanai A and Urano Y (1987) Changing incidence of hepatocellular carcinoma in Japan. Cancer Res 47: 4967–4972 This work was supported in part by a Grant-in-Aid for Cancer Research to S Kawata (Grant No. 07274240) from the Ministry of This work was supported in part by a Grant-in-Aid for Cancer Research to S Kawata (Grant No. 07274240) from the Ministry of Shepherd J, Lobbe SM, Ford I, Isles CG, Lorimer AR, Macfarlane PW, Mackillop JH, Packard CJ, for the West of Scotland Coronary Prevention Study Group (1995) Prevention of coronary heart disease with pravastatin in men with hypercholesterolemia. N Engl J Med 333: 1301–1307 Research to S Kawata (Grant No. 07274240) from the Ministry of Education, Science, and Culture in Japan. Education, Science, and Culture in Japan. Simonetti RG, Camma C, Fiorello F, Politi F, D’amico G and Pagliaro L (1991) Hepatocellular carcinoma. A worldwide problem and the major risk factors. Dig Dis Sci 36: 962–972 Hepatocellular carcinoma. A worldwide problem and the major risk factors. Dig Dis Sci 36: 962–972 APPENDIX Goldstein JL, Helgeson JAS and Brown MS (1979) Inhibition of cholesterol synthesis with compactin renders growth of cultured cells dependent on the low density lipoprotein receptors. J Biol Chem 254: 5403–5409 Current author addresses Habenicht AJR, Glomset JA and Ross R (1980) Relation of cholesterol and mevalonic acid to the cell cycle in smooth muscle and Swiss 3T3 cells stimulated to divide by platelet-derived growth factor. J Biol Chem 255: 5134–5140 Dr Kawata: Second Department of Internal Medicine, Yamagata University School of Medicine, 2-2-2 Iida-Nishi, Yamagata 990-9585, Japan. James GL, Goldstein JL, Brown MS, Rawson TE, Somers TC, McDowell RS, Crowley CW, Lucas BK, Levinson AD and Marsters Jr JC (1993) Benzodiazepine peptidomimetics: protein inhibitor of ras farnesylation in animal cells. Science 260: 1937–1942 Drs Yamasaki, Nagase, Inui, Ito, Tamura, and Matsuzawa: Department of Internal Medicine and Molecular Science, Graduate School of Medicine, B5, Osaka University, 2-2 Yamada- oka, Suita, Osaka 565-0871, Japan. Kandutsch AA and Chen HW (1979) Consequences of blocked sterol synthesis in cultured cells, DNA synthesis and membrane composition. J Biol Chem 252: 409–415 Drs Matsuda and Inada: Department of Internal Medicine, Toyonaka Municipal Hospital, 4-14-1 Shibahara-cho, Toyonaka, Osaka 5675, Japan. Kawata S, Takaishi K, Nagase T, Ito N, Tamura S, Matsuzawa Y and Tarui S (1990) Increase in the active form of 3-hydroxy-3-methylglutaryl coenzyme A reductase in human hepatocellular carcinoma: Possible mechanism for alteration of cholesterol biosynthesis. Cancer Res 50: 3270–3273 Dr Noda: Department of Internal Medicine, Suita Municipal Hospital, 2-13-20 Katayama-cho, Suita, Osaka 564, Japan. Dr. Imai: Department of Internal Medicine, Ikeda Municipal Hospital, 3-1-18 Johnan, Ikeda, Osaka 563; Japan. Koga T, Kawabata K, Arai K, Matsushima N, Koike H, Komai T, Rei M and Nakamura H (1995) Comparative pharmacokinetics of pravastatin and simvastatin. Bull Mol Biol Med 20: 103–105 British Journal of Cancer (2001) 84(7), 886–891 © 2001 Cancer Research Campaign
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Beobachtungen über die Nervenelemente bei Ganoïden und Knochenfischen
Archiv für mikroskopische Anatomie
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public-domain
17,504
Beobachtungen fiber die Nervenelemente bei Ganoi'den und Knochenfischen. Teil I: Der Bau der Nervenzellen. Von Anton Nemiloif Assistent am anatomisch-histol. Laboratorium der Universitiit St. Petersburg. H i e r z u T a f e l I, I I u n d 7 T e x t f i g u r e n . In der letzten Zeit sind in die mikroskopische Technik eine Reihe yon neuen Methoden (yon B j e 1 s c h o w s k i, D o n a g g i o, R a m 5 n C a j a 1 und vielen anderen) eingeftihrt worden, welche unsere Kenntnisse tiber den feineren Bau der Nervenzellen- und -fasern in betr~tchtlichem Make erweitert haben. Ungeachtet dessert sind zahlreiche Fragen tiber die wichtigsten morphologischen Beziehungen des Nervensystems bei weitem noch nicht mit d e r $orgfalt und Genauigkeit festgestellt, welche fiir irgendwelche wissenschaftliche Schlussfolgerungen erforderlich ist. Der Mangel an Tatsachenmateriat, das Fehlen genau festgestellter Befunde lassen eine Verallgemeinerung der letzteren, sowie Schlussfolgerungen aus denselben, welche doch das Endziel einer wissenschaftlichen Untersuchung darstellen, nicht zu. Dieser Umstand veranlasste reich, den histologischen Bau der ~N'ervenzellen. und -fasern vermittelst verschiedener Fixierungs- und Farbungsmethoden aufs neue zu untersuchen. I. U n t e r s u c h u n g s o b j e k t . Als solches wahlte ich verschiedene Repri~sentanten yon Stisswasserfischen. Beim Arbeiten mit dermassen unbestandigen und eigensinnigen Methoden, wie es die Mehrzahl der Untersuchungsverfahren des iNervensystems sind, ist die Auswahl eines passenden Objektes besonders wichtig. Es mtissen nicht nur die Dimensionen der histologischen Elemente des betreffenden Tieres, sondern auch der Grad der A r c h i v f. mikrosk. Anat. Bd. 72. 1 2 Anton Nemiloff: Widerstandsfahigkeit seiner Gewebe dem Untersuchungsverfahrea gegenfiber in Berticksichtigung gezogen werden. Fernerhin ist auch die Zuganglichkeit des betreffenden Objektes, d. h. die MSglichkeit, dasselbe zu jeder Zeit und in beliebiger Menge zu erhalten in Betracht zu ziehen. In Berticksichtigung dieser Forderungen stellen die Fische ein sehr geeignetes Untersuchungsobjekt vor. Fiir meine Untersuchungen benutzte ich sowohl G a n o i d e n (Acipenser ruthenus) als auch verschiedene Knochenfische wie L u c i o p e r c a sandra, Perca fluviatilis, Acerina cernua, Coregonus, Silurus glanis, L o t a v u l g a r i s und andere. Zum Studium des feineren Baues des Nervensystems eignet sich das Gehirn 'und Riickenmark weniger als die peripheren Nerven, da erstere zahlreiehe Gliaelemente enthalten und sich schwer fixieren lassen. Ich stelltc daher haupts~,chlich an Kopf-, Spinal: und teilweise sympathischen Ganglien und an den yon ihnen abgehenden Nervenst~mlmehen meine Untersuchungen an. Die Elemente des Gehirns und Rtiekenmarks sind jedoch zur Kontrolle benutzt worden. Als ein besonders dankbares Objekt erwies sich fiir reich Lota vulgaris. Bereits G o r o n o w i t s c h (18) hat darauf hingewiesen, dass die betri~chtliche Breite der Kopfhiihle, sowie die verh~ltnism~ssig weiche Konsistenz vieler Sehiidelknochen yon Lota eine morphologisehe Untersuchung seines Nervensystems begiinstigt. ~ieinerseits kann ieh noeh hinzufiigen, dass Lota ein ausgezeichnetes histologisches Material darstellt. Die Nervenelemente yon Lota sind der 5[ethylenblauf~rbung leicht zugiinglich. Die Ganglien yon Lota enthalten neben kleinen Elementen und solehen mittlerer Griisse an bestimmten Stellen ungeheuer grosse Zellen und Fasern, welche beinahe mit unbewaffnetem Auge zu erkennen und fiir eine histologische Untersuchung sehr geeignet sind. Der Reichtum an loekerem, yon der Fixierungsfliissigkeit leieht durchdringbarem interzelluliirem Bindegewebe begiinstigt den Erfolg der Fixierung tier Nervenzellen und -fasern; die betri~chtliche GrSsse einiger Gang'lien, z. B. im Verlauf des Vagus, ermSglichen es, dutch dieselben Schnitte in ttollundermark aus freier Hand anzulegen, was ftir das Gelingen der ~ethylenblaufarbung yon grosser Bedeutung ist. Obgleich in vergleichend-anatomischer Hinsicht die Kopfnerven der Fische infolge einer Reihe yon tiefeiagreifendeH sekundgtren Veranderungen in betrachtlichem Mal~e ihren primitiven Charakter eingebfisst haben und nur mit einiger Schwierigkeit einen morphologischen Vergleich mit den Spinalganglien zulassen, benutzte ich dennoch in gleichem Marie sowohl diese als jene, Ftir meine vorwiegend histologischen Ziele hat die Herkunft einer Faser oder Zelle sowie die vergleichend-anatomische Stellung eines Ganglions keine besondere Bedeutung. Nervenelemente bei Ganoiden und Knochenflschen. II. Untersuchungsmethoden. Von den Fixierungsmitteln benutzte ich haupts~chlich das Chromessig:s~uregemisch, die Mischungen yon L e n h o s s ~ k , Flemming, Zenker und H e r m a n n , sowie verschiedene Spezialverfahren wie mit Trictllormilchs~ure, mit der Fliissigkeit yon C a r n o y - G i l s o n , die Silberbehandlung nach R. C a j a l usw. Die Pr~,parate wurden entweder in Paraffin rasch (durch BcrgamotSl) oder h~iufiger in Celloidin-Paraffin oder in reinem CeIloidin eingebettet. Von den F~rbungsverfahren ,babe ich am hiiufigsten die Doppelfi~rbung mit Safranin und Lichtgriin, das H:,tmatoxylinverfahren nach H e i d e n h a i n, die Fi~rbung mit Tolluidinblau-Erythrosin, die W e i g e r t sche Elastinf~trbung und viele andere angewandt. Ausserdem kontrollierte ich meine Beobachtungen an fixiertem Material durch Studien der Elemente nach i n t r a v i t a l e r Fiirbung mit 5iethylenblau, wobei ich entwedcr die Ganglien und Nervenst~mmchen in toto f~rbte oder a u s freier Hand in Hollundermark eingelegte Stiicke in Schnitte zerlegte and die letzteren fiirbte. III. Die Nervenzellen der Kopfo, Spinal- und sympathischen Ganglien. Die Nervenzellen in den Kopf- oder Spiualganglien der Fische unterscheidell sich ihrer GrOsse als auch haupts~tchlich dem Charakter ihrer Fortsatze nach. Die :,iltercn Autoren wie Ch. R o b i n , B i d d c r . W a g n e r , S t a n n i u s (60), S t i e d a (61) und anderc hielten den B a u d e r Spinalganglien bci Fischen fiir ungemein einfach und beschrieben in denselben nut bipolare Zcllen. Auch R a n v i e r (51) weist ill seincm Lehrbuch der Histologie darauf hin, dass die Zellen der Spinalganglien yon Fischen einen scharf ausgepr:,tgten bipolaren Typus aufweisen und empfiehlt insbesonderc die Spinalganglien des Rochens als das geeigneteste 0 b j e k t zum Studium des Verhaltens der Nervenfasern zur 8ubstanz der Ganglienzellen. Im Jahre 1886 unterscheidet G u s t. F r i t s c h (15) bereits zwei Arten y o n Elementen in den Spinal- und Kopfganglien yon Lophius : erstens oppositipolare Ganglienzellen, welche keine typischen Gebilde der Spinalganglien, sondern, wie )[ a x S c h u l t z e darauf besteht, nur lokale zellige Erweiterungen des Achsenzylinders darstellen ; zweitens pseudounipolare oder regentipolare Zellen, mit vielen Forts:,itzen, yon denen einer jedoch in betr~chtlichem 5IaSe dominiert; diese pseudounipolaren Zellen stellen durchaus nicht eine Besonderheit yon Lophius dar, sondern kommen auch anderen Fischen zu. Im Jahre 1893 weist v a n G e h u c h t e n (17) fibrigens wieder d a r a u f hin, dass bei der Mehrzahl der Fische die :Nervenzellen der Spinalganglien bipolar sind und dass somit die Fische im Verlauf des ganzen Lebens die Zellform behalten, welche bei den htiheren Wirbeltieren nur eine ~-bergangsform darstellt und nur einem bestimmten Entwicklungsstadium zukommt. I m 1" 4 Anton Nemiloff: Gegenteil zu v a n G e h u c h t e n fiberzeugte sich B e l a H a l l e r (19) 1898 beim Studium des vagalen Spinalganglions bei verschiedenen Knochenfischen yon der hSheren histologischen Differenzierung dieses Ganglions. So werde~ z.B. bei Barbus ausser den gewShnlichen bipolaren Zellen auch grSssere Elemente angetroffen, welche nicht nur zwei grosse Achsenzylinderforts~tze, sondern auch mehrere kleine sich im Ganglion verzweigende aufweisen. IrJ demselben 5ahre konstatiert E rail Ho 1m g re n (20) beim Studium vermittelst der l~ethylenblaumethode der Spinalganglien yon Selachiern und Teleostiern bei Gadus yon den letzteren und bei Raja und Acanthias yon den ersteren ,,schSne Ubergangsformen zwischen pseudounipolaren und oppositipol bipolaren Spinalganglienzellen". S z a w i n s k a (163) beschreibt wiederum in seiner Arbeit fiber den Bau der l~ervenzellen yon Selachiern s~mtliche Zellen der SpinaIganglien als bipolare, wobei beide Forts~tze entweder yon entgegengesetzten Zellpolen oder mehr oder weniger einander gen~hert abgehen kSnnen. Im Jahre 1899 differenzierte H o 1m g r e n (21) vermittelst einer einfachen Farbung mit Eisenh~matoxylin in den Spinalganglien yon Lophius multipolare Zellen~ hatte jedoch nicht die MSglichkeit, ihre Forts~tze zu verfolgen. Eine ausffihrlichere Beschreibung der Spinalganglienelemente bei Fischen gibt L e v i (34). Nach seinen Untersuchungen werden in den cerebrospinalen Ganglien yon 0rthagoriscus mola Zellen verschiedener GrSsse angetroffen. Die grSsseren derselben enthalten einen Kern yon elipsoider Form, einer~ dicken Aehsenzylinderfortsatz und ausserdem zahlreiche Forts~tze in Gestalt yon Strangen und Balken, welche im peripheren Teil der Zelle ein Netz bilden. Die grossen Zellen sowie diejenigen mittlerer GrSsse sind bipolar, aber mit zahlreiehen lmrzen Fortsatzen besetzt, welehe alsbald nach dem Austritt aus der Kapsel endigen. Fast samtliche kleine Zellen besitzen desgleichen zahlreiche aecessorische Forts~tze, w~hrend yon ihren Aebsenzylinder~ eine betr~chtliehe Anzahl von Kollateralen entspringt. Viele Zellen sin~ yon einem Geflecht dfinner markhaltiger, augenscheinlich sympathischer Fasern umgeben. N a c h meinen, h a u p t s a c h l i c h v e r m i t t e l s t des M e t h y l e n b ] a u v e r f a h r e n s I) ausgef~ihrten U n t e r s u c h u n g e n h a b e n sowohl die K o p f a l s auch die c e r e b r o s p i n a l e n G a n g l i e n einen r e c h t k o m p l i z i e r t e n Bau. D e r v o r w i e g e n d e Z e l l t y p u s i s t in d e r T a t die b i p o 1 a r e Z e l l e (Taf. I, Fig. 1) m i t zwei yon e n t g e g e n g e s e t z t e n Z e l l p o l e ~ abgehenden Achenzylinderfortsatzen. Die GrSsse d i e s e r Z e l l e ~ 1) Ich fertigte Schnitte durch die Kopfganglien (Trigeminus-Facialiskomplex, Vagusgruppe) und die gr6sseren Spinalganglien in Hollundermark aus freier Hand vermittelst eines Rasiermessers an, und f~rbte darauf die Schnitte auf deIn 0bjekttrgger in einer ~/~2proz. bis ~]~+proz. LSsung yon Methylenblau in physiologischer Kochsalzl~sung im Verlauf yon 2--3 Stunden. Bisweilen habe ieh aueh die Ganglien in toto gef~rbt, indem ich dieselben yon oben vermittelst einiger Tropfen l~ethylenblau anfeuchtete, wobei ieh mit einer st~rkeren Lfisung (t/s proz.) begann und darauf auf sehw~chere (t/l~ proz. his U~6proz.) fiberging. Nervenelemente bei Gano'iden und Knochenfischen. ~ariiert, wobei sie jedoch niemals Riesendurchmesser erreichen. Ein Zellfortsatz erstreckt sich zentralwarts, tier andere peripherwarts. Sowohl der zentrale als auch der periphere Fortsatz verlaufen das eine Mal unverzweigt, h~tufig sogar ohne Windungen 9eine weite Strecke, das andere Mal gewShnlich T-f0rmig verzweigt. Beide Fortsi~tze sind meist markhaltig, wobei die Markscheide bald in einiger Enffernung yon dem Zellk(~rper beginnt, bald die unmittelbare Fortsetzung der Markhtille der Zelle selber (conf. welter unten) darstellt. Ausser den bipolaren Elementen werden in dell yon mir untersuchten Ganglien best~ndig typische u n i p o l a r e Z el 1e n (Tar. I, Fig. 2)angetroffen, welche vollkommen den Zellen in den Spinalganglien der hSheren Wirbeltiere gleichen. Sie stellen rundliche, ovale oder keulenf(~rmige Gebilde mit bisweilen aus~gebogenen unregelmassigen Rt~ndern und einem grossen runden Kern dar. Von dem verjtingten Zellende entspringt ein Fortsatz. welcher keinen Knauel bildet, sondern gew0hnlich mehr oder weniger gradlinig verlttuft und yon einer recht dicken Markscheide umgeben ist. Dieser Fortsatz erstreckt sich in einigen ]?~llen weithin unter Abgabe yon marklosen ~(stchen an den Ranvierschen $chntirringen, in anderen Fallen teilt er sich T-f0rmig in einer verhMtnismassig nahen Entfernung yon der Zelle. Die bipolaren und unipolaren Zellen stellen die Hauptmasse tier Zellelemente in den yon mir untersuchten Ganglien dar. Ausserdem habe ich jedoch auch hauptsLtchlich im Verlauf der Gef~tsse in dem dieselben umgebenden Bindegewebe m u l t i p o l a r e I q e r v e n z e l l e n mit zahlreichen Dendriten (Taf. I, Figg. 3, 4, 5) gefunden. Diese Zellen weisen gewShnlich eine unregelmassige ~ieleckige, bisweilen stark ausgebogene und verzweigte Form auf. Ausser einem langen und dtinnen Achsenzylinderfortsatz, welcher bisweilen auf eine weite Strecke hin in dem die Gefasse der Ganglien umgebenden Bindegewebe verfolgt werden kann, ent~pringen yon der Zelle noch zahlreiche Dendriten. Diese sind in einigen Fallen an einer Zelle in grosser Zaht vorhanden, "~erzweigen sich alsbald, zerfallen in eine grosse Anzahl yon :~sten mit varikSsen Verdickungen und endigen nicht weit yon der Zelle. In anderen Fallen ist die Zahl der Dendriten viel geringer, diese .selber sind bedeutend dtinner, beginnen sich erst in betrachtlicher ~Entfernung yon tier Zelle zu verzweigen, wobei sie niemals eine 6 Anton Nemiloff: so grosse Anzahl yon Verzweigungen bilden, wie bei Zellen des anderen Typus. Die Anordnung beiderlei Zellen im Verlauf der Gefasse sowie ihr allgemeiner Habitus veranlassen mich, sie ftir sympathische Elemente zu halten. Die Zellen mit kurzen Dendriteg geh0ren offenbar dem ersten, die ZeIlen mit langen Dendriten dem zweiten Typus sympathischer Zelten an, wie sie yon A. S. D o g i e l (8--11) ftir die hSheren Wirbeltiere und fill' die niedrigen yon S a k u s s e w (55) und mir (43) festgestellt sind. In den Ganglien des N. vagus wird konstant noch ein Typus yon Zellen angetroffen, welche sich durch ihre GrSsse und meistenteils eigenartige Kernform (Tar. II, Figg. 26, 27, 28)~ siehe weiter unten, auszeichnen. Diese Zellen, welche ihrer Gr0sse nach mit Recht als R i e s e n z e I l e n bezeichnet werden mtissen, sind hauptsachlich am unteren Ganglionende konzentriert, wobei sie gew0hnlich einzeln liegen und nut selten in Gruppen yon 3--5. tm oberea Teil des Ganglions werden sie selten angetroffen; in dem Abschnitt des Vagus zwischen (}ehirn und der Ganglienanschwellung ist es mir hie gelungen, sie aufzufinden. In den zahlreichen yon dem Ganglion n. vagi entspringenden und hauptsachlich latero-ventraL verlaufenden Sfftmmchen sind die erwlthnten Zellen sehr zahlreich zwischen den Fasern vorhanden. Sie sind meist in Langsreihen: zwischen den Faserbiindeln angeordnet und stellen den einzigen hier vorkommenden Zelltypus dar. Es scheint, als senken sich diese Zellen aus dem Ganglion langs der Nervenstammchen herab. Besonders zahlreich sind sie in dem st~trksten Hauptst~.mmchen, welches aus dem Ganglion n. vagi entspringt. Bisweilen geht hier die seriale Langswanderung der Zellen plStzlich in eine gew0hnliche hnhaufung derselben tiber, wobei bei grossen Fischen diese Anhliufungen dermassen betrachtlich sind, dass die Stammchen an diesen Stellen gleichsam eine gangli0se Anschwellung oder Verbreiterung, welche sogar mit dem unbewaffneten Auge zu erkennen ist, bilden. Ich habe diese Zellen bei verschiedenen Vertretern der Knochenfische beobachtet; ein besonders gtinstiges Objekt stellt jedoch Lota dar; sie erreichen hier besonders grosse Dimensionen und sind der Methylenblaufarbung Ieicht zuganglich. Offenbar hat auch L e v i (34) diese Zellen bei Orthagoriscus mola gesehen, sie entsprechen wahrscheinlich auch den grossen Elementea im Rtickenmark yon Knochenfischen, welche vielfach beschrieben worden sind, so z. B. yon S a r g e n t (56) bei Ctenolabrus coeruleus, Nervenelemente bei G~no'iden und Knochenfischen. yon K o l s t e r (32) bei Perca fluviatilis, voa D a h l g r e n (5) bei verschiedenen Pleuronectiden, yon F r i t s c h (14, 15) bei Lophius piscatorius, yon T a gl i a n i (64-- 67) bei Orthagoriscus und Solea impar usw. Es ist bemerkenswert, dass auch im Rtickenmark der Fische diese Riesenzellen nach den Beschreibungen der Forscher (conf. die Zeichnung yon S a r g e n t auf pag. 215 d. XV. Bd. yore .,Anatom. Anzeig.") in seriaIe Laagsreihen angeordnet sind. Die R i e s e n z e l l e n (Tar. I, Figg. 6, 7, S, 9) im Ganglion n. vagi sind gewShnlich multipolar. Selten sind dieselben rundlich in der Regel l~nglich-eif6rmig oder unregelmassig v!eleckig mit abgerundeten Ecken. Der Nervenfortsatz entspringt yon tier Zelle mit einem charakteristischen Kegel, ist recht dick, infolgedessen diese Fasern sehr augenfMlig sind. Nicht welt yon der Zelle biegt gewShnlich dieser Fortsatz.wmklig yon seiner urspr~ingliche~l l[ichtung ab und erh~flt eine Markscheide. .Nach einem kfirzeren oder l~mgeren Yerlauf biegt er entweder abermals um und erstreckt .~ich im St~tmmchen riickwhrts oder er teilt sich (h~iufig mehrfach) aa den Ranvierschen Schnfirringea, wobei die Teil~tste im $tSmmchel~ nach verschiedeaen Richtungen veriaufea tutti schl~esslich bisweilen in einer betrhchtlichen Entfernung yon der Zelle dem Beobachter sich entziehen. Mitunter nimmt der Nervenfortsatz seinen Aafang nicht vot~ der Zelle selber, sondern vo,~ einem recht dicken Auswuchs derselbeJl, yon ~velchem auch einige kurze, dicke, in Ptsttchen in nachster Nahe der Zelle endigende Fortsatze entspringen. Die Dendriten entspringen entweder voa dem verlgngerten und in die Lange gezogenem Abschnitt der Riesenzelle, welcher in de~ Nervenfortsatz fibergeht oder allseitig yon der Zelle. Im ersten Fall erscheinen die Dendriten in Gestalt einiger recht dicker, sich yon dem verengten Tell der Zelle absondernder Forts~itze, welche mit zugespitzten Seitenhstchen versehen sind. Sowohl die Forts,~tze selber als auch deren -~ste verfeinern sich allmahlich und endigen entweder zugespitzt oder in Plattchen unweit der Zelle selber. Wenn die Dendriten allseitig yon der Zelle abgehen, erscheinen sie gewShnlich in Gestalt kurzer feiner, mit EndpF,tttchen versehener Fadchen, welche einzeln oder in Bitndeln yon der Zelle entspringen. Bisweilen jedoch stellen die l)eudriten dicke, stark verzweigte oder aber charakteristische, keulenfOrmige Forts~ttze dar. 8 Anton Nemiloff: Sowohl dem Charakter ihrer Dendriten als auch dem ferneren Schicksal ihres Nervenfortsatzes nach erscheinen diese Zellen recht mannigfaltig. Bei einem eingehenderen Studium k(innten dieselbea wahrscheinlich in mehrere charakteristische Typen, wie die spinalen und sympathischen Ganglien der hSheren Wirbeltiere, eingeteilt werden. Fig 1. P e r i z e l l u l ~ t r e s G e f l e c h t um eine Riesenzelle. Die Zelle selber ist ungefi~rbt geblieben und daher unsichtbar, sp perizelluli~res Geflecht; mn ~ eine an alas Geflecht herantretende feine Faser. Ganglion n. vagi. Lota vulgaris. 5Iethylenblau. R e i c h e r t s Obj. 7a. Kamera lucida. Eine jede Riesenzelle i s t yon einem ausserst dichten perizellul~tren Geflecht aus feinen, varikSsen F~dchen umgeben, so dass sie wie in einem Gespinst zu liegen scheint (Taf. I, Fig. 9). An jede Zelle treten gewShnlich (conf. Textfig. 1 und Taf. I, Figg. 9, 10) zwei oder mehrere feine markhaltige Fasern heran, wobei dieselben ihre Markscheide verlieren. Nervenelemente bei Gano'/den und Knochenfischen. Bisweilen teilt sich eine markhaltige Faser zun~tchst an einem R a n v i e r schen Schntirringe, worauf ein Teilast zu einer; der zweite zu einer anderen benachbarten Zelle verl~tuft; beide endigen in je einem perizellularen Gefiecht. Nach Verlust der Markscheide beschreibt die Faser einige Windungen um die Zelle, windet sich gleichsam um dieselbe auf ahne sich zu verzweigen unter Beibehaltung ihrer Individualit~t. Alsdann beginnt sie jedach sich vielfach zu teilen und zerf',tllt in ein ausserst dichtes Netz feiner varik0ser Fasern, welche sich in den verschiedensten Richtungen fiberkreuzen. Das ganze dichte filzartige Geflecht ist iimerhalb der Schichten der um die Zelle angeordneten Bindegewebshfille gelegen. Van dieser Anardnung kann man sich leicht i~berzeugen, sobald man das Getlecht im optischen Durchschnitt betrachtet. Die F•serchen des pericellul~iren Geflechtes dringen nicht in das Protaplasma der Zelle ein. Die feinen, fadenf0rmigen Dendriten der Riesenzellen, welche neben tier Zelle selber endigen, dri~gen in dieses Gettecht ein, wabei ihre Verzweigungen sich mit den Fasern desselben verflechten (Taf. I, Fig. 9). Das Geflecht ist dermassen dicht, dass es unmSglich ist zu entscheiden, ab hier blass ein Kontakt oder eine echte Verschmelzung stattfindet. Die Herkunft der markhaltigen, das perizellul/'tre Geflecht bildenderi Fasern habe ich nicht feststellen kSnnen. Ich habe diese Fasern auf weite Strecken verfolgen k0nnen, schliesslich jedach entziehen sie sich der Beobachtung, so dass es mir nicht gelungen ist, festzustellen, ab sie van Zellen desselben Ganglions herstammen oder van ausw~trts eindringen. In der Bindegewebshfille einiger Riesenzellen wird bisweilen zwischen den Fasern des perizellularen Geflechtes, wie es z. B. auf Tar. I die Fig. 9 illustriert, eine kleine Zelle angetroffen, welche sich recht intensiv in Methylenblau farbt. Ihren Dimensionen, dem Charakter ihres Kernes und Protaplasma nach erinnert dieselbe eher an eine Nervenzelle, welche die Riesenzelle begleitet, als an einen Leukazyten. Die Anwesenheit einer derartigen kleinen Zelle neben einer Riesenzelle, welche, wie welter unten berichtet werden soll, haufig degenerative Prozesse offenbart, erscheint auffallend und l~sst der van B t i h l e r (4) und anderen Farschern ausgesprochenen Betrachtungen tlber den Ersatz untergegangener Elemente im Nervensystem durch neuauswachsende 10 Anton Nemiloff: gedenken. Leider ist es mir nicht gelungen, die Natur und Bedeutung dieses ratselhaften Gebildes naher zu bestimmen; ar~ ihm habe ich weder Fortsatze noch eine deutliche KSrnelung im Protoplasma wahrnehmen kOnnen. Ich kann nur die Vermutung aussprechen, dass es mSglicherweise Neuroblasten sind, welche in einer gewissen Anzahl ftir das ganze Leben im interstitiellen Gewebe des Ganglions nachbleiben und nachher die absterbendel~ Elemente ersetzen. Von den Zellen der Kopf- und Spinalganglien unterscheidez~ sich scharf die Elemente der zentralen Sympathikuskette (Taft I, Fig. l 1), welche bei Fischen nur in dem vorderen KSrperabschnitt deutlich abgesondert ist. Die ZeUen sind hier kleiner, wobei multipolare Elemente vorwiegen. Zwischen den letzteren kSnnen Zellen mit kurzen, verdickten und stark verzweigten Dendriten als auch solche mit allseitig verlaufenden, langen und kurzen, mit charakteristischen rosenkranziOrmigen Verdickungen besetzten Fortsatzen unterschieden werden. Die Zellen sind nicht nur in dem Ganglion selber angeordnet, sondern dringen auch teilweise in die Rami communicantes ein. Auch die yon den sympathischen Ganglien abgehenden Stammchen enthalten auf betrachtlichen Strecken eine grosse Anzahl vo~ Zellelementen. IV. D e r B a u der H i i l l e n der N e r v e n z e l l e n . Die Nervenzellen der Kopf- als auch der Spinalganglien vo~ Fischen sind von einer in den verschiedenen Fallen verschiedenartigen Zellhtille umgeben. Die Literaturangaben fiber den Bau der Htille der Nervenzellen bei Fischen sind recht widersprechend und ungenau. Die ~Iteren Autoren beachten entweder diese Frage nicht oder behandeh~ sie nur voriibergehend. L e y d i g (1851), M a x S c h u l t z e (1859), K e y und R e t z i u s , R a n v i e r und andere beobachteten an tier Peripherie der Ganglienzellen yon Fischen eine markhaltige Schicht. Von den neueren Autoren beschreibt H o l m g r e n (20) in einer kleinen Bemerkung iiber die Spinalganglierr bei Selachiern und Knochenfischen desgleichen ein ,markgleichendes Stratum", welches ibm durch Osmiums~ure zu differenzieren gelungen war. An den Zellpolen war diese Htille deutlich unterbrochen. Obgleich die 0smiumsiiure die verschiedensten Substanzen fi~rbt, erschien es H o l m g r e n dennoch hSchst wahrscheinlich, dass es sich hier um eine tier Markscheide der Nerven verwandte Substanz handele. H o l m g r en richter ausserdem die Aufmerksamkeit Nervenelemente 9 bei Ganoiden und Knochenfischen. auf die Anwesenheit yon Kernen in den Zellelementen des Neurilemms, welches die Ganglienzelle umgibt. In einer spi~teren Arbeit aus dem Jahre 1899 berichtet Holmgren (21), dass die Zelleu der Spinalganglien yon Lophius piscatorius von einer Bindegewebskapsel umgeben sind, welche unmittelbar in die endoneurale Scheide des Achsenzylinders tibergeht und im Zusammenhange mit dem interstitiellen Gewebe des Ganglions steht. Diese Kapsel hat augenscheinlich einen lamell~ren Bau and enth[flt einze]ne, verhMtnism~ssig kleine, ovale oder gestreckte Kerne. Zwischen dieser Kapsel und der Ganglienzelle ist eine Schicht grosskerniger endothelialer Zellen eingeschoben. Nach den Beobachtungen yon Hohngren geht diese diinne, nur aus einer Schicht endothelialer Zellen bestehende Membran in die S ch w an nsche Scheide des Achscnzylinderfortsatzes iiber. Soviel ich auf Gruud meiner vermittelst verschiedener Fixierungs- und Fitrbungsverfahrea angesteUten Beobachtungen beurteilen kann, sind bei Fischen mindestens drei Typen yon Htillen tier Nervenzellen vorhanden~ welche sehr den H(illen derNervenfasern gleichen. Im einfachsten Falle (z. B. die Riesenzellen der Ganglie~ n. vagi) besteht die Htille (conf. Textfig. 4, fk) aus mehreren, konzentrisch um die Zelle angeordneten Bindegewebsschichten. Die Differenzierung des Bindegewebes ist in diesem Falle eiz~e einfache Orientierung seiner Elemente und zwar der Fibrillenbiindel der Zelle gegentiber. Das Bindegewebe selber der Htille ist eine blosse Fortsetzung des tibrigen interstitiellen Gewebes des Ganglions. Es 1;~sst sich hier weder eine einigermasseu deutliche Grenzschicht des Bindegewebes noch eine dichtere Htille oder Schicht erkennen. Auf dem Achsenzylinderfortsatz wird die ftir die Faserhtille charakteristische konzentrische Anordnung allm~thlich undeutlich und schwindet schliesslich vollkommen. Die Zellhfille verschmilzt mit dem interstitiellen Gewebe~ welches den Nervenfortsatz umgibt und yon einigen Autoren als H e n l e s c h e Scheide unterschieden wird. Ich muss jedoch vermerken, class bei Fischen kaum yon einer besonderen H e n l e schen Scheide die Rede sein kann. Das den Nervenfortsatz umgebende interstitielle Gewebe ist, soviel ich habe wahrnehmen k6nnen, niemals in besonderer Weise orientiert. Desgleichen babe ich nach keinerlei Darstellungs- und Farbungsverfahren eine unmittelbar der Faser anliegende Schicht wahrnehmen k0nnen. Niemals geht diese einfachste Art yon Htille in das Neurilemm der Nervenfaser fiber; dieses beginnt in derartigen F~tllen auf dem NerYenfortsatz un- 12 Anton Nemiloff: welt yon dem ZellkSrper und steht in keinem anatomischen Zusammenhang mit dem umgebenden Bindegewebe. Am deutlichsten tritt die erwahnte Htille an Praparaten hervor, welche im Chromessigsauregemisch fixiert und mit Safranin und Lichtgrtin oder mit Hamatoxylin nach H e i d e n h ain gefarbt sind. Bei einer einfachen Farbung mit B(ihmerschem Hamatoxylin und Pikrofuchsin wird desgleichen eine recht elektive Farbung dieser Htille erhalten. Bisweilen tritt auch an Methylenblaupraparaten sehr deutlich die konzentrische Schichtung tier Fibrillenbtindel des interstitiellen.Gewebes um die h'ervenzelleH hervor. In komplizierteren Fallen (Taf. II, Fig. 12) schiebt sich zwischen die Faserschicht und die iNervenzelle eine dtinne, homogene Membran mit eiaer Schicht platter, sternf0rmiger gellen anf der dem Cytoplasma der Zelle zugekehrten Seite ein. Eine derartige H~ille besitzt die Mehrzahl der Zellen der Kopf- und Spinalganglien. In diesen Fallen ist die konzentrische Schichtung des interstitiellen Gewebes um die Zelle weniger deutlich, ja kann sogar dermassen verwischt sein, dass sie nur an der Anordnung der Zellkerne erraten wird. Nach innen yon dieser Htille ist eine strukturlose, diinne Membran vorhanden, deren Innenflache (d. h. der dem Zellk6rper zugewandten Flache) eine Schicht flacher Zellen anliegt, welche vou einigen Forschern, so yon H o l m g r e n , als Endothelzellen beschrieben werden. Diese letzteren erscheinen als flache, sternfSrmige Elemente mit fasrigem Protoplasma, einem grossen, o~r Kern und dtinnen, zarten Fortsatzen. Letztere verasteln sich stark, anastomosieren miteinander und verschmelzen zu einem zarten Netz, welches der Innenflache der oben beschriebenen homogenen Membran anliegt, mit dieser jedoch niemals anatomisch zusammenhangt. Ftir die Differenzierung der erwahnten Membran als auch des ihr anliegenden Zellnetzes eignet sich am meisten das Methylenblau (schwache L6sungen yon 1/4--1/a~ in 0,75~ Chlornatriuml(isung), mit Hiife dessert eine elektive Farbung dieser Gebilde erzielt werden kann. In einigen Fallen bleibt hierbei sowohl die Zelle als auch die homogene Membran ungefarbt, wobei auf dem hellen Untergrunde prachtvoll das zarte blaue, yon den Fortsatzen der sternfOrmigen Zellen gebildete ~Netz hervortritt. In anderen Fallen nimmt wiederum die erwahnte Membran eine intensive Nervenelemente bei Gano'iden und Knochenfischen. 13 blaue Farbe an, wobei sie dermassen deutlich hervortritt, dass jeder Zweifel ausgeschlossen ist. Sie liegt der Zelle nicht dicht an~ sondern umgibt dieselbe bloss, ohne deren Kontur genau zu folgen, wobei sie stellenweise feine Falten bildet. Recht deutlich erscheint diese Htille auch an fixiertea Pr~tp~raten (z. B. nach einer Fixierung in Chromessigs;mregemisch und einer F,trbung mit Ht~matoxylin nach H e i d e n h a i n oder nach Fixierung in dem H e r m a n n s c h e n Gemisch und einer Fitrbung mit Holzessig). Um die morphologische Bedeutung dieser Gebilde beurteile~ zu kSnnen, mfissen ihre Beziehungen zu den entsprechenden Schichten des Nervenfortsatzes berficksichtigt werden. Zu diesem Zweck sind wiederum Methylenblauprhparate und zwar Prhparate in toto die geeignetsten: auf ihnen ist gleichzeitig die Zelle selber, sowie deren Fortstttze httufig auf weite Strecken hin sichtbar, so dass man sich fiber die Beziehungen deren Elemente zueinander orientieren und die auf Schnitten durch fixierte Prt~parate erhaltenen Befunde ergt~nzen kann. Es l;tsst sich deutlich feststellen, dass die erw;thnte Membran unmittelbar, ohne Unterbrechung in das Neurilemm des ~Nervenfortsatzes fibergeht und sich yon diesem durchaus nicht unterscheidet. Das der Innenfl~tche der homogenen Membran anliegende Zellennetz geht desgleichen ohne Unterbrechung und unverttndert unmittelbar in ein gleiches iNetz auf der Innenflache des Neurilemms des Nervenfortsatzes tlber2) Bisweilen ist auch ein unmittelbarer Zusammenhang der Fortsittze einer sternfSrmigen Zelle des Nervenfortsatzes mit den Verzweigungen einer entsprechenden Zelle, die der Hfille der Nervenzelle angeh~rt, zu erkennen. Die Zusammensetzung der H(ille wird ferner noch komplizierter durch das Auftreten einer markhaltigen oder Myelinschicht (z. B. an vielen Zellen des Trigeminus-facialis Ganglienkomplexes). In diesen F~llen sind sowohl die Faserhfille als auch die strukturlose Membran die gleichen wie in dem vorhergehenden. Die der ~) Dieses l~etz ist yon Zellen gebildet, deren Kerne die altbekannten ,,Kerne tier Schwannschen Scheide" darstellen. Die Zellen liegen der S c h w a n n schen Scheide nut an, ohne sich mit ihr zu verbinden. Genaueres fiber den Bau tier Schwannschen Scheide wie fiberhaupt der H~illen der Nervenfasern werde ich in dem zweiten, bereits druckfertigen Teil meiner Arbeit berichten. 14 Anton N e m i l o f f : Innenflache der S c h w a n n schen Scheide anliegenden Zellen weisen jedoch einen etwas abweichenden Charakter auf: ihre Fortsatze sind dicker, das Protoplasma ist deutlicher fasrig und enthalt kleine in Methylenblau stark fiirbbare K0rnchen oder Tr0pfchen. Das yon den Zellfortsittzen gebildete Netz (conf. Tar. III, Fig. 13) ist weniger zart als in den vorhergehenden Fallen; die Netzschlingen sind mehr abgerundet, wobei das Netz selber nicht in einer Ebene angeordnet ist, sondern die Markschicht in deren ganzer Dicke durchsetzt. Die Zellen bilden somit mit ihren verastelten Fortsatzen eine schwammartige, mit Myelin angeffillte Protoplasmamasse und erinnern teilweise ihrem Bau nach an die unltingst (44) yon mir beschriebenen Fettzeilen von Acipenser ruthenus; in Berficksichtigung des Fehlens eines unmittelbaren Zusammenhanges mit der Neurilemmmembran k0nnen diese Zellen richtiger als ,;Markscheidenzellen" bezeichnet werden. Weiterhin (ira zweiten Tell der Arbeit) soll gezeigt werden, dass auch die Markscheide der Nervenfasern, in welche die bier beschriebene Htille der Ner~enzellen tibergeht~ einen gleichen Ban aufweist. Die Kontinuitiit der Markschicht wird an der ~)bergangsstelle der Zelle in die Nervenfaser durchaus nicht gest0rt. In einigen Fiillen ist eine ,Markscheidenzelle" gerade am P o l d e r Nervenzelle gelegen und gehiirt somit zur H~llfte der Markhtille der Nervenzelle, zur Halfte der Markscheide des Fortsatzes an. Bei dea yon mir untersuchten:Fischen ist es mir nicht gelungen, an der (i'bergangsstelle der Nervenzelle in die Faser die ringf0rmigen Gebilde zu -sehen, welche nach H o l m g r e n (20) an den Zellen yon Selachiern (Raja) und Teleostiern (Gadus) und anderen sich intensiv mit Metkylenblau farben. Desgleichen babe ich auch nicht die yon H o l m g r e n beschriebene, distalwarts von dem erwahnten Ring gelegene Verengerung des Achsenzylinders wahrgenommen. Ebenso stimmen auch die yon mir nach der Behandlung der Nervenzelle saint ihren Fortsatzen mit Osmiumsaure erhaltenen Bilder nicat mit denjenigen tiberein, welche R a n v i e r (51) in seinem Lehrbuch und H o l m g r e n (20) in der oben angeftihrten Arbeit gibt. Aui' meinen Praparaten geht die Markschicht ununterbrochen in Gestalt einer gleichmassigen Scheide auf die Fortsatze der Zelle tiber. Nervenelemente bei Gano'/den und Knochenfischen. 15 V. Trophozyten. ') Ich gehe nun zur Beschreibung derjenigen Zellelemente tiber, welche stets in grOsserer oder geringerer Anzahl zwischen der Nervenzelle und der dieselbe umgebenden Htille angetroffen werden. Zwischen dem Cytoplasma der Nervenzelle und ihrer Hfille ist kein praformierter Spaltraum vorhanden, wovon man sich leicht an dem lebenden, in Methylenblau gefarbten Gewebe oder an gut fixierten Prttparaten fiberzeugen kann und wie es auch viele Forscher, z.B. H o l m g r e n und L e n h o s s ~ k (gegen S o l g e r , Tschassownikoff und andere) annehmen. Soviel ich habe wahrnehmen k6nnen, liegt das Cytoplasma stets der Hrille an. wobei es mit seiner elastischen Masse die hier eingeschlossenen Zellelemente an letztere anpresst. Eine AblSsung der Hrille yon dem Cytoplasma ist sehr schwer zu vermeiden; in dieser Beziehung hat mir auch das yon F u c h s (16) vorgeschlagene H~trtungsverfahren nach der Fixierung und zwar mit Alkohol yon 5 0/% dessen Konzentration allmahlich nicht mehr als um 5 ~ gesteigert werden soll, wenig genritzt. Bessere Resultate erzielte icb nicht durch Ab~tnderung der Hartungsbedingungen, sondern der Fixierungsbedingungen (z. B. Erw'~rmen des Chromessigsauregemisches, Einlegen yon sehr kleinen Stricken i n d i e Sublimat15sung, versuchsweise Bestimmung des Optimums der Fixierungsdauer usw.). Zur Frage tiber die morphologische und physiologische Bedeutung der unter der Htille eingeschlossenen Zellen, welche verschieden bezeichnet werden, als ,,endokapsulare Zellen ~, .~Begleitzellen'c, ,,Trophozyten ~c, ,interkapsulttre Zellen" usw., ist bereits ~iel geschrieben worden. Um meine Arbeit nicht auszudehnen, will ich die grosse Literatur tiber diese Zellen hier nicht anftthren, zumal dieselbe recht vollstandig in den Arbeiten you H o l m g r e n (20--31)7 B e r g e n (2), S. R. C a j a l (49--50) nnd anderen zusammengestellt isL Ich gehe ohne weiteres zur Beschreibung meiner Befunde an den Nervenzellen yon Fischen fiber. Ausser den bereits beschriebenen sternf0rmigen, dem Netlrilemm anliegenden Zellen sind bei Fischeu unterhalb tier Hrille ~) Indem ich ttberall in meiner Arbeit den Ausdruck ,,Trophozyten-gebrauche, habe ich durchaus nicht die Absicht, den betreffenden ZeIlelementen irgend eine Rolle bei der Ern~thrung der Nervenzellen zuzuschreiben, sondern benutze nut eine gangbare Bezeichnung derselben. 16 Anton ~Nemiloff: zweierlei Artea yon Zellelementea vorhanden: 1. sternfSrmige~ welche die Trophospongien yon H o l m g r e n bilden uad 2. Leukozyten. Diese Zellen sind nicht schwer zu unterscheiden, zumaI wean sich das Auge an das betreffende Objekt gewShnt hat und morphologische Merkmale erkennt, welche beim ersten Anblick nieht auffallen. Selbst in den F~llen, wenn das Eindringen dec Fortsatze in das Cytoplasma nicht sichtbar ist, unterscheidet sich ein Trophozyt dennoch durch den Charakter seines Protoplasmas und dutch seinen Kern yon einem Leukozyten. Das Protoplasma des letzteren ist mehr oder weniger k6rnig, wahrend das Protoplasma des Trophozyten einen mehr oder weniger deutlichen fibrillaren Bau erkeunea lasst. Der ovale Kern der Trophozyten erscheint auf gut fixiertea Prltparaten gr~isser als der Kern der Leukozyten. Besonders deutlich tritt dieser Unterschied ira Protoplasma und Kern der erwlthnten Zellen an Ganglienpraparaten hervor, welche entweder aach R a b I fixiert und mit Tolluidinblau-Erythrosin gef'~rbt oder im Gemisch yon L e n h o s s ~ k fixiert und mit Hamatoxylin nach H ei d e n h a i n gefarbt worden sind. Die Trophozyten (Taf. II, Fig. 14) der yon mir untersuchten Fische stellen recht grosse, mit zahlreichen Fortstttzen versehene Elemente dar, welche das Cytoplasma der Nervenzelle allseitig umgeben. Die Fortsatze derselben sind recht breit, plattchenf6rmig, mit zugespitzten, eckigen Verbreiterungen, welche im Cytoplasma der Nervenzelle sich verzweigen und, indem sie miteinander anastomosieren, in derselben zu einem dichten Netz eckiger, plattchenf6rmiger Balken 1) verschmelzen. Das genannte Netz durchzieht das ganze Cytoplasma und dringt bis zum Kern vor, ohne jemals in denselben einzudringen. Zwecks Darstellung der Trophospongien habe ich die MehrzahI der spezielI dafter yon H o 1 m g r e n u. a. vorgeschlagene~ Methoden (C a r a o y s Gemisch, Alkohol-Chloroform-Essigs~tur% Pikrinsliure-Sublimat, Pikrinsalpetersaure, Fixierung in Trichloressigsaurel6sung undWeigertsResorcin-Fuchsinfarbgemisch u. a.) versucht, die besten Resultate jedoch mit dem gewOhnlichen (nicht prikrinsaurem Gemisch) yon L e n h o s s ~ k und einer Fitrbung mit H~,tmatoxylin nach H e i d e n h a i a erzielt. Ist der ~) FOr die Trophospongien der Fische sind die pliittchenfSrmigen, mit blattf(irmigen Verbreiterungen besetzten Balken charakteristisch. 17 Nervenelemente bei Ganoiden und Knochenfischen. Schnitt nicht zu dtinn und gtmstig gefallen, so erhielt ich prachtvolle Bilder, auf welchen zweifellos deutlich das Eindringen der Forts~ttze der Trophozyten in das Protoplasma der Nervenzelle und die Bildung yon Trophospongien aus denselben sichtbar war. Einige Forscher, so unl~ngst Dr. H u g o M e r t o n (42), haben die Ansicht ausgesprochen, dass die Trophospongien in einigen Zellen (z. B. in den unipolaren-Ganglienzellen des Zentralnervensystems yon Tethys leporina) augenscheinlich selbst~ndige Gebilde in Gestalt yon wichtigen Bestandteilen der Ganglienzelle darstellen, welche sekundar mit Gliafasern, die in das Cytoplasma der Nervenzelle eindringen, in Verbindung treten. Bei Fischen wenigstens kann jedoch yon einer Selbst':mdigkeit der Trophospongien nicht die Rede sein, da auf Serienschnitten durch Nervenzellen leicht der unmittelbare Zusammenhang der Trophospongienbalken mit einem Fortsatze eines Trophozyten festgestellt werden kann; in diesen Fhllen gelingt es auch leicht, sich davon zu iiberzeugen, dass samtliche in das Cytoplasma eindringenden Forts;ttze der Trophozyten an der Bildung der Trophospongien teilnehmen. Bei derselben Behandlung der Praparate treten in demselben Ganglion an einigen Zellen die Trophospongien ~usserst deutlich hervor, an anderen sind sie kaum wahrnehmbar. In einem Fall ist das Trophospongium in der Mehrzahl der Zellen eines Ganglions zu erkennen, in einem anderen wiederum in keiner einzigen Zelle. Die Anwesenheit yon Trophozyten unter der Hiille gelingt es auch in diesem Falle festzustellen, ihre Fortsatze verschmelzen jedoch gleichsam nach ihrem Eindringen in das Cytoplasma der Nervenzelle mit diesem und werden unkenntlich. H o I m g r e n hat, wie bekannt, interessante Veranderungen an den Trophospongien bei verschiedenen Funktionszusti~nden der Nervenzelle beschrieben. Unter gewissen Bedingungen erfolgt eine Veranderung des Aggregatzustandes d e r Trophospongien, wobei das kSrnige Protoplasma seiner Balken sich stellenweise in Tropfen einer untingierbaren Substanz umwandelt. Bisweilen kann dieser Prozess einer physikalisch-chemischen Umanderung der Trophospongien soweit vorschreiten, dass einzetne TrSpfchen zu hellen Kan~tlchen verschmelzen, welche in diesen Fallen das Cytoplasma der Servenzelle drainieren. In einer Reihe yon Arbeiten (20-- 31) beweist H o 1m g r e n das Vorhandensein eines Zusammenhanges zwischen den erwahnten Veranderungen in den A r c h l y f. m i k r o s k . & n a t . Bd. 72. 2 18 Anton :Nemiloff: verschiedenen Abschnitten des Trophospongiums und dem Stoffwechselprozess in dem Cytoplasma der dasselbe einschliessenden Zelle Es gelang ihm hierbei u. a. den Zusammenhang zwischen der Kanalisation der Trophospongien in den Nervenzellen und dem Anwachsen und Schwund der Tigroidsubstanz in denselbell festzustellen. Viele andere Forscher, welche sich mit dem Studium der Trophospongien in verschiedenen Zellen, besonders in den Nervenzellen, beschaftigt haben, stimmten zum Tell der Ansicht H o l m g r e n s bei, zum Tell berichtigten sie und veranderten dieselbe. So bestreitet T s c h a s s o w n i k o f f (68) nach dem Studium der ,,Saftkan'51chen" in den zentralen und peripheren Nervenzellen der Katze, des Hundes, des Kaninchens, des Meerschweinchens. des Huhns und der Ente, zum Teil mit Hilfe der gewShnlichen Fixierungsmethoden, zula Tell mit Hilfe tier ,,SchwSrzungsmethodc" yon K o l o s s o f f einen Zusammenhang tier Sat'tkaniilchen mit der Zellkapsel der Nervenzelle und nimmt an, dass die Saftkaniilchen fiir die Entfermmg der Stoffwechselprodukte dienen. P e w s n e rINe u f e l d (46) untersuchte (lie Saftkaniilehen in den Nervenzellen des Rilckenmarks verschiedener S~iugetiere und gelangte zur ~'bcrzeugung, dass die intrazellulSren KanSlchen keine eigene Wandung besitzen, in das Protoplasma ebtgelassen sind und morphologisch demselben angehSren; ein kanMisiertes Tv,~phospongium war jedoch in den von ibm untersuehten Zellen nieht vorhanden. R o h d e (53) ist im allgemeinen mit der Lehre H o I m g r e n s yon den Trophospongien einverstanden, nimmt jedoch an, dass dieselben nicht sekundiir in das Cytoplasma der Nervenzelle eindringen, wie e s H o l m g r e n behauptet, und stellt dieselben in innigen Zusammenhang mit der Entwicldung der Gan~lienzelle und ihreln fibrill~iren Bau. Die Trophozyten scien nicht Zellen des interstitiellcn Gewebes, sondern Neurogliaelemente. Infolge Anwesenheit der Trophospongien kSnnen die NervenzeIlen gewissermassen mit den Geschleehtszellen verglichen werden, da beide vermittelst Zellen ern~hrt werden, mit denen sie in innigem genetiscben Zusammenhang steben. In seiner verschiedenen intrazellul~ren Netzapparaten gewidmeten Arbei~ weist B e r g e n (2, darauf hin, dass s:,imtliehe Versuehe, diese Zellen als Trophospongien, Sat'tkanMchen. Centrophormien usw. zu deuten, den tats~tchlichen Befunden nicht vollkommen entsprechen; es wird hierbei dem Umstande Rechnung getragen, dass diese Gebilde bei weitem nicht in allen Zellen eines Typus angetroffen werden. - - D i e Entstehung dieser intrazellul~iren Apparate stellt sich B e r g e n folgendermassen vor, dass im Cytoplasma KSrnchcn oder TrSpfchen auftreten, welche sieh nebencinander in Reihen anordnen und miteinander verschmelzen. Die Substanz dieser KSrnchen besitzt die F~ihigkeit, sich xdtal zu veri~ndern, wobei sie ihr F~irbungsvermOgen vertiert and sich auflOst. Schliesslich fand R a m O n C a j a l (50) mit Hilfe einer besonderen Ab~inderung seines Gruudverfahrens in den Riiekenmarkszellen einen besonderen Nervenelemente be| Gano'/den und Knochenfischen. 19 Apparat in Gestalt eines Netzes yon feinen RS'hren; letztere sind stellenweise erweitert, stellenweise jedoch dermassen verengt, dass sie kaum wahrnehmbar sind. Dieser Apparat nimmt fa~t den ganzen Zellleib ein und entsendet in die Dendriten ein bis zwei blind endigende :-~stchen. .le griisser der ~euron is~, desto komplizierter und gr6sser stellt sich der erwS.hnte Apparat dar. In den kleinsten Zellen sind nur einige miteinander anastomosierende, varik5se :~stchen vorhanden. Hinsichtlich der Bedeutung dieses Apparates .|st RamSu Cajal der Ansieht, dass das Golginetz und das Kan.~|chennetz yon Holm grcn ein Gebilde darstellen und dass dasselbe ein geschlossenes kommunizierendes RShren- und Sinussystem vorstelle. Ohne meine Beobachtu~gen verallgemeinern zu wollen, kau~l Jch dennoch nicht umhin, darauf hinzuweisen, dass es mir ia den yon mir untersuchten Zellen keinmal gelungen war, weder eiue Kanalisation der Tr0phospongiell noch ein Auftreten yon Tr0pfche~ it1 denselben zu erkennen. War das Pr~parat gut fixiert, so war auf s~imtlichen im $chnitt gelegenen I,'ortsatzen der Trophozyten keine Ver~nderung sichtbar, die als Kanalisation im Sinne Holmgrens gedeutet werdeu konnte. Eine Vakuolisierung der Trophozytenforts~tze babe ich nur an solchen Pr~iparate~ beobachtet, welche ungeniigend bearbeitet worden waren. So erhielt ich zufi~llig eine Serie nach S. R. C a j a l mit Silber und nachfolgender Reduktiou desselben durch Pyrogallolgemisch behandelter [ri~parate; infolge Schadhaftigkeit des Thermostateu ~,~Lr die Temperatur ill demse|ben betritchtlich gestiegen, so das.~ Gang|ieustticke mehr a|s 24 Stunden be| einer hohen Temperatur i~ der SilberlSsu~g gelegen batten. ~Nur um mich zu iiberzeugeT~, wieweit die Zellen hierbei deformiert worden sind, fertigte ich aus den oberflachlich eingebetteten Stfickchen Schnitte an. Selbstverst~,tndlich war in diesen [ r a p a r a t e n keine Spur yon Neurofibrillenf~rbuz~g vorhanden, die Kerne waren desgleichen schlecht erhaltem das Protoplasma war jedoch yon einem deutlichen Netz yogi Kanalchen durchzogen. Be| einer Betrachtung derselben mit starker Vergr6sserung habe ich wahrnehmen k0nnen, dass die genannten Kan~,ilchen aus zahlreichen nebeneinander gelegenen Tr(ipfchen bestehen, zwischen denen noch Reste des Trophospongiumprotoplasma erhalten waren. In Anbetracht der ungtinstigen Fixierungsbedingungeu und der starkei~ Deformation der Zellea kann ich diese Vakuolisierung der Fortsatze nur als ein durch die missratene Behandiung hervorgerufenes Kunstprodukt an,erkennen. Ich will jedoch damit durchaus nicht behaupten, dass 2* 20 Anton Nemiloff: jegliehe Kanalisation tier Trophospongien ein Kunstprodukt sei; ich mOchte nur darauf hinweisen, dass ein jegliches derartiges. Gebilde, wie Spa]ten, Kanalchen usw., nut mit grosset Vorsicht beurteilt werden kOnnen, da die tagliche Erfahrung im Laboratorium uns zeigt, wie leicht dieselben in den Praparaten ktinstlich entstehen. Eine besondere Aufmerksamkeit in bezug auf Trophospongien wandte ich denjenigen Nervenzellen zu, in denen irgendwelche morphologische Merkmale einer in ihnen verlaufenden funktionellen, Erscheinung sichtbar w a r e n . - Viete Nervenzellen der Fische erwiesen sich, wie welter unten berichtet werden soll, mit einzelligen Parasiten -- Myxosporidien - - infiziert, welche sie schliesslich zu Grunde richteten, jedenfalls in ihnen starke StSrungen bewirkten. Die Kerne vieler Zellen gaben desgleichen in Berticksichtigung ihrer Form, des Austrittes yon Chromatin aus ihnen, der in ihnen enthaltenen Einschltisse und anderen Merkmalen, Anzeichen yon Prozessen in der Zelle, welche augenscheinlich zum Stoffwechsel in Beziehung stehen. Einige der yon mir untersuchten Zellen waren ausserdem yon dicken mit Leukozyten angeffillten Gangen durchzogen, welches Verhalten abermals nicht zugunsten eines normalen Zustandes dieser Zellen sprach. Ungeachtet dessen ist es mir in allen diesen verschiedenartigen Fallen keinmal gelungen, irgendwelche KanMisation der Trophospongien wahrzunehmen. Auf Grund meiner Praparate kann ich nur aussagen, dass, augenscheinlich in Abhangigkeit yon dem funktionellen Zustande des Protoplasmas der Nervenzelle, das Trophospongium das einreal sichtbar, das andere Mal unsichtbar ist. Was jedoch hierbei in dem Protoplasma der Nervenzelle vor sich geht, und welche Veranderungen dasselbe hierbei erleidet, babe ich nicht sicher feststellen kSnnen. In Berticksichtigung hauptsachlich der physiko-chemischea Ver'anderungen der Trophospongien in einigen Stadien der funktionellen Tatigkeit der Nervenzelle i s t . H o l m g r e n geneigt, die Trophospongien ftir besonders wichtige Gebilde in der Zelle zt~ halten, welche einen bedeutenden Einfiuss auf die Stoffwechselprozesse in derselben austiben. SeIbst vollkommen sicher festgestellte morphologische Beziehungen geben jedoch leider keine gentigend sichere Grundlage ftir streng wissenschaftliche Schltisse: Nervenelemente bei Guno'iden und Knochenfischen. 21 physiologischen Charakters. Wit sind daher genStigt, uns mit Annahmen zu begniigen, welche mehr oder weniger wahrscheinlich sein kOnnen, jedoch keinen Anspruch auf vollkommene Sicherheit machen kSnnen. Wenngleich ich auch die geistreichen Betrachtungen H o l i n g r e a s als ausserst interessant anerkenne, bin ich dennoch geneigt, anzunehmen, dass in einigen Fallen, so in den yon mir untersuchten Nervenzellen der Fische, den Trophospongien mit gleicher Wahrscheinlichkeit eine andere Rolle zugesprocheu werden kann. Das Netz der Fortsatze, welche das Protoplasma durchziehen, macht auf mich wenigstens eher den Eindruck eines Skelettgebildes, dem eine mechanische Bedeutung in der Zelle zukommt. MSglicherweise dient es den weicheren Best~nd[eilen des Protoplasmas als Stiitze, oder aber trennt verschiedene Protoplasmaabschnitte voneinander, oder aber dient zur Isolation der Nervenfibrillenbtindel voneinander, jedenfalls ist mir die Vorstellung gelaufiger, in der ,,Symbiose" der NervenzelIe mit den sternfOrmigen Zellen das Ziel einer mechanischen Erscheinung anzuerkennen, als dieselbe mit den komplizierten Stoffwechselprozessen in Zusammenhang zu bringen. Ein Vergleich der Trophospongien mit den entsprechenden Gebilden in den Nervenzellen wirbelloser Tiere weist darauf hin, dass bei letzteren die mechanische Bedeutung yon Forts~ttzen und Fasern, welche in die ~Nervenzelle eindringen, ill vielen Fallen augenscheinlich ist. Ich erinnere hierbei an die unlangst (1905) yon G o l d s c h m i d t im Biolog. Zentralblatt beschriebenen radittrgestreiften h'ervenzellen des Pferdespulwurms. Die Nervenzellen sind hier gleichsam auf Gliafasern, welche in das Protoplasma derselben allseitig radiar eindringen, aufgereiht. G o 1d s c h m i d t hebt mit Recht die mechanische Rolle dieser Fasern hervor, welche in diesem Fall vollkommen klar zutage tritt. In anderen Fallen sind die Verh~ltnisse mehr "r trotzdem ist, meiner Meinung nach, die mechanische Bedeutung dieser Gebilde in vielen Fallen ausserst deutlich. Vom Standpunkt einer mechanischen Bedeutung der Trophospongien ist die grSssere oder geringere Deutlichkeit derselben mSglicherweise yon dem jeweiligen Zustand des Protoplasmas der Nervenzelle abhangig, infolgedessen das Sttitzgertist in einigen Fallen sich scharf abhebt, in anderen Fallen unklar erscheint oder sogar vollkommen verdeckt wird. 22 Anton Nemiloff: VI. Loukozyton. Ausser Trophozyten werden unter der Hfille der Nervez~zellen, wie bereits erwlthnt, gew(~hnlich in verschieden grosset Zahl Leukozyten angetroffen, welche auch im interstitiellen Gewebe des Ganglions in grosser Zahl vorhanden sind und in demselben stellenweise besondere Anhaufungen bilden, wie bereits H o l m g r e n bei Lophius, Acanthias und Gadus darauf hingewiesen hat. Hinsichtlich der Bedeutung und der Rolle der Leukozyten im Nervengewebe sind in letzter Zeit viele Angaben gemacht wordel~. Bereits P u g n a t (48) fand in den Spinalganglien iilterer Tiere viele GanglienzeUen yon einem Haufen yon Leukozyten umgeben; in einigen Fii,llen waren die letzteren sogar in die Nervenzellen eingedrungen, in welchem FalI er einige Verttnderungen in dem Fiirbungsverm(igen des Protoplasmas der Nervenzelle wahrnahm und einen ]~Iolekularzerfall desselben beobachtete. Mit einigen anderen Forschern nimmt P u g n a t an, dass die Nervenzellen ira. Alter zugrunde gehen und den Leukozyten, wie fiberall so auch hier, es obliegt~ unniitze und abgestorbene Elemente aus dem Organismus zu entfernen. In einer Reihe hauptsiichlich dem Alterungsprozess gewidmeten Arbeiten fiihrt M e t s c h n i k o f f den Gedanken durch, dass die eine Nervenzelle umgebenden Elemente ausgewanderte Leukozyten-Makrophagen sind, welche die Nervenzelle resorbieren. In seinem halbpopuI~tren Buche ,Essais. optimistes ~ (Paris, 1907) resiimiert M e t s c h n i k off seine friiheren Beobachtungen folgenderreassert: Es unterliegt keinem Zweifel, dass bei der Aitersdegeneration die Nervenzellen yon Neuronophagen umgeben werden, welche ihren Inhalt absorbieren und eine mehr oder weniger vollst~,ndige Atrophie derselben bewirken. Eine Neuronophagie beobachtete desgleichen Demoor (6) an Tieren, welche an den Folgen einer bald nach der Geburt ausgeftihrten Trepanation zugrunde gegangen waren, sowie ~ a n o u ~ I i a n (36, 37, 37a) im Rtickenmark yon Hunden und in den Spinalganglien yore )[enschen bei der Tollwut; Mencl (40~ 41) beschreibt genau den Prozess des Eindringens der Leukozyten in die Nervenzelle und beobachtete sogar das Einwandern yon Leukozyten in den Kern und die Zerst(irung desselben; P. Vall~e (69) beschreibt die Neuronophagie bei Altersveriinderungen in dem ~ervensystem yon Hunden usw. In der speziellen medizinischen Literatnr finden sieh desgleichen zahlreiche ttinweise auf eine ZerstSrung der Nervenelemente dutch Leukozyter~. bei verschiedenen Erkrankungen, wie Epilepsie, Abdominaltyphus, Fleck'typhususw. Andererseits ist jedoch auch kein Mangel an Arbeiten vorhanden. welche die phagozytiire Fiihigkeit der Leukozyten im Nervensystem leugne~ und ihnen bier eine andere Rolle zuerteilen. So hat M a r i n e s c o (38, 39) weder im Gehirn noch im Riickenmark ein Eindringen yon Phagozyten in die Nervenze]le beobachtet. Im Protoplasma der Elemente, welche die Nervenzelle nmgeben, gelingt es nie~ Bestandteile der letzteren zu finden, infolgedessen ersteren auch keine phagozytliren Eigenschaften zugesprochen werden kSnnen; sie kSnnen nut einen ,-Nervene|emente bei Gan~;iden und Knochenfischen. 23 Druck auf die Nervenzelle ausiiben und Atrophie derselben als Folge yon Raummangel oder einer Ern~hrungsstSrung bewirken. Eine ak-tive Neuronophagie leugnet auch E x p o s i t o (13), obgleich er ein Resorptionsvermi~gen der Leukozyten und Neurogliaelemente auf abgestorbene Nervenzellen nicht in Abrede stellt. Nach der Ansicht yon de B u c k und de ~[uor (3) ist die Anwesenheit yon Leukozyten in der N~the der Ncrvenzellen durch Reizung ,~der Entziindung bewirkt; es handele sich hier einfach um eine mechanische, hSchstens h~imotaxische Erscheinung und durchaus n i c h t u m einc zellulttre Phagozytosc; derartige Bilder werden in jedem infiltrierten entzilndeten (~ewebe angetroffcn, wobei es Niemandem einf~llt, hier eine Phagozytose anzunehmcn. Auch R a m o n y C a j a l (50) h~lt die erw~hnten Elemente nicht fiir Phagozyten, sondern schreibt ihnen eine stimulierende Wirlmng auf die Ern~hrung und das Wachstum der Nervenfasern zu; seiner 3Ieinung nach sind die Elemente imstande, wichtige Ver~tnderungen der Form und der Forts~ttze der Nervenzelle hervorzurufen (z. B. Glomerulusbildung bei den 8pinalganglienzeIlen). Nach der Ansicht yon Saigo (55a) kommen die lakun~ren Ausbuchtungen an den GanglienzeUen mit eingelagerten Rundzellen in jedem Lebensalter vor. Diese Rundzellen erkl'3.rt er ffir Gliazellen; nicht ftir lymphozyt~tre Elemente. Soviel ich an meinen Pr'aparaten babe wahrnehmen kSnnen, l~sst sich die Anwesenheit yon Leukozyten unter der Htilte der Nervenzellen nicht immer mit einer phagozyt'aren T:atigkeit derselben in Abhangigkeit bringen, wie denn tiberhaupt die I:rage der Phagozytose nur mit grosser Vorsicht behandelt werden muss. Leukozyten umgeben h',tutig in grSsserer oder geringerer Zahl vollkommen normale Nervenzellen, in denen es auf keine Weise gelingt, irgend welche Alterserscheinungen oder iiberhaupt Degenerationserscheinungen darzustellen. In diesen F'allen liegt natih-lich durchaus kein Grund vor, die Leukozyten ftir Phagozyten zu erklaren. Andererseits habe ich durch einzellige Parasite~ vollkommen zerstSrte oder zweifellos degenerierende Nervenzellen mit verSdeten oder kollabierten Kernen gesehen; in derartigen Fallen wtirde die Anwesenheit yon Leukozyten, welchen nach P u g n a t (48) und anderen Forschern es obliegt, aus dem Nerven: gewebe wie auch aus anderen Geweben unntitze und abgestorbene Elemente zu entfernen, durchaus zweckentsprechend sein; dennoch habe ich auch hier keine gr6ssere Anzahl yon Leukozyten als gewShnlich gefunden; im Gegenteil, derartige vertidete oder zerstSrte Zellen waren yon einer geringeren Zahl von Leukozyten umgeben als vollkommen normale Elemente. Jn meinen Praparaten sind mir viele Zellen zu Gesicht gekommen, in welchen, dem Allgemeinzustande des Protoplasma nach zu urteilen, intensive 24 A n t o n l ~ e m i l o ff: physiologische Prozesse vor sich gingen, wobei jedoch dieselben augenscheinlich ohne den stimulierenden Einfluss yon Leukozyten erfolgten, da die Zahl derselben um die 5Tervenzelle sehr gering war und dieselbe sich durchaus nicht yon einer normalen unterschied. Verhaltnismassig selten babe ich ein Eindringen yon Leuko~ zyten in das Protoplasma und sogar in den Kern yon ~'ervenzellen gesehen, welcher Vorgang nach M e t s ch n ik o f f, wie bekannt, nicht eine notwendige Bedingung einer phagozytaren Tatigkeit darstellt. Der Prozess des Eindringens eines Leukozyten beginnt damit, dass am Rande der Zelle, wie auch M e n c l darauf hinweist, eine kleine Delle erscheint, in welche der Leukozyt eintritt, wobei er dieselbe nicht vollkommen ausftillt, sondern yon der Wand derselben durch einen kleinen Raum getrennt ist. Der Leukozyt dringt welter in das Protoplasma ein, wobei der yon ihm zurtickgelegte Weg sich hinter ihm als ein ziemlich breiter, das Protoplasma durchsetzender Kanal darstellt. Wie Men cl (40), so habe auch ich beobachten kbnnen, wie ein Leukozyt auf diese Weise in den Kern eindringen kann. Dringen mehrere Leukozyten gleichzeitig in eine Nervenzelle ein, so entstehen Bilder der Art, wie ich eines auf Taf. II, Fig. 15 abgebildet babe, auf welcher das ganze Protoplasma yon diesen Kanalen durchzogen ist. Dieses Bild erinnert in hohem Grade an das grobe, intrazellulare Netz, welches nach H o 1 m g r e n (29) die Rtickenmarkszellen yon Lophius piscatorius durchzieht oder die intrazellul~tren Kapillaren, welche F r i t s c h (15), H o l m g r e n (21), S t u d n i h k a (62) und andere beschrieben haben. Bei einem sorgfaltigeren Studium des Praparates habe ich mich jedoch stets davon tiberzeugen kOnnen, dass in diesen Kanalen nicht Auslaufer der Kapsel mit Zellelementen und Blutkapillaren, sondern einfach Leukozyten, wie solche gew6hnlich an den ~'ervenzellen unterhalb der Kapsel angetroffen werden, enthalten sind. Die Frage nach der Bedeutung eines derartigen Eindringens yon Leukozyten und ob dasselbe als Phagozytose aufgefasst werden muss oder nicht, muss ich often lassen. Die Wanderung der Leukozyten in dem Zetlprotoplasma kann an und ftir sich ohne jegliche phagozytitre Tatigkeit vor sich gehen; andererseits babe ich in dem Zellprotoplasma der Leukozyten nicht die Anwesenheit yon Bestandteilen der F[ervenzelle nachweisen k0nnen, Nervenelemente bei Gano'iden und Knochenfischen. 25 wahrend in Fallen echter Neuronophagie es den Forschern, so z. B. M a n o u ~ l i a n (37) 1906, bisweilen gelang, in den Phagozyten Cytoplasmareste yon h'ervenzellen (und zwar PigmentkSrner) zu finden: VII. E i n w a c h s e n der Kapsel. V a k u o l e n u n d P a r a s i t e n in d e n N e r v e n z e l l e n . Ausser Kanalen, vermittelst derer in die h'ervenzelle Leukozyten eindringen, sind in dem Protoplasma yon ~Nervenzellen, welche einen degenerativen Charakter aufweisen, haufig noch a n d e r e m i t B i n d e g e w e b e angeftillte Kanale anzutreffen, welche den yon F r i t s c h (15), H o l m g r e n (28), $ t u d n i S k a (62), E c o n o m o (12a), ~Nils A n t o n i (44a) und anderen gesehenen entsprechen. Diese Kanlile entstehen, wie es Fig. 16, Taf. II zeigt, infolge Einwachsens yon Elementen der fibrillaren Htille in das Cytoplasma der h'ervenzelle, wobei dieselben bald breiter, bald schmaler sein kSnnen. Stellenweise verbreitern sie sich und bilden betrachtliche, mit Bindegewebe angeftillte Hohlraume. h'iemals ist der Durchmesser dieser Kanale dermassen gleichmassig als derjenigen, durch welche Leukozytez~ in die h'ervenzelle eindringen. Ist das Bindegewebe bis zu einer gewissen Tiefe in das Cytoplasma eingedrungen, so beginnt es nach verschiedenen Richtungen auszuwachsen, wobei es nicht setten eine zur ursprttnglichen senkrechte Richtung einschlagt: infolgedessen erscheinen die Umrisse der yore Bindegewebe im l~rotoplasma angelegten Gange eigenttimlich gewunden. In einigen Fallen ist das ganze Protoplasma einer Nervenzelle yore Bindegewebe dermafien stark durchwachsen, class es den Eindruck macht, als lagen in dem interstitiellen Bindegewebe Bruchstticke und formlose P~este einer h'ervenzelle. Die Frage, ob mit dem Bindegewebe auch feine Blutgef~isse einwachsen, wage ich nicht zu entscheiden, ich finde jedoch in meinen Praparaten einige Andeutungen daftir und halte daher ein derartiges Einwachsen u Blutgef~ssen ffir durchaus m(iglich. Ein Einwachsen der Htille lasst sich nur an zweifellos degenerierenden Zellen wahrnehmen, in denen der Kern gew0hnlieh vollkommen ver(~det oder kollabiert ist. Es ist mSglich, dass bei diesem ~:orwachsen tier Hiille mit derselben junge INervenelemente vordringen, welche die Stelle der absterbenden Zelle 26 Anton 51emilo ff: einnehmen und dieselbe ersetzen oder sogar Neuroblasten, die nach B t i h l e r und anderen Forschern in den Ganglien vorhanden sind. Sehr haufig fand ich in dem Protoplasma der Nervenzelle verschieden grosse Vakuolen oder vakuolenartige Gebilde, yon denen sowohl in der histologischen ~ls auch medizinischen Literatur bereits viel berichtet worden ist (Taf. II, Fig. 17 und 15v). In den yon mir untersuchten Zellen erscheinen diese Gebilde bald als grosse Vakuolen, welche in einem Teil der Zelle konzentriert waren, bald waren sie in Gestalt kleiner Tropfen im ganzen Cytoplasma zerstreut. Die Vakuolen sind jedenfalls keine konstanten Bestandteite der Zelle, ihre Anwesenheit im Protoplasms. wird jedenfalls yon keinerlei wahrnehmbaren Veranderungen im Kern und anderen Elementen des Neurons begleitet. Mit Hilfe rein histologischer Methoden i s t meiner Ansicht nach die Frage schwer zu 10sen, ob diese Vakuoleu der morphologische Ausdruck irgend welcher normalet physiologischer Prozesse in der Zelle sind oder ob dieselben den pathologischen Erscheinungen zugerechnet werden mtissen (parasitare oder nicht parasit,tre vakuollare Degeneration). In der medizinischen Literatur sind I-Iinweise daftir vorhande~, class in einigen Fallen die Bildung yon Vakuolen im Protoplasma der Nervenzellen durch Eindringen yon Bakterien in dieselben hervorgerufen wird. Bereits L. D r t i n er (12), welcher in seiner Arbeit eine Reihe yon Fallen anftihrt, in denen mikroskopische Parasiten in normaler~ Zellen vorhanden waren, warnt die Forscher vor hierbei mSglichen Irrttimern. Eine gewisse hnzahl yon Zellen war bei den yon mir untersuchten Fischen (besonders bei Lota vulgaris) yon einzelligen P a r a s it e n infiziert, deren Anwesenheit betrachtliche Ver~ anderungen samtlicher Teile der Nervenzelle bewirkte. Ich habe diese Parasiten nicht genau, bestimmt; dieselben geh0ren jedoch augenscheinlich zu den Myxosporidien; meine Praparate entsprechen vollkommen den Abbildungen yon S c h u b e r g und S c h r S d e r (57), welche die Myxosporidien im Nervensystem der Forelle beschrieben hubert. Von anderen Fischen wurden meines Wissens Myxosporidien nur in den Spinalganglienzellen yon Lophius piscatorius beobachtet, wo sie yon H e n n e g u y und darauf yon D o f l e i n (7) beschrieben wurden. Nervenelemente bei Gano'iden und Knochenfischen. 2T Wie die Textfigg. 2 und 3 zeigen, haben die Cysten der Parasiten eine l~tngliche oder ovale Form und sind dermassen im Protoplasma der Zelle gelegen, dass sie den Kern komprimieren und zur Peripherie d~'angen. Bisweilen sind auch in einer Zelle zwei Cysten vorhanden (Textfig. 3). Haufig werden auch in den Praparaten yon Parasiten verlassene und yon denselben bis zur Unkenntlichkeit verunstaltete Zellen angetroffen. Die Gr0sse det" Cysten ist sehr mannigf'altig. Einige ft~llen vollkommen die Zellen an, so dass yore Protoplasma nur ein schmaler Saum nach- Fig. 2. E i n e y o n ein, z e l l i g e n P a r a s i t e n i n f i z i e r t e N e r v e n z e l l e , k ~ Htille der Nervenzelle; i = K e r n ; kn ---~ Kern einer Zelle der Htille ; p = einzeUige P a r a s i t e n ; nz ~ Protoplasma der l~ervenzelle. Ganglion n. vagi. Lota vulgaris. Fixiert; im Gemisch yon L e n h o s s ~ ! k ; F~rbung mit Hii,matoxylin nach H e i d e n h a i n ; in Celloidin-Paraffin eingebettet. R e i c h e r t s Obj. Homog. Immers. ~/1~. Kamera lueida. bleibt, analog der Protoplasmaschicht der Fettzellen. Andere~ Cysten sind wiederum sehr klein, kleiner sogar als der Kern. Wenn nun auf einem Schnitt aus einer derartigen Cyste die Sporen herausgefallen sind, so kann sie leicht for eine grosse Vakuole oder einen intrazellularen Gang oder Kanal gehalten werden. Infolge eines verschiedenen Verhaltens der Sporen des. Parasiten und des Protoplasma der Nervenzelle kommt es vor, dass das Protoplasma der Nervenzelle gut fixiert, w~thrend die Sporen schlecht erbalten sind und zu einer kompakten Masse 28 Anton Nemiloff: verschmelzen, welche sich stark mit dem Farbstoff durchtrankt und die Vorstellung einer eigenartigen Differenzierung des Protoplasma gibt. Bei einer Ftirbung mit Methytenblau werden die Cysten ebenso wie der Kern durchgefarbt. Kurz, es sind hierbei eine Reihe morphologischer Fehler mtiglich, und alas um so mehr, als der Entwicklungszyklus der Nervenparasiten noch bei weitem nicht erforscht ist. -5-' ~ : . : , : . . r ~ . ~' ~+';:~:~2 9 :.W _-nzi ~z O III g ~ ',~,, ~ ~ , ~:.~,."'~.~. _ ....._,_..... _P_ ......................... 'w, , ~i"./:~/,~ i Fig. 3. Eine v~n eil~zclligen P a r a s i t e n i n f i z i e r t e Nervenzelle. k ~ Htille der Nervenzelle ; nz ~ Protoplasma der Nervenzelle: p ~ einzellige Parasiten. Der Kern ist w,m Sehnitt nicht getroffen. Ganglion n. vagi. Lota vulgaris. Fixiert im Gemisch yon Lenhoss4k; gefiirbt mit Hiimatoxylin nach Heidenhain; eingebettet in Celloidin-ParMfin. R e ic h e r t s homog.Immers. ~it,2' TubuslSnge 180 ram. Es bleibt mir noch tibrig, auf eine interessante Eigenheit des Cytoplasma der Nervenzellen yon Fischen hinzuweisen, n~tmlich anf das vollstandige Fehlen des Pigmentes, welches fast konstant in den lqervenelementen der hOheren Wirbeltiere angetroffen wird. 5"ur im Verlauf der Gefasse des Ganglions finden sich kleine Pigmentzellen bindegewebigen Charakters; grosse sternfOrmige Pigmentzellen werden zuweilen in dem das Ganglion umgebenden Bindegewebe beobachtet. Nervenelemente bei Ganoiden und Knochenfischen. 29 VIII. Der B a u des K e r n k 6 r p e r c h e n s und d e s s e n A u s t r i t t in das C y t o p l a s m a . Die Kerne yon ~Nervenzellen der yon mir untersuchtea Fische weisen in morphologischer Hinsicht keine Besonderheiten auf. Sie sind alle blaschenf6rmig, rund oder oval. Die I(ernmembran ist im Vergleich mit derjenigen anderer Zellen betrachtlich dick. Das (echte) KernkOrperchen ist recht gross und enth~tlt fast konstant die yon M a u t h n e r , S c h r a n und vielen anderen beschriebenen, stark lichtbrechenden Gebilde. Soviel ich habe wahrnehmen kannen, sind ill der Mehrzahl der Kernkarperchen nicht je ein derartiges lichtbrechendes Kbrperchen, wie augenscheinlich 0 b ers t e i n e r (45) geneigt war anzunehmen, sondern mehrere vorhanden, worauf auch [R h 2 i 5 k a (54), welcher die Kernkarperchen der Nervenzellen des Rfickenmarks yore Frosch, Meerschweinchen, Katze, Hund, Pferd und Menschen nntersucht hatte, hinweist. Die yon Rfi'~iaka beschriebene oberflachliche Schicht oder H~'llle um diese Gebilde, sowie die yon ihm beschriebenen Karperchen mit gez~hnten l~andern, habe ich auf meinen Praparaten nicht gesehen. Soviel ich habe erkennen k6nnen, gibt es zweierlei Arten M a u t h n e r - S c h r b n s c h e r K6rperchen. Die eine Art stellt blasse, schwacher lichtbrechende Gebilde vor; ihrer betrachtlicheren GrOsse nach gewahren sie den Eindruck yon kleinen, in die Substanz des Kernkarperchens eingelassener Vakuolen. Die andere Art ist kleiner, jedoch starker lichtbrechend und gleicht eher festen, karnigen Einschlfissen als Vakuolen (Taf. II, Fig. 191). Wahrend die Karperchen der ersten Art sowohl in dem peripheren als auch im zentralen Tell des KernkOrperchens angetroffen werden, sind die starker lichtbrechenden Karperchen der zweiten Art vorwiegend in der peripheren Schicht der Kernkarperchensubstanz konzentriert. Haufig ist ein kleines, glanzendes K6rnchen in dem einer Vakuoie gleichenden Karperchen erster Art gelegen. Einige KernkOrperchen entbehren vollkommen der M a u t h n e r- S c h r ~ n schen Karperchen oder enthalten nur einige stark lichtbrechende oder schwach lichtbrechende. Die Gr6sse dieser Gebilde ist desgleichen ausserst mannigfaltig und zwar haufig sogar in einem KernkOrperchen. In verhaltnismltssig seltenen Fallen babe ich den Austritt des KernkOrperchens in das Cytoplasma gesehen (Taf. II, Fig. 18. 30 A n t o n N e m i l o ff: und 20). Das Kernk6rperchen erwies sich hierbei (Taf. II, Fig. 20) recht welt vom Kern entfernt im Cytoplasma eingeschlossen. Auf verschiedenen Praparaten habe ich eine Reihe yon Stadien des Austrittes finden k0nnen, welches, einigen Merkmalen nach, wenigstens in den yon mir untersuchten Zellen sich als Kunstprodukt offenbartc. An einigen gtinstig fixierten und gefttrbten Praparaten verlief yon dem ins Cytoplasma ausgewanderten KernkSrperchen zum Kern hin eine kaum merkbare Spur in Gestalt eines Kanals~ welcher durch den Durchtritt des Kernk0rperchet~s bedingt war. Die Kernmembran ist an der Durchtrittsstelle des KernkSrperchens zerrissen, desgleichen ist auch der Teil des Kernnetzes, welcher dem Kernk0rperchen analog, verletzt. Der tibrige Teil des Kernnetzes offenbarte das Bild eines vollkommen normalen, ruhenden Kernes, welcher sogar keine Spuren der Anzeichen an sich trug, die yon den Autoren bei einem scharf -ausgepr~gten Stoffwechsel zwischen Kern und Protoplasma beschrieben werden. Es wird hierbei der Eindruck gewonnen, als w~tre das KernkOrperchen mit Gewalt aus dem Kern ausgestossen, wobei es das Kernnetz verletzt, die Kernmembran eingerissen hat ul~d tief in das Protoplasma eingedrungen ist. Das Mitgeteilte veranlasst mich nun zur Annahme, dass der Austritt des Kernk0rperchens aus dem Kern keine nattirliche oder funktio~elle Erscheinung darstellt, sondern ktinstlich beim Herausschneideu des Ganglions, oder beim i~%erftihren desselben mit der Pinzette aus einer Fltissigkeit in die andere, oder beim $chueiden auf dem Mikrotom, oder schliesslich bei den wahrend der Fixierung der Gewebe vor sich gehenden chemischen Prozessen erfolgt. Die Kerne einiger Zellen erleiden hierbei irgend einen mechanischen Effekt, infolgedessen das Kernk6rperchen aus dem Kern herausgepresst wird. IX. S t R b c h e n f 6 r m i g e u n d a n d e r e Einschlfisse i m Kern. In den yon mir untersuchten Nervenzellen habe ich ausser den gewShnlichen Kernelementen auch verschiedenartige inkonstante Gebilde und Einschltisse angetroffen. Welter obeu habe ich bereits angegeben, dass in einigen Fi~llen Leukozyten selbst in den Kern tier Nervenzelle eindringen. 51"ervenelementebei Gano'iden und Kncchenfischen. 31 Im Kern werden ausserdem bisweilen noch besondere stabchenf6rmige oder fadenf6rmige Gebilde wahrgenommen, wie ich solche auf Fig. 21, Taf. III abgebildet habe. Dieselben stellen sich bald in Gestalt gerader, gleichmassiger Stabchen, bald als feine, leicht gewundene Bander dar; selten sind sie hufeisenf6rmig oder schlingenfSrmig gekrtimmt; gewShnlich sind diese Gebilde sehr intensiv gefarbt, wobei nur die Enden derselben etwas schwacher tingiert erscheinen. Das Karyoplasma liegt diesen Gebilden niemals unmittelbar an, sondern ist yon denselben durch einen geringen Zwischenraum getrennt. Ebenso erreicllt ein derartiges Stabchen oder Bandchen niemals die Kernmembran, bertihrt dieselbe niemals, sondern endigt stets in einiger Entfernung yon derselben. Diese stabchen- oder fadenfOrmigen Gebilde entsprechen OffGnbar den ,,Krystalloiden "~, ,stabchenf0rmigen Gebilden", ,,intranuklearen $tabcl|en", welche M a n n (35) in den Kernen yon Gehirnzellen von Kaninchen, Le nh o s s 6 k (33) in den Kernen sympathischer Nervenzellen vom Igel, H o l m g r e n (22) in den Kernen spinaler und sympatbiscl~er Ganglienzellen bei $augetieren nnd VSgeln, Sj 5 v all (58) in den Kernen yon Spinalganglienzellen beim Igel, A. $ m i r n o f f (59) in den Kernen yon Spinalganglienzellen bei ei~em viermonatlichen menschlichen Embryo mid R a m 6 n C a j a l (49) in ~'ervenzellen verschiedener Typen beschrieben haben. ~Niemals habe ich beobachten k6nnen, (lass diese Gebilde, wie es H o l m g r e n annimmt, sich aus dem Kern in das Cytoplasma erstrecken oder sogar ausserhalb der Zelle begannen, ebenso wie ich niemals dergleichen regelmassige prismatische Formen gesehen habe, wiG sie S m i r n o f f abbildet. L e n h o s s 6 k hielt, wie bekannt, diese ,intranuklearen Stabchen" ftir .Krystalloide", M a n n fiir eine besondere Form eines Centrosoma, H o ! m g r e n erklart sie einfaeh fiir ratselhaft, wahrend S j 6 v a l l dieselben ftir Gin dauerhafteres Ersatzmaterial als die Tigroidsubstanz halt. Zugunsten eines krystallinischen Charakters dieser Gebilde spricht nur ihr homogenes Aussehen; irgend welehe optische, ftir Krystalle charakteristische Eigenschaften sind nicht fGstzustellen, so dass meiner Meinung nach kein reehter Grund vorliegt, dieselben als krystallinisch zu bezeiebnen; wfirden diese intranukleLtren Stabchen als Krystalloide zu bezeichnen sein, so k6nnten eben- 32 Anion :Nemilo ff: sogut auch die Schollen der Tigroidsubstanz den Krystalloiderl zugezahlt werden. Noch mit weniger Recht k6nnten sie als Centrosome bezeichnet werden, mit welchen sie weder ihrer Form noch ihrer Gr6sse noch ihrer Lagerung in der Zelle nacb, irgend etwas gemein haben. Am einfachsten und natttrlichsten scheint mir die Annahme, dasses sich im gegebenen Fail um irgend welche Stoffwechselprodukte der Zelle handelt, welche sich unter gewissen Bedingungen im Kern verdichten und eine charakteristische st~tbchenf6rmige oder fadenfSrmige Form annehmen. Diese Produkte n~ther bestimmen zu wollen und dieselben durchaus ftir Ablagerungen yon Ersatzmaterial in der Zelle anzunehmen (SjSvall), scheint mir willkt~rlich zu sein, da ja ein pathologischer Charakter dieser Gebilde m6glich ist. Bei tier geringen Wahrscheinlichkeit irgend welcher physiologischer Annahmen nur auf Grund yon anatomischen Befunden ist ja auch die M6glichkeit nicht ausgeschlossen, dass es sich hier um einen einzelligen Parasiten handelt. Eine desgleichen ratselhafte Bedeutung haben auch noch andere Einschlfisse (conf. Textfig. 4, Taft II, Fig. 22), welche hauptsachlich in den Kernen yon Riesenzellen angetroffen werden. Diese stellen sich als grosse Konkretionen verschiedener Form dar, die mit den anderen Kernelementen nicht in unmittelbarem Zusammenhange stehen und sich intensiv in Safranin, Hamatoxylin nach H e i d e n h a i n , Toluidinblau und anderen Farbstofl'en farben. Ihre Form ist sehr mannigfaltig, bald rund oder oval, eif6rmig, bald keulenfSrmig oder kolbenf6rmig, bald kommaf6rmig usw. Sie sind vollkommen homogen, enthalten weder Vakuolen noch KSrner und offenbaren tiberhaupt keine Differenzierung. X. V e r ~ n d e r u n g e n des Kerns. Das gr6sste Interesse gew~thren diejenigen Kernbilder, welche einen morphologischen Ausdruck irgend welcher physiologischer Prozesse. in der Zelle darstellen; dieselben haben bereits vor langerer Zeit die Aufmerksamkeit der Forscher, wie K o r s c h e l t , F l e m m i n g , van B e n e d e n , B a l b i a n i , H e n n e g u y , H o l m g r e n und anderer auf sich gelenkt. Speziell in betreff des Kernes der Nervenzellen und seiner morphologischen Eigenttlmlichkeiten bei verschiedenen funktionellen Zustanden der Zelle sind in den letztea Nervenelemente bei Gane'/den und Knoehenfischen. 33 Fig 4. Einlagerungen ~in d e m K ' e r n e i n e r N e r v e n z e l l e . Der Kern (i) offenbart einige charakteristische Formver~nderungen und stel]enweise Reduktionen, z . B . in der Kernmembran (st). d : Dentriten, nz----:. Protoplasma der Nervenzelle ; fk : fibrillate I~l~ille dcr Nervenzelle ; st ~ Reduktionsstelle der Kernmembran; kr ~ Einlagerun~en. Ganglion n. vagi. Riesenzelle. Lota vulgaris. Fixiert in Chromessigsauregemiscb, gef~rbt in H~matoxylin nach H e i d e n h a i n . Eingebettet in Celloidin-Paraffin. Z e i s s ' homog. Immers. 1/~. Kamera lucida. Archiv f. mikrosk. Anat. Bd. 72. ~ 34 Anton N e m i l o f f : Jahren eine Reihe von Beobachtungen voa Marin esco, H o l m g r e n, Levi, BaronciniL. eBerettaA., P e r r i n de l a T o u c h e et Dide, Guerrini, Rilvington, Giani e Ligorio, RamSn C aj al, H a t ai und vielen anderen verSffentlicht worden. In den Ganglienzellen der Fische habe ich sehr h~'tufig verschiedene Abweichungen yon der gewOhnlichen Kernstruktur tier normalen, ruhenden Kerne angetroffen. In einigen Fallen war z. B. das gesamte Chromatin an der Kernperipherie angeordnet (Tar. II, Fig. 15 und 23). Das ganze Kernnetz war frei yon Chromatink6rnchen, nut dicht an der Kernmembran war eill Saum oder Streifen yon Chromatink6rnchen vorhanden; ein Teil derselben konnte ausserdem auch in dem Cytoplasma in der Nithe des Kernes festgestellt werden. Dieser Streifen nahm entweder die ganze Peripherie des Kernes ein oder konzentrierte sich in einem Teil desselben. Bisweilen war, wie in dem auf Taf. II, Fig. 15, abgebildeten Falle, diese Chromatinkonzentration an der Peripherie des Kernes von dem weiter oben beschriebenen Eindringen yon Leukozyten in die Zelle und den Kern begleitet; in anderen Zellen war jedoch die Chromatinkonzentration mit keinerlei anderweitigen Veritnderungen im Karyo- und Cytol)lasm:t verbunden. Die Kernform war hierbei unverandert. In anderen Fttllen war die Form des Kernes verandert, wobei eine Zu- oder Abnahme tier f~trbbaren KOrnchen in ibm nachweisbar war; die Kernumrisse wurden unregelmitssig, an vielen Stellen desselben traten HOcker oder zungenf0rmige Auswt'tchse auf, und zwar bald nur an einer Stelle des Kernes, wobei die sogenannten Flammenfiguren der Autoren entstanden, bald an der ganzen Peripherie desselben. Es liegt kein Grund vor, diese Bilder ftir Kunstprodukte zu halten, da weder das Cytoplasma, noch die Membran, noch tiberhaupt das ganze Pritparat irgend welche Anhaltspunkte daftir bot. Derartige Formveranderungen des Kernes kOnnen auch noch weiter fortschreiten. Anstatt H6ckern und Auswtichsen treten an der Kernperipherie breite, gelappte Fortsatze auf, und zwar besonders hitufig an de~ oben beschriebenen Riesenzellen. Hierbei entstehen, wie es die Textfigg. 4, 5 und 6, sowie Figg. 24, 25, 26, 27, 28 der Taf. II zeigen, die verschiedenartigsten Kernformen, yon einer bisquitund hufeisenf0rmige~l his zu einer kringelfSrmigen und gelappten, wie in den Zellen des Spinnapparates tier Lepidoptera und einiger Nervenelemente bei Gano'iden und Knochenfischen. 35 anderer Drtisenelemente. Der Kern ist gleichsam bestrebt, vermittelst Lobopodienbildung seine Bertihrungsflache mit dem Cytoplasma zu vergr(issern, in alle Ecken des ZellkSrpers vorzudringen und seinen Einiiuss auf die entferntesten peripheren Teile der Zelle zu erstrecken. Es entstehen hierbei h~ufig Bilder, welche ! nL Fig. 5. Bisquitf~irmiger Kern einer Nervenzelle. nz Protoplasma einer 5Iervenzelle; i --= Kern; nue ~ KernkSrperchen. Ganglion n. vagi. Riesenzelle. Lota vulgaris. Fixiert im (] emisch yon L e n h o s s ~k ; gefitrbt mit H~h~ato• nach H e i d e n h a i n ; eingebettet in CelloidinParaffin. Z eis s' homog. Immersion 1,5 mm; Apert. 1,30. Kamera ]ucida. an die Figuren einer amitotischen Kernteilung (Textfig. 5) erinnern. Ich mSchte diese Streckung des Kernes nicht als Amitose bezeichnen, da in der tiberwiegenden Mehrzahl der Falle es nicht bis z u r B i l d u n g yon Tochterzellen oder Tochterkernen kommt. Zwei kernige Zellen sind, wie bereits H o l m g r e n (21) yon den Ganglien yon Lophius, Acanthias, Raja, Gadus und Rana berichtet, auch in den yon 3* 36 Anton Nemiloff: mir untersuchten Zellen die gr(isste Seltenheit. Auf den Serienschnitten durch eine grosse Anzahl yon Ganglien habe ich nur eine oder zwei Zellen mit zwei oder drei Kernen gesehen; Zellen: mit verzweigten Kernen sind jedoch recht zahlreich vorhanden; wtirden diese Kernformen Teilungsfiguren sein, so mtisste die Zahl der zweikernigen Zellen zweifellos eine viel gr6ssere sein. Bisweilen k6nnen sich freilich bei der Streckung des Kernes und bei der Bildung yon geIappten Fortsatzen desselben yon ihm kleine Abschnitte abschnt~ren oder absondern, welche sp,~terhin eine runde Gestalt annehmen, so dass eine Art Knospung des Kernes vorliegen kann. Das weitere Schicksal eines derartigen, abgeschntirten'Kernteils habe ich leider nicht weiter verfolgel~ k0nnen. Ich glaube jedoch dennoch nicht, dass eine derartige ,Kernknospung" der gew(ihnlichen Amitose gleichgestellt werden kann, welche in anderen Geweben vorkommt und yon Apolant (1), O r z e c h o w s k y (45a) und anderen Forschern auch ftir die Nervenelemente angenommen wird. Die hbschniirung eines Kernabschnittes ist im gegebenen Falle eine Begleiterscheinung, ich m6chte sagen eine zufallige Erscheinung der lebhaften Metabolie des Kernes und keine echte Teilung im gewOhnlichen Sinne derselben. Eher noch k6nnte diese Erscheinung mit den Prozessen einer funktionellen direkten Kernteilung, in der Art, wie sie P l a t e (47) in den Luftr6hren des neuseeliindischen Janellides als regenerative Zel]amitose annimmt. In derartig verzweigten Kernen sind auch einige andere Veranderungen im Vergleich zu ruhenden Kernen sichtbar. Das Kernki~rperchen ist gew0hnlich etwas vergr0ssert, das Kernnetz ist schwach, bisweilen auch gar nicht sichtbar, wahrend die Menge der Chromatink6rnchen und -schollen mehr oder weniger zugenommen hat. Noch tiefergreifende Veranderungen werden an den Riesenzellen beobachtet, die allen Anzeichen nach in der Degeneration begriffen sind. An irgend einer Stelle des verzweigten Kernes wird dessen Htille reduziert (Textfigg. 4 und 6~ Taf. I.I, Fig. 22), wobei die Kernsubstanz sich frei ins Cytoplasma ergiesst und sich mit ihr vermengt. Die Kernmembran schwindet in einigen Fallen nur an dem Ende eines feinen Kernfortsatzes, wobei eine Vermischung der Elemente des Karyo- und Cytoplasmas in beschranktem Mal~e erfolgt. In derartigen Fallen werden auch die grOssten Einschliisse vorgefunden, yon denen weiter Nervenelemente bei G~no'/den u n d K n o c h e n f i s c h e n . 3T oben die Rede war. Ausserdem wird haufig an den v o n d e r erwahnten Berfihrungsstelle des Karyo- und Cytoplasmas am entferntesten gelegenen Abschnitten des Kernes eine gewisse Konzentration der Kernsubstanz wahrgenommen. In anderen Fallen verschwindet die Kernhfille auf eine betr~,tchtliche Strecke, wobei eine recht intensive Vermischung der Kernelemente mit dem Cytoplasma erfolgt. Haufig sind halb oder vollkommen verGdete Kerne sichtbar, welche alsdann kollabieren und als enge Kanale oder Spalten erscheinen, Das ,rk ........ ks ~:~.~ 9ff~j~;'..- :-:~~ .~,?::4.._':~,::2'.',%=.. -:,-.',,~...j,~ :Fig. 6. Kern einer Nervenzelle. n z = P r o t o p l a s m ~ der N e r v e n zelle ; i --~ K e r n ; r k ~--- K e r n e i n s c h l f i s s e ; k s = Stelle, ~n w e l e h e r die K e r n m e m b r a n r e d u z i e r t i s t u n d die K e r n s u b s t a n z sieh in d a s C y t o p l ~ s m ~ e r g i e s s t . G a n g l i o n n. v a g i . Pdesenzelle. L o t ~ vulgaris. Fixiert im Gemiseh yon Lenhossgk; gef~rbt mit H ~ m a t o x y l i n n a e h It e i d e n h e i n ; e i n g e b e t t e t in Celloidin. Z e i s s' h o m o g . I m m e r s . 1,5 r a m ; A p e r t . 1,80. K ~ m e r a lueida. Protoplasma ist in derartigen Fallen mehr oder weniger vakuolisiert m~d enthalt in grosset Zahl K6rnehen, Schollen und stabehenfSrmige Gebilde, die sieh intensiv in Hamotoxylifi naeh Heidenh a i n , in Safl'anin und anderen Farbstoffen farben. Derartige Zellen mit ver6deten und kollabierten Kernen mtissen offenbar als zugrunde gehende oder absterbende Nervenelemente angesehen werden. Bei experimentellen Versuchen gelang es einen Kernschwund nur in Fallen starkerer Verletzungen tier Nervenzelle zu erzielen. So beobachtete R i l v i n g t o n (52) einen Kernschwund in den Nervenzellen bei der Vergiftung eines K~ninchens mit dem Gift der australischen TigerschIange. 38 Anton Nemiloff: XI. I n t e r s t i t i e l l e s G e w e b e in d e n G a n g l i e n der Fischeo ])as interstitielle Gewebe weist auch in den yon mir untersuchten Kopf- und Spinalganglien das gewShnliche Verhalten auf, infolgedessen ich mich dabei nicht welter aufhalten werde. Im Ganglion n. vagi offenbart dasselbe nur eine paradoxe EigenW -n Fig. 7. B i i n d e l q u e r g e s t r e i f t e r M u s k e l f a s e r n im i n t e r s t i t i e l l e n Gewebe eines G a n g l i o n s . gz ~ Ganglienzellen; ig ~ interstitieUes Gewebe; mp ~ quergestreifte Muskelfasern. Ganglion n. vagi. Lota vulgaris. Fixiert im Gemisch yon L e n h o s s ~ k ; gef~rbt mit H~matoxylin nach l ~ e i d e n h a i n . Eingebettet in Celloidin-Paraffin. Z e i s s ' homog. Immers. 1,5 ram; Apert. 1,30. Kamera lucida. tfimlichkeit, indem es kleine Btindel quergestreifter Muskelfasern enthltlt. Ein TeiI d erselben ist an der Peripherie des Ganglions gelagert, unmitteiber unterhalb der Bindegewebshtille desselben. Ein anderer Teil erstreckt sich in Gestalt recht feiner Btindel Nervenelemente bei Gano'/den und Knochenfischen. 39 und sogar einzelner Fasern betr:achtlich weit in das Ganglion selber. Soviel ich auf Quer- und L;mgsschnitten dieser Muskelfaserbtindel habe warnehmen k6nnen, so offenbaren sie keine Unterschiede yon der quergestreiften K($rpermuskulatur. Literaturverzeichnis. Die mit einem * verzeichneten Arbeiten sind nach einem Referat zitiert. 1. A p o l a n t : {)ber die sympathisehen Ganglienzellen der Nager. Arch. f. mikr. Anat., Bd. 47, H. 3. 2. B e r g e n, F. v. : Zm" Kenntnis gewisser 8trukturbilder (,Netzapparate ~, ,Saftkan'alchen ~, ,,Trophospongien =) im Protoplasma verschiedener Zellenarten. Arch. f. mikr. Anat., Bd. 64, H. 3. *3. B u c k , D. de et M o o r , L. de: La neuronophagie. Journal de ~leurol. (Bruxelles-Paris), No. 14, p. 269--274, av. 3 Fig. 190{). 4. B t i h l e r , A.: Untersuehungen iiber den Bau der Nervenzellen. Verh. phys.-me& Gesellschaft, Wiirzburg, Bd. 31, N. F. No. 8, pag. 285--292. ~Iit 2 Taf. 5. D a h l g r c n , U.: The Giant Ganglion Cells in the Spinal Cord of the Order tteterosomata Cope (Anacanthini pleuronectoidei Guentner). Anat. Anz., Bd. 13, 1897, p. 281--293. 6. D e m o o r : Les effets de la trepanation chez les animaux nouveaux-n~s. Travaux de lab. de l'Institut Solvay, T. IV, p. 321. 7. D o f 1e i n , Fr.: Studien zur Naturgeschichte der Protozoen. III. Uber Myxosporidien. Zool. Jahrb., Abt. Anat., Bd. 11. 8. Do g i e l , A.S.: Zur Frage fiber die Ganglien der Darmgefleehte bei den Sgugetieren. Anat. Ariz., Bd. X, No. 16. 9. Derselbe: Zur Frage fiber den feineren Bau des sympathischen Nervensystems bei den Siiugetieren. Arch. f. mikr. Anat., Bd. XLVI, 1895, p. 305--344. 10. Derselbe: Zwei Arten sympathischer iNervenzellen. Anat. A~z., Bd. XI, .No. 22, 1896. 11. Derselbe: Uber den Ban der Ganglien in den Geflechten des Darmes and der Gallenblase des Menschen and der S~ugetiere (hierzu Taf. V--IX). Separat-Abzug aus dem Arch. f. Anat. u. Phys., Anat. Abt., 1899. 12. D r fi n e r, L. : Kern- and Zellendegeneration und ihre Ursache. Jenaische Zeitschr. f. Naturwissenschaft, Bd. 28. *12a. E c o n o m o, C. J. : Beitrgge zur normalen Anatomie der Ganglienzellen. Arch. Psychiatr. u. Nervenkr., Bd. 41, tI. 17 1906, p. 158--201. Mit 5 Tar. "13. E x p o s i t o : La Neuronofagia. Manicomio Interprovinciale V. E. 11 in 51ocera Inferiore. 14. F r i t s e h ~ G. : Uber den Angelapparat des Lophius piscatorius. Sitzungsbericht d. kgl. preuss. Akad. d Wissenschaften zu Berlin, Jahrg. 1884, No. 50~ p. 1145--1151. 40 Anton Nemiloff: 15. Derselbe: g'ber einige bemerkenswerte Elemente des Zentralnervensystems yon Lophius piscatorius L. Arch. f. mikr. Anat., Bd. 27, 1886, p. 13--31, Taf. II[ und IV. 16. F u c h s , H.: tTber die Spinalganglienzellen und Vorderhirnganglienzellen einiger Siiuger. Anat. Hefte, Bd. XXI, H. 1, 1903. "17. G e h u c h t e n , V a n : Contributions s l'~tude des ganglions cdrSbrospinaux. Bruxelles 1892. 18. G o r o n o w i t s c h , N. Dr.: Der Trigemino-facialis-Komplex yon Lota vulgaris. Festschrift zum siebzigsten Geburtstage yon C a r l G e g e n b a u r am 21. Aug. 189{i, dritter Band. Leipzig 1897. 19. H a l l e r , B. Dr.: Dcr Ursprung der Vagusgruppe bei den Teleostiern. Mit Taf. I - - I V u. 1 Textfig. Festschrift zum siebzigsten Geburtstage yon C a r l G e g e n b a u r am 21. Aug. 1896, dritter Band. Leipzig 1897. 20. H o l m g r e n , E m i l : Kurze vorlSufige Mitteilungen fiber die Spinalganglien der Selaehier und Teleostier. Mit 11 Abbild. Anat. Anz., Bd. XV, No. 8, 23. Okt 1898. 21. Derselbe : Zur Kenntnis dec Spinalganglienzellen yon Lophius piscatorius Lin. Mit 2 Abbild. im Text und 32 Fig. auf Taft I X - - X V I I I . Anat. Hefte, Erste Abt. Arbeiten aus anat. Institut, Heft X ~ ' ( V I I I (Bd. XII, H. I), 1899. 22. Dersetbe: Weitere ~[itteihmgen fiber den Bau der Nervenzellen. Mit 13 Abbiht. Anat. Anz., Bd. 16, No. 15 16, 22. Sept. 1899. 2:~. Derselbe: Nvch weitcre Mitteilungen fiber den Bau der Nervenzellen verschiedener Tiere. Anat. Anz., Bd. 17, No. 6/7, 1900. 24. Derselbe: Studien in der feineren Anatomie der Nervenzellen. Anat. Hefte, Bd. 15. H. 1, 1900. 25. Derselbe: Weitere 5Iitteilungen fiber die ,SaftkanMchen ~ der Nervenzellen. Anat. Anz., Bd. 18, No. 11/12, 1900. 26. Derselbe: Beitr~ge zur Morphologie der Zelle. I. Nervenzellen. Anat. Hefte, Bd. 18, H. 2, 1901. 27. Derselbe: Einige Worte fiber alas ,Trophospongium" verschiedener Zellarten. Anat. Anz., Bd. 20, No. 18, 1902. 28. Derselbe: Weiteres fiber das ,Trophospongium ~ der Nervenzellen und der Driisenzellen des Salamander-Pankreas. Arch. f. mikr. Anat., Bd. 60, 1902. 29. Derselbe: L~ber die sogen. ~intrazellulSren F'~den ~ der Nervenzellen von Lophius piscatorius. Mit 7 Abbild. Anat. Anz., Bd. :CXIII, l~o. 2/3, 8. April 1903. 3!). Derselbe: Beitriige zur Morphologie dec Zellen. II. Verschiedene Zellarten. Anat. Hefte, H. 75, Bd. 25, 1904. 3L Derselbe: T)ber die Tropbospongien zentraler Nervenzellen. Arch. f. Anat. u. Phys., 1904, Anat. Abt., H. 1, p. 15--32. Mit 3 Taft 39_. K o l s t e r , R u d . : gTber bemerkenswerte Ganglienzellen im Riickenmark yon Perca fluviatiles. Mit 1 Abbild. Anat. Anz., Bd. XIV, No. 9, p. 250--253. *33. L e n h o s s ~ k : Arch. f. Anat. u. Phys., Anat. Abt, 1897. Nervenelemente bei Gano'/den und Knochenfischen. 41 *34. L e v i , G.: La struttura dei gangli cerebrospinali nei Selaci e nei Teleostei. Sperimentale Anno LX, No. 8, p. 242--248, 1906. 35. M a n n : Histological changes induced im sympath, mat. and sens. Nerve Cells by fonctional activity. Journ. of Anat. and Pbysioh, Vol. 29, 1894. 36. M a n o u ~ l i a n : Des l~sions des ganglions c~r~brospinaux darts la vieillesse. C. lt. Soc. biol., Paris 1903, No. 3, p. 115. 37. Derselbe: Ann. de l'Institut Pasteur, 0ktobre 1906, p. 859 (zitiert nach Metschnikoff, Essais optimistes. 37a. Derselbe: Etude sur le m~canisme de la destruction des cellules nerveuses clans la vieillesse et duns les Stats pathologiques. C. R. Ac. Sc. Paris, 18. f~vr. 1907. 38. M a r i n e s c o , G.: ~I~canisme de la s~nilitd et de la mort des cellules nerveuses. C.R. Acad. Sc. Par., T. 130, No. 17, p. 1136--1139, 1900. 39. Derselbe: Etudes histologiques sur le m~eanisme de s~nilit~. Revue g5nerale des sciences, 30 d~cembre 1904, p. 1116. 40. 5 I e n c l , E.: ZurVakuolisation der Gangiienzellen. 5lit 2 Abbildungen. Anat. Anz., Bd. XXVIII, No. 9/10, 1906. 41. Derselbe: Une petite notice sur la vaeuolisation des cellules nerveuses. Anat. Anz., Bd. XXIX., No. 1/2. 42. 5 I e r t o n , Hugo, Dr.: Lrber ein intracellul~res Netzwerk der Ganglienzellen yon Tethys leporina. Mit 2 Abbild. Anat. Anz., Bd. XXX, 1907, No. 17 und 18. 43 ~ e m i l o f f , A.: Zur Frage der Nerven des Darmkanals bei den Amphibien. 3 Tafeln. Arb. d. St. Petersb. naturforsch. Gesellsch., Abt. f. Zool. u. Physiol., T. XXXII, H. 2, p. 59--88. 44. Derselbe : Zur Frage tiber den B a u d e r Fettzellen bei Acipenser ruthenus. Mit 6 Abbild. Anat. Ariz., Bd. XXVIII, No. 21 u. 22, 1906. 44a. N i l s A n t o n i : ,Deltabildungen ~ ( H o l m g r e n ) und derartige Strukturen bei den Ganglienzellen yon Lophius. Anat. Anz., Bd. XXXI, 1907, No. 7/8. 45. 0 b e r s t e i n e r : Anleitung beim Studium des Baues tier nervSsen Zentralorgane. Leipzig-Wien 1896. "45a. O r z e e h o w s k y : Kernteilungsfiguren in Ganglienzellen. Verh. Psychiatr. u. Neural. Wien Sitzung v. 12. Juni 1906. Wiener klin. Wochenschrift, 1906, No. 34, nach Referat in Neurol. Zentralb., Jahrg. 25, 1906, No. 21, p. 1016. 46. P e w s n e r - N e u f e l d , R.: lJber die Saftkan~lchen in den Ganglienzellen des Riickenmarks und ihre Beziehungen zum pericellul~ren Saftlttckensystem. Anat. Anz., Bd. 23, No. 16/17, 1903, p. 1--23, mit 2 Taft und 1 Figur. 47. P l a t e , L.: Uber regenerative Amitose, Degenerationserscheinungen und Phagocytose in den AtemrShren der Janellen. Hierzu Taf. XXVIII. Arch. f. mikr. Anat., Bd. 51, 1898. 48. P u g n a t , C. A.: De la destruction des cellates nerveuses par les leucocytes chez les animaux '~g~s. C. Rend. Soc. biol. 1898, No. 8, p. 242. 42 Anton Nemiloff: 49. R a m 6 n C a j a l : Un sencillo metodo de coloraeione del reticulo protoplasmico y sus efectos en los diversos centras nerviosos de vertrebratos y invertebratos. Trabajos del lab. de investig, biolog, de la Univ. de Madrid, T. II. p. 129, 1903. 50. Derselbe: Tipos celulares de los ganglios sensitivos del hombre y mamiferos, Trabajos del lab. de investig, biolog, de la Univ. de Madrid. T. IV, fasc. 1. y 2, Madrid 1905. 50 a Derselbe : L'appareil reticulaire de Golgi-Holmgren colors par le nitrate d'argent. Travaux du Laboratoire de recherches biologiques de l'Universit6 de Madrid T. V (X de la ~Revista Trimestral micrografica ~) Fascicule 3 ~ Juillet 1907. 51. R a n v i e r : Traite technique d'histologie, russische ~:bersetzung unter d. Redakt. v. T a r e h a n o f f , St. Petersburg 1881. 52. R i l v i n g t o n , B.: A preliminary communication on the changes in nerve cells after poisoning with the venom of the australian tigersnake (Hoplocephalus Curtus). Journ. Phys. Cambridge, Vol. 28, No. 6, p. 426--430, 9 Fig. 53. Rohdc, E.: Untersuchungen fiber den Bau der Zelle IV. Zum histologischen Wert der Zelle. Zeitschr. wiss. Zoologie, Bd. 78, H. 1, 1904, p. 1--148, 7 Tar., 102 Fig. 54. Rfi~.i~ka, V l a d i s l a v : Zur Geschichte uad Kenntnis der feineren Struktur der Nukleolen zentralcr Nervenzellen. ~lit 1 Abbild. Anat. Anz., Bd. XVI, 8. November 1899, No. 21 u. 22. 55. S a c u s s e w , S.: Die Nervencndigungen im Darmkanal der Fische. Arb. d. Naturf. Gesellschaft in St. Petersburg. Zool. und Physiol. Abteilung~ Bd. XXVIII, Lief. 4 (russ.). 55a. Saigo: Uber die Altersver~nderungen der Ganglienzellen im Gehirn. Virchows Arch., 0kt. 1907, Bd. 190, H. 1. 56. S a r g e n t , P o r t e r E d w a r d : The Giant Ganglion Cells in the Spinal Cord of Ctenolabrus coeruleus. With 10 Fig. Anat. Anz., Bd. XV, 1899, p. 212--225. 57. S c h u b e r g , A. und S e h r S d e r , 0.: Myxosporidien aus dem Nervensystem und der Haut der Baehforelle (Myxobolus neurobius n. sp. und H e n n e g u y a nfisslini n. sp.). Hierzu Taf. III. Arch. f. Protistenkunde, Bd. VI, Jena 1905. 58. S j S v a l l , E i n a r : 0bet die Spinalganglienzellen des Igels. Ein neuer Befund yon krystalloiden Bildungen in Nervenzellen. Die intracellul~ren ,,Kan~lchen" Systeme. Anat. Hefte, Abt. I, H. 58 (Bd. 18, H. I), p. 239 bis 266. Mit 2 Taf. 59. S m i r n o w , A. E.: Einige Beobachtungen fiber den Bau der Spinalganglienzellen bei einem viermonatl, menschl. Embryo. Arch. f. mikr. Anat., Bd. 59, H. 3, p. 459--470. 60. S t a n n i u s , H.: Das peripherische Nervensystem der Fische, anat. und physiol, untersucht. Mit 5 Steintafeln. Rostock 1849. 61. S t i e d a, L.: Studien fiber das zentrale Nervensystem der Knochenfische. Mit Tar. I und II. Zeitschr. f. wissensch. Zoologie, Bd. 18, 1868. Nervenelemente bei Ganoiden und Knochenfischen. 43 62. S t u d n i ~ k a , F. K.: Beitritge zur Kenntnis der Ganglienzellen. III. TJber endocelluliLre und pericelluli~re Blutkapillaren der grossen Ganglienzellen yon Lophius. Sitz.-Ber. bShm. Ges. Wiss. Prag 1903. Mit I Taf. 63. S z a w i n s k a , W.: Recherches sur le syst~me nerveux des S~laciens. Arch. Biol., T. 15, F. 3, p. 463--509 ar. 2 pl. et 6 Fig. 64. T a g l i a n i , G i u l i o : Ricerche anatomiehe intorno alla midolla spinale. del l'0rthagoriscus mola. Monit. Zool. ital., Bd. V, 1894, p. 248--258. 65. Derselbe: Intorno a'cosi detti lobi accessorii e alle cellule giganti della midolla spinale di alcuni Teleostei. Boll. d. Soe. d. nat. in Napoli, Ser. I, Vol. 9, 1895, p. 60--69. 66. Derselbe: Conside~azioni morphologiche intorno alle cellule nervose colossali dell' Amphioxus lanceolatus e alle cellule nervose giganti del midollo spinale di alcuni .Teleostei. ~Ionit. Zool. ital., Vol. 8, 1897, p. 264--275. 67. Derselbe: (~ber die Riesennervenzellen im Riickenmarke yon Solea impar. Anat. Anz., Bd. XV, 1899, p. 234--236. 68. T s e h a s s o w n i k o f f , S. G.: Zur Frage fiber die Herkunft und Bedeutung der ,,Saftkan~lehea" in den Nervenzellen. Fragen tier Neuropsychischen Medizin, Bd. 1, 1903, pag. 1--27, 2 Taft (russiseh). 69. V a l l ~ e , P.: St~r Ies l~sions seniles des ganglions ne[veu• du chien. C. Rend. Soe. biol., Paris 1903, No 3, p. 127--128. Erklarung der Abbildungen auf Tafel I--II. Fig. Fig. Fig. Fig. Fig. Fig. T a f e l I. Bipolare Nervenzelle. k ~ Zellhiille; n ~ Zellkern; ax Zellfortsiitze; pr ~ R a n v i e r s c h e Schntirringe. Ganglion des: Trigeminus - facialis - Komplexes. Lota vulgaris. Methylenblau. Reichert, Obj. 7, Tubusl:,tnge 180. Kamera lucida. 2. U n i p o l a r e Z e l l e . n ~ Kern; Ganglion des Trigeminus-facialis= Komplexes. Lota vulgaris. Methylenblau. Reichert, Obj. 7. Kamera lucida. 3. M u l t i p o l a r e Nervenzelle. d z Dendl'iten; ax ~ Nervenfortsatz. Ganglion n. vagi. Lota vulgaris. Methylenblau. Reichert, Obj. 5. Kamera lucida. 4. M u l t i p o l a r e Nervenzelle. d : Dendriten; ax : Nervenfortsatz. Ganglion n. vagi. Lota vulgaris. Methylenblau. Reichert, Obj. 7 a. Kamera lucida. 5. M u l t i p o l a r e Nervenzelle. d ---- Dendriten; ax ~-~ Nervenfortsatz. Ganglion n. vagi. Lota vulgaris. Methylenblau. Reichert, Obj. 7 a. Kamera lucida. 6. R i e s e n n e r v e n z e l l e . k ~ Hiille;]~d ---- Dendriten; e ---- r~tselhafte kleine Zelle, welche gew(ihn]ich die Riesenzel]en begleitet; ax = Nervenfortsatz. Ganglion n. vagi. Lota vulgaris. Methylenblau. Reichert, Obj. 7 a. Kamera lucida. 1. 44 Anton Nemiloff: Fig. 7. Riesennervenzelle. k ~ tt[ille; d ~ Dendriten; ax == Nervenfortsatz. Ganglion n. vagi. Lota vulgaris. ~[ethylenblau. Reichert, Obj. 7. Kamera lucida. Fig. 8. Riesennervenzelle. k -----fIfille; n = Zellkern; d ~---Dendriten; ax = Nervenfortsatz. Ganglion n. vagi. Lota vulgaris. Reichert, Obj. 7. Kamera lucida. Fig. 9. Riesennervenzelle, yon einem perizellul~ren Geflecht u m g e b e n , d = Dendriten; nz ---~ Nervenzelle; ps = perizellul~res Geflecht; e ~--- r~tselhafte kleine Zelle, welche gewShnlich die Riesenzellen begleitet; ax =: I%rvenfortsatz. Ganglion n. vagi. Lota vulgaris. Reiehert, Obj. 5. Kamera lucida Leitz. :Fig. 10. PerizellulSres G e f l e c h t yon Nervenfasern um Riesenzellen. Infolge der betri~chtlichen Dtinne der Astchen ist es auf der Figur nicht gelungen wiederzugeben, dass dieselben in verschiedenen Ebenen gelegen sind. Das Geflecht erseheint ausserdem auf der Figur zu flach, wahrend es tatsi~chlich stark gewSlbt ist; m n = markhaltige Nervenfaser; pr = R a n v i e r s c h e Schnfirring; ps ---~ perizellul'~res Geflecht. Ganglion n. vagi. Lota vulgaris. Nethylenblau. Reichert, Obj. 7a. Kamera lucida. Fig. 11. Gruppe yon Nervenzellen aus einem sympathischcn G a n g l i o n . k ~ Hiille; n = Kern; d ~ Dendrit; ax ~ Nervenfortsatz. Zentrale sympathische Kette. Lota vulgaris, l~[ethylenblau. Zeiss, Obj. 4,00 mm, apert. 0,95. Kamera lucida. Fig. 12. Fig. 13. T a f e l II. Bau der Hfille einer Nervenzelle. fk ~ fibrill::~re tItille; sk = S c h w a n n s e h e Scheide; c = Protoplasma der Nervenzelle; n = Kern; nu = KernkSrperchen. Spinalganglion. Acipenser ruthenus. H e r m a n n s c h e Fltissigkeit. Zeiss, Homog. Immers. ~/~.-,. Kamera lucida. Bau der Hfille einer Nervenzelle. EinGefleeht gebildet yon Forts~tzen sternfSrmiger Zellen, welche der Innenfl:~che des Neurilemms anliegen; die Balken dieses Geflechtes durchziehen das Mark und bilden ein Gertist desselben. Der Deutlichkeit wegen ist das Geflecht nur auf einer Seite der Zelle abgebildet und diese letztere nicht gezeichnet. Auf der Figur ist es jedoch leider nicht gelungen, wiederzugeben, dass die Netzf'~den in der x3fyelinschicht in verschiedenen Ebenen verlaufen. Beim Fixieren mit Ammoniummolybdat ist in der Markscheide eine Falte entstanden, welche in der Figur nicht gut wiedergegeben ist; schz ~ Sternzellen, welehe tier Innenfl~ehe des Neurilemms anliegen; n = Kern einer Sternzelle; spl---~ das yon den Forts'~tzen der sternfSrmigen Zellen gebildete Netz, welches ein Gertist der l~Iarkscheide darstellt: rk = Falte, die sich im Pr'~parat nach tier Fixierung gebildet hat. Ein Ganglion des Trigeminus-facialis Komplexes. Lota vulgaris. Methylenblau. Zeiss, Homog. Immers. ~/~. Kamera lucida. Nervenelemente bei Ganoiden und Knoehenfischen. Fig. 14. Fig. 15. Fig. 16. Fig. 17. Fig. 18. Fig. 19. 45 Trophospongien einer Nervenzelle im Durchschnitt. k ~ Htille der Hervenzelle ; n : Kern einer Hiillenzelle ; c ---- Protoplasma der Nervenzelle; t r ~ Trophozyt; t n ~ Kern eines Trophozyten; trp ~- Fortsi~tze yon Trophozyten (Trophospongien); n z - - Kern der Nervenzelle; nuc ~--- KernkSrperchen. Acipenser rathenus. Fixiert im Gemisch yon L e n h o s s ~ k; gef~trbt mit Hiimatoxylin nach t t e i d e n h a i n ; e i n g e b e t t e t in Celloidin-Paraffin. Zeiss, Homog. Immers. 1,5 ram, Apert. 1,30. K a m e r a lucida. Eindringen yon Leukozyten in eine Nervenzelle. K ---- Htille einer Nervenzelle ; k n ---- Kern einer Hfillenzelle ; nz ~-Kern der Nervenzelle; chr ~ Chromatin teilweise aus dem K e r n ausgetreten; 1 ---- Leukozyt; lg ~ die bei seinem Vordringen in dem Cytoplasma yon dem Leukozyten zurtickgelassene Spur in Gestalt eines Kanals. Cerebrospinales Ganglion. Acipenser ruthenus. Fixiert in Chromessigsi~uregemisch; gefSrbt mit Safranin und Lichtgrtin; eingebettet in CelIoidin-Paraffin. Zeiss, Homog. Immers. 1,5 mm~ Apert. 1,30. K a m e r a lucida. Einwachsen der Bindegewebshtille in eine absterbende Nervenzelle. Nur der Rand der Nervenzelle ist abgebi]det. nz ~ Cytoplasma der Nervenzelle; k ~ fibrill~re Hiille. Aus einer Schnittserie; auf den folgenden Sehnitten wiichst die Hiille ungeffdlr senkrecht zur Schnittebene (resp. Ebene der Zeichnung) vor, darauf wieder gegen das Zentrum der Zelle. Ganglion n. vagi. Riesenzelle. Lota vulgaris. Fixiert in Chromessigsiiuregemisch, gef~rbt mit Eisenh:cimatoxylin; eingebettet in Paraffin. Zeiss, Homog. Immers. 1/1.. K a m e r a lucida. Vakuolisierung des Protoplasma einer Nervenzelle. nz = Protoplasma der Nervenzelle; v = Vakuolen; n ---~Kern der Nervenzelle; nuc ~ KernkSrperchen Spinalganglion. Fixiert in Chromessigsi~uregemisch; gefitrbt in Safranin und Lichtgrtin; eingebettet in Celloidin-Paraffin. Zeiss, Homog. Immers. ~/1~., Tubusli~nge 180. Kamera lucida. Austritt des KernkSrperchens i n alas C y t o p ! a s m a und Vakuolen. n ~ Kern der Nervenzelle; nuc ---- K e r n k6rperehen wi~hrend seines Austrittes aus dem K e r n ; nz = Protoplasma der Nervenzelle; v ~ Vakuolen; Spinalganglion. Acipenser ruthenus. Fixiert in Chromessigs~uregemisch; gef~rbt in H~matoxylin nach H e i d e n h a i n und B o r d e a u x , R. ; eingebettet ir~ Celloidin-Paraffin. Zeiss, Homog. Immers. I/~, Tubusl~nge 180 ram. Kamera lucida. Bau des KernkSrperchens einer Nervenzelle. sl = starklichtbrechende Gebilde in der Substanz des KernkSrperehens; 1 ----- schwiieher lichtbreehende Gebilde in der Substanz des K e r n kiirperchens. Spinalganglion. Acipenser ruthenus. Fixiert im Gemisch yon L e n h o s s ~ k ; gefi~rbt mit Hi~matoxylin nach H e i d e n h a i n ; eingebettet in Celloidin. Zeiss, Homog. Immers. 1,5 ram, Apert. 1,30. Kamera lucida. 46 Fig. 20. Anton Nemiloff: Nervenelemente bei Ganoiden etc. Austritt des Kernkiirperchens in das Cytoptasma. nz ---- Protoplasma der Nervenzelle; i -~-- K e r n ; s ~--- die vom Kernkiirperchen bei seinem D u r c h t r i t t durch das Cytoplasma nachgelassene Spar; nuc : KernkSrperchen. Spinalganglion. Acipenser ruthenus. Fixiert im Gemisch yon L e n h o s s ~ k; gef~trbt mit Safranin; eingebettet in Celloidin-Paraffin. Zeiss, Homog. Immers. 1,5 ram, Apert. 1,30. K a m e r a lucida. Fig. 21. S t i i b e h e n f S r m i g e s Gebilde im Kern. nz ---~ Cytoplasma; i ---- Kern; nuc ---- KernkSrperchen; kr ---- intranuklei~res, sti~bchenf(irmiges Gebilde. Ganglion n. vagi. Lota vulgaris. Fixiert ill einer ges~ttigten SublimatISsung in pbysiologischer KochsalzlSsung ; gefiirbt mit H~tmatoxylin nach H e i d e n h a i n - B o r d e a u x R. ; eingebettet in Celloidin. Zeiss, Homog. Immers. 1/12. K a m e r a lucida. Fig. 22. E i n s c h l i i s s e im Kern einer Nervenzelle. Der Kern offenbart charakteristisehe Ver~nderungen der Form sowie stellenweise Reduktion der Kernmembran. r ~ intranukle~res Gebilde; i ---- Kern; i s ~ Stelle einer Reduktion der Kernmembran. Ganglion n. vagi. Riesenzelle. Lota vulgaris. Fixiert im Gemisch yon L e n h o s s 4 k; gefi~rbt mit Eisenh~matoxylin ; eingebettet in P a raffin. Reichert, Homog. Immers. 18b. Kamera lucida. Fig. 23. K o n z e n t r a t i o n des Chromatins im peripheren Teil des Kerns ciner Nervenzelle. ~ ~ Hfille; kn ~ Kern einer Hiillenzelle; 1 ~ Leukozyt ; i --~Kern; nuc ~ KernkSrperchen : chr ~ Chromatin. Spinalganglien. Acipenser ruthenus. Fixiert in Chromessigsiiuregemisch; gefSrbt in Safranin-Lichtgriin; eingebettet in Celloidin-Paraffin. Zeiss, Homog. Immers. 1,5 mm. kpert. 1,3(}. Kamera lucida. Fig. 24. G e l a p p t e r Kern einer 5IervenzelIe. nz ~ Cytoplasma der 1Nervenzelle; i ~- K e r n ; nnc ~ Kernkiirperchen. Ganglion n. vagi. L o t a ~,ulgaris. Fixiert im Gemisch yon L e n h o s s ~ k ; gef~trbt mit H~imatoxylin nach H e i d e n h a i n ; eingebettet in Celloidin-Paraffin. Zeiss, Homog. Immers. 1/~2. Kamera lueida. Fig. 25. G e l a p p t e r Kern einer Nervenzelle. k ~ Htille der Nervenzelle ; i ~ Kern der Nervenzelle ; nz ---- Cytoplasma. Gang|. n. vagi. Lota vulgaris. Fixiert im Gemiseh yon L e n h o s s ~ k ; gef~rbt in H~matoxylin naeh H e i d e n h a i n ; eingebettet in Celloidin-Paraffin. Zeiss: Homog. Immers. ~/12. Kamera lucida. Fig. 26--28. G e l a p p t e K e r n e yon Nervenzellen. k ~ Hiilh.; nz ~ Frotoplasma; i ~ Kern. Ganglion n. vagi. Lota vulgaris. Methylenblau. Reiehert, Obj. 5. Kamera lueida. Fig. 29. E i n B f i n d e l q u e r g e s t r e i f t e r ~uskelfasern im interstitiellen Gewebe eines Ganglions. mp~quergestreifte Muskelfasern; mn ----- Kerne der quergestreiften Muskelni ig interstitielles Gewebe. Ganglion n. vagi. Chromessigs~uregemisch. Hi~matoxylin nach H e i d e n h a i n . Zeiss, Homog. Immers. ~/,~. Kamera lucida. Samtl. Zeichnungen sind mit Hfilfe d. Zeichenprisma yon Leitz ausgefiihrt worden. ~ 7_ B -o C7: ;~;!, J i; I i I \~'~~ ,} ";:" . ~.t .~ i'~
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Garden-based interventions and early childhood health: a protocol for an umbrella review
Systematic reviews
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Abstract Background: Garden-based interventions have the potential to impact young children’s health in a number of ways, including enhancing dietary intake, increasing outdoor physical activity, diversifying the gut microbiome, and promoting general wellbeing. A number of recent systematic reviews have either included or focused on garden- based interventions for young children. However, most prior reviews including young children only focus on one health outcome or one setting, making a full summary of prior research assessing the impact of garden-based interventions nonexistent. As such, this umbrella systematic review aims to synthesize the literature on health outcomes of garden-based interventions for young children. Methods: This protocol outlines the systematic steps we will take to conduct an umbrella review on health-related outcomes of garden-based interventions in children younger than 6 years of age. We will systematically search PubMed, PsycINFO, ERIC, CINAHL, Embase, Scopus, OVID-Agricola, and CAB Direct, including all systematic reviews and meta-analyses fitting the pre-determined inclusion/exclusion criteria. We will double screen at each phase of the review: title/abstract, full text, data extraction, and quality appraisal. We will assess the quality of included reviews using A Measurement Tool to Assess Systematic Reviews (AMSTAR 2). Based on the potential for stark variability in what how reviews report child health outcomes, we will analyze the reviews both narratively and quantitatively, reporting summary of findings tables and iteratively mapping the results. This protocol aligns with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols statement (PRISMA-P). Discussion: This umbrella review aims to summarize the role that garden-based interventions play in health promotion for young children. We will focus on a number of diverse child health outcomes in an effort to comprehensively synthesize the evidence to inform future garden-based interventions, research, and policy. Systematic review registration: PROSPERO CRD42019106848 Systematic review registration: PROSPERO CRD42019106848 Systematic review registration: PROSPERO CRD42019106848 Keywords: Gardening, Young children, Farm to preschool © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Garden-based interventions and early childhood health: a protocol for an umbrella review Kara Skelton1* , Ann Herbert1 and Sara E. Benjamin-Neelon2 Skelton et al. Systematic Reviews (2019) 8:310 https://doi.org/10.1186/s13643-019-1229-8 Skelton et al. Systematic Reviews (2019) 8:310 https://doi.org/10.1186/s13643-019-1229-8 Background and food systems knowledge [1–3]. Research on garden- based interventions in youth and adult populations have shown associations between gardening and reductions in anger, stress, anxiety, and body mass index (BMI). They have also demonstrated improvements in cognitive func- tioning, life satisfaction, mood, and overall quality of life [4–7]. There is growing evidence that garden-based inter- ventions may have additional benefits for young children, such as stress reduction and improved mental health and academic performance, suggesting interventions which are garden-based may be able to improve multiple aspects of health simultaneously [5, 8]. However, previous systematic Garden-based interventions have the potential to improve a wide range of child health outcomes, including enhan- cing dietary intake, increasing outdoor physical activity, diversifying the gut microbiome, and promoting general wellbeing. This may be due, in part, to the potential of garden-based interventions to promote healthy eating and physical activity, while enriching children with food origin * Correspondence: kara.skelton@jhu.edu 1Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, HH904, Baltimore, MD 21205, USA Full list of author information is available at the end of the article * Correspondence: kara.skelton@jhu.edu 1Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, HH904, Baltimore, MD 21205, USA Full list of author information is available at the end of the article Review methodology While a number of systematic reviews on garden-based interventions for children exist [5, 6, 8, 10, 11, 22–24], there has yet to be a comprehensive umbrella review that summarizes the wide array of health benefits of garden- based interventions for young children. As noted above, existing systematic reviews on garden-based interventions for children focus primarily on single health outcomes, such as fruit and vegetable intake [11] or academic per- formance [10]. Additionally, most reviews examined only one type of gardening program (e.g., farm-to-preschool) rather than exploring the multiple settings in which garden-based interventions can be implemented [24]. Although there is a published review that looks more broadly at the health impacts of gardening in school-aged children, it included only one study with preschool-aged children [8]. Additionally, due to the diversity in settings, types, and benefits of garden-based interventions, we aim to holistically evaluate and summarize existing systematic reviews on garden-based interventions and health out- comes for young children in a single umbrella review. Given the existence of systematic reviews on garden-based interventions that focus on or include young children, we will conduct an umbrella review, in accordance with the Joanna Briggs Institute Methodology for Umbrella Reviews. The systematic review methodology outlined in this paper will be used to strategically locate, synthesize, and evaluate published systematic review- and meta-analysis-level evi- dence on the role of garden-based interventions in the health promotion of young children. Umbrella reviews are able to systematically assess the highest levels of evidence for an overall topic, while evaluating the quality of the evi- dence concurrently [25, 27]. Therefore, this umbrella re- view highlights strengths, as well as gaps, in the evidence for garden-based interventions. We will assess the quality of included systematic reviews on garden-based interventions, including both random- ized studies and non-randomized studies, and with and without a control or comparison group, appraising meth- odological characteristics through the use of A Measure- ment Tool to Assess Systematic Reviews (AMSTAR 2). Through this critical appraisal tool, this umbrella review will also enable researchers and other stakeholders to de- termine the quality of existing systematic review-level evi- dence on garden-based interventions for young children. The following question will guide this umbrella review: What role can garden-based interventions play in health promotion for children aged 6 years and younger? To successfully answer this question, we will explore the fol- lowing objectives: 1. Skelton et al. Systematic Reviews (2019) 8:310 Page 2 of 8 2. To determine which garden-based interventions are effective at improving child health and well-being outcomes; reviews have primarily focused on single health outcomes [9–12], leaving large gaps in what is known about the hol- istic health and wellbeing impacts of gardening programs for young children. 3. To identify the most prominent measures used to detect and assess the health and wellbeing impacts of garden-based interventions in young children; Prior garden-based intervention studies in young children have found some improvement in dietary outcomes, such as fruit or vegetable intake, willingness to try new foods, and even BMI [13–15]. Younger children may be more willing to taste and accept novel foods than older children [16], and exposure to fruits and vegetables by age 5 years is vital for establishing habitual consumption later in life [17]. Previous research has also shown that hands-on experiences through garden-based interventions may increase fruit and vegetable consumption more than an intervention that merely in- creases availability [3, 18]. Additionally, garden-based inter- ventions have been utilized as a form of therapy for an array of disorders and diseases, such as autism spectrum disorder [19] and childhood cancer [20]. The benefits of improved dietary and physical activity behaviors and increased nutri- tion knowledge acquired from these interventions may have the potential to seep through into other child health out- comes, such as enhanced academic performance and im- proved mental health [10, 21]. However, few review articles have considered and assessed diverse child health outcomes within the same article 4. To critically evaluate available garden-based interventions on child health outcomes both narratively and quantitatively; 5. To identify gaps in the literature and to highlight potential areas of improvement for the scientific field of garden-based interventions, including, but not limited to study design, measurement, and child health outcomes. Review methodology To identify and synthesize existing review articles, ranging from narrative reviews to meta-analyses, on garden-based interventions for young children; Protocol development This umbrella review protocol follows the Joanna Briggs In- stitute Methodology for Umbrella Reviews [25]. This proto- col was also developed to align with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols (PRISMA-P) 2015 statement [26] (Additional file 1) and has been registered with the PROSPERO database for systematic reviews (#CRD42019106848). Intervention This umbrella review will include systematic reviews that focus on or include garden-based interventions. As there is no single definition of garden-based interventions due to their complexity and variation in type and setting, we have defined this term for the purposes of this review. Thus, we define garden-based interventions as any intervention that engages children in active learning about nutrition, food sys- tems, agriculture, or environmental health through connec- tions with outside fruit or vegetable gardens or farms, raised garden beds, greenhouses, container gardens, microfarms, or other alternative gardening methods. We will also include farm-to-school and farm-to-child care programs, which typ- ically link children with fruit and vegetables from local farms or gardens. For young children, garden-based interventions can occur in an array of settings, including homes, early care and education programs (e.g., center-based child care or preschool), community centers, community gardens, after- school programs, and summer camps. Similarly, there are numerous ways in which garden-based interventions can be implemented. Some garden-based interventions are standa- lone programs, and others may be integrated into broader nutrition education programs that incorporate additional in- terventions simultaneously. For the purposes of this um- brella review, we will include reviews of any garden-based interventions that meet the above criteria. This criterion is intentionally broad to allow for a range of reviews and inter- ventions to be included in this review. Inclusion criteria We used the population, intervention, context, outcome and study design (PICOS) structure in formulating the Page 3 of 8 Skelton et al. Systematic Reviews (2019) 8:310 Page 3 of 8 scope of this umbrella review [27]. This enabled us to precisely delineate a priori inclusion criteria for the um- brella review. We will apply the inclusion criteria at both the review and individual study level. For example, there may be a review that meets our inclusion criteria, but further examination at the individual study level reveals there are no studies included within the review that meet inclusion criteria. In this case, we would exclude the review. In other words, there must be at least one individual-level study that meets all inclusion criteria for us to include the review. take place in any county or climate, or in a rural or urban setting. Similarly, the garden-based interventions could be designed for any type of young child, including those of any gender and socioeconomic status. Garden- based interventions that are focused on children with certain health conditions, special developmental and or psychological considerations, will also be included. Outcomes We will consider reviews that include any child-level health or wellbeing outcomes. These include but are not limited to weight or BMI, the gut microbiome, health-related behav- iors (e.g., diet, physical activity, social interaction), academic (e.g., knowledge or cognition), and mental health. We will also include qualitative outcomes, including major themes and concepts relating to garden-based interventions, where reported. We will also consider adverse or unintended con- sequences where noted in reviews. We will include reviews that report both child and parent-level health outcomes, but only the child-level outcomes will be extracted and included in the analysis. We will exclude reviews that focus solely on parent-, school-, or community-related outcomes. Types of studies For this review, we will include only systematic reviews. In- cluded reviews could have conducted meta-analysis or nar- rative synthesis as part of their analysis. We will define a systematic review with guidance from the PRISMA-P 2015 statement. A systematic review will be defined as a review which (a) has an explicit set of aims; (b) employs a reprodu- cible methodology, including a systematic search strategy and selection of studies; and (c) is a systematic presentation and synthesis of the characteristics and findings of included studies [26]. We will exclude review articles that do not meet this definition of a systematic review. We will also ex- clude individual primary studies. There are no limitations for study designs included in the reviews; any systematic review reporting data about child-level health and overall wellbeing benefits of garden-based interventions for children younger than 6 years will be included. We will include systematic reviews that are randomized (e.g., randomized controlled trial), quasi-randomized, and non-randomized designs (e.g., pre-post design, non-randomized trial). We will exclude systematic reviews that examine qualitative studies. We will include only full review articles published after 1990, as is best practice with umbrella review methodology [27]. Additionally, we will include only peer-reviewed litera- ture (i.e., we will exclude dissertations and conference ab- stracts) (Table 1). Participants This umbrella review will include systematic reviews that in- clude children younger than 6 years of age. For inclusion, re- views do not have to be focused solely on our age range of interest. However, children younger than 6 years must be within the included age range of at least one included article included in the review. We will not exclude participants based on gender or any other socioeconomic-related factors. Pilot search We conducted a pilot search strategy for all databases listed above (Table 2). We utilized key terms and con- trolled vocabulary for each database. We used five key review papers as “targets” to ensure the pilot search lo- cated the types of articles we wanted to include. The pilot search included all search terms. As we wanted to make sure we were not losing a large number of system- atic reviews due to the date restrictions, we ran the pilot search without date restrictions. As we did not find any relevant systematic reviews on this topic for any data- base prior to 1990, we will include the restriction in the final search strategy. Additionally, we slightly adapted search terminology to ensure we capture all relevant farm-to-school and farm-to-childcare reviews. Adapta- tion involved the inclusion of additional terminology and removal of terminology that was not relevant to yield all potentially eligible reviews. The final search strategy to be used for the umbrella review is presented in Additional file 2. Search strategy Database search Similarly, when included systematic reviews have been cited more than 200 times, the citation searches will be limited to the first 200 most recent citations. As Cochrane reviews are updated fre- quently and may be published in peer-reviewed journals in addition to the Cochrane database, we may retrieve more than one review published by the same author(s) on the same topic (e.g., an update of an existing review). If this circumstance arises, we will only include the most re- cent version of the review. However, we will cite to previ- ous versions of the review. Search terms We will search the abovementioned electronic databases using database-specific controlled vocabulary and key terms. We developed this search strategy using terms for gardening and young children that have been utilized in previous reviews [8, 23, 24, 28] as well as additional terms that were selected to capture the breadth of the body of literature. To ensure completeness, we drafted the search strategy in collaboration with a Medical Search strategy Database search We will not employ any limitations related to the con- text in which the garden-based interventions take place. Reviews can include garden-based interventions that We will search the following databases from 1990 onward: PubMed, PsycINFO, ERIC, CINAHL, Embase, Scopus, Skelton et al. Systematic Reviews (2019) 8:310 Page 4 of 8 Table 1 Study inclusion and exclusion criteria Inclusion criteria Exclusion criteria Study type Systematic reviews, with or without meta-analysis All other study types (e.g., qualitative systematic review, non-systematic reviews, individual studies) Study period Reviews published in or after 1990 Reviews published prior to 1990 Participants Children younger than 6 years of age Children 6 years of age and older Primary outcomes Any child-level health or wellbeing outcome Any non-child-level outcomes (e.g., parent or community-related outcomes) Intervention/program type Garden-based interventions or programs Reviews that do not include garden-based interventions or programs Reviews that do not include garden-based interventions or programs OVID-Agricola, and CAB Direct. Additionally, we will search systematic review databases, including the Cochrane Register of Systematic Reviews, the Joanna Briggs Institute Database of Systematic Reviews and Im- plementation Reports, and PROSPERO. We will also search the first 200 results of Google Scholar, when sorted in relevance ranking, for review and meta-analyses articles. Additionally, we will conduct reference list and citation searches for all included articles. Similarly, when included systematic reviews have been cited more than 200 times, the citation searches will be limited to the first 200 most recent citations. As Cochrane reviews are updated fre- quently and may be published in peer-reviewed journals in addition to the Cochrane database, we may retrieve more than one review published by the same author(s) on the same topic (e.g., an update of an existing review). If this circumstance arises, we will only include the most re- cent version of the review. However, we will cite to previ- ous versions of the review. Librarian who specializes in systematic reviews and an expert in early childhood gardening research. OVID-Agricola, and CAB Direct. Additionally, we will search systematic review databases, including the Cochrane Register of Systematic Reviews, the Joanna Briggs Institute Database of Systematic Reviews and Im- plementation Reports, and PROSPERO. We will also search the first 200 results of Google Scholar, when sorted in relevance ranking, for review and meta-analyses articles. Additionally, we will conduct reference list and citation searches for all included articles. Study screening The lead and second reviewer will carry out the initial database search. To manage the blinded title and ab- stract screening process, we will utilize Covidence Soft- ware (Covidence Systematic Review Software, Veritas Table 2 Pilot search results, from 1990 to January 9, 2019 PubMed PsycINFO ERIC CINAHL Scopus Embase Google Scholar CAB Direct Agricola Search strategy details in Additional file 2 10, plus MeSH terms 10, plus DE terms 10, plus SU terms 10, plus MJ terms 10 10, plus Emtree terms 1 AND 2 AND 3 10, plus PG terms 1 AND 2 AND 3 Number of hits 12,601 518 610 498 1,753 92 200 378 0 Target papers Savoie-Roskos ✓ ✓ ✓ ✓ ✓ Davis ✓ ✓ Ohly ✓ ✓ ✓ ✓ Masset ✓ ✓ Table 2 Pilot search results, from 1990 to January 9, 2019 P bM d P INFO ERIC CINAHL S Page 5 of 8 Page 5 of 8 Skelton et al. Systematic Reviews (2019) 8:310 Page 5 of 8 Health Innovation, Melbourne, Australia). As citations are imported into Covidence, they will automatically be de-duplicated based on an exact match of the title, date, and author. Following the comprehensive search, screen- ing of the titles and abstracts will occur independently by three reviewers split into two teams. Within Covi- dence, each citation will be screened, using a priori inclusion and exclusion criteria and then categorized as “No,” “Maybe” or “Yes.” Through Covidence, the citation will be automatically filtered into one of three lists: “Irrelevant,” “Resolve Conflicts,” and “Full text review.” For a citation to be added to the “Irrelevant” list, a “No” must be cast by both reviewers; if there is a disagree- ment between the two reviewers, the citation will move to the “Resolve Conflicts” list. A citation will move auto- matically to “Full text review” with any combination of “Maybe” and “Yes” received by a team of reviewers. Dis- agreements between reviewers will be resolved using consensus, and by a third reviewer if necessary. that are relevant to the umbrella review questions; (8) funding sources for each review; (9) main findings rele- vant to the review question; and (10) comments or notes regarding included studies. Quality appraisal Quality appraisal In addition to data extraction, a quality appraisal for each systematic review will be conducted using the AMSTAR 2, which is updated to allow for both random- ized and observational studies [29]. The recent update to the original AMSTAR tool addresses the more modern need for policy and research decision making that ac- count for “real-world observational evidence” [29]. AMSTAR 2 is an appraisal tool consisting of 16 items with the following response options: Yes, Partial Yes, No. The AMSTAR has been evaluated and shown to be both valid and reliable [30]. Please note that AMSTAR 2 was not intended to be scored, and as such we will not score this tool. To evaluate quality, two reviewers will in- dependently extract relevant data based on the AMSTAR 2 for each included article. Any disagreements between re- viewers will be resolved among themselves first through discussion and by a third reviewer if the reviewers are un- able to achieve consensus. We will not exclude reviews based on results of their quality assessment. Rather, we will conduct the quality assessment to critique the strength of evidence generated. Once the list of citations moving forward to full-text review is complete, the research team will gather articles in their full-text, PDF form with assistance from a med- ical librarian. During full text screening, both reviewers must agree on a final inclusion/exclusion decision as well as the accompanying rationale. If the authors can- not determine eligibility after full-text review, we will contact the review authors to assist in determining eligi- bility. We will document all reasons for exclusion throughout the full text screening phase in Covidence. After exhausting all efforts to retrieve full-text for a citation, the full text cannot be retrieved, it will be ex- cluded. Additionally, should there be duplicates at this level, we will exclude them. Only those articles meeting all inclusion criteria will move forward for data abstrac- tion. The number of included studies from search through data extraction will be automatically created using a PRISMA flow diagram within Covidence. Study screening For each review article, we will also extract information for individual primary stud- ies meeting inclusion criteria, including, but not limited to citation details, child characteristics, setting, interven- tion type and design, results, limitations, and conclu- sions to enable us to account for overlap at the primary study level. We will be limited to data extraction at the individual study level based on what is presented in the review. The data extraction form is included as Additional file 3. We will contact corresponding au- thors for any missing data or for clarification of un- clear items. Reporting of findings For this umbrella review, we will report a summary of findings from all included reviews based on data synthe- sis, presenting a comprehensive overview of what is known in the literature on the role of garden-based in- terventions in health promotion for children aged 6 years and younger. We will create the summary of findings ta- bles from extracted data, directly mapping findings to our research questions per the Joanna Briggs Institute methodology for conducting an umbrella review [25] and the Cochrane Handbook’s Methodology for con- ducting an overview of reviews [32]. We will take a mixed-methods approach to synthesizing the review lit- erature, utilizing both qualitative methods (e.g., narrative synthesis) and quantitative methods (e.g., numerical pat- terns or associations). In line with the research questions guiding this umbrella review, we plan to highlight the strengths and weakness of included systematic reviews, as well as describe any evidence gaps we identify. We also plan to report on effectiveness of garden-based interventions. For this, we will present a grid of interven- tion components and child health and well-being out- comes, noting directionality of each outcome. We plan to summarize the setting, outcome measures, numbers of children, and pooled results from each review, includ- ing implications for future research and practice through tables and narration, as appropriate. When reporting findings in tabular form, we will present child health outcomes across included reviews, stratifying tables by review methodology (e.g., all evidence gained from re- views of randomized controlled trials) and child health outcome (e.g., reporting evidence on academic perform- ance separately from nutrition outcomes). For child health outcomes, we anticipate reporting tabular results in the following categories: child nutrition outcomes, academic performance, education, mental health and so- cial skills, gut microbiome, and physical activity. For child nutrition outcomes, we anticipate a need to break down results further, in which case we will report results in the following categories: (1) intake, reporting separ- ately on fruit and vegetable intake as allowed; (2) selec- tion, reporting fruit and/or vegetable selection and preference outcomes; and (3) biometric and anthropo- metric outcomes (e.g., body mass index, wasting, etc.) Where tabular presentations of results are presented, they will be accompanied by detailed descriptions. As we are including a broad range of health outcomes, we expect included reviews to report on child health out- comes in different ways and will be limited to what is re- ported. Confidence in evidence During the full text data extraction phase, two reviewers will independently extract article data directly into Covi- dence. Using recommendations for relevant data fields for umbrella reviews from Aromataris et al. 2015 [27], we will collect the following data, at minimum, from each eligible systematic review: (1) citation details; (2) purpose/objectives of the included review; (3) review methodology (e.g., meta-analysis, narrative synthesis); (4) study population (e.g., age, demographic characteristics), setting (e.g., country, setting of garden-based interven- tion), and context; (5) search strategy and results (e.g., number of databases sources and searched, date range, inclusion of gray literature); (6) number of included studies, citation, type, and country of origin of studies; (7) child-level health and wellbeing outcomes reported For included studies, we will report on confidence in findings using the information presented in each review. This could be in the form of a quality of evidence tool, such as the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) measures [31]. However, there are many additional tools that existing reviews can use to assess the confidence in evidence, which may cause variations in how this aspect is re- ported in reviews. As such, we will report on the exact tool used for included reviews and their associated find- ings, iteratively making the decision on how to display confidence in findings based on the information re- ported in each individual review. If a review is included in which the authors did not conduct an assessment of Page 6 of 8 Skelton et al. Systematic Reviews (2019) 8:310 Skelton et al. Systematic Reviews confidence in evidence, the review team will not conduct any de novo assessments. In this instance, there will be no confidence in evidence presented for that review. by the following age groups: infancy (less than 12 months of age), toddlers (12 months of age–less than 36 months of age), and preschool (3 years of age–less than 6 years of age). However, we will be limited in this strati- fication by how included reviews report on health out- comes by age. For example, if a review stratifies findings by age (e.g., preschool, school-age), we will report our results accordingly. Similarly, if a review does not separ- ate results by age, we will only be able to report what is reported in the review. In this instance, results that can- not be disaggregated by age will be reported separately within our review. Reporting of findings We will aim to report health outcomes stratified Additionally, we will create a table summarizing the AMSTAR 2 results for each included review. As is best practice, we will report the entire umbrella review in ac- cordance with PRISMA guidelines. Due to the potential for overlap of primary studies in the review articles, we will report the number of times individual studies are included across multiple reviews. We will systematically identify any occurrences of over- lap across systematic reviews by noting individual stud- ies included in more than one review. We will also explore the consistency of reporting at the individual level across reviews [33] to determine if there is any overlap. We will explore this through the use of The Cochrane Handbook’s template for mapping individual primary studies contained within included systematic re- views [32]. For example, one review article may report on one specific child health outcome of an individual study, while another review includes the same study but reports on a different (perhaps secondary) health out- come. In this case, we would not consider this overlap. However, if reviews are reporting the same outcomes from the same study, we will highlight this overlap. If we do find there is overlap, we will calculate the corrected covered area [34] and report on this measure in the re- view paper. We will also consider overlap when inter- preting results of the review. Author details 1 Author details 1Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, HH904, Baltimore, MD 21205, USA. 2Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, HH755, Baltimore, MD 21205, USA. 1Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, HH904, Baltimore, MD 21205, USA. 2Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, HH755, Baltimore, MD 21205, USA. Abbreviations AMSTAR: A Measurement Tool to Assess Systematic Reviews; ECE: Early care and education; PICO: Population, intervention, context, outcome and study design; RoB: Risk of bias AMSTAR: A Measurement Tool to Assess Systematic Reviews; ECE: Early care and education; PICO: Population, intervention, context, outcome and study design; RoB: Risk of bias Acknowledgements None. Acknowledgements None. Discussion For this umbrella review, we aim to (1) identify and synthesize existing review and meta-analysis articles on garden-based interventions for young children; (2) iden- tify the most prominent measures used to detect and as- sess the impacts of garden-based interventions in young children; (3) critically evaluate the available evidence both narratively and quantitatively; and (4) identify gaps in the literature and describe areas of improvement for the scientific field of garden-based interventions, includ- ing, but not limited to study design, measurement, and child health outcomes. In doing so, we will provide a very comprehensive overview of what is known in the literature about the health and wellbeing impacts of gardening programs for young children. Page 7 of 8 Page 7 of 8 Skelton et al. Systematic Reviews (2019) 8:310 Page 7 of 8 Skelton et al. Systematic Reviews (2019) 8:310 Skelton et al. Systematic Reviews (2019) 8:310 This umbrella review has several strengths. First, this umbrella review fills a considerable gap in the literature by providing a holistic overview of existing evidence of the health and wellbeing benefits of garden-based inter- ventions for young children, identifying strengths of current evidence and highlighting areas for improve- ment. To date, this type of umbrella review does not exist. Second, this review will examine knowledge gaps in the field and elaborate on how these gaps could be addressed by future research. Summarizing this informa- tion will be an asset to both researchers and public health professionals aiming to improve the health and wellbeing of young children. Additionally, this umbrella review will be conducted using the most systematic pro- cedures available at this time. Adhering to these guide- lines helps ensure that we procedure a high-quality umbrella review that will be a useful and trusted re- source for interested parties. Received: 12 March 2019 Accepted: 11 November 2019 Received: 12 March 2019 Accepted: 11 November 2019 Competing interests Competing interests The authors declare that they have no competing interests. Availability of data and materials N/A Ethics approval and consent to participate N/A Anticipated challenges for this review include the need to extract relevant information from existing review arti- cles. We realize there are numerous benefits to garden- based interventions throughout the life span. However, we only focused on children younger than 6 years, as this is an area where garden-based interventions in an ECE, community, or home setting could make a substantial impact. We limited our search to peer-reviewed litera- ture published after 1990, but do not believe this will exclude any relevant studies based on the pilot search strategy. However, we realize the exclusion of non-peer reviewed literature may eliminate high-quality reviews, which is another limitation. We will elaborate on add- itional limitations in regard to findings in the narration of the review. Another limitation of this review will be the potential for study overlap across reviews. Knowing this potential risk, we will examine and report on any overlap in the review. Consent for publication N/A Authors’ contributions KS drafted the initial manuscript and critically reviewed and revised the manuscript. SBN provided oversight and critically reviewed and revised the manuscript. AH reviewed and edited the manuscript. All authors approved the final manuscript as submitted and agreed to be accountable for all aspects of the work. Funding Availability of data and materials N/A References 1. Hanbazaza MA, Triador L, Ball GD, Farmer A, Maximova K, Alexander First N, et al. The impact of school gardening on Cree children’s knowledge and attitudes toward vegetables and fruit. Can J Diet Pract Res. 2015;76(3):133–9. 2. Morgan PJ, Warren JM, Lubans DR, Saunders KL, Quick GI, Collins CE. The impact of nutrition education with and without a school garden on knowledge, vegetable intake and preferences and quality of school life among primary-school students. Public Health Nutr. 2010;13(11):1931–40. 2. Morgan PJ, Warren JM, Lubans DR, Saunders KL, Quick GI, Collins CE. The impact of nutrition education with and without a school garden on knowledge, vegetable intake and preferences and quality of school life among primary-school students. Public Health Nutr. 2010;13(11):1931–40. 3. Parmer SM, Salisbury-Glennon J, Shannon D, Struempler B. School gardens: an experiential learning approach for a nutrition education program to increase fruit and vegetable knowledge, preference, and consumption among second-grade students. J Nutr Educ Behav. 2009;41(3):212–7. 4. Soga M, Gaston KJ, Yamaura Y. Gardening is beneficial for health: a meta- analysis Preventive Medicine Reports 2017;5:92–9 3. Parmer SM, Salisbury-Glennon J, Shannon D, Struempler B. School gardens: an experiential learning approach for a nutrition education program to increase fruit and vegetable knowledge, preference, and consumption among second-grade students. J Nutr Educ Behav. 2009;41(3):212–7. 4. Soga M, Gaston KJ, Yamaura Y. Gardening is beneficial for health: a meta- analysis. Preventive Medicine Reports. 2017;5:92–9. Despite anticipated limitations, conducting this um- brella review on the role of gardening for health promo- tion in young children could be of great importance for researchers, public health professionals, and policymakers. By summarizing the current evidence for and simultan- eously identifying strengths, weaknesses, and limitations for garden-based interventions, we hope to strengthen the quality of future research in this area. Further, we hope to support and highlight evidence-based interventions that improve the health and wellbeing of young children. 5. Ozer EJ. The effects of school gardens on students and schools: conceptualization and considerations for maximizing healthy development. Health Educ Behav. 2007;34(6):846–63. 6. Robinson-O'Brien R, Story M, Heim S. Impact of garden-based youth nutrition intervention programs: a review. J Am Diet Assoc. 2009;109(2):273–80. 7. Wang D, MacMillan T. The benefits of gardening for older adults: a systematic review of the literature. Activities, Adaptation & Aging. 2013;37(2):153–81. Supplementary information Supplementary information accompanies this paper at https://doi.org/10. 1186/s13643-019-1229-8. Additional file 1. PRISMA-P Checklist. Additional file 2. Search Strategy. References Additional file 3. Data Extraction Form. Supplementary information Supplementary information Supplementary information accompanies this paper at https://doi.org/10. 1186/s13643-019-1229-8. Additional file 1. PRISMA-P Checklist. Additional file 2. Search Strategy. Additional file 3. Data Extraction Form. pp y Supplementary information accompanies this paper at https://doi.org/10. 1186/s13643-019-1229-8. Additional file 1. PRISMA-P Checklist. Additional file 2. Search Strategy. Additional file 3. Data Extraction Form. 11. Savoie-Roskos MR, Wengreen H, Durward C. Increasing fruit and vegetable intake among children and youth through gardening-based interventions: a systematic review. J Acad Nutr Diet. 2017;117(2):240–50. Page 8 of 8 Page 8 of 8 Skelton et al. Systematic Reviews (2019) 8:310 Skelton et al. Systematic Reviews (2019) 8:310 12. McCormick R. Does access to green space impact the mental well-being of children: a systematic review. Journal of Pediatric Nursing. 2017;37:3–7. 13. Brouwer RJN, Neelon SEB. Watch Me Grow: a garden-based pilot intervention to increase vegetable and fruit intake in preschoolers. BMC public health. 2013;13(1):363. 13. Brouwer RJN, Neelon SEB. Watch Me Grow: a garden-based pilot intervention to increase vegetable and fruit intake in preschoolers. BMC public health. 2013;13(1):363. 14. Meinen A, Friese B, Wright W, Carrel A. Youth gardens increase healthy behaviors in young children. Journal of Hunger & Environmental Nutrition. 2012;7(2-3):192–204. 15. Castro DC, Samuels M, Harman AE. Growing healthy kids: a community garden- based obesity prevention program. Am J Prev Med. 2013;44(3 Suppl 3):S193–9. 16. Howard AJ, Mallan KM, Byrne R, Magarey A, Daniels LA. Toddlers’ food preferences. The impact of novel food exposure, maternal preferences and food neophobia. Appetite. 2012;59(3):818–25. 17. Nicklaus S, Remy E. Early origins of overeating: tracking between early food habits and later eating patterns. Current Obesity Reports. 2013;2(2):179–84. 18. Evans A, Ranjit N, Rutledge R, Medina JL, Jennings R, Smiley A, et al. Exposure to multiple components of a garden-based intervention for middle school students increases fruit and vegetable consumption. Health Promotion Practice. 2012. 19. Flick KM. The application of a horticultural therapy program for preschool children with autism spectrum disorder. Journal of Therapeutic Horticulture. 2012;22(1). 20. Blair CK, Madan-Swain A, Locher JL, Desmond RA, de Los SJ, Affuso O, et al. Harvest for health gardening intervention feasibility study in cancer survivors. Acta Oncologica. 2013;52(6):1110–8. 21. Blair D. The child in the garden: an evaluative review of the benefits of school gardening. The Journal of Environmental Education. 2009;40(2):15–38. 22. Appleton KM, Hemingway A, Saulais L, Dinnella C, Monteleone E, Depezay L, et al. Supplementary information Increasing vegetable intakes: rationale and systematic review of published interventions. European journal of nutrition. 2016;55(3):869–96. 23. Blair D. The child in the garden: an evaluative review of the benefits of school gardening. Program Evaluation. 2009;40(2):15–38. 24. Hoffman JA, Schmidt EM, Wirth C, Johnson S, Sobell SA, Pelissier K, et al. Farm to preschool: the state of the research literature and a snapshot of national practice. Journal of Hunger & Environmental Nutrition. 2017;12(4):443–65. Journal of Hunger & Environmental Nutrition. 2017;12(4):443–65. 25. Aromataris E, Fernandez RS, Godfrey C, Holly C, Khalil H, Tungpunkom P. Methodology for JBI umbrella reviews; 2014. 26. Moher D, Shamseer L, Clarke M, Ghersi D, Liberati A, Petticrew M, et al. Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement. Systematic reviews. 2015;4(1):1. 27. Aromataris E, Fernandez R, Godfrey CM, Holly C, Khalil H, Tungpunkom P. Summarizing systematic reviews: methodological development, conduct and reporting of an umbrella review approach. International journal of evidence-based healthcare. 2015;13(3):132–40. 28. Sisson SB, Krampe M, Anundson K, Castle S. Obesity prevention and obesogenic behavior interventions in child care: a systematic review. Preventive medicine. 2016;87:57–69. 29. Shea BJ, Reeves BC, Wells G, Thuku M, Hamel C, Moran J, et al. AMSTAR 2: a critical appraisal tool for systematic reviews that include randomised or non-randomised studies of healthcare interventions, or both. bmj. 2017;358:j4008. 30. Shea BJ, Grimshaw JM, Wells GA, Boers M, Andersson N, Hamel C, et al. Development of AMSTAR: a measurement tool to assess the methodological quality of systematic reviews. BMC medical research methodology. 2007;7(1):10. 31. Lewin S, Booth A, Glenton C, Munthe-Kaas H, Rashidian A, Wainwright M, et al. Applying GRADE-CERQual to qualitative evidence synthesis findings: introduction to the series. BioMed Central; 2018. 31. Lewin S, Booth A, Glenton C, Munthe-Kaas H, Rashidian A, Wainwright M, et al. Applying GRADE-CERQual to qualitative evidence synthesis findings: introduction to the series. BioMed Central; 2018. 32. Pollock M, Fernandes R, Becker L, Pieper D, Hartling L. Chapter V: Overviews of Reviews. Draft Version. 2018 8 Oct 2018. In: Cochrane Handbood for Systematic Reviews of Interventions [Internet]. London: Cochrane; [1-38]. Available from: https://training.cochrane.org/handbook/version-6/chapter-V. 33. Pollock A, Campbell P, Brunton G, Hunt H, Estcourt L. Selecting and implementing overview methods: implications from five exemplar overviews. Systematic Reviews. 2017;6(1):145. 34. Pieper D, Antoine S-L, Mathes T, Neugebauer EAM, Eikermann M. Systematic review finds overlapping reviews were not mentioned in every other overview. Supplementary information Journal of Clinical Epidemiology. 2014;67(4):368–75. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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Promoting solution phase discharge in Li–O2 batteries containing weakly solvating electrolyte solutions
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Promoting solution phase discharge in Li-O2 batteries containing weakly solvating electrolyte solutions Xiangwen Gao1‡, Yuhui Chen1‡, Lee Johnson1 and Peter G. Bruce1* 1 Departments of Materials and Chemistry, Parks Road, University of Oxford, OX1 3PH, UK Xiangwen Gao1‡, Yuhui Chen1‡, Lee Johnson1 and Peter G. Bruce1* 1 Departments of Materials and Chemistry, Parks Road, University of Oxford, OX1 3PH, UK * Author to whom correspondence should be addressed * Author to whom correspondence should be addressed Abstract Th d ti d th h th f ll i l t The reduction proceeds through the following general steps: The reduction proceeds through the following general steps: O2 + Li+ + e- → LiO2 (1) 2LiO2 → Li2O2 + O2 (2) LiO2 + Li+ + e- → Li2O2 (3) (1) (2) (3) O2 + Li+ + e- → LiO2 (1) 2LiO2 → Li2O2 + O2 (2) LiO2 + Li+ + e- → Li2O2 (3) (3) Whether Li2O2 grows in solution or as a film on the electrode surface depends on the solubilit Whether Li2O2 grows in solution or as a film on the electrode surface depends on the solubility of the LiO2 intermediate; if LiO2 dissolves in the electrolyte solution then Li2O2 grows in solution. Solubility of LiO2 depends on the strength of the cation and anion solvation, i.e. on the solvent and salt donor and acceptor numbers15,22-24. However, the very properties that make a good solvent for LiO2, (high polarity) often makes the solvent more susceptible to nucleophilic attack or proton abstraction by the reactive O2- radical, leading to undesirable side-reactions25,26. The challenge is to form Li2O2 in solution on discharge in low donor number (weakly solvating) solvents. Soluble catalysts or salts with high donor numbers (DN) can in principle promote solution phase growth of Li2O2 in low donor number solvents (e.g. ethers)22,27-30. High DN salts have been shown to increase the capacity 4 fold and reduce the discharge overpotential by 30-50 mV over low DN salts22. Viologens27,28, phthalocyanines29 and quinones30 have been investigated as possible soluble reduction catalysts. While the studies of such catalysts are important, in most cases there is little or no direct evidence demonstrating that they promote formation of Li2O2 in solution and not on the electrode surface because they rely on electrochemical measurements alone. Yet past work on Li-O2 batteries has shown how essential it is to provide more than electrochemical evidence in this field31. In some cases, soluble catalysts show an increase in discharge voltage (lower overpotential) as small as e.g. 40 mV28,29, which is very unlikely to be sufficient to shut-off the direct reduction of O2 to Li2O2, essential to stop detrimental Li2O2 film formation. Also, none of the previous studies in low donor number solvents exhibited a significant increase in capacity on discharge at a relatively high rate, which is important for a successful Li-O2 battery. Abstract On discharge, the lithium-O2 battery can form a Li2O2 film on the cathode surface, leading to low capacities, low rates and early cell death, or it can form Li2O2 particles in solution, leading to high capacities at relatively high rates and avoiding early cell death. Achieving discharge in solution is important and may be encouraged by the use of high donor or acceptor number solvents or salts that dissolve the LiO2 intermediate involved in the formation of Li2O2. However, the characteristics that make high donor or acceptor number solvents good (e.g. high polarity) result in them being unstable towards LiO2 or Li2O2. Here we demonstrate that introduction of the additive 2,5-Di-tert- butyl-1,4-benzoquinone (DBBQ) promotes solution phase formation of Li2O2 in low polarity and weakly solvating electrolyte solutions. Importantly, it does so while simultaneously suppressing direct reduction to Li2O2 on the cathode surface, which would otherwise lead to Li2O2 film growth and premature cell death. It also halves the overpotential during discharge, increases the capacity 80-100 fold and enables rates > 1 mA cm-2areal for cathodes with capacities of > 4 mAh cm-2areal. The DBBQ additive operates by a new mechanism that avoids the reactive LiO2 intermediate in solution. 1 The high theoretical specific energy of the rechargeable Li-O2 battery has generated intense interest in the possibility of a practical device that could deliver energy storage significantly in excess of today’s lithium-ion batteries1-9. However, major challenges hinder the development of such a technology1-6,10-14. Typically a Li-O2 battery is composed of a lithium metal anode separated by an aprotic electrolyte solution from a porous O2 cathode. The reaction at the cathode involves, on discharge, the reduction of O2 to form Li2O2, with oxidation of the latter on charge. Growth of Li2O2 on the cathode surface leads to low capacities, poor rates and early cell death15-17. In contrast, if Li2O2 can be induced to grow in the electrolyte solution then high discharge capacities at relatively high rates and avoiding early cell death is possible15. It is clearly important to operate a Li-O2 battery in which Li2O2 grows in solution. A number of groups have elucidated the mechanism of O2 reduction to Li2O2 on discharge1 A number of groups have elucidated the mechanism of O2 reduction to Li2O2 on discharge15,16,18-21. CV studies with DBBQ The potential at which O2 is reduced to Li2O2 (the discharge plateau in a Li-O2 cell) is lower than the thermodynamic potential for O2/Li2O2, 2.96 V. A CV corresponding to this process is shown in Fig. 1. To promote O2 reduction to Li2O2 in solution in low DN solvents while suppressing the direct reduction of O2 to form a Li2O2 film, which would otherwise passivate the electrode15,16,21, it is necessary to carry out the reduction of O2 to Li2O2 in solution at a higher potential than the surface reaction, which also has the advantage of increasing the cell discharge potential closer to its thermodynamic potential of 2.96 V (reducing the overpotential). To achieve this, molecules with a redox potential somewhat higher than the potential at which O2 is reduced (discharge plateau in a Li- O2 cell) are required. Quinones were selected as they are known to exhibit potentials in the relevant range30,32. Several quinones were investigated but most were found not to enhance O2 reduction, see Supplementary Fig. S1. Electrolyte preparation and cell assembly are described in the Supplementary Information. DBBQ, in contrast, showed promising electrochemistry, Fig. 1. The cyclic voltammograms for DBBQ obtained in 1 M LiTFSI in tetraethylene glycol dimethyl ether (TEGDME) and dimethoxyethane (DME) at a gold electrode under Ar exhibit quasi-reversible behavior, Fig. 1 and Supplementary Fig. S2. In the presence of O2, the reduction peak is enhanced significantly. Such a CV is similar to that of a catalyzed reduction33, where a redox active species, in this case DBBQ, is reduced and then takes part in a chemical reaction, here with O2 to form Li2O2, resulting in the rapid regeneration of more DBBQ, giving rise to the increased reduction current. The reduction potential is significantly higher than for the direct reduction of O2, Fig. 1, thus effectively suppressing the direct reduction of O2 to Li2O2 films on the electrode surface. The mechanism of O2 reduction by DBBQ is discussed further later; demonstration of the efficiency of DBBQ in promoting Li2O2 formation in solution and not on the electrode surface, as well as increasing the discharge potential of Li-O2 cells is presented below. Figure 1 | CVs demonstrating the significant effect DBBQ has on O2 reduction in ethers. CVs for DBBQ in 1 M LiTFSI in (a) TEGDME and (b) DME. CVs under Ar (blue) and O2 (red) and for direct O2 reduction without DBBQ (black). Abstract Here we demonstrate that addition of DBBQ (2,5-Di-tert-butyl-1,4-benzoquinone) to a weakly solvating (low DN) electrolyte solution, LiTFSI in ether22, promotes O2 reduction to Li2O2 in solution while halving the discharge overpotential (increasing the discharge potential), suppressing the growth of a Li2O2 film on the electrode surface thus postponing cell death, increasing the discharge capacity 80-100 fold and permitting discharge at relatively high rates > 1 mA cm-2areal for an electrode capacity of > 4 mAh cm-2areal. It operates by a new mechanism that does not involve the reactive LiO2 as an intermediate; the new mechanism also decouples the link between the nature of the 2 electrolyte solution (solvating power) and the nature of the product (particles or surface film). The search for truly stable electrolyte solutions for Li-O2 batteries will focus on very low polarity and hence weakly solvating solvents. The significance of the present work is that if such stable solvents can be identified then DBBQ provides a route to solution growth of Li2O2 and hence potentially high rates, high capacities and sustained cycling, avoiding early cell death. Enhancing the discharge of Li-O2 cells with DBBQ Li-O2 cells were constructed as described in the Supplementary Information (Methods Section). The cathode was a binder-free carbon-fiber gas diffusion layer (GDL, Freudenberg), similar to cathodes used widely for aprotic O2 cells20,34. Carbon electrodes are relatively stable on discharge35, which is our focus here. The anode consisted of LixFePO4, as used in previous Li-O2 studies instead of Li metal in order to avoid any oxidation of the anode by O2 36. The LixFePO4 potential vs. Li+/Li, 3.45 V, was used to express all potentials in this work on the Li scale. The electrolyte solution was in all cases 1 M LiTFSI dissolved in the low donor and acceptor number ethers, TEGDME or DME. Cells containing TEGDME and DME saturated with O2 (under 1 atm. of O2), were each discharged at several different areal current densities with and without DBBQ, Fig. 2. In the absence of DBBQ, the cells died rapidly, exhibiting very small capacities and poor rate capability, in accord with previous observations3,37. The cells with DBBQ discharged under the same conditions exhibited a dramatic improvement, delivering up to 80 to 100 times higher discharge capacities before end of life. In TEGDME with DBBQ, a capacity of 10.6 mAh cm-2areal (equivalent to 9.1 mg of Li2O2) was obtained at a current density of 0.2 mA cm-2areal, while in DME with DBBQ, 7.3 mAh cm-2areal (equivalent to 6.3 mg of Li2O2) was obtained at 0.5 mA cm-2areal and 4 mAh cm-2areal (equivalent to 3.4 mg of Li2O2) at 1 mA cm-2 areal. Moreover, areal current densities of 0.5 mA cm-2 (in TEGDME) and 2 mA cm-2 (in DME) were achieved, while halving the discharge overpotential, compared with the performance in the absence of DBBQ. To estimate the contribution of DBBQ reduction itself to the capacity, the cells were discharged under Ar, for DME and TEGDME, and at the same current densities as in Fig. 2. The discharge curves are given in Supplementary Fig. S3. A negligible capacity was observed. These values are all within the limits of the theoretical capacity for DBBQ reduction of 12.5 mAh m-2BET. It has been shown that the limit of Li2O2 film growth is 6 nm17, which equates to a maximum capacity of 15 mAh m-2BET (0.4 mAh cm-2areal). As is evident in Fig. 2, the cells without DBBQ exhibit end of life below this limit, indicating that Li2O2 formation is predominantly by the surface route. CV studies with DBBQ DBBQ concentration was 10 mM and CVs were carried out at planar Au electrodes, scan rate 100 mV s-1. Figure 1 | CVs demonstrating the significant effect DBBQ has on O2 reduction in ethers. CVs for DBBQ in 1 M LiTFSI in (a) TEGDME and (b) DME. CVs under Ar (blue) and O2 (red) and for direct O2 reduction without DBBQ (black). DBBQ concentration was 10 mM and CVs were carried out at planar Au electrodes, scan rate 100 mV s-1. 3 Enhancing the discharge of Li-O2 cells with DBBQ Whereas cells containing DBBQ are able to exceed the limit of film growth by an order of magnitude, signaling predominantly solution growth of Li2O2. 4 4 Figure 2 | Significant effect of DBBQ on discharge in ethers. Load curves of oxygen reduction at gas diffusion electrode discharged in 1 M LiTFSI in (a) TEGDME and (b) DME with 10 mM DBBQ (solid lines) and without DBBQ (dash lines) under O2 at various areal current densities from 0.1 mA cm-2 to 2 mA cm-2. (c,d) enlarged section of load curves recorded without DBBQ in a,b. 200 μl of electrolyte was used. The roughness factor of the cathode is 270. The amounts of Li2O2 formed on discharge were 10.0, 9.1 and 5.2 mg cm-2areal in TEDGME and 9.1, 6.3, 3.4 and 2.0 mg cm-2areal in DME. e 2 | Significant effect of DBBQ on discharge in ethers. Load curves of oxygen reduction at gas diffusio Figure 2 | Significant effect of DBBQ on discharge in ethers. Load curves of oxygen reduction at gas diffusion electrode discharged in 1 M LiTFSI in (a) TEGDME and (b) DME with 10 mM DBBQ (solid lines) and without DBBQ (dash lines) under O2 at various areal current densities from 0.1 mA cm-2 to 2 mA cm-2. (c,d) enlarged section of load curves recorded without DBBQ in a,b. 200 μl of electrolyte was used. The roughness factor of the cathode is 270. The amounts of Li2O2 formed on discharge were 10.0, 9.1 and 5.2 mg cm-2areal in TEDGME and 9.1, 6.3, 3.4 and 2.0 mg cm-2areal in DME. Figure 2 | Significant effect of DBBQ on discharge in ethers. Load curves of oxygen reduction at gas diffusion electrode discharged in 1 M LiTFSI in (a) TEGDME and (b) DME with 10 mM DBBQ (solid lines) and without DBBQ (dash lines) under O2 at various areal current densities from 0.1 mA cm-2 to 2 mA cm-2. (c,d) enlarged section of load curves recorded without DBBQ in a,b. 200 μl of electrolyte was used. The roughness factor of the cathode is 270. The amounts of Li2O2 formed on discharge were 10.0, 9.1 and 5.2 mg cm-2areal in TEDGME and 9.1, 6.3, 3.4 and 2.0 mg cm-2areal in DME. Enhancing the discharge of Li-O2 cells with DBBQ To confirm that Li2O2 grows primarily in solution, away from the electrode surface, in the presence of DBBQ, despite the use of low donor/acceptor solvents, the discharged cathodes with and without DBBQ were extracted and examined by SEM. The results are shown in Fig. 3. In both TEGDME and DME, in the absence of DBBQ, the surfaces of the carbon fibers that constitute the GDL were covered with a film and there was no evidence of Li2O2 particles. In contrast, identical cells discharged under the same conditions, except for the presence of DBBQ, show substantial growth of particles in the pores of the electrodes and with the toroidal morphologies expected for Li2O2, Fig. 3. Equally important is that DBBQ suppresses film growth on the electrode surface. This is shown in Fig. 3 (c,g) where there is little evidence of film growth when DBBQ was present until close to cell death. There will always be some direct reduction to form Li2O2 on the surface, even at the higher potential where DBBQ is reduced, as the direct reduction to form a Li2O2 film is suppressed but not eliminated completely. It has been proposed recently that the presence of H2O can itself promote Li2O2 toroid formation in Li-O2 batteries16,20. Care was taken to rigorously dry the solvents, electrodes and all cell components used here. The H2O content at the beginning and end of discharge did not exceed 30 ppm, considerably smaller than the quantities required to promote toroid formation; at least 200500 ppm H2O is needed16,20. Overall, the SEM images demonstrate that DBBQ has successfully displaced the O2 reduction away from the electrode surface, promoting growth of large Li2O2 particles in the adjacent solution within the pores of the electrode. 5 Figure 3 | SEM images showing the Li2O2 morphologies on discharge in 1 M LiTFSI in ethers with and without DBBQ. (a) the pristine GDL; (b-e) discharge in TEGDME and (f-i) in DME. (b,f) full discharge without DBBQ; (c,g) half discharge with 10 mM DBBQ and (d,e,h,i) full discharge with DBBQ. Figure 3 | SEM images showing the Li2O2 morphologies on discharge in 1 M LiTFSI in ethers with and without DBBQ. (a) the pristine GDL; (b-e) discharge in TEGDME and (f-i) in DME. (b,f) full discharge without DBBQ; (c,g) half discharge with 10 mM DBBQ and (d,e,h,i) full discharge with DBBQ. Enhancing the discharge of Li-O2 cells with DBBQ To demonstrate the particles observed in SEM are indeed Li2O2, powder X-ray diffraction (PXRD), infrared spectrometry (IR) and Raman spectroscopy were carried out on the porous electrodes extracted from the cells. The results are presented in Fig. 4. The PXRD pattern collected on the GDLs discharged in ethers exhibits only peaks associated with Li2O2. The results are confirmed by the IR and Raman spectra in Fig. 4, which also show Li2O2 as the primary product. Although ethers are one of the more stable solvents in Li-O2 batteries, it is known that they are not completely stable38. Small peaks associated with lithium acetate/formate and some Li2CO3 are evident as minor by-products in the IR, as identified previously for discharge in ethers39. There is little evidence of LiOH. To investigate the presence of any soluble by-products, NMR was carried out on the electrolyte solutions. The details are described in the Supplementary Information. In addition to the peaks 6 associated with the electrolyte solutions, only a tiny peak assigned to lithium acetate was observed, Supplementary Fig. S4. In-situ differential electrochemical mass spectrometry (DEMS) was carried out to investigate the gas consumption on discharge. The procedure is described in the Supplementary information and the results are presented in Fig. 5. No gases were detected other than O2 and in particular there was no evidence of CO2, consistent with the degree of side-reactions in ethers being small. The total O2 consumed and total charge passed were measured and the integral gave a ratio of electrons to oxygen consumed of 2.03 e-/O2, consistent with the dominant reaction on discharge involving Li2O2 formation38,40. These results are in accord with charge/mass ratios seen previously for ethers38. Taken together, the PXRD, IR, Raman and DEMS indicate that the dominant product on discharge in the presence of DBBQ in ethers is Li2O2 and that it forms relatively large particles in the pores rather than on the surfaces of the porous electrode. The amount of Li2O2 present in the electrode was quantified by chemical analysis using TiOSO4 as described in the Supplementary information. The yield of Li2O2 (observed mass/mass predicted from charge passed) with DBBQ was 95% and 86% in DME and TEGDME, respectively. This compares with 91% and 81% reported previously for DME and TEGDME in the absence of DBBQ38. Enhancing the discharge of Li-O2 cells with DBBQ The slightly higher yields indicates that the relatively high surface area of the Li2O2 film that grows on the electrode in the absence of DBBQ leads to more decomposition of the electrolyte solution than is the case for the large particles in solution. It has also been suggested that LiO2 is responsible for solvent decomposition on discharge26,41,42 and as discussed below, our analysis points to a mechanism that avoids this reactive intermediate. 7 7 Figure 4 | Characterization of the discharge product confirming Li2O2 is dominant. (a) PXRD pattern, (b) IR and (c) Raman spectra of GDLs discharged in 10 mM DBBQ - 1 M LiTFSI in TEGDME and DME under O2. aracterization of the discharge product confirming Li2O2 is dominant. (a) PXRD ctra of GDLs discharged in 10 mM DBBQ - 1 M LiTFSI in TEGDME and DME und Figure 4 | Characterization of the discharge product confirming Li2O2 is dominant. (a) PXRD pattern, (b) IR and (c) Raman spectra of GDLs discharged in 10 mM DBBQ - 1 M LiTFSI in TEGDME and DME under O2. 8 Figure 5 | In-situ DEMS in DBBQ-TEGDME showing 2.03 e- per O2 consumption, consistent with formation of Li2O2. (a) discharge current (blue), O2 consumption (green) and CO2 evolution (red) in 10 mM DBBQ - 1 M LiTFSI in TEGDME; (b) voltage profile of the DEMS cell. Cyclic voltammetry was applied. e-/O2 ratio was obtained from the integral of charge passed and total O2 consumption. Figure 5 | In-situ DEMS in DBBQ-TEGDME showing 2.03 e- per O2 consumption, consistent with formation of Li2O2. (a) discharge current (blue), O2 consumption (green) and CO2 evolution (red) in 10 mM DBBQ - 1 M LiTFSI in TEGDME; (b) voltage profile of the DEMS cell. Cyclic voltammetry was applied. e-/O2 ratio was obtained from the integral of charge passed and total O2 consumption. Attempts to charge the cells after discharge proved fruitless, see Supplementary Fig. S5. This is to be expected since the Li2O2 is not well connected to the electrode surface and therefore direct electrochemical oxidation will be difficult. Therefore, especially in the presence of a reduction mediated discharge, it will be necessary to employ an oxidation mediator to charge the cell, as described previously36,43-45. The mechanism of O2 reduction in the presence of DBBQ As mentioned above, DBBQ does not operate as an electrocatalyst like, for example, the phthalocyanines described previously29,46, for which O2 is bound to the electrocatalyst before, during and after reduction. Neither does it operate as a redox shuttle, transferring electrons from the electrode surface to reduce O2 in solution to LiO2 and further to Li2O2 by an outer sphere reaction. Instead, it operates by a different mechanism that changes the pathway of O2 reduction to Li2O2 avoiding the reactive LiO2 as an intermediate. The reduction of quinones, such as DBBQ, in Li+ electrolyte solutions under Ar is known to form Li- quinone complexes, in this case LiDBBQ, Fig. 147-49. In the presence of O2 the reduction potential for DBBQ/LiDBBQ does not change, Fig. 1, indicating that the same reduction reaction (DBBQ to LiDBBQ) occurs, i.e. there is no binding of O2 to DBBQ prior to the initial electron transfer, unlike the phthalocyanines29, the first step is as shown in equation (4). However, the reduction current is enhanced significantly, Fig. 1. The observed CV is similar to that of an ECcat reaction, electrochemical 9 reduction followed by a chemical step, in which the reduced form of the redox couple takes part in a chemical reaction that re-generates the oxidized form of the couple to feed the reduction33. Here DBBQ is re-generated from LiDBBQ by the latter reducing O2 in a chemical step, which goes on to form Li2O2. In the absence of DBBQ, reduction of O2 to Li2O2 proceeds via the LiO2 intermediate15,16,18-21, and it is the need to reach the potential for formation of LiO2 that pins the O2 reduction at a potential (discharge plateau in a Li-O2 cell) significantly negative of the standard potential for Li2O2 formation, 2.96 V, Fig. 1. Where the energetics of an intermediate dictates the potential required to carry out an electrochemical reaction this is referred to as a “thermodynamic overpotential”50. In the presence of DBBQ O2 reduction effectively takes place at the potential for DBBQ reduction, Fig. 1, i.e. at a significantly higher potential than would be the case if O2 reduction was occurring via the LiO2 intermediate in solution. This indicates that O2 reduction does not follow the usual path via the LiO2 intermediate but involves formation of a different intermediate complex between LiDBBQ and O2. The mechanism of O2 reduction in the presence of DBBQ By complexing Li+ and O2 with DBBQ- the reaction path and hence free energy of the intermediate (now a complex of the form LiDBBQO2 not LiO2) is lowered (Fig. 6) and the potential correspondingly raised, as seen in the higher voltage for the discharge plateau in galvanostatic discharge of Li-O2 cells, Fig. 2. The sequence of proposed reaction steps at the cathode on discharging a Li-O2 cell containing DBBQ is summarized in equations (4) to (6). Equation (4) is the initial electrochemical reduction. Equations (6a) and (6b) are examples of possible steps by which the intermediate formed in (5) could disproportionate or react with another LiDBBQ, to form Li2O2 that grows from solution, as observed in for example Fig. 3. Confirmation that LiDBBQ and O2 react together to form Li2O2 was obtained by a direct chemical experiment in which O2 was bubbled through a solution containing LiDBBQ and the quantity of Li2O2 measured by TiOSO4 titration, see supplementary information for details. 10 DBBQ(sol) + Li+(sol) + e- → LiDBBQ(sol) (4) LiDBBQ(sol) + O2(sol) ⇌ LiDBBQO2(sol) (5) 2 LiDBBQO2(sol) → Li2O2(s) + O2(sol) + 2 DBBQ(sol) (6a) LiDBBQ(sol) + LiDBBQO2(sol) → Li2O2(s) + 2 DBBQ(sol) (6b) DBBQ(sol) + Li+(sol) + e- → LiDBBQ(sol) (4) LiDBBQ(sol) + O2(sol) ⇌ LiDBBQO2(sol) (5) 2 LiDBBQO2(sol) → Li2O2(s) + O2(sol) + 2 DBBQ(sol) (6a) LiDBBQ(sol) + LiDBBQO2(sol) → Li2O2(s) + 2 DBBQ(sol) (6b) LiDBBQ(sol) + O2(sol) ⇌ LiDBBQO2(sol) (5) 2 LiDBBQO2(sol) → Li2O2(s) + O2(sol) + 2 DBBQ(sol) (6a) LiDBBQ(sol) + LiDBBQO2(sol) → Li2O2(s) + 2 DBBQ(sol) (6b) 10 10 Figure 6 | Schematics (left) of reactions on discharge and (right) the effect of DBBQ on the potential determining step. DBBQ is reduced at the electrode surface forming LiDBBQ, and then LiDBBQ reacts with O2, producing Li2O2 and itself being regenerated to DBBQ. Schematic of free energy plot is at E0 for O2/ Li2O2. Figure 6 | Schematics (left) of reactions on discharge and (right) the effect of DBBQ on the potential determining step. DBBQ is reduced at the electrode surface forming LiDBBQ, and then LiDBBQ reacts with O2, producing Li2O2 and itself being regenerated to DBBQ. Schematic of free energy plot is at E0 for O2/ Li2O2. These reactions can be summarized by the schematic shown in Fig. 1. Abraham KM, Jiang Z. A polymer electrolyte-based rechargeable lithium/oxygen battery. J Electrochem Soc 1996, 143(1): 1-5. Methods Methods and any associated references are available in the online version of the paper. The mechanism of O2 reduction in the presence of DBBQ 6, and the consequences of this scheme are relatively simple electron transfer and dominate solution phase product formation that translate into high rates and capacities during cell discharge. As noted above, DBBQ does not act as a conventional catalyst, it does not bind O2 and facilitate LiO2 formation by stabilizing the superoxide intermediate. Instead DBBQ is reduced to LiDBBQ that binds O2 to form LiDBBQ, (equation 5). The characteristics that make DBBQ suitable for this function are, a reduction potential positive of the potential for formation of LiO2 formation thus avoiding direct formation of LiO2, a reduction potential negative of the overall reduction potential to Li2O2 such that a driving force remains to push the reaction towards peroxide formation and the ability to bind O2 when in the reduced form (LiDBBQ). Outlook O2 reduction to Li2O2 by the DBBQ mediated route brings a number of benefits. The electrochemistry at the electrode surface is now DBBQ reduction rather than direct formation of Li2O2, in an electrolyte solution that does not dissolve LiO2 (weakly solvating electrolyte solution). As a result, Li2O2 formation is moved into solution without the need for high donor/acceptor number solvents or salts. DBBQ shuts down the direct formation of a Li2O2 film on the cathode, thus postponing cell death, increasing capacity 80-100 fold and facilitates discharge rates of > 1 mA cm-2areal for cathodes with capacities of > 4 mAh cm-2areal. The discharge potential is also increased (overpotential is halved). O2 reduction to Li2O2 in the presence of DBBQ follows a new route that avoids the reactive LiO2 in solution. The search for truly stable electrolyte solutions for Li-O2 batteries will focus on very low polarity and hence weakly solvating solvents. The significance of the present work is that if such stable solvents can be identified then DBBQ provides a route to solution growth of Li2O2 and hence potentially high rates, high capacities and sustained cycling, avoiding early cell death. These results demonstrate the importance of moving to a mediated reaction on reduction and imply that the future of the lithium-air battery involves the mediated formation and decomposition of lithium peroxide, where the latter fulfills the role of storage medium only. References 1. Abraham KM, Jiang Z. A polymer electrolyte-based rechargeable lithium/oxygen battery. J Electrochem Soc 1996, 143(1): 1-5. 11 2. Bruce PG, Freunberger SA, Hardwick LJ, Tarascon J-M. Li-O2 and Li-S batteries with high energy storage. Nat Mater 2012, 11(1): 19-29. 3. Girishkumar G, McCloskey B, Luntz AC, Swanson S, Wilcke W. Lithium−air battery: promise and challenges. J Phys Chem Lett 2010, 1(14): 2193-2203. 4. Shao Y, Park S, Xiao J, Zhang J-G, Wang Y, Liu J. Electrocatalysts for nonaqueous lithium–air batteries: status, challenges, and perspective. ACS Catal 2012, 2(5): 844-857. 5. Christensen J, Albertus P, Sanchez-Carrera RS, Lohmann T, Kozinsky B, Liedtke R, et al. A critical review of Li/air batteries. J Electrochem Soc 2012, 159(2): R1-R30. 6. Black R, Adams B, Nazar LF. Non-aqueous and hybrid Li-O2 batteries. Adv Energy Mater 2012, 2(7): 801-815. 7. Choi NS, Chen Z, Freunberger SA, Ji X, Sun YK, Amine K, et al. Challenges facing lithium batteries and electrical double-layer capacitors. Angew Chem Int Ed 2012, 51(40): 9994- 10024. 8. Etacheri V, Marom R, Elazari R, Salitra G, Aurbach D. Challenges in the development of advanced Li-ion batteries: a review. Energy Environ Sci 2011, 4(9): 3243-3262. 9. Zhang T, Imanishi N, Shimonishi Y, Hirano A, Takeda Y, Yamamoto O, et al. A novel high energy density rechargeable lithium/air battery. Chem Commun 2010, 46(10): 1661-1663. 10. Luntz AC, McCloskey BD. Nonaqueous Li-air batteries: a status report. Chem Rev 2014, 114(23): 11721-11750. 11. Li F, Zhang T, Zhou H. Challenges of non-aqueous Li-O2 batteries: electrolytes, catalysts, and anodes. Energy Environ Sci 2013, 6(4): 1125-1141. 12. Thackeray MM, Chan MKY, Trahey L, Kirklin S, Wolverton C. Vision for designing high-energy, hybrid Li ion/Li–O2 cells. J Phys Chem Lett 2013: 3607-3611. 13. Scrosati B, Hassoun J, Sun Y-K. Lithium-ion batteries. A look into the future. Energy Environ Sci 2011, 4(9): 3287-3295. 14. Sharon D, Hirshberg D, Afri M, Garsuch A, Frimer AA, Aurbach D. Lithium-oxygen electrochemistry in non-aqueous solutions. Isr J Chem 2015, 55(5): 508-520. 12 15. Johnson L, Li C, Liu Z, Chen Y, Freunberger SA, Ashok PC, et al. The role of LiO2 solubility in O2 reduction in aprotic solvents and its consequences for Li–O2 batteries. Nat Chem 2014, 6(12): 1091-1099. 16. Aetukuri NB, McCloskey BD, Garcia JM, Krupp LE, Viswanathan V, Luntz AC. Solvating additives drive solution-mediated electrochemistry and enhance toroid growth in non- aqueous Li-O2 batteries. Nat Chem 2015, 7(1): 50-56. 17. References Luntz AC, Viswanathan V, Voss J, Varley JB, Nørskov JK, Scheffler R, et al. Tunneling and polaron charge transport through Li2O2 in Li–O2 batteries. J Phys Chem Lett 2013, 4(20): 3494-3499. 18. Hummelshoj JS, Luntz AC, Norskov JK. Theoretical evidence for low kinetic overpotentials in Li-O2 electrochemistry. J Chem Phys 2013, 138(3): 034703. 19. Laoire CO, Mukerjee S, Abraham KM, Plichta EJ, Hendrickson MA. Influence of nonaqueous solvents on the electrochemistry of oxygen in the rechargeable Lithium−air battery. J Phys Chem C 2010, 114(19): 9178-9186. 20. Schwenke KU, Metzger M, Restle T, Piana M, Gasteiger HA. The influence of water and protons on Li2O2 crystal growth in aprotic Li-O2 cells. J Electrochem Soc 2015, 162(4): A573- A584. 21. Adams BD, Radtke C, Black R, Trudeau ML, Zaghib K, Nazar LF. Current density dependence of peroxide formation in the Li-O2 battery and its effect on charge. Energy Environ Sci 2013, 6(6): 1772-1778. 22. Burke CM, Pande V, Khetan A, Viswanathan V, McCloskey BD. Enhancing electrochemical intermediate solvation through electrolyte anion selection to increase nonaqueous Li-O2 battery capacity. Proc Natl Acad Sci U S A 2015, 112(30): 9293-9298. 23. Aurbach D, Hirshberg DH, Sharon D, Afri M, Garsuch A, Frimer AA. The catalytic behavior of lithium nitrate in Li-O2 batteries. The 228th ECS Meeting; 2015 October 11 – 15, 2015; Phoenix, AZ; 2015. 24. Gunasekara I, Mukerjee S, Plichta EJ, Hendrickson MA, Abraham KM. A study of the influence of lithium salt anions on oxygen reduction reactions in Li-air batteries. J Electrochem Soc 2015, 162(6): A1055-A1066. 25. Khetan A, Luntz A, Viswanathan V. Trade-offs in capacity and rechargeability in nonaqueous Li–O2 batteries: Solution-driven growth versus nucleophilic stability. J Phys Chem Lett 2015, 6(7): 1254-1259. 25. Khetan A, Luntz A, Viswanathan V. Trade-offs in capacity and rechargeability in nonaqueous Li–O2 batteries: Solution-driven growth versus nucleophilic stability. J Phys Chem Lett 2015, 6(7): 1254-1259. 25. Khetan A, Luntz A, Viswanathan V. Trade-offs in capacity and rechargeability in nonaqueous Li–O2 batteries: Solution-driven growth versus nucleophilic stability. J Phys Chem Lett 2015, 6(7): 1254-1259. 13 26. Sharon D, Afri M, Noked M, Garsuch A, Frimer AA, Aurbach D. Oxidation of Dimethyl Sulfoxide Solutions by Electrochemical Reduction of Oxygen. J Phys Chem Lett 2013, 4(18): 3115-3119. 27. Lacey MJ, Frith JT, Owen JR. A redox shuttle to facilitate oxygen reduction in the lithium air battery. Electrochem Commun 2013, 26(0): 74-76. 28. References Yang L, Frith JT, Garcia-Araez N, Owen JR. A new method to prevent degradation of lithium- oxygen batteries: reduction of superoxide by viologen. Chem Commun 2015, 51(9): 1705- 1708. 29. Sun D, Shen Y, Zhang W, Yu L, Yi Z, Yin W, et al. A solution-phase bifunctional catalyst for lithium-oxygen batteries. J Am Chem Soc 2014, 136(25): 8941-8946. 30. Matsuda S, Hashimoto K, Nakanishi S. Efficient Li2O2 formation via aprotic oxygen reduction reaction mediated by quinone derivatives. J Phys Chem C 2014, 118(32): 18397-18400. 31. Imanishi N, Luntz AC, Bruce PG. The Lithium Air Battery: Fundamentals. Springer, 2014. 32. Guin PS, Das S, Mandal PC. Electrochemical reduction of quinones in different media: a review. Int J Electrochem 2011, 2011: 1-22. 33. Saveant J-M. Elements of molecular and biomolecular electrochemistry: an electrochemical approach to electron transfer chemistry. A JOHN WILEY & SONS, INC., Hoboken, New Jersey., 2006. 34. Hartmann P, Bender CL, Vracar M, Durr AK, Garsuch A, Janek J, et al. A rechargeable room- temperature sodium superoxide (NaO2) battery. Nat Mater 2013, 12(3): 228-232. 35. Ottakam Thotiyl MM, Freunberger SA, Peng Z, Bruce PG. The carbon electrode in nonaqueous Li-O2 cells. J Am Chem Soc 2013, 135(1): 494-500. 36. Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. Charging a Li–O2 battery using a redox mediator. Nat Chem 2013, 5: 489–494. 37. Lu Y-C, Kwabi DG, Yao KPC, Harding JR, Zhou J, Zuin L, et al. The discharge rate capability of rechargeable Li-O2 batteries. Energy Environ Sci 2011, 4(8): 2999-3007. 38. McCloskey BD, Valery A, Luntz AC, Gowda SR, Wallraff GM, Garcia JM, et al. Combining accurate O2 and Li2O2 assays to separate discharge and charge stability limitations in nonaqueous Li–O2 batteries. J Phys Chem Lett 2013, 4(17): 2989-2993. 14 39. Freunberger SA, Chen Y, Drewett NE, Hardwick LJ, Barde F, Bruce PG. The lithium-oxygen battery with ether-based electrolytes. Angew Chem Int Ed 2011, 50(37): 8609-8613. 40. Chen Y, Freunberger SA, Peng Z, Barde F, Bruce PG. Li-O2 battery with a dimethylformamide electrolyte. J Am Chem Soc 2012, 134(18): 7952-7957. 41. Adams BD, Black R, Williams Z, Fernandes R, Cuisinier M, Berg EJ, et al. Towards a stable organic electrolyte for the Lithium oxygen battery. Adv Energy Mater 2015, 5(1): 1400867. 42. Zhang Z, Lu J, Assary RS, Du P, Wang H-H, Sun Y-K, et al. Increased Stability Toward Oxygen Reduction Products for Lithium-Air Batteries with Oligoether-Functionalized Silane Electrolytes. Acknowledgements P.G.B. is indebted to the EPSRC and the RCUK Energy programme including SUPERGEN for financial support. Author contributions ‡These authors contributed equally to this work. X.G. and Y.C. designed experiments and analyzed the data. X.G. performed electrochemical and characterization of discharge products. Y.C. performed the UV-vis spectroscopy experiments and analyzed the data. P.G.B, X.G., Y.C., L.J. interpreted the data. P.G.B. wrote the paper. References J Phys Chem C 2011, 115(51): 25535-25542. 43. Vincent Giordani, Wesley Walker, Vyacheslav Bryantsev, Jasim Uddin, Strahinja Zecevic, Dan Addison, et al. Freely Diffusing Oxygen Evolving Catalysts for Rechargeable Li-O2 Batteries. abstract for 16th IMLB 2012 Jeju Korea; 2012; 2012. p. S6-3. 44. Bergner BJ, Schurmann A, Peppler K, Garsuch A, Janek J. TEMPO: a mobile catalyst for rechargeable Li-O2 batteries. J Am Chem Soc 2014, 136(42): 15054-15064. 45. Lim HD, Song H, Kim J, Gwon H, Bae Y, Park KY, et al. Superior rechargeability and efficiency of lithium-oxygen batteries: hierarchical air electrode architecture combined with a soluble catalyst. Angew Chem Int Ed 2014, 53(15): 3926-3931. 46. Trahan MJ, Jia Q, Mukerjee S, Plichta EJ, Hendrickson MA, Abraham KM. Cobalt phthalocyanine catalyzed lithium-air batteries. J Electrochem Soc 2013, 160(9): A1577- A1586. 47. Lee M, Hong J, Seo DH, Nam DH, Nam KT, Kang K, et al. Redox cofactor from biological energy transduction as molecularly tunable energy-storage compound. Angew Chem Int Ed 2013, 52(32): 8322-8328. 48. Hanyu Y, Honma I. Rechargeable quasi-solid state lithium battery with organic crystalline cathode. Sci Rep 2012, 2: 453. 49. Peover ME, Davis JD. The influence of ion-association on the polarography of quinones in dimethylformamide. J Electroanal Chem (1959) 1963, 6(1): 46-53. 50. Koper MTM. Thermodynamic theory of multi-electron transfer reactions: implications for electrocatalysis. J Electroanal Chem 2011, 660(2): 254-260. 51. Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. A stable cathode for the aprotic Li-O2 battery. Nat Mater 2013, 12(11): 1050-1056. 15 52. Hartmann P, Bender CL, Sann J, Durr AK, Jansen M, Janek J, et al. A comprehensive study on the cell chemistry of the sodium superoxide (NaO2) battery. Phys Chem Chem Phys 2013, 15(28): 11661-11672. 52. Hartmann P, Bender CL, Sann J, Durr AK, Jansen M, Janek J, et al. A comprehensive study on the cell chemistry of the sodium superoxide (NaO2) battery. Phys Chem Chem Phys 2013, 15(28): 11661-11672. Competing financial interests The authors declare no competing financial interests. 52. Hartmann P, Bender CL, Sann J, Durr AK, Jansen M, Janek J, et al. A comprehensive study on the cell chemistry of the sodium superoxide (NaO2) battery. Phys Chem Chem Phys 2013, 15(28): 11661-11672. 52. Hartmann P, Bender CL, Sann J, Durr AK, Jansen M, Janek J, et al. A comprehensive study on the cell chemistry of the sodium superoxide (NaO2) battery. Physical Chemistry Chemical Physics 2013, 15(28): 11661-11672. 51. Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. A stable cathode for the aprotic Li-O2 battery. Nature Materials 2013, 12(11): 1050-1056. Materials and methods TEGDME was distilled under vacuum and DME was distilled under Ar. All solvents were further dried for several days over freshly activated molecular sieves (type 4Å, Aldrich) before use. The final water content was < 10 ppm (determined by Karl Fischer titration). Lithium bis(trifluoromethane)sulfonimide (LiTFSI, Aldrich) was dried at 70 oC under vacuum over several days. 3,5-di-tert-butyl-o-benzoquinone, 2,5-di-tert-butyl-1,4-benzoquinone (DBBQ) and thymoquinone were obtained from Aldrich. The prepared electrolyte solutions contain < 10 ppm water content (determined by Karl Fischer titration). High purity N5.5 O2 (BOC) was used in all measurements. O2 gas flow was further dried by an in-line moisture trap filled with activated 3 Å molecular sieves. All materials were stored in an Ar-filled glove box. Cyclic voltammetry (CV) was performed using a VMP3 electrochemical workstation (Biologic) and a multi-necked, air-tight glass cell within a glove box. The measurements were carried out at room temperature and IR correction was used. 2 mm diameter polycrystalline Au disks (BAS Inc.) were employed as the working electrodes. A platinum wire served as the counter electrode and a partially oxidized LiFePO4 composite electrode behind a Vycor frit served as the reference electrode, as described previously15. 16 Swagelok Li-O2 cells were constructed as described previously51. Binder-free gas diffusion layers (GDL, H2315, Quintech) served as the O2 electrode. The porosity of the GDLs is 80 %, roughness factor (total surface area/ areal area) is 90 and the Brunauer-Emmett-Teller surface area is below 1 m2 g-134. Three pieces of GDLs (4 mm x 4 mm) were stacked to form the cathode giving a final roughness factor of 270 (3 x 90), a glass fibre filter (Waterman) was used as the separator and a partially oxidized LiFePO4 electrode was used as the anode. The two-phase LixFePO4 has a fixed potential of 3.45 V vs. Li+/Li. 200 µl of electrolyte solution was used, consisting of either TEGDME or DME containing 1 M LiTFSI with DBBQ as indicated in the main article. All cell components were dried at 90 oC under vacuum prior to use. Assembled cells were placed in glass tubes, which were filled with dried O2 inside the glove box. Cells were discharged inside an Ar-filled glove box. Characterisations of discharged electrodes For post-cycling characterisation, the cells were dissembled in a glovebox and the cathode and separators were rinsed with a small amount of TEGDME or DME, the resulting solutions were subjected to Karl Fischer titration to determine the water content after discharge. The electrodes were rinsed again with DME and dried prior to further characterisation. The morphology of discharge electrodes were observed by FE-SEM using a Zeiss-Merlin. PXRD was carried out with a Rigaku X-ray diffractometer in an air-sensitive holder. FTIR spectra were measured with a Thermo IR spectrometer (Nicolet 6700) in a N2-filled glove box. Raman spectra were measured with a Rinishaw Invia spectrometer (10 mW laser power at 785 nm) with an air-sensitive sample holder. For NMR analysis, 100 µl of electrolyte was extracted from the discharge electrodes and separators then diluted with 0.7 ml of CDCl3, measurements were recorded on a Bruker spectrometer (400 MHz). A DEMS cell was constructed as described previously40. A GDL served as working electrode and a partially oxidised LiFePO4 composite electrode served as anode. The electrolyte solution was 10 mM DBBQ in 1 M LiTFSI in TEGDME. A continuous 95% O2 / 5% Ar gas flow was purged through the cell as a carrier gas at a flow rate of 0.3 ml min-1. The quantity of Li2O2 formed was determined by UV-vis spectrometry (Thermo Evolution 200) using a UV-vis titration method reported previously20,52. The unwashed discharged electrode and separators were added to a vial containing a known amount of water; Li2O2 reacts with water to produce H2O2 in solution. 1 ml of this solution was mixed with 2 ml of 2 % TiOSO4 dissolved in 1 M H2SO4 solution and a yellowish complex [Ti(O2)]2+ (λmax= 405 nm) was formed. The UV-vis absorption spectrum of the solution was measured and compared to a calibration curve, which was obtained by measuring solutions with known amounts of commercial Li2O2 (Aldrich). The purity of commercial Li2O2 was determined by titration using KMnO4 and this was taken into account when constructing the calibration curve. References 17
https://openalex.org/W4315565727
https://journals.unisba.ac.id/index.php/JRK/article/download/1511/988
Indonesian
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Gambaran Pengetahuan tentang Penyakit Tuberkulosis Paru pada Keluarga Penderita di Puskesmas X
Jurnal Riset Kedokteran
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Gambaran Pengetahuan tentang Penyakit Tuberkulosis Paru pada Keluarga Penderita di Puskesmas X Achmad Cesario Ludiana, Yuliana Ratna Wati* Prodi Pendidikan Kedokteran, Fakultas Kedokteran, Universitas Islam Bandung, Indonesia. Creative Commons Attribution- NonCommercial-ShareAlike 4.0 International License. Creative Commons Attribution- NonCommercial-ShareAlike 4.0 International License. Volume : 2 No. : 2 Halaman : 107-116 Terbitan : Desember 2022 Kata Kunci : Keluarga Penderita; Tingkat Pengetahuan; Tuberkulosis Paru. Kata Kunci : Keluarga Penderita; Tingkat Pengetahuan; Tuberkulosis Paru. @ 2022 Jurnal Riset Kedokteran Unisba Press. All rights reserved. A R T I C L E I N F O A R T I C L E I N F O Article history : Received : 25/8/2022 Revised : 19/12/2022 Published : 21/12/2022 Creative Commons Attribution- NonCommercial-ShareAlike 4.0 International License. Volume : 2 No. : 2 Halaman : 107-116 Terbitan : Desember 2022 Article history : Received : 25/8/2022 Revised : 19/12/2022 Published : 21/12/2022 Article history : Received : 25/8/2022 Revised : 19/12/2022 Published : 21/12/2022 Article history : Penelitian ini bertujuan mengetahui gambaran pengetahuan tentang penyakit tuberkulosis paru pada keluarga penderita TB Paru di Puskesmas X Kabupaten Bandung. Penelitian bersifat deskriptif dengan pendekatan purposive sampling. Subjek penelitian adalah keluarga penderita TB Paru di Puskesmas X Kabupaten Bandung. Data didapatkan menggunakan kuesioner. Keluarga pasien diteliti sebanyak 66 subjek terdiri dari 54,4% laki- laki, 33,3% berpendidikan menengah atas, 63.6% berstatus ekonomi rendah, 74,2% dari suku Sunda, 74,2% responden bekerja, 34,8% berusia antara 46- 55 tahun, dan status hubungan keluarga dengan pasien 88.89% adalah orang tua. Tingkat pengetahuan keluarga penderita TB Paru mengenai tanda-tanda penyakit TB Paru (74,2%), pencegahan (77,3%), dan pengobatan (56,1%) adalah baik. Tingkat pengetahuan mengenai cara penularan (43,9%), Pengawas Minum Obat (PMO) (48,5%), dan komplikasi (48,5%) adalah cukup. Tingkat pengetahuan mengenai penyebab (39,4%) adalah kurang. Secara umum tingkat pengetahuan keluarga tentang penyakit TB Paru adalah cukup. A. Pendahuluan Menurut WHO (World Health Organization) Tuberkulosis (TB) merupakan salah satu penyakit paling mematikan di dunia. Seperempat dari populasi dunia, terinfeksi kuman TB. Berdasarkan WHO Global Tuberculosis Report tahun 2018, terdapat secara keseluruhan kasus TB baru sebanyak 6,4 juta, dimana setara dengan 64% dari insidensi TB yaitu 10,0 juta kasus. Kematian akibat tuberkulosis secara global diperkirakan sebanyak 1,3 juta.[1] WHO Global Tuberculosis Report tahun 2018, juga menjelaskan angka insidensi TB di Indonesia pada tahun 2017 sebanyak 319 per 100.000 penduduk dan angka kematian penderita tuberkulosis 40 per 100.000 penduduk. Data tersebut menunjukan Indonesia berada pada peringkat ke-2.[1] Pada tahun 2017 ditemukan jumlah kasus tuberkulosis meningkat, dari pada tahun 2016. Jumlah kasus tertinggi yang dilaporkan terdapat di provinsi dengan jumlah penduduk yang besar yaitu Jawa Barat, Jawa Timur dan Jawa Tengah. Kasus tuberkulosis di tiga provinsi tersebut sebesar 43% dari jumlah seluruh kasus tuberkulosis di Indonesia. Akibat tingginya angka penyakit tuberkulosis maka dibutuhkan sosialisasi mengenai pencegahan dan pengetahuan tentang penyakit. [2] Menurut Kementrian Kesehatan Case Detection Rate (CDR) tertinggi pada tahun 2017 adalah DKI Jakarta (104,7%), sedangkan CDR terendah adalah Jambi (24,2%). Jawa Barat berada di peringkat ke-6 di Indonesia dengan nilai CDR 53,2%, hal ini menunjukkan bahwa di Jawa Barat penemuan kasus TB sudah baik, karena fasilitas kesehatan sudah cukup mumpuni dan merata sehingga cukup mudah untuk dijangkau oleh masyarakat. CDR Provinsi Jambi cukup rendah, hal ini dapat terjadi karena kurangnya fasilitas yang mendukung. Angka kejadian Tuberkulosis Paru di Jambi memang kecil atau pengetahuan dan kesadaran masyarakat akan gejala penyakit TB cukup rendah. [3] Data dari profil kesehatan Departemen Kesehatan Provinsi Jawa Barat tahun 2017 Case Notification Rate (CNR) tuberkulosis per 100.00 penduduk dari tahun 2003-2017 cenderung meningkat, dibandingkan tahun 2016. Pada tahun 2017 terdapat tiga kabupaten/kota dengan Case Notification Rate semua kasus tuberkulosis yang tinggi yaitu di Kota Sukabumi (400 kasus), Cirebon (396 kasus), dan Bandung (386 kasus). Hal ini menunjukkan angka penularan penyakit TB Paru relatif cukup tinggi dan pengendalian kasus TB Paru cukup rendah karena kurangnya pemahaman masyarakat mengenai pencegahan penyakit TB Paru dan kurangnya edukasi tentang pencegahan maupun tentang penyakit TB Paru. Adapun CNR (Case Notification Rate) yang terendah yaitu Kabupaten Bekasi. [2] Menurut Profil Kesehatan Kabupaten Bandung tahun 2019 angka keberhasilan pengobatan tuberkulosis di Kabupaten Bandung 90,50%. Keberhasilan pengobatan tertinggi di Puskesmas Sukajadi, Sudi, Sukamanah, Pangalengan dan Cileunyi dengan angka keberhasilan 100%. Wilayah dengan angka keberhasilan terendah yaitu Puskesmas Nagrak 75,83% dan Puskesmas X 73,95%. A B S T R A C T This research is aimed to know about the general knowledge of pulmonary tuberculosis in the families of this patients at X Community Health Center, Bandung District. This research uses descriptive method with purposive sampling techniques. The subjects of this research are the families of pulmonary tuberculosis patients at X Community Health Center, Bandung District. The data were obtained using questionnaires. The families of the patients, whom were studied, are 66 subjects consists of 54,4% men, 33,3% with high school level of education, 63,6% with low economic status, 74,2% are Sundanese, 74,2% are workers, 34,8% aged between 46 to 55 years old, and the relation between the families and the patients is 88,89% parents. The pulmonary TB patients’ families’ level of knowledge regarding the signs & symptoms (74,2%), the prevention (77,3%), and the treatment (56,1%) is good. The level of knowledge regarding the mode of transmission (43,9%), Drug-Taking Supervisor (48,5%), and the complication (48,5%) is sufficient. The level of knowledge regarding the causes (39,4%) is low. In general, the pulmonary TB patients’ families’ level of knowledge is sufficient. Keywords : Family of The Patients; Knowledge level; Pulmonary Tuberculosis. Corresponding Author : *yulianaratnawati@unisba.ac.id Indexed : Garuda, Crossref, Google Scholar DOI : https://doi.org/10.29313/jrk.vi.1511 Corresponding Author : *yulianaratnawati@unisba.ac.id Indexed : Garuda, Crossref, Google Scholar DOI : https://doi.org/10.29313/jrk.vi.1511 107/116 Achmad Cesario Ludiana et al. Gambaran Pengetahuan tentang Penyakit Tuberkulosis,... A. Pendahuluan [5] Kepatuhan minum obat bisa mengakibatkan rendahnya tingkat keberhasilan pengobatan TB paru, Hal ini dikarenakan kepatuhan minum obat merupakan salah satu keberhasilan dalam pengobatan TB. Kepatuhan adalah suatu sikap yang merupakan respon yang muncul hanya apabila individu tersebut dihadapkan pada suatu stimulus yang menghendaki adanya reaksi individual. Jika individu tidak mematuhi apa yang telah menjadi ketetapan dapat dikatakan tidak patuh. Kepatuhan minum obat dipengaruhi oleh beberapa variabel yaitu variabel umur, pendidikan, penghasilan, pengetahuan, sikap, dan peran PMO (Pengawas Minum Obat). [6] Menurut Niven, keluarga dapat menjadi faktor yang sangat berpengaruh dalam menentukan keyakinan dan kesehatan individu juga dapat juga menentukan program pengobatan yang mereka dapatkan. Dukungan dari anggota keluarga merupakan faktor penting dalam kepatuhan terhadap pengobatan.[6] Penelitian tentang dukungan keluarga dalam keberhasilan pengobatan banyak diteliti, salah satunya penelitian yang dilaksanakan Rachmawati, Laksmiati dan Soenarsongko. Menurut penelitian tersebut dukungan keluarga mempunyai peran yang sangat penting bagi kepatuhan pasien TB paru. Selain sebagai pihak yang selalu mendukung untuk kesembuhan, keluarga juga bertanggung jawab sebagai Pengawas Minum Obat (PMO) yang nantinya akan berperan untuk mengawasi dan mengingatkan secara terus menerus kepada pasien agar pasien meminum obatnya secara teratur dan tepat waktu sesuai dengan dosis yang sudah ditetapkan 108/116 Volume 2, No. 2, Desember 2022 Jurnal Riset Kedokteran (JRK) oleh petugas, dukungan keluarga dalam keberhasilan pengobatan pada pasien TB tidak terlepas dari faktor pengetahuan keluarga itu sendiri. [6] B. Metode Penelitian Metode penelitian ini adalah deskriptif dengan menggunakan pendekatan penelitian cross sectional. Cross sectional yaitu penelitian yang dilakukan pada satu waktu. Pemilihan sampel diawali dengan survei pada populasi. Sampel yang dipilih adalah yang memenuhi kriteria inklusi dan eksklusi. Populasi didapat dari keluarga penderita TB Paru di Puskesmas X Kabupaten Bandung. Besar sampel dihitung dengan menggunakan rumus Lemeshow didapatkan jumlah sample yaitu 66 subjek dengan Kriteria inklusi pada penelitian ini adalah keluarga penderita TB Paru yang berobat di Puskesmas X Kabupaten Bandung, dan kriteria eksklusi tidak menjadi caregiver penderita karena caregiver sudah di edukasi oleh puskesmas setempat, dan keluarga yang tidak serumah. Kemudian subjek diberikan kuisioner yang memberikan gambaran dari pengetahuan, penyebab, tanda tanda, penularan, komplikasi, pengawas minum obat, pencegahan dan pengobatan. Dalam hal ini ingin mengetahui gambaran pengetahuan penyakit TB Paru pada keluarga penderita di Puskesmas X Kabupaten Bandung. Variabel dalam penelitian ini adalah pengetahuan tentang penyakit TB Paru. Data penelitian diperoleh dari alat penelitian berupa kuesioner. Kuesioner dibagikan kepada responden dengan cara memberikan link google formulir yang akan diberikan oleh peneliti dan akan dibantu diarahkan oleh tenaga kesehatan setempat yang telah dilatih. Kuesioner diisi oleh masing-masing responden dan tidak boleh diwakilkan. C. Hasil dan Pembahasan Telah dilakukan penelitian mengenai Gambaran Pengetahuan Tentang Penyakit Tuberkulosis Paru Pada Keluarga Penderita Tuberkulosis Paru di Puskesmas X Kabupaten Bandung. Sampel yang memenuhi kriteria inklusi yaitu keluarga penderita TB Paru yang berobat di Puskesmas X Kabupaten Bandung dan eksklusi yaitu keluarga yang tidak menjadi caregiver dikarenakan caregiver sudah di edukasi terlebih dahulu oleh puskesmas, yaitu sebanyak 66 orang. e-ISSN 2798-6594 | p-ISSN 2808-3040 109/116 Tabel 1. Karakteristik Keluarga Penderita Penyakit TB Paru Karakteristik *Frekuensi Persen Jenis Kelamin Laki-laki 36 54.5 Perempuan 30 45.5 Usia <17 tahun 1 1.5 17-25 tahun 6 9.1 26-35 tahun 6 9.1 36-45 tahun 17 25.8 46-55 tahun 23 34.8 56-65 tahun 12 18.2 >65 tahun 1 1.5 Tabel 1. Karakteristik Keluarga Penderita Penyakit TB Paru Tabel 1. Karakteristik Keluarga Penderita Penyakit TB Paru e-ISSN 2798-6594 | p-ISSN 2808-3040 e-ISSN 2798-6594 | p-ISSN 2808-3040 Achmad Cesario Ludiana et al. Gambaran Pengetahuan tentang Penyakit Tuberkulosis,... Karakteristik *Frekuensi Persen Suku Betawi 1 1.5 Jawa 7 10.6 Sunda 58 87.9 Pekerjaan Bekerja 49 74.2 Tidak Bekerja 17 25.8 Pendidikan SD 21 31.8 SMP 16 24.2 SMA/SMK 22 33.3 PERGURUAN TINGGI (D1-S3) 7 10.6 Penghasilan <RP.3.200.000 42 63.6 RP.3.200.000 10 15.2 RP.3200.000-RP.5.000.000 14 21.2 Hubungan Dengan Pasien Anak 17 25.8 Istri 11 16.7 Orang Tua 18 27.3 Saudara Kandung 4 6.1 Suami 16 24.2 Jenis Pengobatan Pasien Baru 61 92.4 Pasien Kambuh 5 7.6 Volume 2, No. 2, Desember 2022 Jurnal Riset Kedokteran (JRK) ISSN 2798 6594 | ISSN 2808 3040 111/116 Tabel 2. Distribusi Frekuensi Indikator Pengetahuan Keluarga Penderita Tuberkulosis Paru Indikator Frekuensi % Penyebab Tuberkulosis Paru Baik 18 27.3 Cukup 22 33.3 Kurang 26 39.4 Tanda-tanda Tuberkulosis Paru Baik 49 74.2 Cukup 0 0 Kurang 17 25.8 Cara penularan Tuberkulosis Paru Baik 11 16.7 Cukup 29 43.9 Kurang 26 39.4 Pencegahan Tuberkulosis Paru Baik 51 77.3 Cukup 13 19.7 Kurang 2 3.0 Pengobatan Tuberkulosis Paru Baik 37 56.1 Cukup 22 33.3 Kurang 7 10.6 Pengawasan Minum Obat Tuberkulosis Paru Baik 14 21.2 Cukup 32 48.5 Kurang 20 30.3 Komplikasi Tuberkulosis Paru Baik 29 43.9 Cukup 32 48.5 Kurang 5 7.6 Jurnal Riset Kedokteran (JRK) Jurnal Riset Kedokteran (JRK) Tabel 2. C. Hasil dan Pembahasan Distribusi Frekuensi Indikator Pengetahuan Keluarga Penderita Tuberkulosis Paru Indikator Frekuensi % Penyebab Tuberkulosis Paru Baik 18 27.3 Cukup 22 33.3 Kurang 26 39.4 Tanda-tanda Tuberkulosis Paru Baik 49 74.2 Cukup 0 0 Kurang 17 25.8 Cara penularan Tuberkulosis Paru Baik 11 16.7 Cukup 29 43.9 Kurang 26 39.4 Pencegahan Tuberkulosis Paru Baik 51 77.3 Cukup 13 19.7 Kurang 2 3.0 Pengobatan Tuberkulosis Paru Baik 37 56.1 Cukup 22 33.3 Kurang 7 10.6 Pengawasan Minum Obat Tuberkulosis Paru Baik 14 21.2 Cukup 32 48.5 Kurang 20 30.3 Komplikasi Tuberkulosis Paru Baik 29 43.9 Cukup 32 48.5 Kurang 5 7.6 Tabel 2. Distribusi Frekuensi Indikator Pengetahuan Keluarga Penderita Tuberkulosis Paru Penyebab Tuberkulosis Paru Penyebab Tuberkulosis Paru Komplikasi Tuberkulosis Paru e-ISSN 2798-6594 | p-ISSN 2808-3040 Achmad Cesario Ludiana et al. Gambaran Pengetahuan tentang Penyakit Tuberkulosis,... Hasil pengkategorian indikator pengetahuan tentang TB Paru adalah sebagai berikut. Pada indikator penyebab dari 66 orang, 26 orang (39,4%) memiliki tingkat pengetahuan yang kurang. Pada indikator tanda- tanda dari 66 orang, 49 orang (74,2%) memiliki tingkat pengetahuan yang baik. Pada indikator cara penularan dari 66 orang, 29 orang (43,9%) memiliki tingkat pengetahuan yang cukup. Pada indikator pencegahan dari 66 orang, 51 orang (77.3%) memiliki tingkat pengetahuan yang baik. Pada indikator pencegahan dari 66 orang, 37 orang (56.1%) memiliki tingkat pengetahuan yang baik. Pada indikator pengawasan dari 66 orang, 32 orang (48,5%) memiliki tingkat pengetahuan yang cukup. Pada indikator komplikasii dari 66 orang, 32 orang (48,5%) memiliki tingkat pengetahuan yang cukup. Berikut merupakan kategorisasi tingkat pengetahuan berdasarkan persentase terbanyak. Tabel 3. Kategorisasi Tingkat Pengetahuan Keluarga Penderita TB Paru Tingkat Pengetahuan Jumlah Persentase Baik (>75%) 21 31.8 Cukup (56%-75%) 44 66.7 Kurang (<56%) 1 1.5 Jumlah 66 100 Tabel 3. Kategorisasi Tingkat Pengetahuan Keluarga Penderita TB Paru Hasil pengkategorian tingkat pengetahuan tentang TB Paru adalah sebagai beirkut. Dari 66 orang, 21 orang (31,8%) memiliki tingkat pengetahuan yang baik, 44 orang (66,7%) memiliki tingkat pengetahuan yang cukup dan 1 orang (1,5%) memiliki tingkat pengetahuan yang kurang. Tabel 4. Hubungan Karakteristik Keluarga Penderita TB Paru dengan tingkat pengetahuan 12/116 Volume 2, No. 2, Desember 2022 Tabel 4. Hubungan Karakteristik Keluarga Penderita TB Paru dengan tingkat pengetahuan Karakteristik Pengetahuan Total Baik Cukup Kurang N % N % N % Jenis kelamin Laki-laki 9 25.00 27 75 0 0.00 36 Perempuan 12 40.00 17 57 1 3.33 30 Total 21 31.82 44 67 1 1.52 66 Usia <17 tahun 0 0.00 1 100.00 0 0.00 1 17-25 tahun 3 50.00 3 50.00 0 0.00 6 26-35 tahun 3 50.00 3 50.00 0 0.00 6 36-45 tahun 3 17.65 14 82.35 0 0.00 17 46-55 tahun 7 30.43 16 69.57 0 0.00 23 56-65 tahun 5 41.67 6 50.00 1 8.33 12 Volume 2, No. Penyebab Tuberkulosis Paru 2, Desember 2022 Jurnal Riset Kedokteran (JRK) ISSN 2798-6594 | p-ISSN 2808-3040 113/116 Karakteristik Pengetahuan Total Baik Cukup Kurang N % N % N % >65 tahun 0 0.00 1 100.00 0 0.00 1 Total 21 31.82 44 67 1 1.52 66 SUKU Betawi 0 0.00 1 100.00 0 0.00 1 Jawa 2 28.57 5 71.43 0 0.00 7 Sunda 19 32.76 38 65.52 1 1.72 58 Total 21 31.82 44 67 1 1.52 66 Pekerjaan Bekerja 14 28.57 35 71.43 0 0.00 49 Tidak Bekerja 7 41.18 9 52.94 1 5.88 17 Total 21 31.82 44 67 1 1.52 66 Pendidikan SD 5 23.81 16 76.19 0 0.00 21 SMP 3 18.75 13 81.25 0 0.00 16 SMA/SMK 8 36.36 13 59.09 1 4.55 22 PERGURUAN TINGGI (D1-S3) 5 71.43 2 28.57 0 0.00 7 Total 21 31.82 44 67 1 1.52 66 Penghasilan <RP.3.200.000 12 28.57 30 71.43 0 0.00 42 RP.3.200.000 2 20.00 8 80.00 0 0.00 10 RP.3200.000-RP.5.000.000 7 50.00 6 42.86 1 7.14 14 Total 21 31.82 44 67 1 1.52 66 Hubungan Dengan Pasien Anak 9 52.94 7 41.18 1 5.88 17 Istri 4 36.36 7 63.64 0 0.00 11 chmad Cesario Ludiana et al. Gambaran Pengetahuan tentang Penyakit Tuberkulosis,... Achmad Cesario Ludiana et al. Gambaran Pengetahuan tentang Penyakit Tuberkulosis,... Karakteristik Pengetahuan Total Baik Cukup Kurang N % N % N % Orang Tua 2 11.11 16 88.89 0 0.00 18 Saudara Kandung 1 25.00 3 75.00 0 0.00 4 Suami 5 31.25 11 68.75 0 0.00 16 Total 21 31.82 44 67 1 1.52 66 Jenis pengobatan Pasien Baru 18 29.51 42 68.85 1 1.64 61 Pasien Kambuh 3 60.00 2 40.00 0 0.00 5 Total 21 31.82 44 67 1 1.52 66 Keluarga Penderita tuberkulosis paru di Puskesmas X Kabupaten Bandung, dari 36 orang berjenis kelamin laki-laki sebanyak 27 orang (75%) berpengetauan cukup, dan dari 30 orang berjenis kelamin perempuan sebanyak 17 orang (57%) berpengetahuan cukup. Pembahasan Dari tabel 1 menunjukkan bahwa responden yang terbanyak berjenis kelamin laki-laki yaitu sebanyak 36 responden atau 54.5%, sedangkan perempuan berjumlah 30 responden atau 45.5%. Pengetahuan mengenai TB Paru lebih baik terjadi pada laki-laki dibandingkan wanita karena laki-laki sebagian besar mengetahui penyebab ataupun penularan TB Paru.[7] Dari tabel 4.1 di atas menunjukkan bahwa responden adalah keluarga pasien yang terbanyak berusia 46-55 tahun sebanyak 23 responden atau 34,8%, usia 36-45 tahun yakni 17 responden atau 25.8%, usia 56-65 tahun yakni 12 responden atau 18,2%. Penelitian ini juga didukung penelitian dari Hasriani, usia seseorang mempengaruhi tingkat pengetahuan. Sehingga semakin tinggi usia keluarga penderita, maka pasien akan mempunyai pengetahuan tentang penyakit Tuberkulosis Paru yang semakin baik pula. Sehingga hal ini akan menyebabkan keluarga penderita akan lebih paham dengan pecegahan dan pengobatan, yang pada akhirnyan akan mendukung keberhasilan pengobatan penderita tuberkulosis paru.[8] Dari tabel 1 di atas menunjukkan bahwa responden yang terbanyak berpendidikan tamat SMA sebanyak 22 responden atau 33,3%, SD yakni 21 responden atau 31.8%, tamat SMP yakni 16 responden atau 24,2%, dan sedangkan tamat akademik/sarjana yakni 7 responden atau 10.6%. Pendidikan merupakan suatu kegiatan, usaha manusia atau proses perubahan perilaku menuju kedewasaan dan penyempurnaan kehidupan manusia. Tolak ukur pendidikan seseorang dapat diketahui dari pengetahuan dan sikapnya. Berdasarkan data dari kuisioner 60% responden sudah lulus dari pendidikan dasar sehingga responden dinilai sudah mampu menerima informasi tentang suatu penyakit, terutama penyakit tuberkulosis paru, dimana panyakit tuberkulosis paru membutuhkan pengetahuan yang baik untuk membantu keberhasilan pengobatan. Semakin tinggi tingkat pendidikan responden, maka semakin baik penerimaan informasi tentang pengobatan penyakitnya sehingga akan semakin teratur pengobatannya. Hasil penelitian ini didukung oleh penelitian dari Cemy Nur Fitria bahwa semakin tinggi pendidikan akan mampu memberikan persepsi yang positif terhadap pengobatan pada pasien Tuberkulosis Paru.[9] Dari tabel 1 menunjukkan bahwa responden terbanyak bekerja adalah 49 responden atau 74.2%, sedangkan tidak bekerja yakni 17 responden atau 25,8%. Pekerjaan responden dapat disimpulkan memiliki penghasilan yang kurang atau rendah biasanya akan lebih mengutamakan kebutuhan primer dari pada pemeliharaan kesehatan seperti yang disampaikan Amira bahwa umumnya individu yang mempunyai penghasilan kurang menyebabkan kemampuan memperoleh status gizi menjadi kurang baik dan kurang seimbang sehingga berdampak pada menurunnya status kesehatan.[10] Dari tabel 1 menunjukkan berdasarkan penghasilan bahwa responden berpenghasilan <Rp 3.2 juta adalah 42 responden atau 63.6%, berpenghasilan antara Rp 3.2-Rp 5 juta adalah 14 responden atau 21.2% dan berpenghasilan Rp 3.2 juta sebanyak 10 orang atau 15.2%. Penyebab Tuberkulosis Paru Keluarga penderita tuberkulosis paru di Puskesmas X Kabupaten Bandung, dari 1 orang berusia <17 tahun sebanyak 1 orang (100%) berpengetahuan cukup, dari 6 orang berusia 17-25 tahun sebanyak 3 orang (50%) berpengetahuan cukup, dan baik dari 6 orang berusia 26-35 tahun sebanyak 3 orang (50%) berpengetahuan cukup dan baik, dari 17 orang berusia 36-45 tahun sebanyak 14 orang (82.35%) berpengetahuan cukup, dari 23 orang berusia 46-55 tahun sebanyak 16 orang (69.57%) berpengetahuan cukup, dari 12 orang berusia 56-65 tahun sebanyak 6 orang (50%) berpengetahuan cukup, dan dari 1 orang berusia >65 tahun sebanyak 1 orang (100%) berpengetahuan cukup. Keluarga penderita tuberkulosis paru di Puskesmas X Kabupaten Bandung, dari 1 orang suku Betawi sebanyak 1 orang (100%) berpengetahuan cukup, dari 7 orang suku jawa sebanyak 5 orang (71.43%) berpengetahuan cukup, dan dari 58 orang suku sunda sebanyak 58 orang (65.12%) berpengetahuan cukup. Keluarga penderita tuberkulosis paru di Puskesmas X Kabupaten Bandung, dari 49 orang bekerja sebanyak 35 orang (71.43%) berpengetahuan cukup, dan dari 17 orang tidak bekerja sebanyak 9 orang (52.94%) berpengetahuan cukup. Keluarga penderita tuberkulosis paru di Puskesmas X Kabupaten Bandung, dari 16 orang berpendidikan SMP sebanyak 13 orang (81.25%) berpengetahuan cukup, dari 22 orang berpendidikan SMA/SMK sebanyak 13 orang (59.09%) berpengetahuan cukup, dan dari 7 orang berpendidikan PT sebanyak 5 orang (71.43%) berpengetahuan baik. Keluarga penderita tuberkulosis paru di Puskesmas X Kabupaten Bandung, dari 42 orang berpenghasilan <Rp 3.200.000 sebanyak 30 orang (71.43%) berpengetahuan cukup, dari 10 orang berpenghasilan Rp 3.200.000 sebanyak 8 orang (80%) berpengetahuan cukup, dan dari 14 orang berpenghasilan Rp 3.200.000–Rp 5.000.000 sebanyak 7 orang (50%) berpengetahuan baik. Keluarga Penderita Tuberkulosis Paru di Puskesmas X Kabupaten Bandung, dari 17 orang hubungannya dengan pasien adalah anak sebanyak 9 orang (52.94%) berpengetahuan baik, dari 11 orang hubungannya dengan pasien adalah istri sebanyak 7 orang (63.64%) berpengetahuan cukup, dari 18 orang hubungannya dengan pasien adalah orang tua sebanyak 16 orang (88.89%) berpengetahuan cukup, dari 4 orang hubungannya dengan pasien adalah orang tua sebanyak 3 orang (75%) berpengetahuan cukup, dan dari 18 orang hubungannya dengan pasien adalah suami sebanyak 11 orang (68.75%) berpengetahuan cukup. Keluarga penderita tuberkulosis paru di Puskesmas X Kabupaten Bandung, dari 61 orang pasien baru sebanyak 42 orang (68.85%) berpengetahuan cukup, dan dari 5 orang pasien kambuh sebanyak 3 orang (60%) berpengetahuan baik. Volume 2, No. 2, Desember 2022 114/116 Jurnal Riset Kedokteran (JRK) Pembahasan Hasil dari penelitian ini sejalan dengan hasil penelitian Purwanto juga menyebutkan bahwa tingkat pengetahuan TB paru lebih rendah pada orang dengan pendapatan kurang dari Upah Minimum Regional (UMR) adalah 5 kali lebih besar dari pada keluarga pasien dengan pendapatan lebih dari UMR.[8] Dari tabel 1 diperoleh data responden memiliki pengetahuan yang baik yakni sebanyak 44 orang (66.7%), berpengetahuan cukup baik yakni 21 orang (31.8%) dan berpengetahuan kurang baik sebanyak 1 orang (1.5%). Keluarga pasien tuberkulosis paru yang memiliki pengetahuan yang baik dan cukup baik tentang penyebab, tanda-tanda, cara penularan, pencegahan, pengobatan, pengawasan, komplikasi, maka diharapkan akan memberikan pengertian kepada keluarga yang menderita Tuberkulosis Paru sehingga pasien akan patuh dan teratur dalam minum obat. Sehingga akan sangat membantu sekali dalam proses penyembuhannya.[8] Baik dan cukup baik pengetahuan responden tersebut karena mereka sudah mendapatkan paparan informasi. Paparan informasi yang semakin lama akan semakin baik dan semakin mudah diperoleh, akan mempengaruhi tingkat pengetahuan seseorang. Informasi tersebut pada keluarga penderita diperoleh dari berbagai sumber. Hal ini sesuai teori pengetahuan menurut Notoatmojo, bahwa pengetahuan merupakan hasil dari tahu, dan ini terjadi setelah orang melakukan pengindraan terhadap suatu obyek tertentu. Pengindraan terjadi melalui panca indra manusia, yakni indra penglihatan, pendengara, penciuman, rasa dan raba. Sebagian besar pengetahuan manusia diperoleh melalui mata dan telinga. Hal ini sesuai penelitian Yessica, H.T, persepsi dan e-ISSN 2798-6594 | p-ISSN 2808-3040 115/116 Achmad Cesario Ludiana et al. Gambaran Pengetahuan tentang Penyakit Tuberkulosis,... pengetahuan orang tua yang baik tentang penyakit Tuberkulosis Paru memberikan pengaruh yang signifikan terhadap keberhasilan pengobatan pasien.[11] Keterbatasan yang dialami peneliti adalah waktu dan regulasi pelayanan Kesehatan di Puskesmas X Kabupaten Bandung yang terkendala karena pandemi sehingga pelayanan poli TB dibatasi jumlah pasien perharinya dan kapasitas ruangan dikurangi sehingga peneliti membutuhkan waktu yang cukup lama untuk mengumpulkan data responden, dan keadaan pandemi yang membuat peneliti tidak bisa datang ke tempat penelitian yaitu Puskesmas X Kabupaten Bandung. D. Kesimpulan Simpulan dari penelitian ini adalah keluarga penderita tuberkulosis paru di Puskesmas X Kabupaten Bandung sebagian besar berjenis kelamin laki-laki, berusia antara 46-55 tahun, status bekerja, berpenghasilan kurang dari Rp. 3.200.000, hubungan dengan pasien adalah orang tua dan merupakan pasien baru sebanyak 61 orang. Keluarga Penderita Tuberkulosis Paru di Puskesmas X Kabupaten Bandung adalah sebagian besar berpengetahuan cukup baik dan baik. Hal ini terlihat dari indikator pengetahuan seperti penyebab, tanda-tanda, cara penularan, pencegahan, pengawas minum obat, komplikasi, dan keluarga penderita tuberkulosis paru di Puskesmas X Kabupaten Bandung yang memiliki pengetahuan cukup 44 orang (66,7%) berjenis kelamin laki laki yaitu sebanyak 27 orang (75%), berumur 45-55 tahun yaitu sebanyak 16 orang (69,57%), suku Sunda yaitu sebanyak 58 orang (65,12%), memiliki pekerjaan yaitu 35 orang (71,43%), riwayat pendidikan 13 orang dengan pendidikan SMP (81,25%), penghasilan <Rp.3.200.000 yaitu sebanyak 30 orang (71,43%), hubungan dengan anggota keluarga suami yaitu sebanyak 11 orang (68,85%), dan jenis pengobatan baru yaitu sebanyak 42 orang (68,85%). Daftar Pustaka [1] WHO, “WHO TB burden report 2018 [Internet],” Work. Heal. Saf., vol. 63, p. 476, 201 [2] Dinkes Jabar, “Profil Kesehatan Jawa Barat 2017,” 2018. [3] K. K. Republik Indonesia, “Pedoman Nasional Pengendalian Tuberkulosis-Keputusan Menteri Kesehatan Republik Indonesia Nomor 364,” J ICT, 2011. [4] Aini Agnia, “Tingkat Kepatuhan Pengobatan Pasien Fase Intensif Berdasarkan Karakteristik Pasien TB di Puskesmas X,” J. Ris. Kedokt., 2022. [5] Dinas Kesehatan, “Profil Kesehat Kabupaten Bandung 2019,” 2019. [6] Freeman, “Tingkat pengetahuan,” J Chem Inf Model, vol. 53, no. 9, pp. 1689–99, 2013. [7] I. Y. Y. U. E. Siswanto, “Hubungan Pengetahuan dan Dukungan Keluarga dengan Kepatuhan Minum Obat Anti Tuberkulosis di Puskesmas Andalas Kota Padang,” J Kesehat Andalas, vol. 4, no. 3, pp. 724–8, 2018. [8] S. S. A. H. W. Setiarni, “Hubungan Antara Tingkat Pengetahuan, Status Ekonomi Dan Kebiasaan Merokok Dengan Kejadian Tuberkulosis Paru Pada Orang Dewasa Di Wilayah Kerja Puskesmas Tuan-Tuan Kabupaten Ketapang Kalimantan Barat,” J Kesehat Masy (Journal Public Heal., vol. 5, no. 3, 2019. [9] F. C. M. A. Nur, “Hubungan Tingkat Pengetahuan Tentang Tuberkulosis Dengan Kepatuhan Minum Obat Di Puskesmas Banyuanyar Surakarta,” Jikk, vol. 7, no. 1, pp. 41–5, 2019. [10] Permatasari A, “Pemberantasan Penyakit TB Paru dan Strategi Dots,” Univ Stuttgart, pp [11] Depkes RI, “Kementerian Kesehatan Republik Indonesia,” Kementeri Kesehat RI, 2018. Volume 2, No. 2, Desember 2022 116/116
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Factors Affecting Renewable Energy Technology Adoption Policies of 50 States and District of Columbia in the United States
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Factors Affecting Renewable Energy Technology Adoption Policies of 50 States and District of Columbia in the United States Samantha Roberts  University of Utah Tristan Roland  Prairie View A&M University Ananda S Amarasekara  (  asamarasekara@pvamu.edu ) Prairie View A&M University https://orcid.org/0000-0002-2052-3947 Samantha Roberts  University of Utah Tristan Roland  Prairie View A&M University Ananda S Amarasekara  (  asamarasekara@pvamu.edu ) Prairie View A&M University https://orcid.org/0000-0002-2052-3947 Factors Affecting Renewable Energy Technology Adoption Policies of 50 States and District of Columbia in the United States Introduction Energy policy in the United States engages federal, state, county and city level governmental actions related to the generation, distribution and consumption of different classical or non-renewable and renewable resources based energy. At all levels these energy policies are enacted and enforced through legislation and regulation. Fossil fuels are central to the traditional non-renewable sector and the renewable energy includes solar, wind and hydroelectric power as major sources. Given the multiple policymakers at all levels of government in the United States, energy policy is complicated and interconnected. Unlike in many parts of the world the state governments of the United States have a major role in exercising their local energy policies at the state level (Mazmanian et al. 2020). Generally, the state energy policy has several stakeholders; including citizens, state- level interest groups, agencies, corporations or businesses and elected state officials. In addition, several factors can affect the viability of energy policies, such as the accessibility of energy resources, the cost of extracting certain forms of energy, weather conditions, geography, consumer demand as well as the potential environmental impacts. In recent years a number of researchers around the world have studied the nexus between renewable energy economic policy and the environmental sustainability of countries; however, there is only a handful of studies on United States (Saint Akadiri et al. 2020), (Aslan et al. 2018), (Mayer 2018), (Koondhar et al. 2018). According to a recent study by Ahmed and co workers the transition to renewable energy in US is impossible without massive public renewable energy research and development budgets along with sustained federal as well as state policies (Ahmed et al. 2021). These efforts in the United States showed significant fluctuations over the preceding three decades and economic policy uncertainty was also highly volatile. Furthermore, they have emphasized the need for stable environmental policies in achieving long-​term environmental benefits (Ahmed et al. 2021). In another study on the impact on natural resources, population growth and environmental quality in the US, Khan et al. have encouraged policymakers in the USA to establish policies that control the excessive use of natural resources, promote sustainable lifestyles, develop energy-efficient carbon pricing, and fix the ecological budget to secure a sustainable future for the country (Khan et al. 2021). Their investigation indicates long-​run associations among the variables and reveal an inverse relation of natural resources and renewable energy consumption. Research Article License:   This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/11 Introduction Furthermore, a positive relationship of non-​renewable energy consumption, population growth, and bio capacity with the ecological footprint and CO2 emissions was also noted during this work (Khan et al. 2021). There are few limited studies on adoption of specific renewable energy technologies, focusing on a state or a region of the US (Pitt et al. 2018), (Pol and Ford 2020). For instance, a 2019 study analyzed the solar photovoltic technology adoption in Pacific Northwest region of the US (Cho et al. 2019). This study found a co-relation between solar adoption trends and higher education levels in the populations. Furthermore, researchers could identify certain areas in the state of Oregon ideal for energy companies to promote, educate and incentivize home solar program, in order to bolster the adoption (Cho et al. 2019). However, as far as we are aware there are no reports on sustainable energy technology adoption trends in separate states in the United States. In an attempt to fill this void and as a continuation of our efforts in the development (Amarasekara 2013) and evaluation of sustainable energy technologies in US we have studied recent energy technology adoption trends in 50 states and district of Columbia in the United States and their co-relation to a selected set of eight contributing factors. The variables: percentage of high school graduates (HS); college graduates (CD); total population (TP); area (TA); water covered area (PW); annual income (AI); and registered democrats (RD) were selected as predictor variables for this study. Furthermore, willingness of individual states to adopt modern renewable energy sources wind (WE), solar (SE), hydro (HE), geothermal (GE) and biomass energy (BE) for electrical energy generation and the current trends are focused in this study. The electrical energy generated by nuclear energy is not taken into account in this contemporary renewable energy trend analysis as nuclear fission electricity generation is in rapid decline in the past 30 years (Markard et al. 2020). Furthermore, nuclear energy is not a part of this sustainability revolution and in a number of large economies such as China, India, United Kingdom and Germany power generation from non-hydro renewables has already surpassed the electricity generation from nuclear power plants (IEA 2019). In addition, recent sharp falls in the cost of renewable energy technologies such as solar cells are likely to undermine the economic competitiveness of nuclear energy still further (IRENA 2018). Abstract Renewable energy policies and adoption of new renewable energy technologies in different states of the United states are not uniform. The factors affecting the trends in adopting electrical energy generation using sustainable resources: wind, solar, hydro, geothermal and biomass as well as registered all electric vehicles in 50 states and district of Columbia in the United States was analyzed using multivariate linear regression analysis. Eight contributing factors: percentages of high school graduates; college graduates; total population; land area; percentage of water covered area; average annual income and registered democrats in the state were selected as predictor variables. Among eight factors considered, percentage of registered democrats was found as the most influencing factor (p = 0.00543) determining the renewable electrical energy adoption. The transition to all electric cars strongly co-related to higher average annual income of the population (p = 0.00141). In conclusion, an aggressive education campaign by environmentalist and pro-sustainability groups may help in de-coupling the energy and environment policies in the United States from political ideologies in order to achieve a more sustainable future. Introduction We have considered the education standards of the population as a key influencing factor in adopting sustainable technologies. A study on educational attainment in the United States shows that percentage of high school graduates increased from 41 to 91% and college graduates Page 2/11 increased from 8 to 38% during the period of from 1960 to 2020; however this increase is not uniform throughout the US and there are considerable irregularities among regions and states (Statista 2022). There are several links, suggesting that education level and cognitive ability of the population should be related to social awareness of costs and benefits of renewable energy use and consequent public acceptance (Eshchanov et al. 2021). Research studies have demonstrated less of a preference for smaller, immediate rewards versus larger, delayed rewards in more highly educated and intelligent groups of people (Shamosh and Gray 2008). Similarly, there is evidence for the co-relation between education level of a society and the abilities to play important role in mitigating environmental degradation (Salahodjaev 2016). In the United States total population (TP) of a state and the total land area (TA) are two independent variables; for instance the small state New Jersey with a high population has a population density of approximately as one thousand times the population density of Alaska (States101 2022). The land area of a state is an important factor in adopting renewable energy technologies such as wind (WE) and hydro (HE) as well; therefore we have included total population (TP) and the total area (TA) of states as two other variables. The water covered land area of a state may have a bearing on the ability of a state to generate hydroelectric power, as most of these power stations are built near a large water reservoir; additionally, water covered area percentage is independent from the total land area of the state as some large areas of the western United states are arid land with minimal annual rainfall (Moore et al. 2021). The median annual income (AI) of a population is an important factor in determining the tendency to adopt renewable energy technologies. This factor is generally independent form most of the other factors considered such as: total population (TP), area (TA), water covered area (PW), and registered democrats (RD); however may have an association to the education of the population in the states. Introduction Nevertheless, we have considered annual income (AI) as another variable as this can be correlated to the tendency of embracing more expensive and newest renewable energy technologies such as electric vehicles and roof-top solar panels. Another important factor may be the political ideology; unlike in many parts of the developed world, the renewable energy policy in the United States has a greater bearing on the political affiliation of the decision makers. The US withdrawal from Paris agreement in June 2017 under a republican administration and immediate reentry under democratic control is a reflection of this political bias (Marlow et al. 2021), (Ali et al. 2021). This phenomena is common to federal, state and local government in the US; therefore we have included the percentage of registered democrats in a state as one of the factors influencing the renewable energy adoption trends and decisions. Methodology Multivariable linear regression used to predict an outcome variable (y) on the basis of multiple distinct predictor variables (x) was applied in all analysis. This multivariable linear regression model can be expressed by the following Eq. (1) where b values are regression weights or coefficients. y = b0 + b1x1 + b2x2 + b3x3 + b4x4 + b4x5 + …….. + bnxn (1) y = b0 + b1x1 + b2x2 + b3x3 + b4x4 + b4x5 + …….. + bnxn (1) The open source R programming environment at: www.r-project.org was used in data analysis. This research analysis is based on the hypothesis that recent renewable energy technology adoption trends in 50 states and district of Columbia in the United States are co-related to eight contributing factors: percentage of high school graduates (HS), college graduates (CD), total population (TP), area (TA), water covered area (PW), annual income (AI) and registered democrats (RD). Data Availability Data Availability Page 3/11 Page 3/11 Table 1 Datasets related to this article Data Source Available data https://www.eia.gov/state/seds/; www.eia/electricity/data/state Electricity generation of states https://www.census.gov/programs-surveys/popest/technical-documentation/research/evaluation-estimates/2020-evaluation- estimates/2010s-state-total.html Population data of states https://www.census.gov/geographies/reference-files/2010/geo/state-area.html Land and water area of states https://www.census.gov/search-results.html?searchType=web&cssp=SERP&q=median%20income Median income of residence in a state https://data.census.gov/cedsci/table? q=educational%20attainment&g=0100000US,.04000.001_0400000US72&tid=ACSST1Y2019.S1501&tp=true&hidePreview=true Educational attainment of residence in a state https://www.archives.gov/electoral-college/2020 Electoral college results by state https://www.statista.com/statistics/1080003/political-party-identification-state-us/ Identification with political parties by state https://afdc.energy.gov/data Bio-Energy and electric vehicles by state Results And Discussion Percentage of renewable electrical energy in the state (PRE) In the first phase of the study co-relation between percentage of all forms of combined renewable electrical energy produced in the state (PRE) to eight predictor variables were studied using multivariate regression analysis according to the Eq. (2): outcome: PRE = b0 + b1x1 + b2x2 + b3x3 + b4x4 + b5x5 + b6x6 + b7x7 + b8x8 (2) x1 = HS, x2 = CD, x3 = PD, x4 = TP, x5 = TA, x6 = PW, x7 = AI, x8 = RD where the predictor variables are: percentage of high school graduates (HS); percentage of college degree graduates (CD); population density of the state (PD); total population of the state (TP); area of the state (TA); percentage of water covered area of the state (PW); average annual personal https://www.census.gov/geographies/reference-files/2010/geo/state-area.html https://www.archives.gov/electoral-college/2020 https://www.statista.com/statistics/1080003/political-party-identification-state-us/ https://afdc.energy.gov/data ome: PRE = − 3.63 + 3.98 HS + 0.432 CD − 0.0000727 PD − 0.00000000197 TP + 0.000000678 TA − 0.664 P Three predictor variables with p < 0.02 are significantly co-related to the renewable electrical energy generation in a state as shown in Table 2. The percentage of registered democrats with p = 0.00543 is the most influencing factor determining the tendency of the state policy makers to implement renewable resources based electrical energy generation. The population density (p = 0.01964) and percentage of high school graduates (p = 0.02033) are also showing significant influences. The populations with higher education levels are likely to adopt renewable resources based energy and sustainable environmental policies and similar inclinations are seen in other parts of the world as well (Karasmanaki and Tsantopoulos 2019). In addition, area of the state (p = 0.05995) and water covered area (p = 0.05012) also shows strong positive and negative co-relations. Percentage of combined renewable electrical energy in the state (PRE) shows positive coefficients for HS, CD, TA and RD; whereas negative coefficients are found for PD, TP, PW and AI. Therefore the analysis predicts an increase in percentage of combined renewable electrical energy in the state (PRE) for the increase in predictor variables HS, CD, TA and RD. In contrary the model predicts a decrease in percentage of combined renewable electrical energy in the state (PRE) for the increase in predictor variables PD, TP, PW and AI. ercentages of renewable electrical energy components: wind (WE), solar (SE), hydro (HE), geothermal (GE) Percentages of renewable electrical energy components: wind (WE), solar (SE), hydro (HE), geothermal (GE) and biomass energy (BE) In the second phase, we have expanded the analysis in previous section; where we have studied the co-relations of percentages of individual components of renewable energy: wind (WE), solar (SE), hydro (HE), geothermal (GE) and biomass (BE) based renewable electrical energy in states to the same eight predictor variables as in previous study. Multivariate regression analysis was carried out using R for the model: outcome: WE/SE/HE/GE/BE = b0 + b1x1 + b2x2 + b3x3 + b4x4 + b5x5 + b6x6 + b7x7 + b8x8 (4) x1 = HS, x2 = CD, x3 = PD, x4 = TP, x5 = TA, x6 = PW, x7 = AI, x8 = RD Percentage of renewable electrical energy in the state (PRE) (3) can be written as follows: outcome: PRE = − 3.63 + 3.98 HS + 0.432 CD − 0.0000727 PD − 0.00000000197 TP + 0.000000678 TA − 0.664 PW − 0.00000884 AI + 1.74 RD ( Multivariate regression analysis p values for the outcome: percentage of combined renewable electrical energy in the state (PRE) Predictor variable p High school graduates, % (HS) 0.02033 College degree graduates, % (CD) 0.72897 Population density, per sq. mile (PD) 0.01964 Total population (TP) 0.71355 Area of the state, sq. mile (TA) 0.05995 Water covered area % (PW) 0.05012 Average annual income, $ (AI) 0.1324 Registered democrats, % (RD) 0.00543 The model Eq. (3) can be written as follows: Percentage of renewable electrical energy in the state (PRE) In the first phase of the study co-relation between percentage of all forms of combined renewable electrical energy produced in the state (PRE) to eight predictor variables were studied using multivariate regression analysis according to the Eq. (2): outcome: PRE = b0 + b1x1 + b2x2 + b3x3 + b4x4 + b5x5 + b6x6 + b7x7 + b8x8 (2) x1 = HS, x2 = CD, x3 = PD, x4 = TP, x5 = TA, x6 = PW, x7 = AI, x8 = RD outcome: PRE = b0 + b1x1 + b2x2 + b3x3 + b4x4 + b5x5 + b6x6 + b7x7 + b8x8 (2) x1 = HS, x2 = CD, x3 = PD, x4 = TP, x5 = TA, x6 = PW, x7 = AI, x8 = RD x1 = HS, x2 = CD, x3 = PD, x4 = TP, x5 = TA, x6 = PW, x7 = AI, x8 = RD where the predictor variables are: percentage of high school graduates (HS); percentage of college degree graduates (CD); population density of the state (PD); total population of the state (TP); area of the state (TA); percentage of water covered area of the state (PW); average annual personal income of the state (AI); and registered democrats in the state (RD), and the results are shown in Table 2. where the predictor variables are: percentage of high school graduates (HS); percentage of college degree graduates (CD); population density of t state (PD); total population of the state (TP); area of the state (TA); percentage of water covered area of the state (PW); average annual personal income of the state (AI); and registered democrats in the state (RD), and the results are shown in Table 2. Page 4/11 Page 4/11 Table 2 Multivariate regression analysis p values for the outcome: percentage of combined renewable electrical energy in the state (PRE) Predictor variable p High school graduates, % (HS) 0.02033 College degree graduates, % (CD) 0.72897 Population density, per sq. mile (PD) 0.01964 Total population (TP) 0.71355 Area of the state, sq. mile (TA) 0.05995 Water covered area % (PW) 0.05012 Average annual income, $ (AI) 0.1324 Registered democrats, % (RD) 0.00543 The model Eq. (6) Percentages of renewable electrical energy generated using hydro (HE) The regression analysis p values for hydro based renewable electrical energy generation in states are shown in Table 5. The p values are relatively high for all the variables studied and the lowest value of 0.145 is for area of the state. This results is logical as states with large land areas are likely to have rivers and waterways that can be dammed for hydroelectric power generation. Interestingly, the water coverage percent, mostly counting lakes in a state shows a much higher p as these are still water bodies. Page 6/11 1 2 3 4 5 6 7 8 Percentages of renewable electrical energy generated using wind (WE) Percentages of renewable electrical energy generated using wind (WE) The results of multivariate regression analysis study on wind energy based renewable electrical energy generation in states are shown in Table 3. The two variables: area of the state and the percentage of registered democrats showed significantly low p values in comparison to other variables as shown in Table 3. As expected states with large land area and suitable geographic terrains can produce more wind energy than smaller states. In addition, political affiliation of the policy makers can also be an important influence in adopting wind energy electricity generation in a state, as evident from the second lowest p value in Table 3. Percentage of renewable electrical energy generated using wind (WE) shows positive coefficients for PW, AI and RD; whereas negative coefficients are found for HS, CD, PD, TP and TA. Therefore the analysis predicts an increase in percentage of electrical energy generated using wind (WE) for the increase in predictor variables PW, AI and RD. In contrary the model predicts a decrease in percentage of renewable electrical energy generated using wind (WE) for the increase in predictor variables HS, CD, PD, TP and TA Page 5/11 Page 5/11 Table 3 Multivariate regression analysis p values for the outcome: percentage of wind based renewable electrical energy in the state (WE) Predictor variable p High School graduates, % (HS) 0.248 College degree graduates, % (CD) 0.6761 Population density, per sq. mile (PD) 0.3733 Total population (TP) 0.3881 Area of the state, sq. mile (TA) 0.0643 Water covered area % (PW) 0.2835 Average annual income, $ (AI) 0.3548 Registered democrats, % (RD) 0.1014 The model Eq. (5) can be written as follows: Table 3 electrical energy in the state (WE) Predictor variable p High School graduates, % (HS) 0.248 College degree graduates, % (CD) 0.6761 Population density, per sq. mile (PD) 0.3733 Total population (TP) 0.3881 Area of the state, sq. mile (TA) 0.0643 Water covered area % (PW) 0.2835 Average annual income, $ (AI) 0.3548 Registered democrats, % (RD) 0.1014 The model Eq. (5) can be written as follows: 1.08 HS − 0.29 CD − 0.000015 PD − 0.00000000259 TP + 0.000000371 TA + 0.199 PW + 0.000003 AI + 0.5 Percentages of renewable electrical energy generated using solar (SE) Percentages of renewable electrical energy generated using solar (SE) The results of multivariate regression analysis study on solar energy based renewable electrical energy generation in states are shown in Table 4. The popular roof-top solar panel in home energy generation appear to be strongly co-related to the population density of the state with p =  0.00000761 with a positive co-relation. Percentage of renewable electrical energy generated using solar (SE) shows positive coefficients for HS, PD, TP, PW and RD; whereas negative coefficients are found for CD, TA and AI. Therefore the analysis predicts an increase in percentage of electrical energy generated using solar (SE) for the increase in predictor variables HS, PD, TP, PW and RD. In contrary the model predicts a decrease in percentage of renewable electrical energy generated using solar (SE) for the increase in predictor variables CD, TA and AI. Table 4 Multivariate regression analysis p values for the outcome: percentage of solar based renewable electrical energy in the state (SE) Predictor variable p High School graduates, % (HS) 0.312 College degree graduates, % (CD) 0.294 Population density, per sq. mile (PD) 0.00000761 Total population (TP) 0.561 Area of the state, sq. mile (TA) 0.419 Water covered area % (PW) 0.622 Average annual income, $ (AI) 0.781 Registered democrats, % (RD) 0.859 The model Eq. (6) can be written as follows: Table 4 Multivariate regression analysis p values for the outcome: percentage of solar based renewable electrical energy in the state (SE) Predictor variable p High School graduates, % (HS) 0.312 College degree graduates, % (CD) 0.294 Population density, per sq. mile (PD) 0.00000761 Total population (TP) 0.561 Area of the state, sq. mile (TA) 0.419 Water covered area % (PW) 0.622 Average annual income, $ (AI) 0.781 Registered democrats, % (RD) 0.859 The model Eq. (6) can be written as follows: The model Eq. (6) can be written as follows: The model Eq. (6) can be written as follows: outcome: SE = − 0.121 + 0.214 HS − 0.167 CD + 0.000194 PD + 0.000000000396 TP − 0.0000000363 TA + 0.0207 PW − 0.000000205 AI + 0.0134 RD ( ) outcome: HE = 1.23–1.29 HS − 0.818 CD + 0.0000140 PD − 0.0000000002.76 TP + 0.000000442 TA − 0.244 PW + 0.00000478 AI − 0.0318 RD (7) Percentages of renewable electrical energy generated using geothermal (GE) mile (PD) 0.000413 Total population (TP) 0.481 Area of the state, sq. mile (TA) 0.399 Water covered area % (PW) 0.375 Average annual income, $ (AI) 0.483 Registered democrats, % (RD) 0.799 The model Eq. (8) can be written as follows: outcome: GE = − 0.0958 + 0.134 HS − 0.153 CD + 0.00000984 PD + 0.000000000324 TP − 0.0000000256 TA − 0.02.52 PW + 0.000000349 AI + 0.013 RD (8) Percentages of renewable electrical energy generated using biomass (BE) Table 6 Multivariate regression analysis p values for the outcome: percentage of geothermal based renewable electrical energy in the state (GE) Predictor variable p High School graduates, % (HS) 0.349 College degree graduates, % (CD) 0.157 Population density, per sq. mile (PD) 0.000413 Total population (TP) 0.481 Area of the state, sq. mile (TA) 0.399 Water covered area % (PW) 0.375 Average annual income, $ (AI) 0.483 Registered democrats, % (RD) 0.799 The model Eq. (8) can be written as follows: Table 6 Multivariate regression analysis p values for the outcome: percentage of geothermal based renewable electrical energy in the state (GE) Predictor variable p High School graduates, % (HS) 0.349 College degree graduates, % (CD) 0.157 Population density, per sq. mile (PD) 0.000413 Total population (TP) 0.481 Area of the state, sq. mile (TA) 0.399 Water covered area % (PW) 0.375 Average annual income, $ (AI) 0.483 Registered democrats, % (RD) 0.799 The model Eq. (8) can be written as follows: The model Eq. (8) can be written as follows: outcome: GE = − 0.0958 + 0.134 HS − 0.153 CD + 0.00000984 PD + 0.000000000324 TP − 0.0000000256 TA − 0.02.52 PW + 0.000000349 AI + 0.013 ( ) outcome: HE = 1.23–1.29 HS − 0.818 CD + 0.0000140 PD − 0.0000000002.76 TP + 0.000000442 TA − 0.244 PW + 0.00000478 AI − 0.0318 RD (7) Percentages of renewable electrical energy generated using geothermal (GE) Geothermal electrical energy generation is rare in US; however, we have counted this new source as it is a rapidly developing trend in the last couple of years (Ball 2021), (Ayling 2021). A distinctly low p value of 0.000413 was found for population density of a state, as shown in Table 6. This may be due to the fact that so far only a few very large states with small populations have tapped this promising sustainable source for electricity generation. Percentage of renewable electrical energy generated using geothermal (GE) shows positive coefficients for HS, PD, TP, AI and RD; whereas negative coefficients are found for CD, TA and PW. Therefore the analysis predicts an increase in percentage of electrical energy generated using geothermal (GE) for the increase in predictor variables HS, PD, TP, AI and RD. In contrary the model predicts a decrease in percentage of renewable electrical energy generated using geothermal (GE) for the increase in predictor variables CD, TA and PW. Table 6 Multivariate regression analysis p values for the outcome: percentage of geothermal based renewable electrical energy in the state (GE) Predictor variable p High School graduates, % (HS) 0.349 College degree graduates, % (CD) 0.157 Population density, per sq. mile (PD) 0.000413 Total population (TP) 0.481 Area of the state, sq. mile (TA) 0.399 Water covered area % (PW) 0.375 Average annual income, $ (AI) 0.483 Registered democrats, % (RD) 0.799 Page 7/11 Table 6 Multivariate regression analysis p values for the outcome: percentage of geothermal based renewable electrical energy in the state (GE) Predictor variable p High School graduates, % (HS) 0.349 College degree graduates, % (CD) 0.157 Population density, per sq. mile (PD) 0.000413 Total population (TP) 0.481 Area of the state, sq. mile (TA) 0.399 Water covered area % (PW) 0.375 Average annual income, $ (AI) 0.483 Registered democrats, % (RD) 0.799 The model Eq. (8) can be written as follows: outcome: GE = − 0.0958 + 0.134 HS − 0.153 CD + 0.00000984 PD + 0.000000000324 TP − 0.0000000256 TA − 0.02.52 PW + 0.000000349 AI + 0.013 RD (8) Percentages of renewable electrical energy generated using biomass (BE) Page 7/11 Table 6 Multivariate regression analysis p values for the outcome: percentage of geothermal based renewable electrical energy in the state (GE) Predictor variable p High School graduates, % (HS) 0.349 College degree graduates, % (CD) 0.157 Population density, per sq. Table 5 Multivariate regression analysis p values for the outcome: percentage of hydro based renewable electrical energy in the state (HE) Multivariate regression analysis p values for the outcome: percentage of hydro based renewable electrical energy in the state (HE) electrical energy in the state (HE) Predictor variable p High School graduates, % (HS) 0.363 College degree graduates, % (CD) 0.44 Population density, per sq. mile (PD) 0.585 Total population (TP) 0.951 Area of the state, sq. mile (TA) 0.145 Water covered area % (PW) 0.386 Average annual income, $ (AI) 0.334 Registered democrats, % (RD) 0.95 The model Eq. (7) can be written as follows: outcome: HE = 1.23–1.29 HS − 0.818 CD + 0.0000140 PD − 0.0000000002.76 TP + 0.000000442 TA − 0.244 PW + 0.00000478 AI − 0.0318 RD (7) Percentages of renewable electrical energy generated using geothermal (GE) outcome: HE = 1.23–1.29 HS − 0.818 CD + 0.0000140 PD − 0.0000000002.76 TP + 0.000000442 TA − 0.244 PW + 0.00000478 AI − 0.0318 RD (7) Percentages of renewable electrical energy generated using geothermal (GE) Page 6/11 Page 6/11 Percentage of renewable electrical energy generated using hydro (HE) shows positive coefficients for PD, TA and AI; whereas negative coefficients are found for HS, CD, TP, PW and RD. Therefore the analysis predicts an increase in percentage of electrical energy generated using hydro (HE) for the increase in predictor variables PD, TA and AI. In contrary the model predicts a decrease in percentage of renewable electrical energy generated using hydro (HE) for the increase in predictor variables HS, CD, TP, PW and RD. Page 7/11 RD (8) Percentages of renewable electrical energy generated using biomass (BE) Page 7/11 Percentages of renewable electrical energy generated using biomass (BE) The regression analysis results for biomass based renewable electrical energy generation in states are shown in Table 7. A high co-relation is found with percentage of college degree graduates with p values of 0.039. However, the coefficient for this correlation is negative, indicating that increase in percentage of college graduates can result a decrease in renewable electrical energy generation in the state using biomass (BE). The regression analysis results for biomass based renewable electrical energy generation in states are shown in Table 7. A high co-relation is found with percentage of college degree graduates with p values of 0.039. However, the coefficient for this correlation is negative, indicating that increase in percentage of college graduates can result a decrease in renewable electrical energy generation in the state using biomass (BE). Percentage of renewable electrical energy generated using biomass (BE) shows positive coefficients for HS, PD, TP, AI and RD; whereas negative coefficients are found for CD, TA and PW. Therefore the analysis predicts an increase in percentage of electrical energy generated using biomass (BE) for the increase in predictor variables HS, PD, TP, AI and RD. In contrary the model predicts a decrease in percentage of renewable electrical energy generated using biomass (BE) for the increase in predictor variables CD, TA and PW. Table 7 Multivariate regression analysis p values for the outcome: percentage of biomass based renewable electrical energy in the state (BE) Predictor variable p High School graduates, % (HS) 0.365 College degree graduates, % (CD) 0.039 Population density, per sq. mile (PD) 0.568 Total population (TP) 0.471 Area of the state, sq. mile (TA) 0.821 Water covered area % (PW) 0.787 Average annual income, $ (AI) 0.172 Registered democrats, % (RD) 0.135 The model Eq. (9) can be written as follows: outcome: GE = − 0.0958 + 0.134 HS − 0.153 CD + 0.00000984 PD + 0.000000000324 TP − 0.0000000256 TA − 0.0252 PW + 0.0000000349 AI +  0 0130 RD (9) outcome: GE = − 0.0958 + 0.134 HS − 0.153 CD + 0.00000984 PD + 0.000000000324 TP − 0.0000000256 TA − 0.0252 PW + 0.0000000349 AI +  0.0130 RD (9) The model Eq. (10) can be written as follows: outcome: PEV = 0.00148–0.00672 HS − 0.00673 CD − 0.0000000116 PD + 0.0000000000678 TP + 0.0000000857AI + 0.00511 RD (10) outcome: PEV = 0.00148–0.00672 HS − 0.00673 CD − 0.0000000116 PD + 0.0000000000678 TP + 0.0000000857AI + 0.00511 RD (10) outcome: PEV = 0.00148–0.00672 HS − 0.00673 CD − 0.0000000116 PD + 0.0000000000678 TP + 0.0000000857AI + 0.00511 RD (10) Conclusion And Policy Implications In addition, total population of the state and percentage of democrats in the state are also co- related to the electric automobile adoption; again showing the strong influence in political ideology on sustainability adoption in US. However, the recent advancements in battery materials, recycling technologies as well as anticipated introduction of a number electric car models by major US automakers in the next 2–5 years may expect to lower the electric car prices to match the gasoline models, boosting the affordability of electric cars. Our study has implications for renewable energy technology adoption policies of state and at federal level in the US. This multivariate regression analysis clearly demonstrate a significant co-relation between the political affiliation and total renewable electrical energy percentage as well as to some of the individual components of sustainable energy transformation. Then there are variables such as land area, water cover and population with limited control; where as political bias is a more flexible variable and can be manipulated. Therefore, an aggressive education campaign by environmentalist and pro-sustainability groups may help in de-coupling the energy and environment policies in the United States from political ideologies in order to achieve a more sustainable future. Conclusion And Policy Implications We have analyzed the factors influencing the renewable electrical energy generation and transition to fully electric cars in 50 states and district of Columbia in the United States. This communication reports the possible underlying factors that determines why some states in the US are far behind in adopting sustainable energy technologies, and some are ahead in new electrical energy generation using sources such as solar and wind as well as in use of all electric cars. We have found that political inclination of state's population as the most co-related factor in determining the adoption of sustainable electrical energy generation technologies. In contrary to most other developed countries, sustainability and environment has become highly politicized issues in the United States. This may be due to two reasons: firstly, extensive lobbying by large oil and fossil fuel power companies in US have persuaded the policy makers to dismiss and ignore environmental implications of fossil fuels. This symbiosis is particularly strong in the republican side of the aisle at both federal and state levels. Secondly, the traditional conservative principals of less government control or freedom to make your own decisions and less taxes, commonly identified as republican core values are often misinterpreted for the continuation of the anti-sustainability agenda of large oil and fossil fuel power companies. In further investigation of co-relation between renewable electrical energy sources and policies; we have analyzed the individual components: wind, solar, hydro, geothermal and biomass energy and their co-relation to eight selected variables as well. The sustainable energy technologies such as wind and hydroelectric power generation that require large land areas showed the expected co-relations to larger states. Solar energy electrical power generation is showing the highest level of energy penetration in last couple of years and is expected to revolutionize the domestic electrical energy supply in US. In our analysis, solar electrical energy adoption strongly co-related to the population density and somewhat co-related to the percentage of college degree graduates in a state, indicating that educated urban populations are in the forefront of solar roof-top adoption. The transition to fully electric battery powered automobiles is another major indicator in sustainability revolution. Our study shows a very strong co- relation between electric vehicle adoption and the average annual income. This result is logical as the current fully electric cars cost as twice or more than an equivalent gasoline powered car. Authorship Contribution Statement Samantha Roberts: data collection; literature review; methodology; analysis using R, Tristan Roland: data collection; analysis using R, Ananda S. Amarasekara: conceptualization; writing, editing. Competing interests Authors declare that they have no known competing financial interests or personnel relationships that could have appeared to influence the work reported in this paper. Authorship contribution statement Authorship contribution statement Samantha Roberts: data collection; literature review; methodology;  analysis using R, Tristan Roland: data collection;  analysis using R, Ananda S. Amarasekara: conceptualization; writing, editing. Acknowledgements We thank United States National Science Foundation grant:  NSF DMS -1950677, REU Site: Mathematical Modeling in the Sciences, for financial support. ( ) Percentage of fully electric vehicles registered in a state (PEV) In the third phase of the study, co-relation between percentage of fully electric vehicles registered in a state (PEV) and six selected predictor variables were studied using multivariate regression analysis. The results for electric vehicles registered in a state analyzed using six variables: percentage of high school graduates (HS); college graduates (CD); total population (TP); annual income (AI); and registered democrats (RD) are shown in Table 8. The average annual income shows a very small p value of 0.00141, indicating a strong co-relation between the personnel income and purchasing a fully electric vehicle. Currently, on average fully electric battery powered cars are more expensive than gasoline cars, therefore personnel annual income appears to be the most important factor in determining the acceptance of this renewable energy technology. Percentage of fully electric vehicles registered in a state (PEV) shows positive coefficients for TP, AI and RD; whereas negative coefficients are found for HS, CD and PD. Therefore the analysis predicts an increase in percentage of fully electric vehicles registered in a state (PEV) for the increase in predictor variables TP, AI and RD. In contrary the model predicts a decrease in percentage of fully electric vehicles registered in a state (PEV) for the increase in predictor variables HS, CD and PD. Page 8/11 Table 8 Multivariate regression analysis p values for the outcome: percentage of fully electric vehicles registered in a state (PEV) Predictor variable p High School graduates, % (HS) 0.410 College degree graduates, % (CD) 0.251 Population density, per sq. mile (PD) 0.937 Total population (TP) 0.011 Average annual income, $ (AI) 0.00141 Registered democrats, % (RD) 0.077 The model Eq. (10) can be written as follows: Page 8/11 Table 8 Multivariate regression analysis p values for the outcome: percentage of fully electric vehicles registered in a state (PEV) Predictor variable p High School graduates, % (HS) 0.410 College degree graduates, % (CD) 0.251 Population density, per sq. mile (PD) 0.937 Total population (TP) 0.011 Average annual income, $ (AI) 0.00141 Registered democrats, % (RD) 0.077 The model Eq. (10) can be written as follows: The model Eq. (10) can be written as follows: References Ball PJ (2021) A review of geothermal technologies and their role in reducing greenhouse gas emissions in the USA. J Energy Res Technol 143:010903 7. Ball PJ (2021) A review of geothermal technologies and their role in reducing greenhouse gas emissions in the USA. J Energy Res Technol 143:010903 8. Barbose GL, Forrester S, Darghouth NR, Hoen B (2020) Income Trends among US Residential Rooftop Solar Adopters. Lawrence Berkeley National Lab.(LBNL), Berkeley, CA. (United States), 8. Barbose GL, Forrester S, Darghouth NR, Hoen B (2020) Income Trends among US Residential Rooftop Solar Adopters. Lawrence Berkeley National Lab.(LBNL), Berkeley, CA. (United States), 9. Cho Y, Shaygan A, Daim TU (2019) Energy technology adoption: Case of solar photovoltaic in the Pacific Northwest USA Sustainable Energy. Technol Assessments 34:187–199. doi:https://doi.org/10.1016/j.seta.2019.05.011 9. Cho Y, Shaygan A, Daim TU (2019) Energy technology adoption: Case of solar photovoltaic in the Pacific Northwest USA Sustainable Energy. Technol Assessments 34:187–199. doi:https://doi.org/10.1016/j.seta.2019.05.011 10. Eshchanov B, Abdurazzakova D, Yuldashev O, Salahodjaev R, Ahrorov F, Komilov A, Eshchanov R (2021) Is there a link between cognitive abilities and renewable energy adoption: Evidence from Uzbekistan using micro data Renewable and Sustainable Energy Reviews 141:110819 10. Eshchanov B, Abdurazzakova D, Yuldashev O, Salahodjaev R, Ahrorov F, Komilov A, Eshchanov R (2021) Is there a link between cognitive abilities and renewable energy adoption: Evidence from Uzbekistan using micro data Renewable and Sustainable Energy Reviews 141:110819 11. Fardi Asrami R, Sohani A, Saedpanah E, Sayyaadi H (2021) Towards achieving the best solution to utilize photovoltaic solar panels for residential buildings in urban areas. Sustainable Cities and Society 71:102968. doi:https://doi.org/10.1016/j.scs.2021.102968 11. Fardi Asrami R, Sohani A, Saedpanah E, Sayyaadi H (2021) Towards achieving the best solution to utilize photovoltaic solar panels for residential buildings in urban areas. Sustainable Cities and Society 71:102968. doi:https://doi.org/10.1016/j.scs.2021.102968 12 IEA (2019) W ld E I t t 2019 R t I t ti l E A P i 12. IEA (2019) World Energy Investment 2019 Report. International Energy Agency, Paris 2. IEA (2019) World Energy Investment 2019 Report. International Energy Agency, Paris Renewable power generation costs in 2017 Report. International Renewable Energy Agency, Abu Dhabi 3. IRENA I (2018) Renewable power generation costs in 2017 Report. International Renewable Energy Age 14. Karasmanaki E, Tsantopoulos G (2019) Exploring future scientists' awareness about and attitudes towards renewable energy sources. Energy Policy 131:111–119. doi:https://doi.org/10.1016/j.enpol.2019.04.032 14. References 1. Ahmed Z, Cary M, Shahbaz M, Vo XV(2021) Asymmetric nexus between economic policy uncertainty, renewable energy technology budgets, and environmental sustainability: Evidence from the United States Journal of cleaner production:127723 1. Ahmed Z, Cary M, Shahbaz M, Vo XV(2021) Asymmetric nexus between economic policy uncertainty, renewable energy technology budgets, and environmental sustainability: Evidence from the United States Journal of cleaner production:127723 2. Al-Aboosi FY, Al-Aboosi AF (2021) Preliminary Evaluation of a Rooftop Grid-Connected Photovoltaic System Installation under the Climatic Conditions of Texas (USA. Energies 14:586 2. Al-Aboosi FY, Al-Aboosi AF (2021) Preliminary Evaluation of a Rooftop Grid-Connected Photovoltaic System Installation under the Climatic Conditions of Texas (USA. Energies 14:586 Ali S, Xu H, Ahmad N (2021) Reviewing the strategies for climate change and sustainability after the US de AHP–GMCR-based conflict resolution approach Environment, Development and Sustainability:1–32 3. Ali S, Xu H, Ahmad N (2021) Reviewing the strategies for climate change and sustainability after the US defiance of the Paris Agreement: An AHP–GMCR-based conflict resolution approach Environment, Development and Sustainability:1–32 3. Ali S, Xu H, Ahmad N (2021) Reviewing the strategies for climate change and sustainability after the US defiance of the Paris Agreement: An AHP–GMCR-based conflict resolution approach Environment, Development and Sustainability:1–32 4. Amarasekara AS (2013) Handbook of cellulosic ethanol. John Wiley & Sons 5. Aslan A, Destek MA, Okumus I (2018) Bootstrap rolling window estimation approach to analysis of the Environment Kuznets Curve hypothesis: evidence from the USA Environmental. Sci Pollution Res 25:2402–2408 5. Aslan A, Destek MA, Okumus I (2018) Bootstrap rolling window estimation approach to analysis of the Environment Kuznets Curve hypothesis: evidence from the USA Environmental. Sci Pollution Res 25:2402–2408 5. Aslan A, Destek MA, Okumus I (2018) Bootstrap rolling window estimation approach to analysis of the evidence from the USA Environmental. Sci Pollution Res 25:2402–2408 6. Ayling B Unlocking the potential of low-temperature geothermal resources for direct-use applications in the USA. In: Symposium on the Application of Geophysics to Engineering and Environmental Problems 2021, 2021. Society of Exploration Geophysicists and Environment and Engineering … pp 166–166 6. Ayling B Unlocking the potential of low-temperature geothermal resources for direct-use applications in the USA. In: Symposium on the Application of Geophysics to Engineering and Environmental Problems 2021, 2021. Society of Exploration Geophysicists and Environment and Engineering … pp 166–166 7. References Karasmanaki E, Tsantopoulos G (2019) Exploring future scientists' awareness about and attitudes towards renewable energy sources. Energy Policy 131:111–119. doi:https://doi.org/10.1016/j.enpol.2019.04.032 15. Khan I, Hou F, Le HP (2021) The impact of natural resources, energy consumption, and population growth on environmental quality: Fresh evidence from the United States of America. Sci Total Environ 754:142222 15. Khan I, Hou F, Le HP (2021) The impact of natural resources, energy consumption, and population growth on environmental quality: Fresh evidence from the United States of America. Sci Total Environ 754:142222 16. Kim H-J et al (2020) A comprehensive review of Li-ion battery materials and their recycling techniques Electronics 9:1161 6. Kim H-J et al (2020) A comprehensive review of Li-ion battery materials and their recycling techniques 17. Koondhar MA, Qiu L, Li H, Liu W, He G (2018) A nexus between air pollution, energy consumption and growth of economy: a comparative study between the USA and China-based on the ARDL bound testing approach. Agric Econ 64:265–276 18. Kovač M, Stegnar G, Al-Mansour F, Merše S, Pečjak A (2019) Assessing solar potential and battery instalment for self-sufficient buildings with. simplified model Energy 173:1182–1195 19. Mahalik MK, Mallick H, Padhan H (2021) Do educational levels influence the environmental quality? The role of renewable and non-renewable energy demand in selected BRICS countries with a new policy perspective. Renewable Energy 164:419–432 20. Mangiante MJ et al Economic and technical assessment of rooftop solar photovoltaic potential in Brow Computers(2020)Environment and Urban Systems80:101450doi:https://doi.org/10.1016/j.compenvur 20. Mangiante MJ et al Economic and technical assessment of rooftop solar photovoltaic potential in Brownsville, Texas USA, Computers(2020)Environment and Urban Systems80:101450doi:https://doi.org/10.1016/j.compenvurbsys.2019.101450 21. Markard J, Bento N, Kittner N, Nunez-Jimenez A (2020) Destined for decline? Examining nuclear energy from a technological innovation systems perspective. Energy Res Social Sci 67:101512 21. Markard J, Bento N, Kittner N, Nunez-Jimenez A (2020) Destined for decline? Examining nuclear energy from a technological innovation systems perspective. Energy Res Social Sci 67:101512 22. Marlow T, Miller S, Roberts JT(2021) Bots and online climate discourses: Twitter discourse on President Trump’s announcement of US withdrawal from the ParisAgreement Climate Policy:1–13 22. Marlow T, Miller S, Roberts JT(2021) Bots and online climate discourses: Twitter discourse on President Trump’s announcement of US withdrawal from the ParisAgreement Climate Policy:1–13 23. Mayer A (2018) The fiscal impacts of energy: Perspectives from local governments in the Mountain 23. References Mayer A (2018) The fiscal impacts of energy: Perspectives from local governments in the Mountain West. USA Energy Policy 122:186–193 23. Mayer A (2018) The fiscal impacts of energy: Perspectives from local governments in the Mountain West. USA Energy Policy 122:186–193 23. Mayer A (2018) The fiscal impacts of energy: Perspectives from local governments in the Mountain West. USA Energy Policy 122:186–193 24. Mazmanian DA, Jurewitz JL, Nelson HT (2020) State Leadership in US Climate Change and Energy Policy: The California Experience. J Environ 23. Mayer A (2018) The fiscal impacts of energy: Perspectives from local governments in the Mountain West. USA Energy Policy 122:186–193 24. Mazmanian DA, Jurewitz JL, Nelson HT (2020) State Leadership in US Climate Change and Energy Policy: The California Experience. J Environ Dev 29:51–74 24. Mazmanian DA, Jurewitz JL, Nelson HT (2020) State Leadership in US Climate Change and Energy Policy: The California Experience. J Environ Dev 29:51–74 24. Mazmanian DA, Jurewitz JL, Nelson HT (2020) State Leadership in US Climate Change and Energy Policy: The California Experience. J Environ Dev 29:51–74 25. Mehmood U (2021) Contribution of renewable energy towards environmental quality: The role of education to achieve sustainable development goals in G11 countries Renewable Energy 25. Mehmood U (2021) Contribution of renewable energy towards environmental quality: The role of education to achieve sustainable development goals in G11 countries Renewable Energy 26. Moore RA, Martinetti D, Bigg EK, Christner BC, Morris CE (2021) Climatic and landscape changes as drivers of environmental feedback that influence rainfall frequency in the United States. Glob Change Biol 27:6381–6393 26. Moore RA, Martinetti D, Bigg EK, Christner BC, Morris CE (2021) Climatic and landscape changes as drivers of environmental feedback that influence rainfall frequency in the United States. Glob Change Biol 27:6381–6393 27. Pitt D, Michaud G, Duggan A (2018) Analyzing the costs and benefits of distributed solar energy in Virginia (USA): a case study of collaborative energy planning. J Environ Planning Manage 61:2032–2049 27. Pitt D, Michaud G, Duggan A (2018) Analyzing the costs and benefits of distributed solar energy in Virginia (USA): a case study of collaborative energy planning. J Environ Planning Manage 61:2032–2049 Page 10/11 28. Pol MV, Ford KH (2020) Offshore Wind Energy and the Fishing Industry in the Northeastern USA. Modern Fisheries Engineering. CRC Press, pp 115–124 28. Pol MV, Ford KH (2020) Offshore Wind Energy and the Fishing Industry in the Northeastern USA. References Modern Fisheries Engineering. CRC Press, pp 115–124 29. Saint Akadiri S, Alola AA, Alola UV, Nwambe CS (2020) The role of ecological footprint and the changes in degree days on environmental sustainability in the USA Environmental. Sci Pollution Res 27:24929–24938 29. Saint Akadiri S, Alola AA, Alola UV, Nwambe CS (2020) The role of ecological footprint and the changes in degree days on environmental sustainability in the USA Environmental. Sci Pollution Res 27:24929–24938 0. Salahodjaev R (2016) Does intelligence improve environmental sustainability? Empir test Sustainable 30. Salahodjaev R (2016) Does intelligence improve environmental sustainability? Empir test Sustainable Dev 24:32–40 30. Salahodjaev R (2016) Does intelligence improve environmental sustainability? Empir test Sustainable Dev 24:32–40 31. Sanguesa JA, Torres-Sanz V, Garrido P, Martinez FJ, Marquez-Barja JM (2021) A Review on Electric Vehicles: Technologies and Challenges Smart Cities 4:372–404 31. Sanguesa JA, Torres-Sanz V, Garrido P, Martinez FJ, Marquez-Barja JM (2021) A Review on Electric Vehicles: Technologies and Challenges Smart Cities 4:372–404 32. Shamosh NA, Gray JR (2008) Delay discounting and intelligence: A meta-analysis. Intelligence 36:289–305 32. Shamosh NA, Gray JR (2008) Delay discounting and intelligence: A meta-analysis. Intelligence 36:289–305 32. Shamosh NA, Gray JR (2008) Delay discounting and intelligence: A meta-analysis. Intelligence 36:2 33. States101 (2022) Populations in US States. http//www.states101.com/populations 34. Statista (2022) Statista. https://www.statista.com/statistics/184260/educational-attainment-in-the 34. Statista (2022) Statista. https://www.statista.com/statistics/184260/educational-attainment-in-the-us/ 35. Zafar MW, Shahbaz M, Sinha A, Sengupta T, Qin Q (2020) How renewable energy consumption contribute to environmental quality? The role of education in OECD countries. J Clean Prod 268:122149 Figures Figure 1 Legend not included with this version. Figures Figure 1 Legend not included with this version. Page 11/11
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First Report of the Carolina Spiral Nematode, <i>Scutellonema brachyurus</i>, from Soil of a Garden in Crete, Greece
Journal of nematology
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First Report of the Carolina Spiral Nematode, Scutellonema brachyurus from Soil of a Garden in Crete, Greece Abstract: Members of the genus Scutellonema can cause substantial crop losses to ornamental and cultivated plants directly by feeding ectoparasitically on plant roots (Bridge et al., 2005; Coyne et al., 2006). In May 2015, a soil sample from a house garden from Heraklion city in Crete, Greece, was sent for diagnosis of plant-parasitic nematodes. In this place, there had been cactus (Opuntia sp.) plants (probably imported), which were uprooted 3 to 4 years earlier. After that, the area was cropped with cucumber (Cucumis sativus L.) in spring–summer and leaf vegetables such as spinach (Spinacia oleracea L.) and chicory (Cichorium intybus L.) in autumn–winter. The soil was collected 1 mon after the end of chicory crop. A population density (ca. 30 individuals/100 cm3 of soil) of spiral nematodes (Scutellonema sp.) was found by extracting soil with the wet sieving and decanting method (Cobb, 1918). Morphological and molecular analyses of females identified the species as Scutellonema brachyurus (Steiner, 1938) Andrassy, 1958. The morphology of females was characterized by a hemispherical lip region with four to six annuli, morphometric data for 12 females were L, 640 to 760 mm; a, 24.6 to 30.6; b, 5.8 to 7.4; c, 69.1 to 99.3; c0.5 to 0.6; stylet, 24.5 to 27.5 mm with anterior part shorter than posterior; and spermatheca nonfunctional and male absent. The morphology agreed with the description of S. brachyurus (van den Berg et al., 2013). Alignment indicated that the D2-D3 and ITS sequences (KU059494 and KU059495, respectively) showed 99% and 100% to 99% similarity, respectively, to other sequences of S. brachyurus (type A) deposited in GenBank from the United States, Italy, and Korea (JX472037-JX472046, DQ328753, FJ485643; and JX472069, JX472070, JX472071, respectively), differing from one to six nu- cleotides. Phylogenetic analyses using Bayesian inference of these sequences placed the Scutellonema sp. in a highly supported (100%) clade that included all S. brachyurus (type A) sequences deposited in GenBank (van den Berg et al., 2013). All identification methods were consistent with S. brachyurus. To our knowledge, this is the first report of S. brachyurus for Greece. As the cucumbers and the leaf vegetables cultivated in the area were seed planted, we consider that the nematode originated most probably from the cactus plants which had been previously root ball planted. Scutellonema brachyurus may represent a threat for ornamental and cultivated plants production in Crete, Greece. First Report of the Carolina Spiral Nematode, Scutellonema brachyurus from Soil of a Garden in Crete, Greece The nematode has been already reported, mainly in greenhouses of six European countries (CABI and EPPO, 2006). In most of these cases, it is hypothesized that the nematode was introduced by imported plant material. Key words: Crete detection Scutellonema brachyurum spiral nematodes Key words: Crete, detection, Scutellonema brachyurum, spiral nematodes. Cobb, N. A. 1918. Agricultural technology circular. Washington, DC: U.S. Department of Agriculture, Bureau of Plant Industry. No 1, pp. 48. Received for publication December 20, 2015. 1Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, National Agricultural Research Foundation, Hellenic Agricultural Organization-DEMETER, PO Box 2228, 71003 Heraklion, Crete, Greece. 2Institute for Sustainable Agriculture, CSIC, Avenida Menendez Pidal s/n, 14004 Cordoba, Spain. E-mail: pcastillo@ias.csic.es; p.castillo@csic.es. This paper was edited by Andrea Skantar. CABI and EPPO 2006. Distribution maps of plant diseases, 1st ed. October, pp. Map 990. Cobb, N. A. 1918. Agricultural technology circular. Washington, DC: U.S. Department of Agriculture, Bureau of Plant Industry. No 1, pp. 48. van den Berg, E., Tiedt, L. R., Coyne, D. L., Ploeg, A. T., Navas- Cortes, J. A., Roberts, P. A., Yeates, G. W., and Subbotin, S. A. 2013. Morphological and molecular characterisation and diagnostics of some species of Scutellonema Andrassy, 1958 (Tylenchida: Hoplolaimidae) with a molecular phylogeny of the genus. Nematology 15:719–745. Steiner, G. 1938. Nematodes infesting red spider lilies. Journal of Agricultural Research 56:1–8. Journal of Nematology 48(1):7–7. 2016.  The Society of Nematologists 2016. Journal of Nematology 48(1):7–7. 2016.  The Society of Nematologists 2016. pp Steiner, G. 1938. Nematodes infesting red spider lilies. Journal of Agricultural Research 56:1–8. van den Berg, E., Tiedt, L. R., Coyne, D. L., Ploeg, A. T., Navas- Cortes, J. A., Roberts, P. A., Yeates, G. W., and Subbotin, S. A. 2013. Morphological and molecular characterisation and diagnostics of some species of Scutellonema Andrassy, 1958 (Tylenchida: Hoplolaimidae) with a molecular phylogeny of the genus. Nematology 15:719–745. Received for publication December 20, 2015. 1 This paper was edited by Andrea Skantar. LITERATURE CITED Andrassy, I. 1958. Hoplolaimus tylenchiformis Daday, 1905 (syn. H. coronatus Cobb, 1923) und die Gattungen der Unterfamilie Hoplolaiminae Filip’ev, 1936. Nematologica 3:44–56. Steiner, G. 1938. Nematodes infesting red spider lilies. Journal of Agricultural Research 56:1–8. Bridge, J., Coyne, D., and Kwoseh, C. K. 2005. Nematode parasites of tropical root and tuber crops. Pp. 221–258 in M. Luc, R. A. Sikora, and J. Bridge, eds. Plant parasitic nematodes in subtropical and tropical agriculture, 2nd ed. Wallingford, UK: CABI Publishing. Coyne, D. L., Tchabi, A., Baimey, H., Labuschagne, N., and Rotifa, I. 2006. Distribution and prevalence of nematodes (Scutellonema bradys and Meloidogyne spp.) on marketed yam (Dioscorea spp.) in West Africa. Field Crops Research 96:142–150. 7
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https://europepmc.org/articles/pmc6629714?pdf=render
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Two new species of the tribe Hemisphaeriini (Hemiptera, Fulgoromorpha, Issidae) from southwestern China
ZooKeys
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Keywords Fulgoroidea, morphology, Oriental region, planthoppers, taxonomy http://zoobank.org/6E4B7AAE-AA59-4516-9A9B-6D74D4B11F4A Citation: Yang L-J, Yang L, Chang Z-M, Chen X-S (2019) Two new species of the tribe Hemisphaeriini (Hemiptera, Fulgoromorpha, Issidae) from southwestern China. ZooKeys 861: 29–41. https://doi.org/10.3897/zookeys.861.32594 Abstract Two new species of the tribe Hemisphaeriini: Ceratogergithus brachyspinus Yang & Chen, sp. nov. (Yun­ nan) and Neohemisphaerius clavatus Yang & Chen, sp. nov. (Guizhou) are described and illustrated. A checklist to Hemisphaeriini genera is provided. The generic characteristics of the genera Ceratogergithus Gnezdilov, 2017 and Neohemisphaerius Chen, Zhang & Chang, 2014 are redefined. Checklists and keys to the species of each genus are given. Two new ZooKeys 861: 29–41 (2019) doi: 10.3897/zookeys.861.32594 http://zookeys.pensoft.net Two new ZooKeys 861: 29–41 (2019) doi: 10.3897/zookeys.861.32594 http://zookeys.pensoft.net Two new ZooKeys 861: 29–41 (2019) doi: 10.3897/zookeys.861.32594 http://zookeys.pensoft.net ribe Hemisphaeriini fro RESEARCH ARTICLE Copyright Liang-Jing Yang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Liang-Jing Yang1,2,4, Lin Yang1,2, Zhi-Min Chang1,2,3, Xiang-Sheng Chen1,2,3 Liang-Jing Yang1,2,4, Lin Yang1,2, Zhi-Min Chang1,2,3, Xiang-Sheng Chen1,2,3 1 Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China 2 The Provincial Special Key Laboratory for Development and Utilization of Insect Resources, Guizhou University, Guiyang, Guizhou, 550025, China 3 College of Animal Science, Guizhou University, Guiyang, Guizhou, 550025, China 4 Office of Academic Affairs, Liupanshui normal College, Liupanshui, Guizhou 55300, China Corresponding author: Xiang-Sheng Chen (chenxs3218@163.com) cademic editor: Mike Wilson  |  Received 21 December 2018  |  Accepted 14 May 2019  |  Published 8 July http://zoobank.org/6E4B7AAE-AA59-4516-9A9B-6D74D4B11F4A Two new species of the tribe Hemisphaeriini (Hemiptera, Fulgoromorpha, Issidae) from southwestern China Liang-Jing Yang1,2,4, Lin Yang1,2, Zhi-Min Chang1,2,3, Xiang-Sheng Chen1,2,3 Introduction Hemisphaeriini Melichar, 1906 is the second largest tribe of the planthopper family Is­ sidae with currently 25 genera and 181 species known (Bourgoin 2018). It was erected by Melichar (1906) as family Hemisphaeridae but more recently Gnezdilov (2003, 2013a) downgraded it to the tribe level. Sun et al. (2015) raised the group again to the Copyright Liang-Jing Yang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Liang-Jing Yang et al. / ZooKeys 861: 29–41 (2019) 30 subfamily level based on partial sequences of the nuclear Wingless (Wg) and 18S rDNA genes and Wang et al. (2016) enlarged the subfamily based on 18S, 28S, COXI and Cytb genes to include four tribes (Kodaianellini, Sarimini, Parahiraciini, Hemispha­ eriini). However, here we prefer to follow Gnezdilov (2013a) and treat the group as a tribe of the subfamily Issinae which was also followed by Meng et al (2017). Hemisphaeriini are characterized as follows: body hemispherical; vertex with ante­ rior margin approximately transverse or triangularly elongate; pronotum with convex anterior margin; forewings thick and convex, claval suture present or absent, venation reticulate; hindwings single-lobed, being either well developed, i.e., longer than half length of forewings, venation reticulate, or rudimentary, shorter than half length of forewings, venation simple. The tribe Hemisphaeriini is divided into two groups based on the presence or absence of the forewing claval suture. The genera Neohemisphaerius and Paramongo­ liana both have the forewing claval suture developed. The genus Neohemisphaerius was erected by Chen et al. (2014) for three species (N. wugangensis, N. yangi and N. signifer Walker, 1851) having a forewing with distinct claval suture. Recently Zhang et al. (2016) reviewed Neohemisphaerius, transferred species N. signifer Walker, 1851 to Hemisphaerius Schaum, 1850 and described species N. guangxiensis Zhang, Chang & Chen, 2016. The genus Ceratogergithus was erected by Gnezdilov (2017) for three spe­ cies (C. chelates, C. pseudotessellatus and C. spinosus) having a forewing without a claval suture and pygofer with a large horn-shaped process on posterior margin. In this paper, we describe and illustrate two new species of the tribe Hemisphaeriini, give a checklist to Hemisphaeriini genera, redefine the generic characteristics and provided checklists and keys to the species of these two genera. Introduction Hemisphaeriini are usually collected in broad-leaved forest, although some species are also found on Poaceae in open areas (Gnezdilov 2013b). The species Neohemi­ sphaerius clavatus Yang & Chen, sp. nov. was captured on Bambusa emeiensis.It maybe the second species that feeds exclusively on bamboos (host plant Bambusa emeiensis; Fig. 36), the other species is Rotundiforma nigrimaculata, Meng, Wang & Qin, 2013, whose host plants may be Gigantochloa ligulata Gamble and Dendrocalamus sp. (Meng, Wang & Qin, 2013). Materials and methods The morphological terminology follows Chan and Yang (1994) and Bourgoin et al. (2015), except those for male genitalia following Gnezdilov (2003). Dry specimens were observed by stereoscopic microscope Leica M125 for illustration and descrip­ tion. All measurements are in millimeters (mm). The genital segments were separated and macerated in 10% NaOH, transferred to glycerine for observing and drawing. Illustrations of the specimens were made with a Leica MZ 12.5 stereomicroscope. Photographs of the types were taken by KEYENCE VHX-1000C. Two new species of the tribe Hemisphaeriini from southwestern China 31 The type specimens are deposited in the Institute of Entomology, Guizhou Univer­ sity, Guiyang, China (GUGC) and one paratype of Neohemisphaerius clavatus Yang & Chen, sp. nov. in the Natural History Museum, London (BMNH). Checklist of genera of Hemisphaeriini Bolbosphaerius Gnezdilov, 2013; Brunei, Vietnam. Bolbosphaerius Gnezdilov, 2013; Brunei, Vietnam. p Bruneastrum Gnezdilov, 2015; Borneo. Ceratogergithus Gnezdilov, 2017; China: Hainan, Yunnan. Choutagus Zhang, Wang & Che, 2006; China: Guangxi, Hainan. Clypeosmilus Gnezdilov & A. Soulier-Perkins, 2017; Northern Vietnam. Euxaldar Fennah, 1978; Vietnam. Epyhemisphaerius Chan & Yang, 1994; China: Taiwan. Euhemisphaerius Chan & Yang, 1994; China: Taiwan. Gergithus Stål, 1870; India, Indonesia, Malaysia, Myanmar, Sri Lanka, Southern Chi­ na, Thailand. Gergithus Stål, 1870; India, Indonesia, Malaysia, Myanmar, Sri Lanka, Southern Chi­ na, Thailand. h Gergithoides Schumacher, 1915; Japan, Southern China, Vietnam. g p Gnezdilovius Meng, Webb & Wang, 2017; Southern China, Vietnam, Japan. Gnezdilovius Meng, Webb & Wang, 2017; Southern China, Vietnam, Japan. Hemisphaerius Schaum, 1850; China, India, Indonesia, Japan, Malaysia, Mya New Guinea, Philippines, Sri Lanka, Thailand, Vietnam. New Guinea, Philippines, Sri Lanka, Thailand, Vietnam. pph Hemisphaeroides Melichar, 1903; Sri Lanka. Hemisphaeroides Melichar, 1903; Sri Lanka. Hemiphile Metcalf, 1952; Indonesia. Hemiphile Metcalf, 1952; Indonesia. Hysteropterissus Melichar, 1906; New Guinea. Hysteropterissus Melichar, 1906; New Guinea. Hysterosphaerius Melichar, 1906; Singapore. Hysterosphaerius Melichar, 1906; Singapore. Ishiharanus Hori, 1969; Vietnam. Ishiharanus Hori, 1969; Vietnam. Macrodaruma Fennah, 1978; Southern China, Vietnam. Maculergithus Constant & Pham, 2016; Northern Vietnam, Southern China. Maculergithus Constant & Pham, 2016; Northern Vietna Mongoliana Distant, 1906; Japan, Southern China. Neogergithoides Sun, Meng & Wang, 2012; China: Guangxi, Guangdong, Hainan, Yunnan, Vienam. Neogergithoides Sun, Meng & Wang, 2012; China: Guangxi, Guangdong, Hainan, Yunnan, Vienam. Neogergithoides Sun, Meng & Wang, 2012; China: Guangxi, Guangdong, Hainan, Yunnan, Vienam. Neohemisphaerius Chen, Zhang & Chang, 2014; Southern China. Ophthalmosphaerius Gnezdilov, 2017; Southern China: Yunnan. Ophthalmosphaerius Gnezdilov, 2017; Southern China: Yunnan. Paramongoliana Chen, Zhang & Chang, 2014; China: Guizhou. Paramongoliana Chen, Zhang & Chang, 2014; China: Guizhou. Rotundiforma Meng, Wang & Qin, 2013; China: Yunnan. Taxonomy Family Issidae Spinola, 1839 Subfamily Issinae Spinola, 1839 Tribe Hemisphaerini Melichar, 1906 Liang-Jing Yang et al. / ZooKeys 861: 29–41 (2019) 32 Type species. Ceratgergithus spinosus (Che, Zhang & Wang, 2007). yp p g g p g g Diagnosis. Vertex subsquare or transverse. Metope wide, without median carinae. Postclypeus with distinct median carinae, elevated above the level surface of base of the frons (Figs 6, 7) or without carinae (Chen et al. 2014: figs 2–14D–E, 2–15D–E). Forewings without claval suture and shoulder-like projections (Chen et al. 2014: figs 2–14A–C, 2–15A–C) or with claval suture developed through its whole length, basally depressed (Figs 1, 2). Hindwing one lobed, longer than half length of forewing. Py­ gofer of male symmetrical (in lateral view), posterior margin with a large horn-shaped process in upper half. Anal tube of male apically enlarged (in dorsal view). Distribution. China: Hainan, Yunnan.h Discussion. This genus is similar to Gergithus and Neohemisphaerius, but can be clearly separated from Gergithus by the posterior margin of the pygofer with a large horn-shaped process (Fig. 12) and the aedeagus without pair of short ventral directed toward its apex. It differs from the genus Neohemisphaerius by having a frons without a median carina, with colored marking, a hindwing well developed and longer than half the length of the forewing, and venation reticulate. Genus Ceratogergithus Gnezdilov, 2017 Type species. Ceratgergithus spinosus (Che, Zhang & Wang, 2007). Ceratogergithus brachyspinus Yang & Chen, sp. nov. http://zoobank.org/CA131906-B935-4958-8B37-BEB4B11CE542 Figs 1, 2, 5–18 Figs 1, 2, 5–18 Type material. Holotype: ♂, China: Yunnan, Daweishan National Nature Reserve (103°20'E, 23°07'N), 8 May 2016, L.-J. Yang. Paratypes: 1♂, same data as holotype; 1♂, same data as holotype, except 19 August, 2017, Y.-J. Sui. All in GUGC. Description. Male body length (from apex of vertex to tip of forewing): 5.16–5.31 mm (n = 3); male forewing 4.43–4.58 mm (n = 3); male hindwing 3.30–3.47 mm (n = 3). Coloration (Figs 1, 2, 5–7). Vertex straw-yellow to pale green, all margins brown­ ish (Fig. 5). Frons with brick-red markings, margins brownish (Fig. 7). Clypeus dark brown. Eyes reddish brown to greenish-brown (Figs 6, 7). Pronotum straw-yellow, margins brown (Fig. 5). Mesonotum (Fig. 5) fulvous, with fuscous subtriangular mark­ ing. Forewing fulvous, with three white markings irregular, costal margin white from middle to subapical part (Figs 1, 2, 8). Hindwing brownish and hyaline. Head and thorax (Figs 5–9). Vertex shorter in middle than width at base (0.41: 1.00), transverse, anterior margin weakly convex, posterior margin angularly concave, disc depressed and all margins elevated (Figs 1, 5). Frons longer along midline than maximal width (1.53: 1.00) (Fig. 7), smooth, without median carina or pustules, apical margin nearly straight, margins carinate, disc slightly elevated (in frontal view) (Fig. 7) and arcuate (in lateral view) (Fig. 6). Clypeus with median carina obvious, postclypeus distinctly elevated (Figs 6, 7). Ocelli absent. Pronotum longer than vertex (1.56: 1.00), slightly depressed, margins elevated (Fig. 5). Mesonotum subtriangular, longer than pro­ notum (3.23:1.00) (Fig. 5), without median and lateral carinae, anterior margin nearly transverse (Fig. 5). Forewings about 2 times longer than maximal width (Figs 1, 2), with claval suture developed through its whole length, without “shoulder” basally, venation obscure. Hindwing 0.70 times as long as forewings (Figs 8, 9), reaching pygofer; venation reticulate (Fig. 9). Hind tibiae with two lateral teeth. Metatibiotarsal formula: 7–8–2. Male genitalia (Figs 10–19). Anal tube 1.35 times as long as wide (in dorsal view) (Fig. 10), enlarged apically, apical margin deeply notched medially, bent ventrad (in lateral view) (Fig. 11). Pygofer symmetrical, posterior margin with large horn-shaped process in apical fourth (Fig. 12). Genital style subquadrate (in lateral view), moderate­ ly long, depressed in base near ventral margin, caudo-ventral angle rounded (Fig. 12). Capitulum with neck and small lateral tooth directed cephalad and big lateral tooth on posterior margin, directed laterad (Figs 12, 13). Connective cup-shaped (Figs 14, 15). List of Ceratogergithus species Ceratogergithus chelates (Che, Zhang & Wang, 2007); China: Hainan. Ceratogergithus pseudotessellatus (Che, Zhang & Wang, 2007); China: Hainan. Ceratogergithus spinosus (Che, Zhang & Wang, 2007); China: Hainan. Ceratogergithus brachyspinus Yang & Chen, sp. nov.; China: Yunnan. Key to species of the genus Ceratogergithus (male) 1 Clypeus with distinct median carina. Forewing with claval suture developed (Figs 6–8).......................................C. brachyspinus Yang & Chen, sp. nov. – Clypeus without median carina. Forewing without claval suture..................2 2 Forewing with four pale green transverse fasciae. Anal tube with apical mar­ gins strongly convex (in dorsal view) (Che et al. 2007: figs 26, 28)................ ................................................................C. chelates (Che, Zhang & Wang) – Forewing and anal tube not as above............................................................3 3 Forewing yellowish hazel. Anal tube with apical margins slightly concave (Che et al. 2007: figs 16, 18)..................C. spinosus (Che, Zhang & Wang) – Forewing dark with 3 large elongate spots in basal half, with 6 or 7 smaller elongate spots at apical margin in apical half. Anal tube margin nearly trun­ cate (Che et al. 2007: figs 53, 55).................................................................. .................................................C. pseudotessellatus (Che, Zhang & Wang) Key to species of the genus Ceratogergithus (male) Two new species of the tribe Hemisphaeriini from southwestern China 33 Ceratogergithus brachyspinus Yang & Chen, sp. nov. http://zoobank.org/CA131906-B935-4958-8B37-BEB4B11CE542 Figs 1, 2, 5–18 Ceratogergithus brachyspinus Yang & Chen, sp. nov. http://zoobank.org/CA131906-B935-4958-8B37-BEB4B11CE542 Figs 1, 2, 5–18 Penis twisted medially (Figs 16, 17). Phallobase asymmetrical, with basal tooth process directed caudad (Figs 16, 17a), with pair of short lateral hooks in basal third, directed basad (Figs 16, 17b, e); dorso-lateral lobes of phallobase membranous in api­ cal two-fifth (Figs 16, 19), with two differently shaped processes of different length directed apically: one process slender and short, arising in apical fourth (Figs 16–19c), other one arising in basal third, extended ventrad, with subapical process horn-shaped (Figs 17–19d). Ventral lobe of phallobase apically convex (in ventral view), shorter than dorso-lateral lobes (Fig. 18). Liang-Jing Yang et al. / ZooKeys 861: 29–41 (2019) 34 g J g g y Figures 1–4. Dorsal and lateral habitus of two new species adult (male), 1, 2 Ceratogergithus brachyspinus Yang & Chen, sp. nov. 3, 4 Neohemisphaerius clavatus Yang & Chen, sp. nov. Scale bars: 0.5 mm.hi Figures 1–4. Dorsal and lateral habitus of two new species adult (male), 1, 2 Ceratogergithus brachyspinus Yang & Chen, sp. nov. 3, 4 Neohemisphaerius clavatus Yang & Chen, sp. nov. Scale bars: 0.5 mm. Figures 1–4. Dorsal and lateral habitus of two new species adult (male), 1, 2 Ceratogergithus brachyspinus Yang & Chen, sp. nov. 3, 4 Neohemisphaerius clavatus Yang & Chen, sp. nov. Scale bars: 0.5 mm. Etymology. The specific name is derived from the Latin words “brachys”and “spi­ na”, referring to the short lateral hooks on the basal third of the phallobase. Etymology. The specific name is derived from the Latin words “brachys”and “spi­ na”, referring to the short lateral hooks on the basal third of the phallobase. Host plant. Unknown. Distribution. Southwestern China (Yunnan).h Remarks. This species can be distinguished from all the other species of genus Ceratogergithus by the following characteristics: Frons with brick-red markings (Fig. 7); Two new species of the tribe Hemisphaeriini from southwestern China 35 Figures 5–19. Ceratogergithus brachyspinus Yang & Chen, sp. nov. adult (male), 5 head and thorax, dorsal view 6 head and thorax, lateral view 7 face, front view 8 fore wing 9 hindwings 10 anal tube, dor­ sal view 11 anal tube, lateral view 12 pygofer and genital style, lateral view 13 capitulum of gonostylus, dorsal view 14 connective, lateral view 15 connective, caudal view 16 penis, right lateral view 17 penis, left lateral view 18 penis, ventral view 19 penis, dorsal view. Scale bars: 0.5 mm. Figures 5–19. Ceratogergithus brachyspinus Yang & Chen, sp. nov. Genus Neohemisphaerius Chen, Zhang & Chang, 2014 Type species. Neohemisphaerius wugangensis Chen, Zhang & Chang, 2014. Diagnosis. Body hemispherical. Vertex about 2.5–3.9 times as wider than long along midline, anterior margin straight, posterior margin angulately excavated. Frons elongate, with median carina, lateral margins elevated. Clypeus with median carina moderately convex, median carinae with or without a tubercle process in middle. Pro­ notum depressed, edges elevated. Mesonotum subtriangular, anterior margin approxi­ mately straight. Forewings hemispherical, claval suture developed, without shoulder- like projections basally. Hindwing rudimentary, shorter than half length of forewing, venation indistinct and simple. Hind tibiae with 2 lateral teeth. Metatibiotarsal for­ mula: (9, 10)–(4, 5)–2. Anal tube of male wide and short. Phallobase with pair of ventral hooks directed basad. Distribution. China (Guangdong, Guangxi, Hunan, Guizhou). Discussion. Neohemisphaerius is similar to Hemisphaerius Schaum, 1850 and Gergithus Stål, 1870, but it differs from the two genera by having a frons with a me­ dian carina, and forewings with a claval suture developed. The genus Neohemisphaerius runs close to Paramongoliana in the key by Meng et al. (2017). It differs from Para­ mongoliana in: frons with median carinae, without a row of pustules along the lateral margins; clypeus distinctly convex on disc in midline; forewings with irregular mark­ ings; phallobase with pair of ventral hooks directed basad. List of Neohemisphaerius species Neohemisphaerius clavatus Yang & Chen, sp. nov.; China: Guizhou. Neohemisphaerius guangxiensis Zhang, Chang & Chen, 2016; China: Guangxi. Neohemisphaerius wugangensis Chen, Zhang & Chang, 2014; China: Hunan. Neohemisphaerius yangi Chen, Zhang & Chang, 2014; China: Guangdong. Key to species of the genus Neohemisphaerius (males; modified from Zhang et al. 2016) 1 Frons with disc rugose (Fig. 22); clypeus with distinct median carinae (Fig. 22); forewings with three subparallel dark stripes, slanted caudad (Figs 3, 4); anal tube (in dorsal view) with apical margin concave medially (Fig. 25); Phal­ lobase asymmetrical (Figs 33–35).............N. clavatus Yang & Chen, sp. nov. – Frons with disc smooth (Zhang et al. 2016: figs 3, 16, 20); clypeus with a hump-shaped median carinae (Zhang et al. 2016: figs 2, 16, 19); anal tube not as above; phallobase symmetric..............................................................2 Ceratogergithus brachyspinus Yang & Chen, sp. nov. http://zoobank.org/CA131906-B935-4958-8B37-BEB4B11CE542 Figs 1, 2, 5–18 adult (male), 5 head and thorax, dorsal view 6 head and thorax, lateral view 7 face, front view 8 fore wing 9 hindwings 10 anal tube, dor­ sal view 11 anal tube, lateral view 12 pygofer and genital style, lateral view 13 capitulum of gonostylus, dorsal view 14 connective, lateral view 15 connective, caudal view 16 penis, right lateral view 17 penis, left lateral view 18 penis, ventral view 19 penis, dorsal view. Scale bars: 0.5 mm. clypeus with distinct median carina, postclypeus distinctly elevated (Figs 6, 7); fore­ wing fulvous, with three white irregular markings, with claval suture developed, basally depressed (Figs 1, 2). Liang-Jing Yang et al. / ZooKeys 861: 29–41 (2019) 36 Key to species of the genus Neohemisphaerius (males; modified from Zhang et al. 2016) 1 Frons with disc rugose (Fig. 22); clypeus with distinct median carinae (Fig. 22); forewings with three subparallel dark stripes, slanted caudad (Figs 3, 4); anal tube (in dorsal view) with apical margin concave medially (Fig. 25); Phal­ lobase asymmetrical (Figs 33–35).............N. clavatus Yang & Chen, sp. nov. – Frons with disc smooth (Zhang et al. 2016: figs 3, 16, 20); clypeus with a hump-shaped median carinae (Zhang et al. 2016: figs 2, 16, 19); anal tube not as above; phallobase symmetric..............................................................2 Two new species of the tribe Hemisphaeriini from southwestern China 37 2 Forewings pale brown, with two black patches at costal margin (Zhang et al. 2016: figs 1, 2, 4–5); anal tube with apical margin medially convex (in dorsal view) (Zhang et al. 2016: fig. 12)..........................................N. guangxiensis – Forewings black brown, with 4 or 5 light yellow patches (Zhang et al. 2016: figs 13, 14); anal tube not as above..............................................................3 3 Frons with obscurely short median carinae; anal tube with apical margin round (Chen et al. 2014: figs 2–36: H); a pair of ventral hooks of phallobase longer than half length of aedeagus.................................................. N. yangi – Frons with distinctly long median carina; apical margin of anal tube sinuate (in dorsal view) (Chen et al. 2014: fig. 2–35: H); a pair of ventral hooks of phallobase shorter than fifth length of aedeagus (Chen et al. 2014: figs 2–35: M, K)...................................................................................N. wugangensis 2 2 Forewings pale brown, with two black patches at costal margin (Zhang et al. 2016: figs 1, 2, 4–5); anal tube with apical margin medially convex (in dorsal view) (Zhang et al. 2016: fig. 12)..........................................N. guangxiensis – Forewings black brown, with 4 or 5 light yellow patches (Zhang et al. 2016: figs 13, 14); anal tube not as above..............................................................3 3 Frons with obscurely short median carinae; anal tube with apical margin round (Chen et al. 2014: figs 2–36: H); a pair of ventral hooks of phallobase longer than half length of aedeagus.................................................. N. yangi – Frons with distinctly long median carina; apical margin of anal tube sinuate (in dorsal view) (Chen et al. 2014: fig. 2–35: H); a pair of ventral hooks of phallobase shorter than fifth length of aedeagus (Chen et al. 2014: figs 2–35: M, K)...................................................................................N. wugangensis Neohemisphaerius clavatus Yang & Chen, sp. nov. http://zoobank.org/DE9C89F6-24C8-4E2F-9EF1-E4354252141F Figs 3, 4, 20–36 Type material. Holotype: ♂, China: Guizhou, Duyun, Doupengshan (107°07'E, 25°51'N), L.-J. Yang, 19 August 2017; paratypes 2♂♂, same data as holotype; 3♂♂, same data as holotype except J.-K. Long, 8 August 2016. GUGC and one paratype in BMNH. yp p J g g p yp Description. Male body length: 4.53–4.76 mm (n = 5); male forewings 4.23–4.38 mm (n = 5); male hindwing 1.17–1.42 (n = 5). Coloration (Figs 3, 4, 20–22). Head fulvous, margins of vertex and frons brown (Figs 20, 22). Clypeus with dark brown strip on each side of median carinae (Figs 21, 22). Rostrum brown (Figs 21, 22). Eyes dark brown, antennae brown (Fig. 21). Pro­ notum and mesonotum yellow brown, mesonotum with anterior margin dark brown in the middle (Fig. 20). Forewings yellowish and slightly pellucid, with three dark brown irregular stripes subparallel, slanted caudad, venation mostly fulvous (Figs 3, 4). Hindwing brownish hyaline. Legs brown. Abdomen yellowish. Head and thorax (Figs 5–9). Vertex longer in middle than maximal width (0.37:1.00), quadrangular, anterior margin nearly straight, posterior margin angularly concave, mar­ gins elevated (Fig. 20). Frons rough, basally narrow, longer than maximal width in basal third (1.45:1.00), with median carinae, margins elevated (Figs 21–22). Clypeus with me­ dian carinae moderately convex, arcuate in lateral view (Figs 21–22). Pronotum longer than vertex in midline (1.63:1.00), slightly depressed, without carinae and pustules (Fig. 20). Mesonotum subtriangular, about 3 times longer than pronotum, anterior margin approximately straight (Fig. 20). Forewings about 1.70 times longer than maximal width, with claval suture developed through its whole, venation obscurely reticulate (Figs 3, 23). Hindwings rudimentary, shorter than half length of forewing, venation simple (Fig. 24). Hind tibiae with 2 lateral teeth. Metatibiotarsal formula of hind leg: 10–4–2. Liang-Jing Yang et al. / ZooKeys 861: 29–41 (2019) 38 g g g y Figures 20–35. Neohemisphaerius clavatus Yang & Chen, sp. nov. adult (male), 20 head and thorax, dor­ sal view 21 head and thorax, lateral view 22 head and thorax, front view 23 forewing 24 hindwing 25 anal tube, dorsal view 26 anal tube, lateral view 27 pygofer, lateral view 28 genital styles, lateral view 29 ca­ pitulum of gonostylus, dorsal view 30 connective, lateral view 31 penis left lateral view 32 penis, right lateral view 33 penis, ventral view 34 apical penis, dorsal view 35 penis, dorsal view. Scale bars: 0.5 mm. Figures 20–35. Neohemisphaerius clavatus Yang & Chen, sp. nov. Neohemisphaerius clavatus Yang & Chen, sp. nov. http://zoobank.org/DE9C89F6-24C8-4E2F-9EF1-E4354252141F Figs 3, 4, 20–36 adult (male), 20 head and thorax, dor­ sal view 21 head and thorax, lateral view 22 head and thorax, front view 23 forewing 24 hindwing 25 anal tube, dorsal view 26 anal tube, lateral view 27 pygofer, lateral view 28 genital styles, lateral view 29 ca­ pitulum of gonostylus, dorsal view 30 connective, lateral view 31 penis left lateral view 32 penis, right lateral view 33 penis, ventral view 34 apical penis, dorsal view 35 penis, dorsal view. Scale bars: 0.5 mm. Male genitalia (Figs 25–35). Anal tube pyriform, midline longer than broad (in dorsal view) (Fig. 25). Pygofer nearly rectangular (in lateral view), narrow, anterior and posterior margin subparallel (Fig. 27). Genital styles subtriangular (in lateral view), dorsal margin with triangular process, disc with fingerlike process below capitulum Male genitalia (Figs 25–35). Anal tube pyriform, midline longer than broad (in dorsal view) (Fig. 25). Pygofer nearly rectangular (in lateral view), narrow, anterior and posterior margin subparallel (Fig. 27). Genital styles subtriangular (in lateral view), dorsal margin with triangular process, disc with fingerlike process below capitulum Two new species of the tribe Hemisphaeriini from southwestern China 39 Figure 36. Host plant of Neohemisphaerius clavatus Yang & Chen, sp. nov. in Doupengshan, Duyun (Guizhou, China). Photograph by L.-J. Yang. Figure 36. Host plant of Neohemisphaerius clavatus Yang & Chen, sp. nov. in Doupengshan, Duyun (Guizhou, China). Photograph by L.-J. Yang. (Fig. 28). Capitulum with subapical tooth and lateral tooth (Figs 28, 29). Connective short and thick (Fig. 30). Phallobase asymmetrical, with process clavate, arched in basal third (in lateral view), directed basad, H-shaped (in dorsal view) (Figs 31, 32, 34a), process apically and phallobase basally with transparently membranous process with pair of strong hooks directed caudad (Figs 31–34b, c). Ventral lobe with pair of hooks asymmetrical in apical third, directed cephalad (Figs 31–34h, i); Lateral lobe bifurcate. Dorsal lobe with apical margin slightly notched medially (in dorsal view), with four differently sheet-shaped subapical processes (Figs 34–35d, e, f, g), the smallest near the left middle (Figs 34, 35g), with a short carinae left dorsally near its middle (Fig. 35j).h Etymology. The name of new species is derived from the Latin words “clavate”, referring to the club-shaped process of the aedeagus in basal third (in lateral view). Host plant. Bambusa emeiensis. Distribution. Southwestern China (Guizhou).h Remarks. This species resembles N. wugangensis, N. Acknowledgments We are grateful to Dr. Mick Webb (Department of Entomology, The Natural History Museum, U. K.) for proofreading and advice. This work was supported by the Nation­ al Natural Science Foundation of China (No. 31472033, 31601886), the Program of Science and Technology Innovation Talents Team, Guizhou Province (No. 20144001), the Program of Excellent Innovation Talents, Guizhou Province (No. 20154021), the International Cooperation Base for Insect Evolutionary Biology and Pest Control (No. 20165802), the Project Funded by China Postdoctoral Science Foundation (No. 2017M613002), the Science and Technology Project of Guiyang (No. 2017525), the Academic New Cultivation and Innovation Exploration Special Project of Guizhou University(No. 20175788) and the Science and Technology Program in Guizhou Province ( No. 20177267, 20181032). Neohemisphaerius clavatus Yang & Chen, sp. nov. http://zoobank.org/DE9C89F6-24C8-4E2F-9EF1-E4354252141F Figs 3, 4, 20–36 yangi and N.guangxiensis, but can be distinguished by the following characteristics: Frons rough (Fig. 22), disc flat, slightly depressed; clypeus with median carinae without a tubercles process in middle Liang-Jing Yang et al. / ZooKeys 861: 29–41 (2019) 40 (Fig. 22); forewings yellowish brown, with three dark stripes subparallel (Figs 3, 4); anal tube with apical margin concave medially (in dorsal view) (Fig. 25); Phallobase asymmetrical, with process clavate in basal third (in lateral view), process directed ba­ sad, H-shaped (in dorsal view) (Figs 31, 32a, 34a). References Bourgoin T (2018) FLOW (Fulgoromorpha Lists on the Web): a world knowledge base dedi­ cated to Fulgoromorpha. Version 8, updated 30 September 2018. http://hemiptera-data­ bases.org/flow/ Bourgoin T, Wang RR, Asche M, Hoch H, Soulier-Perkins A, Stroiński A., Yap S, Szwedo J (2015) From micropterism to hyperpterism: recognition strategy and standardized homology-driven terminology of the Forewing venation patterns in planthoppers (Hemiptera: Fulgoromor­ pha). Zoomorphology 134(1): 63–77. https://doi.org/10.1007/s00435-014-0243-6 Chan ML, Yang CT (1994) Issidae of Taiwan (Homoptera: Fulgoroidea). Chen Chung Book, Taichung, 188 pp. Chen XS, Zhang ZG, Chang ZM (2014) Issidae and Caliscelidae (Hemiptera: Fulgoroidea) from China. Guizhou Science and Technology Publishing House, Guiyang, 242 pp. Gnezdilov VM (2003) Review of the family Issidae (Homoptera, Cicadina) of the European fauna, with notes on the structure of ovipositor in planthoppers. Chteniya pamyati N.A. Kholodkovskogo (Meetings in memory of N.A. Cholodkovsky), St. Petersburg 56(1): 1–145. ( ) y ( p ) p fauna, with notes on the structure of ovipositor in planthoppers. Chteniya pamyati N.A. Kholodkovskogo (Meetings in memory of N.A. Cholodkovsky), St. Petersburg 56(1): 1–145. Gnezdilov VM (2013a) Modern classification and the distribution of the family Issidae Spinola (Homoptera, Auchenorrhyncha, Fulgoroidea). Entomologicheskoe Obozrenie 92(4): 724–738. Gnezdilov VM (2013b) Notes on planthoppers of the tribe Hemisphaeriini (Homoptera, Ful­ goroidea, Issidae) from Vietnam with description of a new genus and new species. Zoolog­ ichesky Zhurnal 92(6): 659–663. [English translation published in Entomological Review (2013) 93(8): 1024 1028] https://doi org/10 1134/S0013873813080095 Gnezdilov VM (2013a) Modern classification and the distribution of the family Issidae Spinola (Homoptera, Auchenorrhyncha, Fulgoroidea). Entomologicheskoe Obozrenie 92(4): 724–738. Gnezdilov VM (2013b) Notes on planthoppers of the tribe Hemisphaeriini (Homoptera, Ful­ goroidea, Issidae) from Vietnam with description of a new genus and new species. Zoolog­ ichesky Zhurnal 92(6): 659–663. [English translation published in Entomological Review (2013), 93(8): 1024–1028] https://doi.org/10.1134/S0013873813080095 Two new species of the tribe Hemisphaeriini from southwestern China 41 Gnezdilov VM (2017) Addenda to the revisions of the genera Gergithus Stål and Hemisphae­ rius Schaum (Hemiptera, Auchenorrhyncha, Fulgoroidea, Issidae). Entomological Review 97(9): 1338–1352. https://doi.org/10.1134/S0013873817090123 Melichar DL (1906) Monographie der Issiden (Homoptera). Abhandlungen der k. k. Zoolo­ gisch-botanischen Gesellschaft in Wien 3: 1–327. Meng R, Wang YL, Qin DZ (2013) A new genus of the tribe Hemisphaeriini (Hemiptera: Ful­ goromorpha: Issidae) from China. Zootaxa 3691(2): 283–290. References https://doi.org/10.11646/ zootaxa.3691.2.7 Meng R, Webb MD, Wang YL (2017) Nomenclatural changes in the planthopper tribe Hemi­ sphaeriini (Hemiptera: Fulgoromorpha: Issidae), with the description of a new genus and a new species. European Journal of Taxonomy 298: 1–25. https://doi.org/10.5852/ ejt.2017.298 Sun YC, Meng R, Wang YL (2015) Molecular systematics of the Issidae (Hemiptera: Ful­ goroidea) from China based on wingless and 18S rDNA sequence data. Entomotaxonomia 37(1): 15–26. Wang ML, Zhang YL, Bourgoin T (2016) Planthopper family Issidae (Insecta: Hemiptera: Fulgoromorpha): linking molecular phylogeny with classification. Molecular Phylogenet­ ics and Evolution 105: 224–234. https://doi.org/10.1016/j.ympev.2016.08.012 Zhang ZG, Chang ZM, Chen XS (2016) Review of the planthopper genus Neohemisphaerius (Hemiptera, Fulgoroidea, Issidae) with description of one new species from China. Zook­ eys 568: 13–21. https://doi.org/10.3897/zookeys.568.6700
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The Crest Affair: Judicial Independence and Yukon’s Supreme Court
˜The œnorthern review/Northern review
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Commentary The Hon. Ronald Veale* Andrea Bailey* *The Hon. Ronald Veale, Chief Justice, Supreme Court of Yukon *Andrea Bailey, JD, Whitehorse, Yukon The Northern Review 50 (2020): 219–234 https://doi.org/10.22584/nr50.2020.011 The Hon. Ronald Veale, Chief Justice, Supreme Court of Yukon *Andrea Bailey, JD, Whitehorse, Yukon The Northern Review 50 (2020): 219–234 https://doi.org/10.22584/nr50.2020.011 Introduction Th e Yukon’s 1986 “Crest Aff air” has entered into local legal lore as a contest about judicial independence. It was that and more. In addition to galvanizing the general public to take note of the Yukon courts as an independent institution, the resulting proceedings before the Law Society of Yukon resolved a live question about the professional obligations of the Yukon minister of justice as a member of the bar. As well, the Crest Aff air is simply a good story, given that it took place at a time of confl ict between the Yukon’s Minister of Justice, the Senior Judge of the Yukon Supreme Court, and the president of the Law Society. In the context of a small jurisdiction with outspoken personalities and robust local media, the Crest Aff air led to lively public debate and generated a signifi cant amount of news coverage, some of which is recounted here. Th e Crest Aff air took place shortly after the unveiling of the newly built Whitehorse courthouse, which featured a locally-carved1 Yukon coat of arms2 mounted behind the judge in each of the fi ve courtrooms. Although striking pieces of art with a vivid rendering of the Yukon malamute and the blue, red, and gold shapes representing Yukon’s mountains, rivers, and resources,3 Senior Judge  Harry  Maddison ordered that the coat of arms be removed from the Supreme Court courtrooms. Th e Minister of Justice, Roger Kimmerly,4 refused to do so and, in the face of his refusal, Judge Maddison acted on his own motion, 219 compelling their removal by court order. Although the immediate presence of the coat of arms in the courtrooms was resolved in this manner relatively quickly, the disagreement between the Senior Judge and the Minister continued to play out for much of the next two years. Indeed, the broader context for the Crest Aff air is replete with clashes between the Minister of Justice, the Court, and the Law Society of Yukon, and many of these clashes were seized on by local commentators and media. Introduction Th ere were disagreements about courtroom carpets, clothes hangers, and rosewood furniture; a fi ght over a “bridge to nowhere”; a fairly unconventional use of court robes; an informal boycott of the government building’s opening; and, pushing the dispute into a diff erent forum, a lawyer’s complaint to the law society alleging the Minister called the Senior Judge of the Supreme Court “silly,” thereby insulting the public and demonstrating disrespect for the administration of justice, contrary to his professional obligations as a lawyer. Beyond these colourful facts, however, the Crest Aff air started an important conversation and educated many in the Yukon about the independence of the courts and the role of the judiciary. Although the story may be unfamiliar to many of today’s Yukon lawyers, the Crest Aff air marks an important chapter in the territory’s legal history. A New Courthouse By the mid-1980s, there was consensus about the need for a new courthouse in Whitehorse. Th e old courthouse was located above the post offi ce in the federal building on Main Street. Th ere were no public bathrooms, few chairs, and people in custody were escorted to court in handcuff s through the single public hallway. f While the preference of the bar and the judiciary was for a stand-alone courthouse, for practical reasons the Yukon government wanted to house both the courts and government offi ces in one building. Ultimately, a compromise was reached whereby courts and government would coexist in one building, but with clear physical delineation between their facilities.5 Th e design and planning of the shared building were carried out by a committee, which included both the Senior Judge and the Minister of Justice. During the unveiling of the plans, however, the Minister publicly introduced the facility as a new “Territorial Government Building” in which “a wing … has been set aside for court rooms and associated activities and is known as the Law Courts.” Given the explicit discussions about how to structure a shared facility, it may be suspected that the Senior Judge and the Minister of Justice had diff ering views about whether the courthouse was in fact “a wing” of the government building. The Northern Review 50 | 2020 220 But, in any event, at least everyone could agree that the new space was a marked improvement from the “two territorial courtrooms and one supreme courtroom stuff ed into the aging, stale-aired Main Street federal building.”6 f Th e striking new building, which is substantially unchanged today, was ultimately built with two separate sides, divided by an airy atrium that houses a variety of maintained plants and a popular koi pool. Th e north side, the Law Centre, holds government offi ces; and the south side, the Yukon Courts, includes the Supreme and Territorial Court courtrooms, the shared court registry, judges’ chambers, and the law library. In a nod to the fact that the building houses two branches of government, the north and south sides each have a distinct street address. Despite the clear spatial separation provided by the atrium, a specifi c element of the design provoked a small political skirmish that foreshadowed the dispute over the crests in the courthouse. A New Courthouse Th e atrium had been constructed with a broad walkway connecting the government side of the building with the second-fl oor courtrooms on the court side. Prior to the building’s opening, Judge Maddison ensured that a wall closed the walkway on the government side of the building so that there could be no perception of preferred court access by the Minister of Justice or government lawyers. Th e intended bridge, since dubbed “the bridge to nowhere” and now fi lled with plants, still raises questions (and eyebrows) when it is seen for the fi rst time. i Tensions between the executive and judicial branches of government also erupted over judicial furnishings. Th e legislature’s concerns about the costs of the building, coupled with a government position about using Yukon-built furniture in government offi ces, had led to very deliberate choices for Yukon public servants. However, pursuant to federal guidelines for judges, Yukon’s Supreme Court judge could order up to $20,000 worth of new furniture, to be paid for by the territory.7 Known to be a man of refi ned taste, Judge Maddison ordered a $20,000 rosewood ensemble from Edmonton, which included a desk, coff ee table, credenza, and bookcase. Although Minister Kimmerly complained about this being “exorbitant”8 in the media, it was out of his hands. An August 1 Whitehorse Star article9 also reported that Judge Maddison had “expressed dissatisfaction with the type of green carpet chosen for his new offi ce” and that, further, there was “some contention between Judge Maddison and the government over a special type of garment hanger system installed in his new offi ce.” Possibly in retaliation for these perceived excesses, Minister Kimmerly cut the budget for chairs in the courtrooms from $400 apiece to $200.10 Although the $13 million building was opened for business on July 4, 1986, it was in a state of partial completion at the time, and its formal opening did not take place until October 1. A decision had been made in March 1986 to name the 221 Veale and Bailey | The Crest Affair building the Andrew Philipsen Law Centre, in honour of a Conservative Justice Minister who had died in a motor vehicle accident while in offi ce, and whom Premier Tony Penikett referred to as “the principal author” in the construction of the new building. A New Courthouse Th is did not sit well with the Law Society of Yukon, which publicly objected to the courthouse being associated with a politician. While the government took steps to address this legitimate concern through clear labelling of “Th e Law Courts” on the wall on the south side of the atrium, the opening ceremony was nonetheless reportedly the subject of an informal boycott by lawyers and judges.11 Th e various confl icts surrounding the new building did not arise in a vacuum. Indeed, for reasons unrelated to the courthouse, tensions were at a high point between the government and the bar and courts. Th ese included chronic underfunding of the law library and a dispute about the cost of the territory’s “out of control” legal aid system, then administered through the law society, and over which Minister Kimmerly threatened to impose legislated caps.12 Indeed, in mid-1986, it appears that the Law Society was at the point of threatening to sue the government.13 As well, in March 1986, in response to pressure in the legislative assembly, Minister Kimmerly announced a $100,000 review into the territory’s justice system at large, inviting the public to tell a two-member panel what they felt was “wrong with the justice system.”14 Given his promise not to involve any lawyers or judges, one can readily infer his views about where the problems originated. Th e Crest Aff air became part of this volatile mix in October 1986. Th e Crest is In the Courtrooms! Presumably in the earlier spirit of cooperation that dissipated after the building’s planning phase, the Minister of Justice and the Senior Judge had agreed that a Yukon coat of arms would be placed on the wall behind the judge in the two Supreme Court courtrooms and three Territorial Court courtrooms.h Th e coats of arms were on display without public controversy from the time of the building’s opening in July. Th en, on September 24, Judge Maddison abruptly ordered that they be removed and refused to preside over matters until they were. Waiting for this to happen, Maddison J. adjourned his ongoing proceedings, and Justice Perry Meyer, a visiting Supreme Court deputy judge who was sitting on a lengthy and signifi cant constitutional case, took the unusual step of “shrouding” the crest in his courtroom with a lawyer’s black robe.15 The Northern Review 50 | 2020 222 Minister Kimmerly wasted no time in responding to this state of aff airs. Th at same day, he was quoted in the Whitehorse Star as saying “the entire matter is silly” and that “the cloaking over of the coat of arms is insulting to the public.” He went on to observe that “[i]t is this kind of thing that brings the court and the judiciary into public ridicule and contempt.” Not willing to ignore such commentary, Judge Maddison took the unusual step of delivering public comments from the bench on September 26, explaining his opposition to the coat of arms in his courtroom. As reported in the Whitehorse Star,16 the Judge said that he intended no disrespect, but that he believed the crest is a symbol of the government and, as a judge, he must not be seen as a servant of the Yukon government. Th is was especially important to emphasize in the new facility, because, as Maddison J. Th e Crest is In the Courtrooms! pointedly said, the courtrooms were located in a “government administration building and not a courthouse.” Th e president of the law society also took the opportunity to make public comment about the matter.17 Bruce Willis cited the bar’s ongoing concerns about law library funding and the naming of the building, and described the coats of arms in the courtrooms as “another example [of] interference with the courts’ ability to control themselves.” In the meantime, and virtually immediately after hearing Minister Kimmerly’s comments, Elizabeth Th omas, a former Yukon Crown prosecutor visiting from Ontario, fi led a formal complaint with the law society. Her concerns were based on a CBC Radio news clip that included Minister Kimmerly’s response to the “shrouding” of the coats of arms, and specifi cally reporting that: When the Justice Minister heard about all of this … he was upset. He called it silly … It brings the repute of the courts and the judiciary into disrespect in the Yukon, and I’m extremely saddened by the whole thing. Th e provincial crests appear in all provincial courtrooms, and the territories shouldn’t be any diff erent at all. Th ere’s no independence issue here at all in my view. Th e position of the government is that the Yukon crest will appear in Yukon courtrooms, including the Supreme Court Room, and a, ah that justice will be done in the presence of a symbol of the Yukon territory. Ms. Th omas complained that, as a member of the law society, Minister Kimmerly’s comments amounted to conduct deserving of censure. Veale and Bailey | The Crest Affair 223 Th e Crest is Out of the Courtrooms! Th e Crest is Out of the Courtrooms! As noted, Judge Maddison had provided oral reasons for the removal order on September 26: Th e reason that Court business is conducted in specially designed rooms is not only for the purpose of providing an appropriate forum for dispute resolution between citizens, and between citizens and various branches of government, but is also to symbolize that what is going on is quite independent of any other branch of government. … it is essential to the perceived fairness of the judicial process and the independence of the judiciary that this symbolic presence of the Territorial Government, a frequent litigant, is eliminated. … I have concluded that, in the interest of the due and impartial administration of justice, that the tradition of the past continue; that there be no insignia in the courtroom. Accordingly, Mr. Clerk has been instructed to cover the Crest. Th e coats of arms were accordingly removed over the weekend. However, anxious to appeal Judge Maddison’s decision, the following week the Justice Minister directed government lawyers to fi le a draft order that rendered the Court’s direction into writing. Minister Kimmerly is quoted as saying the order would become appealable once signed by the Judge, and “if [he] refuses to sign it, the coats of arms will simply be put back up.”18 Judge Maddison issued his written order on October 3, 1986, stating that the Government of Yukon had unilaterally installed the crest in each courtroom and refused to remove the “decoration” when requested to do so. He noted the refusal of the Government of Yukon to remove the Yukon coats of arms and ordered the Clerk of the Court to remove them. Maddison J. provided further written reasons for his Order on October 6, again clearly situating his objections to the coats of arms as countering a threat to the independence of the courts and judiciary: Where the crest is understood to be and is asserted by the government as a symbol of government, it cannot but leave the impression with the citizen that the court is part of, not independent of that government. Th is is particularly signifi cant when that Government is a party to proceedings taking place in these courtrooms, as it frequently is. Th e Crest is Out of the Courtrooms! Th e importance of the The Northern Review 50 | 2020 224 symbolism is heightened when the court rooms are housed in a government administration building, not a separate court facility. It is critical to the public’s understanding that the judicial process is impartial that the independence of the judiciary be preserved and the symbolic predominance of the Yukon Government be removed. Th is fundamental principle of independent and impartial justice is refl ected, for example, in s. 11(d) of the Charter of Rights and Freedoms which accords an accused person a fair and public hearing by an independent and impartial tribunal. No one must think that this court is in any way an agency or arm of the legislative or executive arms of government. Th e Public Response and a Resolution in the Courthouse Th e Whitehorse Star published a perceptive editorial on September 26, the day after Judge Maddison made his order. After noting that, as a symbol of government, the coat of arms is as appropriately used by the judiciary as by the executive,19 the newspaper observed that the debate was “a reaction to a perception that the executive is making the judiciary’s job diffi cult on a number of points,” but that, nevertheless, “Justice Minister Roger Kimmerly should not be making orders about the interior of a judge’s courtroom.” Th e editorial continued on: … If a superior judge is to have control of his or her own courtroom on the important legal and procedural issues, as our laws require, then surely there must be similar independence on the minor issues – minor issues that go to the dignity of the court. Simply by maintaining the crests will stay where they are, Kimmerly is showing he, as a politician and cabinet minister, feels he has some control over what goes on in the courtrooms. It may only be control over a decoration on a wall, but that is important symbolically. An independent judiciary is more than independence in fact or point of law – it is independence in public perception. If Justice Maddison’s view, even if it is wrong, is that the crest is a symbol of the executive, then he should have the right to have it removed. Th e Whitehorse Star also published a Letter to the Editor by Lynn Gaudet, a lawyer who was then the program manager with the Yukon Public Legal Education Association.20 In a half-page piece, she explained why an independent judiciary is important to our system of law and why it is that the legal system gives judges the right to control their courtrooms.21 Veale and Bailey | The Crest Affair 225 In the face of public response that was clearly running against him, the Justice Minister retreated and advised that he would not be appealing the order of Maddison J. after all. He is quoted in the Whitehorse Star as saying that the controversy was “not doing anybody any good ... I sincerely hope that the issue dissolves and is forgotten about.”22 He also alluded to a “solution” that he had discussed with Nathan Nemetz, the then-Chief Justice of the Yukon Court of Appeal. Th e Public Response and a Resolution in the Courthouse While not explicitly stated, the proposed solution seems likely to have been to install the Royal Coat of Arms of the United Kingdom in the Supreme Court courtrooms; a display that follows the practice in British Columbia.23 In a second editorial, the Whitehorse Star expressed relief that the matter had been resolved, calling the argument “rather silly, but nevertheless serious.” It also noted that the government’s “hard-nosed attitude … showed to many that the government was prepared to interfere with the courts,” but that the longer the debate continued the more “ludicrous the matter looked to the vast majority of people.” While a truce was thus reached in the forum of public opinion, Minister Kimmerly’s accounting before the law society was just getting underway (Figure 1). Th e Law Society Complaint On October 10, 1986, Minister Kimmerly wrote the Law Society of Yukon in response to Ms. Th omas’s discipline complaint. He stated, among other things, that the comments were justifi ed given his role in the government: It is of course my constitutional responsibility to maintain and defend the role of the Executive in our form of Government and it is my fi rm belief that I was discharging that duty under these circumstances. I am cognizant of my role with respect to the judiciary and my responsibilities in that regard, and my comments on this particular issue were, in my view, responsible to both of my aforesaid duties. Having reviewed the complaint and Minister Kimmerly’s response, Grant Macdonald, the chair of the discipline committee, found that Mr. Kimmerly’s conduct was not deserving of censure, in part due to the role he played in his political offi ce. The Northern Review 50 | 2020 226 Figure 1. Editorial cartoon depicting Minister Kimmerly with a tube of Crest toothpaste Rick Peterson, Whitehorse Star, October 7, 1986. Figure 1. Editorial cartoon depicting Minister Kimmerly with a tube of Crest toothpaste. Rick Peterson, Whitehorse Star, October 7, 1986. 227 Veale and Bailey | The Crest Affair Ms. Th omas appealed that fi nding to the full executive of the law society, and while not unanimous, on January 20, 1987, the executive advised: A consensus was reached, subject to Mr. Kilpatrick’s dissent, that Mr. Kimmerly, during the interview in question, acted in his capacity as Minister of Justice and while his remarks may have been impolite and impolitic, he could not be found to be deserving of censure or disciplinary action by the Executive and furthermore that Mr. Macdonald had acted properly as Discipline Chairman in this case. Dissatisfi ed, Ms. Th omas applied to the Supreme Court of Yukon for an order quashing the decision of the executive. Dissatisfi ed, Ms. Th omas applied to the Supreme Court of Yukon for an order quashing the decision of the executive. Minister versus Courts and Law Society, Round 2 Concurrent with the developments in the complaint before the law society was a judicial council issue that was also attracting media attention and being linked to more fundamental tensions between the branches of government, and indeed between the same individual actors. As noted somewhat noirishly by the Whitehorse Star, “[b]eneath the surface debate … brew petty politics and cool personal relationships between Kimmerly and other main players—Supreme Court Justice Harry Maddison and key members of the law society.”24 In a nutshell, Minister Kimmerly was unhappy with the judicial candidates he was being presented with for appointments, and the implication was that it was because there were too many lawyers on the judicial council that then, as now, vetted judicial applicants. As with other aspects of the legal system, the Minister believed that a majority of lay people should sit on the council because lawyers and the law society necessarily favoured the “professional elite.” Th e Minister proposed either presenting his own list of candidates to the council or having the Public Service Commission department of the Yukon Territorial Government prepare a list. In a gambit that ultimately failed, the Minister did present twelve names selected by the Department of Justice to the council in July 1988, only to have it decline to consider them. At the same time that the law society executive was considering the Kimmerly complaint, it was also separately considering the broader issue of judicial independence. On May 21, 1987, David Gates, the newly-elected law society president, advised the media that the society was striking a committee to study the issue of the Court’s independence from government.25 Th is step had been decided on at the society’s recent annual general meeting and was prompted by the clashes between the courts and the executive branch, including the naming of the law centre, the removal of the coats of arms, the public dispute about the cost of Judge Maddison’s furnishings, as well as more-recent comments by Minister Kimmerly about the high salaries of federal judges and his advocacy with respect to changing the process for judicial appointments by altering the composition of judicial council. Dissatisfi ed, Ms. Th omas applied to the Supreme Court of Yukon for an order quashing the decision of the executive. She was successful. In its review, the law society did not have access to the September 25 CBC interview with the Minister, which was the basis of Th omas’s complaint. Deputy Judge Wachowich, to whom tape recordings were made available, agreed that this omission provided a suffi cient basis on which to quash the law society’s decision. Accordingly, on May 12, 1987, Justice Wachowich returned the matter to the law society, ordering the executive to consider the additional evidence fi led, including the tape recordings provided by the CBC, in its reconsideration. Th e executive of the law society met on May 15, 1987, to review all of the evidence relating to the discipline complaint. On May 25, it publicly announced that it was referring the matter to a Committee of Inquiry for a full hearing. Seizing his opportunity while the inquiry was being convened, on July 10, 1987, the Minister of Justice applied to the Supreme Court of Yukon for an order prohibiting the law society from proceeding with the discipline complaint, on the grounds that he was at all times acting in his capacity as Minister of Justice and not as a member of the Law Society of Yukon. Th e petition characterized the discipline citation as an unlawful attempt to interfere with the Government of Yukon. On July 17, 1987, Deputy Judge Bracco dismissed Minister Kimmerly’s petition, fi nding that the Law Society of Yukon had proper and reasonable grounds for issuing the citation. He concluded that the principle of ministerial immunity asserted by Minister Kimmerly had not been established. Th e matter was therefore remitted to the Law Society’s Committee of Inquiry for a full and fair inquiry into the Minister’s conduct, and to test an important proposition about the extent to which a minister is accountable to the law society, despite their role in government. The Northern Review 50 | 2020 228 Th e Committee of Inquiry Although the dust-ups between the courts and the Minister continued throughout 1987 and into 1988 and beyond, the Crest Aff air did receive its fi nal resolution in July 1988, with formal hearings before the law society’s Committee of Inquiry over two days, and written reasons released by the panel on July 25. h Th e law society was represented by counsel before the Committee of Inquiry,26 and the issue was framed as whether the specifi c comments made to 229 Veale and Bailey | The Crest Affair CBC Radio amounted to conduct deserving of censure. Th is term is defi ned in the Legal Profession Act as conduct that “is contrary to the public interest or that harms the standing of the legal profession generally, or that is contrary to the code of legal conduct.” In particular, the Committee of Inquiry focused on the Minister’s assertion that “Yukoners have been insulted,” “It is silly,” and “It brings the repute of the courts and judiciary into disrespect in the Yukon and I am extremely saddened by the whole thing.” Th e Committee of Inquiry found that what Minister Kimmerly had called “silly” was the shrouding of the coats of arms. It was neither a reference to the courts, nor to Judge Maddison personally. Although Ms. Th omas suggested that there was some “ulterior motive” to the Minister’s comments, this point was not pressed by the law society and the committee declined to further describe or make a fi nding about it.27 i Both the law society and Minister Kimmerly presented expert opinion evidence in support of their arguments. Th e expert lawyer called by the law society testifi ed that the Minister had breached the code of professional conduct with respect to his role in public offi ce and with respect to the administration of justice. Ron Veale, who was acting as counsel for the law society, argued that while a lawyer can properly state a view that a Court is wrong, they cannot publicly state that a Court’s actions are “silly.” Additionally, rather than making a public statement to various media outlets, the Minister should have pursued his grievance through the Canadian Judicial Council. Here, the Minister’s comments, which he alliteratively described as the “petulant pique of a politician,” lowered public confi dence in the justice system and were deserving of censure. Th e Committee of Inquiry In contrast, one of the lawyers called by the Minister, John D. McAlpine, QC, from Vancouver, opined that the Supreme Court had itself “thrown down the gauntlet” in a public way requiring a response from the Minister of Justice, and that, in the context, the Minister’s comments were “sensible,” “understandable,” and a valid exercise of his freedom of speech. Minister Kimmerly’s counsel, Richard Peck QC, argued that to censure the Minister’s comments would be to curtail a lawyer’s fundamental right to speak out on matters of principle. Quoting from Justice Dubin of the Ontario Court of Appeal, he protested that “the Courts are not fragile fl owers that will wither in the heat of controversy.” Comments made in good faith without malice and without attempting to impair the administration of justice are fair game. The Northern Review 50 | 2020 230 In a relatively sparsely-reasoned decision, the Committee of Inquiry accepted that a member holding public offi ce is bound by the same standards of professional conduct required of a practising lawyer, and in some instances held to an even higher duty. However, here, Minister Kimmerly, as Minister of Justice, had found himself in circumstances where he was obliged to respond to the Court’s actions. While his words may not have been well-chosen, the committee was mindful “of the realities of political life and the position of the member as Minister of Justice at the end of a telephone in Haines Junction when told of the shrouding of the Coat of Arms.” After balancing the Minister’s obligations to the profession against his freedom to make a fair and reasonable comment, the committee concluded that the comments of the Minister of Justice were not deserving of censure and dismissed the complaint. Th us ended this chapter of Yukon history.28 Conclusion Despite the fraught background and interpersonal confl ict, and the perception by some that the matter was a “tempest in a teapot,” or “silly” as the Minister of Justice described it, the independence of the Yukon’s judiciary and the broader relationships between the Court, executive, and the bar were nevertheless at the heart of the Crest Aff air, and the incident raised public awareness of how these important institutions intersect. For one thing, the law society complaint clarifi ed that the Minister was still subject to its disciplinary process, despite his role in public life. Th irty years later, this precedent remains one of the few considerations of the potentially confl icting duties of a lawyer-politician in Canadian law.29 As well, particularly from the perspective of Ron Veale who, after playing a minor role in the controversy, later assumed Judge Maddison’s role at the helm of Yukon’s Supreme Court, the Crest Aff air was not a mere idiosyncrasy of the bench but a necessary intervention that advanced public understanding of the independence of the judiciary from the Government of Yukon and the Department of Justice. While the Crest Aff air arose on the heels of the seminal case of Valente v Th e Queen,30 in the years since, various appellate courts, including the Supreme Court of Canada, have continued to refi ne our understanding of the important role that court and judicial independence play in Canadian society. Indeed, this principle lies at the heart of our system of government. An independent judiciary is not the right of a judge—it is a right of the public to the confi dence that a case will be adjudicated fairly, on its merits, and without the exercise of political or other pressure. Veale and Bailey | The Crest Affair 231 As noted above, Yukon’s Supreme Court and Territorial Court continue to share a building with offi ces of the Yukon Department of Justice. Th e second fl oor walkway between the two institutions is still a bridge to nowhere. Now, however, the relationship between the branches of government is one of mutual respect and shared responsibility for delivering a standard of justice that is rightly the envy of many Canadians. Notes 1. Th e artist was Colin Sawrenko. One of his pieces is on display on the government side of the building, near the elevators. A second coat of arms is outside the building on the courthouse side. hi 1. Th e artist was Colin Sawrenko. One of his pieces is on display on the government side of the building, near the elevators. A second coat of arms is outside the building on the courthouse side. hi 2. Th e “crest” forms part of the Yukon coat of arms; specifi cally, it is the part on top of the shield, which consists of the Yukon malamute (or husky) on a mound of snow.h 2. Th e “crest” forms part of the Yukon coat of arms; specifi cally, it is the part on top of the shield, which consists of the Yukon malamute (or husky) on a mound of snow.h 3. Th e technical description, as registered with the Canadian Heraldic Authority, is “Arms: Azure two pallets wavy Argent between two piles reversed Gules fi mbriated Argent, each charged with two bezants, on a chief Argent a cross Gules surmounted by a roundel Vair; Crest: A husky statant on a mount of snow proper.” 4. Roger Kimmerly was a lawyer and had been a magistrate in the Yukon before making a move into politics. 5. Evidence of Timothy Preston before the Law Society Commission of Inquiry, refl ected in Law Society of Yukon v Kimmerly, [1988] LSDD No. 1. l 6. Becky Striegler, “New comfort and security”, Whitehorse Star (August 26, 1986). 7. Jim Butler, “Judges order new furniture outside: Costs taxpayers $50,000”, Whitehorse Star (August 1, 1986). Th e additional $30,000 refl ects that the legislature and/or executive approved $10,000 to furnish each of the offi ces used by the three resident Territorial Court judges. 7. Jim Butler, “Judges order new furniture outside: Costs taxpayers $50,000”, Whitehorse Star (August 1, 1986). Th e additional $30,000 refl ects that the legislature and/or executive approved $10,000 to furnish each of the offi ces used by the three resident Territorial Court judges. 8. While considered “exorbitant” at the time, all of these items have been in consistent use by resident Supreme Court judges, and Judge Maddison’s furniture may well have ultimately cost taxpayers less in the long run. 8. Notes While considered “exorbitant” at the time, all of these items have been in consistent use by resident Supreme Court judges, and Judge Maddison’s furniture may well have ultimately cost taxpayers less in the long run. 9. Butler, supra note 7. 9. Butler, supra note 7. 10. Ibid 11. Becky Streigler, “Courts dedicated: Many lawyers, judges boycott”, Whitehorse Star (October 10, 1986). According to the article, the only lawyers attending were two federal Crown attorneys, lawyers from the Yukon Department of Justice, and one lawyer who was also an MLA. One of the Yukon’s three resident judges attended. hf 12. Th is was ultimately resolved when a tariff schedule was agreed on in September 1986. The Northern Review 50 | 2020 232 13. Becky Streigler, “Minister interfering with justice, law society says”, Whitehorse Star (September 25, 1986). 14. Jim Butler, “Justice inquiry team appointed”, Whitehorse Star (April 9, 1986). 15. Becky Striegler, “Crest called symbol of government; judge refuses to hear case in decorated courtroom”, Whitehorse Star (September 25, 1986). 16. Becky Streigler, “Judge explains why he wants crest out”, Whitehorse Star (September 26, 1986), citing comments made by then Law Society of Yukon President Bruce Willis. 17. Streigler, supra note 13. 18. Becky Striegler, “Gov’t may appeal court’s crest order”, Whitehorse Star (October 1, 1986). 19. Indeed, the commissioner has granted the Territorial Court, as a branch of government, the right to use the Yukon coat of arms, and it does so today in its courtrooms and on its letterhead. 20. And also, it appears, a former law partner of Roger Kimmerly. i 21. “Courts rely on public confi dence: Letter to the Editor”, Whitehorse Star (October 1, 1986). 22. Becky Striegler, “Gov’t gives up coat of arms battle”, Whitehorse Star (October 6, 1986). 23. On December 18, 2009, Ron Veale, now Chief Justice of Yukon, discovered the Royal Crest in the court’s basement storage and placed it behind the bench in Courtroom #1. 24. Jim Butler, “Kimmerly plans changes to method of picking judges,” Whitehorse Star (May 15, 1987). 25. “Law Society studying judicial independence,” Whitehorse Star (May 22, 1987). 26. Ron Veale, as a lawyer, represented the Law Society of Yukon.h 27. Th e decision of the Committee of Inquiry is available online through Quicklaw at Law Society of Yukon v Kimmerly, [1988] LSDD No. 1. 28. Notes As a postscript, it is worth noting that, in an editorial published on July 4, 1988 (“Silly evidence”), the Whitehorse Star quoted earlier CBC reporting that Judge Maddison had in fact called the coats of arms “tacky.” It also cited evidence presented at the law society hearing about letters authored by Maddison J., in which he had agreed to their presence in the courtrooms, provided they “were smaller and of better quality.” Th is evidence was not mentioned in the committee’s decision, but the Whitehorse Star opined that, in light of it, the protracted proceedings were themselves bringing the administration of justice into disrepute. h 29. Th is subject has since been considered in an article by Andrew Flavelle Martin, “Legal Ethics Versus Political Practices: Th e Application of the Rules of Professional Conduct to Lawyer-Politicians” (2012) 91:1 Canadian Bar Review 1, 2013 CanLIIDocs 182, online: <http://www.canlii.org/t/28h2>. 29. Th is subject has since been considered in an article by Andrew Flavelle Martin, “Legal Ethics Versus Political Practices: Th e Application of the Rules of Professional Conduct to Lawyer-Politicians” (2012) 91:1 Canadian Bar Review 1, 2013 CanLIIDocs 182, online: <http://www.canlii.org/t/28h2>. 29. Veale and Bailey | The Crest Affair 233 30. [1985] 2 SCR 673. In Valente, the Supreme Court of Canada considered whether an Ontario provincial court judge was suffi ciently independent to meet the requirement of s. 11(d) of the Charter. In answering the question affi rmatively, Le Dain J. articulated the nature and content of judicial independence, including a recognition of its individual and institutional aspects. Broadly speaking, judicial independence requires security of tenure, fi nancial security, and institutional independence over matters of administration bearing directly on the exercise of a court’s judicial function. Authors Th e Honourable Ronald Veale is Chief Justice, Supreme Court of Yukon. Th e Honourable Ronald Veale is Chief Justice, Supreme Court of Yuko Th e Honourable Ronald Veale is Chief Justice, Supreme Court of Yukon. Andrea Bailey is legal counsel with the Yukon Department of Justice. Any views and opinions expressed in this article are those of the author and do not necessarily refl ect any views and opinions of the Yukon Department of Justice or the Government of Yukon. The Northern Review 50 | 2020 234
https://openalex.org/W4379962060
https://zenodo.org/record/7933388/files/serpil_pagenumber%20%283%29.pdf
English
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The Effect of Fattening Time on Fattening Performance, Slaughter and Carcass Characteristics in Tuj Male Lambs
Zenodo (CERN European Organization for Nuclear Research)
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DOI: http://dx.doi.org/10.5281/zenodo.7933388 Araştırma Makalesi / Research Article The Effect of Fattening Time on Fattening Performance, Slaughter and Carcass Characteristics in Tuj Male Lambs MAS JAPS 8(2): 256–264, 2023 MAS JAPS 8(2): 256–264, 2023 The Effect of Fattening Time on Fattening Performance, Slaughter and Carcass Characteristics in Tuj Male Lambs Serpil ADIGÜZEL IŞIK1* , Mehmet SARI2 , Muammer TİLKİ3 , Kadir ÖNK1 1Kafkas University, Faculty of Veterinary Medicine, Department of Animal Science, Kars 2Kırşehir Ahi Evran University, Agriculture Faculty, Department of Animal Science, Kırşehir 3Karadeniz Technical University, Department of Veterinary, Macka Vocational School, Trabzon *Sorumlu yazar (Corresponding author): serpiladiguzel78@hotmail.com Abstract The research was carried out in 39 Tuj male lambs with an average weight of 29 kg, weaned at the age of 2.5 and 3 months, reared in the Education, Research and Application Farm of the Faculty of Veterinary Medicine of Kafkas University. In the study, intensive fattening was done by using lamb rearing feed and ad libitum roughage in 3 groups, 13 lambs in each group, and 6 lambs were slaughtered on the 60th, 75th and 90th days in the first, second and third groups, respectively. slaughter and carcass characteristics were examined. At the beginning, middle and end of the experiment, body weights and some body measurements were taken from the lambs in the morning before the animals were fed, and the live weights were recorded by weighing the lambs every 2 weeks during the experiment. At the end of the study, the difference between the groups was found to be significant in terms of anterior shank circumference measured in the middle of the trial in the sixty-day fattening group (P<0.05). Again, at the end of the experiment, the differences between the groups in terms of anterior shank circumference were significant (P<0.05, P<0.01). The difference between the groups was found to be significant in terms of anterior shank circumference measured in the middle of the trial in the group that was fed for seventy-five days (P<0.05). The difference between the groups was found to be significant in terms of anterior shank circumference measured in the middle of the trial in the group that was fed for ninety days (P<0.05). Again, in the 90-day group, the differences between the groups in terms of anterior shank circumference taken at the end of the trial were significant (P<0.01), while the differences between other body measurements taken at other periods in all groups were insignificant (P>0.05). Keywords: Tuj lamb, fattening shape, fattening performance, slaughter and carcass characteristics 256 MAS JAPS 8(2): 256–264, 2023 profitability (Koçak, 2019). Tuj breed, which is the subject of this study, is bred around Kars, Ardahan and Iğdır. Pure breeds are found in Arpaçay District of Kars and Çıldır District and villages of Ardahan (Aksoy et al., 2001). Although 6 months old lambs are sold in Kars province, they are not sent to slaughter. They are sold to breeders or people who breed yearling lambs. Abstract Yearling lambs are overwintered by the breeders or the fatteners and sold to slaughterhouses, combines, and slaughterers to be slaughtered when they are 20-21 months old in autumn the following year. This situation increases the costs such as feed, shelter, labour, vaccination and treatment. In addition, since yearling lambs are kept in the pasture period for the second time, the pastures are worn out due to heavy grazing (İlaslan and Geliyi, 1984). Considering these reasons, it is thought that by fattening lambs and yearling lambs in Kars, the pastures will be less worn out and more male lambs will gain more live weight (Aksoy, 1996). In this study, the effect of fattening period on fattening performance and carcass characteristics of Tuj male lambs was investigated. 1. Introduction Turkey's natural and environmental conditions and family traditions create a favourable environment for sheep and goat breeding to be widely practised and to have an important place in livestock breeding. Because sheep and goat breeding is a lower cost livestock breeding activity compared to cattle breeding (Elmalı Aksu et al., 2010). According to the data of Turkish Statistical Institute (TUIK), a total of 22 million ovine animals were slaughtered in 2021, and 480 thousand 488 tonnes (24.61%) of the 1 million 952 thousand tonnes of red meat production is provided by sheep and goats (TUIK, 2023). The most important income item in sheep breeding is obtained from lamb meat production. In this context, an economically effective fattening practice should be carried out in order to raise lambs to a certain live weight in a certain period of time. The determination and implementation of technical and economic conditions in lamb fattening instead of traditional production will positively affect both the profitability of enterprises and mutton production (Karaoğlu et al., 2001). As there are differences among species in terms of growth and development and thus meat production ability, there are also great differences among breeds and groups within breeds (Laçin and Aksoy, 2003). Differences within the same breed are greatly affected by gender and environmental conditions (Akçapınar, 2000). However, it has been reported that the most economical and fastest lamb fattening is intensive fattening after weaning (Koçak, 2009). As in all livestock farms, the main objective in lamb fattening is to increase profitability. However, for a profitable and efficient breeding, it is necessary to know the cost factors, especially feed costs, and to control the costs (Çiçek and Sakarya, 2003; Demir et al., 2015). In addition, in fattening enterprises, live weight gain in lambs to be fattened, feed consumption, feed utilisation ability and the relationships between them are also important factors that directly affect 2. Material and Method In the study, 39 male lambs raised in Kafkas University Education Research and Application Farm were used. After the lambs were vaccinated against internal and external parasites, a one-week feed acclimatisation period was applied and then they were divided into 3 groups with 13 lambs in each group. These groups were given ad libitum concentrate feed and 300 g of medium quality dry meadow grass daily for each lamb during fattening and clean water was kept in front of them during the experiment. Concentrate feed was prepared in a private feed factory and hay was purchased from the Veterinary Faculty Farm. Body measurements (body height, body length, chest circumference, chest depth, front shank and back shank circumference) were taken three times for each group at the beginning, middle and end of the experiment. During the experiment, 257 MAS JAPS 8(2): 256–264, 2023 lambs were weighed every 2 weeks in the morning before feeding and their live weights were determined during fattening. At the end of the fattening period determined for each group, lambs were slaughtered after weighing and slaughter and carcass characteristics (hot and cold carcass weights, hot and cold yield, skin, head, feet, heart-lungs, spleen, kidney, kidney fat, stomach (full, empty), small and large intestine weights (full, empty), rump, arm, loin (fillet), back (chop), tail, rump- neck and others weights, MLD cross- sectional area were determined during cold carcass dismemberment. MLD cross- sectional area in the carcass was determined according to the method reported by Colomer-Rocher et al. (1988) by taking a copy of the cross-section made between the 12th-13th ribs on tracing paper and measuring it with the help of millimetre paper. Shell fat thickness was also determined by measuring with callipers from the same place. Carcass measurements were taken after slaughtering. Measuring stick and measuring tape were used to take the measurements. The left side of the carcass was separated into thigh, arm, skirt, neck, shoulder head, back-lumbar and tail and weights were taken. The carcass parts were weighed with an electronic scale sensitive to 1 g. The values obtained from the carcass parts were multiplied by two and the values of the whole carcass were obtained (Colomer-Rocher et al. 1988). Statistical analyses were performed using Minitab 12.0 package programme. The significance of the differences between groups was analysed by ANOVA and the significance of the differences between two groups was analysed by t test. 3. Results At the end of the experiment, the differences between the groups were significant (P<0.05, P<0.01), but the differences between the body measurements taken at other periods were 258 MAS JAPS 8(2): 256–264, 2023 body measurements taken in other periods were insignificant (P>0.05). the differences between the groups in terms of forelimb circumference were significant (P<0.01), but the differences between the Table 2. Various body measurements (cm) determined at the beginning, middle and end of the experiment in the group fattened for sixty days Features Chest circumference Front shank circumference Rear shank circumference Body length Height at Withers Chest depth Trial Head - - - - - - 60 day 75.99±2.85 7.44±0.13 8.63±0.15 57.89±1.62 60.98±1.06 27.57±0.78 75 day 74.05±2.04 7.61±0.09 8.74±0.19 58.01±1.04 59.02±0.91 26.35±0.60 90 day 75.39±2.03 7.49±0.11 8.72±0.17 58.72±1.34 59.02±1.05 26.38±0.68 Mid-trial - * - - - - 60 day 79.52±2.71 7.71±0.13b 9.30±0.16 60.55±1.48 61.38±1.12 27.93±0.52 75 day 79.77±2.36 8.18±0.09a 9.37±0.13 60.00±1.14 60.62±0.83 27.34±0.54 90 day 80.55±2.22 8.04±0.12ab 9.30±0.17 60.74±1.11 59.74±0.86 27.38±0.52 End of trial - ** - - - - 60 day 83.19±2.66 7.99±0.20b 9.99±0.25 63.30±1.58 61.80±1.25 28.31±0.65 75 day 85.71±2.81 8.77±0.14a 10.02±0.17 62.07±1.54 62.29±0.96 28.37±0.69 90 day 85.89±2.55 8.62±0.14a 9.90±0.20 62.84±1.09 60.50±0.82 28.42±0.54 The difference between groups with different letters in the same column is significant. -: P>0.05 insignificant,. *: P<0.05, **: P<0.01, ***: P<0.001. Table 2. Various body measurements (cm) determined at the beginning, middle and end experiment in the group fattened for sixty days ody measurements (cm) determined at the beginning, middle and end of the up fattened for sixty days Table 3. Various body measurements determined at the beginning, middle and end of the experiment in the group fattened for seventy-five days Chest Front shank Rear shank Body Height at Chest Table 3. Various body measurements determined at the beginning, middle and end of the exper the group fattened for seventy-five days Table 3. 3. Results The live weights of lambs weighed every two weeks are given in Table 1. In the analyses, no significant difference was found between the groups in terms of live weights (P>0,05). Table 1. Live weight of lambs in various periods (kg) Day Groups 60 day 75 day 90 day importance Beginning 35.43±2.49 35.32±2.42 35.70±2.15 - 14 38.68±2.76 38.51±2.53 39.27±2.27 - 28 40.77±2.94 40.22±2.60 41.15±2.27 - 42 43.37±3.05 42.75±2.66 43.11±2.48 - 56 - 44.91±2.75 45.27±2.56 - 70 - 46.15±2.80 46.48±2.51 - 84 - - 48.89±2.34 - 90 - - 51.17±2.18 The difference between groups with different letters on the same line is significant. -: P>0.05, insignificant *: P<0.05, **: P<0.01, ***: P<0.001. The difference between groups with different letters on the same line is significant. -: P>0.05, insignificant *: P<0.05, **: P<0.01, ***: P<0.001. insignificant (P>0.05). In the group fattened for 75 days, the difference between the groups was found to be significant (P<0.05) in terms of front shank circumference taken in the middle of the experiment. The differences between the body measurements taken in other periods were insignificant (P>0.05). In the ninety-day fattening group, the difference between the groups was found to be significant (P<0.05) in terms of forelimb shank circumference measurements taken in the middle of the experiment. At the end of the experiment, In Tables 2, 3 and 4, various body measurements taken at the beginning, middle and end of the experiment of the groups fed for different periods are given respectively. The difference between the groups was found to be significant (P<0.05) in terms of forelimb circumference taken in the middle of the experiment in the group fed for sixty days. At the end of the experiment, the differences between the groups were significant (P<0.05, P<0.01), but the differences between the body measurements taken at other periods were In Tables 2, 3 and 4, various body measurements taken at the beginning, middle and end of the experiment of the groups fed for different periods are given respectively. The difference between the groups was found to be significant (P<0.05) in terms of forelimb circumference taken in the middle of the experiment in the group fed for sixty days. 3. Results Various body measurements determined at the beginning, middle and end of the experiment in the group fattened for seventy-five days Features Chest circumference Front shank circumference Rear shank circumference Body length Height at Withers Chest depth Trial Head - - - - - - 60 day 75.99±2.85 7.44±0.13 8.63±0.15 57.89±1.62 60.98±1.06 27.57±0.78 75 day 74.05±2.04 7.61±0.09 8.74±0.19 58.01±1.04 59.02±0.91 26.35±0.60 90 day 75.39±2.03 7.49±0.11 8.72±0.17 58.72±1.34 59.02±1.05 26.38±0.68 Mid-trial - * - - - - 60 day 80.31±2.69 7.77±0.14b 9.45±0.18 61.14±1.48 61.47±1.14 28.01±0.51 75 day 81.04±2.44 8.31±0.10a 9.51±0.13 60.44±1.20 60.98±0.84 27.56±0.56 90 day 81.69±2.28 8.17±0.12ab 9.43±0.17 61.19±1.08 59.91±0.83 27.61±0.51 End of trial - - - - - - 75 day 81.10±6.50 8.64±0.18 10.17±0.21 64.61±1.20 61.65±0.81 29.56±0.65 90 day 88.98±2.60 8.82±0.16 10.26±0.21 63.70±1.10 62.38±1.20 30.78±1.90 The difference between groups with different letters in the same column is significant. -: P>0.05 insignificant,. *: P<0.05, **: P<0.01, ***: P<0.001. 259 MAS JAPS 8(2): 256–264, 2023 Table 4. Various body measurements (cm) determined at the beginning, middle and end of the experiment in the group fattened for ninety days Features Chest circumference Front shank circumference Rear shank circumference Body length Height at Withers Chest depth Trial Head - - - - - - 60 day 75.99±2.85 7.44±0.13 8.63±0.15 57.89±1.62 60.98±1.06 27.57±0.78 75 day 74.05±2.04 7.61±0.09 8.74±0.19 58.01±1.04 59.02±0.91 26.35±0.60 90 day 75.39±2.03 7.49±0.11 8.72±0.17 58.72±1.34 59.02±1.05 26.38±0.68 Mid-trial - ** - - - - 60 day 81.67±2.67 7.88±0.17b 9.71±0.21 62.16±1.51 61.63±1.19 28.15±0.54 75 day 83.25±2.61 8.53±0.12a 9.75±0.14 61.21±1.35 61.60±0.88 27.95±0.61 90 day 83.68±2.40 8.38±0.13a 9.65±0.18 61.97±1.07 60.19±0.81 27.99±0.51 End of trial - - - - - - 90 day 88.83±2.23 8.09±1.14 9.88±0.12 66.02±0.66 61.82±0.91 29.67±0.76 The difference between groups with different letters in the same column is significant. -: P>0.05 insignificant,. *: P<0.05, **: P<0.01, ***: P<0.001. . Various body measurements (cm) determined at the beginning, middle and end of the ent in the group fattened for ninety days carcass and large intestine full and empty weights, but the differences between the groups were insignificant (P>0.05) in terms of other characteristics. Table 5 shows various slaughter characteristics of different groups. When Table 5 was analysed, it was found that the differences between the groups were significant (P<0.05, P<0.01) in terms of hot Table 5. 3. Results Various slaughter characteristics of lambs (g, kg) Features Fattening time 60 day (n=6) 75 day (n=6) 90 day (n=6) importance Cutting weight (kg) 46.28±2.97 47.32±2.04 51.98±2.39 - Hot carcass weight (kg) 16.90±0.92b 18.83±0.93ab 21.43±1.36a * Skin weight (kg) 5.65±0.46 6.02±0.54 6.10±0.45 - Head weight (kg) 2.45±0.08 2.49±0.13 2.73±0.16 - Foot weight (g) 838.30±50.30 948.30±34.70 898.30±59.70 - Heart-lung weight (g) 828.30±62.10 836.70±37.50 818.30±24.40 - Liver weight (g) 680.00±36.10 623.33±36.20 651.67±20.40 - Spleen weight (kg) 73.33±9.55 76.67±8.03 66.67±4.22 - Kidney weight (g) 148.33±13.50 141.67±16.20 123.33±5.58 - Testes weight (g) 366.70±32.60 438.30±71.80 373.30±52.40 - Stomach full weight (kg) 6.60±0.42 5.47±0.39 5.47±0.38 - Empty stomach weight (kg) 1.47±0.10 1.43±0.09 1.42±0.07 - Small intestine full weight (kg) 2.09±0.12 2.02±0.13 2.02±0.15 - Small intestine empty weight (kg) 1.00±0.14 0.88±0.06 0.68±0.06 - Large intestine full weight (kg) 1.73±0.26b 1.08±0.11a 1.07±0.07a * Large intestine empty weight (kg) 0.55±0.06b 0.34±0.02a 0.36±0.03a ** The difference between groups with different letters in the same column is significant. -: P>0.05 insignificant,. *: P<0.05, **: P<0.01, ***: P<0.001. Table 5. Various slaughter characteristics of lambs (g, kg) P<0.01, P<0.001) for body depth, rump length II and rump circumference I in Table 7, and insignificant (P>0.05) for the other parameters given in Tables 6 and 7. P<0.01, P<0.001) for body depth, rump length II and rump circumference I in Table 7, and insignificant (P>0.05) for the other parameters given in Tables 6 and 7. P<0.01, P<0.001) for body depth, rump length II and rump circumference I in Table 7, and insignificant (P>0.05) for the other parameters given in Tables 6 and 7. Carcass parameters of different groups are given in Tables 6 and 7. The differences between the groups were found to be significant (P<0.05) for rump, arm and loin weights in Table 6, significant (P<0.05, 260 MAS JAPS 8(2): 256–264, 2023 Table 6. Various carcass parameters of lambs (kg, mm, cm²) Features Fattening time 60 day (n=6) 75 day (n=6) 90 day (n=6) importance Thigh weight (kg) 5.23±0.58b 6.26±0.18ab 7.11±0.38a * Arm weight (kg) 3.43±0.39b 4.27±0.24ab 4.74±0.26a * Loin (fillet) weight (kg) 1.55±0.17b 2.14±0.30ab 2.50±0.14a * Back (chop) weight (kg) 3.39±0.53 4.00±0.15 4.97±0.53 - Tail weight (kg) 3.94±0.36 3.35±0.39 3.73±0.42 - Weight of neck and neck (kg) 1.40±0.15 1.72±0.18 2.02±0.20 - MLD shell oil thickness (mm) 0.30±0.02 0.34±0.03 0.35±0.02 - MLD cross-sectional area (cm2) 21.10±2.48 18.37±1.22 20.62±1.30 - The difference between groups with different letters in the same column is significant. 3. Results -: P>0.05 insignificant,. *: P<0.05, **: P<0.01, ***: P<0.001. Table 6. Various carcass parameters of lambs (kg, mm, cm²) Table 7. Various carcass parameters of lambs (cm) Features Fattening time 60 day (n=6) 75 day (n=6) 90 day (n=6) importance Karkas uzunluğu I (cm) 50.72±1.86 55.38±1.38 54.02±1.78 - Karkas uzunluğu II (cm) 71.55±1.27 68.82±1.00 69.90±2.30 - Gövde derinliği (cm) 26.53±0.40b 25.68±0.36b 23.15±0.74a ** But uzunluğu I (cm) 39.53±0.77 40.38±0.57 41.12±0.72 - But uzunluğu II (cm) 60.47±6.38b 72.63±1.06b 33.60±0.91a *** But çevresi I (cm) 38.35±1.66b 41.87±0.82ab 42.93±0.67a * But çevresi II (cm) 31.21±1.33 31.93±0.49 34.38±0.76 - Kol uzunluğu (cm) 23.20±2.51 21.40±0.33 21.63±0.30 - Kol çevresi (cm) 15.67±0.73 15.22±0.43 16.40±0.27 - The difference between groups with different letters in the same column is significant. -: P>0.05 insignificant,. *: P<0.05, **: P<0.01, ***: P<0.001. Table 7. Various carcass parameters of lambs (cm) between the live weights of the lambs in the groups since the birth periods of the lambs were not close to each other and they were at different ages. The end of fattening weights in all three groups were higher than the end of fattening weight (34.24 kg) reported by Işık and Kaya (2011) at the end of 90-day trial in their study on the determination of fattening performance of Tuj breed lambs grazing on pasture, and higher than the end of fattening weight (38 kg) obtained in pasture fattening with Tuj lambs weaned at Kars Experimental and Breeding Station and weighing 19 kg on average (Eliçin et al. 1988). This may be due to the fact that the lambs used in the studies were at different ages and had different starting weights and the studies were conducted as pasture fattening. In some studies (İlaslan and Geliyi 1979, Ulusan and Aksoy 1996), the live weights determined with Tuj and Morkaraman lambs during the pasture period were lower than the results of this study. It can be said that this may be due to the different ages and 4. Discussion In this study, rump, arm and neck weight values reported in all three groups were higher than the values of rump weight (6.29, 6.36 and 6.47 kg), arm weight (3.51, 3.66 and 3.75 kg) and neck weight (1.52, 1.55 and 1.66 kg) reported by Sarı et al. (2012) in pasture, pasture+200 and pasture+400 g groups in Tuj lambs. In a study conducted in Tuj and Morkaraman lambs reared under semi-intensive conditions (Kırmızıbayrak et al. 2003), the rump weight (5.66 kg) of Tuj male lambs was similar to the group fed for 60 days, while the values reported in the other two groups were higher. The results were higher than the values of arm weight (2.95 kg), back-lumbar weight (2.61 kg) and MLD cross-sectional area (9.84 cm2) determined in the same study, while the values of thigh weight (6.04 kg) reported in Morkaraman breed male lambs were similar in the 75-day group and arm weight (3.26 kg) was similar in the 60-day group. In the same study, back-lumbar weight (2.91 kg) and MLD cross-sectional area (10.46 cm2) were lower than the experimental results. The measurements of chest circumference, anterior shank circumference, posterior shank circumference, body length, body height and chest depth of each group were taken 3 times at the beginning, middle and end of the experiment. In the 60-day fattening group, the difference between the groups in terms of anterior shank circumference at the middle and end of the experiment was significant (P<0.05, P<0.01), while the differences found in terms of different body measurements in other periods were found to be insignificant (P>0.05). Again, the differences between the groups in terms of the front shank circumference measurements taken in the middle of the experiment in the 75 and 90 days fattening groups were significant (P<0.05, P<0.01, respectively), while the differences in the other periods were found to be insignificant (P>0.05). The chest girth measurements obtained at different periods were higher than the values (44.57, 46.49, 57.52, 59.05, 68.67 cm) determined by Akçapınar et al. (2002) at 45th and 90th days in Karayaka and Bafra lambs and at 180th day in Karayaka under the conditions of Lalahan Livestock Research Institute, while the value reported for Bafra at 180th day (71.83 cm) was similar to the value reported at the beginning of the experiment for all three groups. 4. Discussion The chest girth measurements obtained at different periods were higher than the values (44.57, 46.49, 57.52, 59.05, 68.67 cm) determined by Akçapınar et al. (2002) at 45th and 90th days in Karayaka and Bafra lambs and at 180th day in Karayaka under the conditions of Lalahan Livestock Research Institute, while the value reported for Bafra at 180th day (71.83 cm) was similar to the value reported at the beginning of the experiment for all three groups. Again, the results of the study were higher than the values (41.12, 42.67; 18.61, 19.72; 42.57, 44.27 cm) determined at 45th day for Karayaka and Bafra lambs in the same study in terms of MAS JAPS 8 weights of the lambs included in the experiment. The differences between the groups were found to be insignificant (P>0.05) in terms of various slaughter characteristics of lambs (skin, head, feet, heart-lung, liver, spleen, kidney, testes, stomach full and empty, small intestine full and empty) except for the weights of large intestine full and empty (P<0.05, P<0.01). This may be due to the fact that the growth in the internal organs and extremities was completed to a great extent when the age and weight of the lambs at the beginning of fattening were considered. In terms of carcass parameters, rump, arm and loin weights were 5.23±0.58, 6.26±0.18, 7.11±0.38; 3.43±0.39, 4.27±0.24, 4.74±0.26 and 1.55±0.17, 2.14±0.30, 2.50±0.14, respectively. While the differences between the groups were significant (P<0.05) in terms of the related traits, the differences between the groups were found insignificant (P>0.05, Table 6) in terms of other carcass parameters (back, tail, rump and neck weight, MLD shell fat thickness and MLD cross-sectional area). Among the carcass parameters expressed in cm units in Table 7, the differences between the groups were significant (P<0.05, P<0.01, P<0.001) for body depth, rump length II and rump circumference I, while the differences were insignificant for the other parameters (P>0.05, Table 7). The hot carcass weight values reported in all three fattening groups were higher than the hot carcass weight values (20.66, 21.36 and 22.15 kg) reported by Sarı et al. (2012) in pasture, pasture+200 and pasture+400 g groups in Tuj lambs. 4. Discussion On days 0, 14, 28, 42, 56, 56, 70, 84 and 90, the mean body weights of lambs belonging to the groups were 35.43±2.49, belonging to the groups were 35.43±2.49, 35.32±2.42, 35.32±2.42; 38.68±2.76, 38.51±2.53, 38.51±2.53; 40.77±2. 94, 40.22±2.60, 41.15±2.27; 43.37±3.05, 42.75±2.66, 43.11±2.48; 2nd and 3rd groups 44.91±2.75, 44.91±2.75, 46.15±2.80, 46.48±2.51; 3rd group 48.89±2.34 and 51.17±2.18 kg. The average live weight of lambs in the three groups at the beginning of the experiment was 35 kg. Slaughter weights of the three groups were 46.28±2.97, 47.32±2.04, 51.98±2.39, respectively. While there was no significant statistical difference between the groups in terms of slaughter weight, hot carcass weights were determined as 16.90±0.92, 18.83±0.93, 21.43±1.36 kg, respectively, and the difference between the 1st and 2nd groups was found significant (P<0.05). The fact that there was no difference between the groups in terms of slaughter weights is thought to be due to the high variation 261 MAS JAPS 8(2): 256–264, 2023 56–264, 2023 was similar to the group fed for 60 days, while the values reported in the other two groups were higher. The results were higher than the values of arm weight (2.95 kg), back-lumbar weight (2.61 kg) and MLD cross-sectional area (9.84 cm2) determined in the same study, while the values of thigh weight (6.04 kg) reported in Morkaraman breed male lambs were similar in the 75-day group and arm weight (3.26 kg) was similar in the 60-day group. In the same study, back-lumbar weight (2.91 kg) and MLD cross-sectional area (10.46 cm2) were lower than the experimental results. The measurements of chest circumference, anterior shank circumference, posterior shank circumference, body length, body height and chest depth of each group were taken 3 times at the beginning, middle and end of the experiment. In the 60-day fattening group, the difference between the groups in terms of anterior shank circumference at the middle and end of the experiment was significant (P<0.05, P<0.01), while the differences found in terms of different body measurements in other periods were found to be insignificant (P>0.05). Again, the differences between the groups in terms of the front shank circumference measurements taken in the middle of the experiment in the 75 and 90 days fattening groups were significant (P<0.05, P<0.01, respectively), while the differences in the other periods were found to be insignificant (P>0.05). 4. Discussion Again, the results of the study were higher than the values (41.12, 42 67; 18 61 19 72; 42 57 44 27 cm) weights of the lambs included in the experiment. The differences between the groups were found to be insignificant (P>0.05) in terms of various slaughter characteristics of lambs (skin, head, feet, heart-lung, liver, spleen, kidney, testes, stomach full and empty, small intestine full and empty) except for the weights of large intestine full and empty (P<0.05, P<0.01). This may be due to the fact that the growth in the internal organs and extremities was completed to a great extent when the age and weight of the lambs at the beginning of fattening were considered. In terms of carcass parameters, rump, arm and loin weights were 5.23±0.58, 6.26±0.18, 7.11±0.38; 3.43±0.39, 4.27±0.24, 4.74±0.26 and 1.55±0.17, 2.14±0.30, 2.50±0.14, respectively. While the differences between the groups were significant (P<0.05) in terms of the related traits, the differences between the groups were found insignificant (P>0.05, Table 6) in terms of other carcass parameters (back, tail, rump and neck weight, MLD shell fat thickness and MLD cross-sectional area). Among the carcass parameters expressed in cm units in Table 7, the differences between the groups were significant (P<0.05, P<0.01, P<0.001) for body depth, rump length II and rump circumference I, while the differences were insignificant for the other parameters (P>0.05, Table 7). The hot carcass weight values reported in all three fattening groups were higher than the hot carcass weight values (20.66, 21.36 and 22.15 kg) reported by Sarı et al. (2012) in pasture, pasture+200 and pasture+400 g groups in Tuj lambs. In this study, rump, arm and neck weight values reported in all three groups were higher than the values of rump weight (6.29, 6.36 and 6.47 kg), arm weight (3.51, 3.66 and 3.75 kg) and neck weight (1.52, 1.55 and 1.66 kg) reported by Sarı et al. (2012) in pasture, pasture+200 and pasture+400 g groups in Tuj lambs. In a study conducted in Tuj and Morkaraman lambs reared under semi-intensive 262 MAS JAPS 8(2): 256–264, 2023 Akçapınar, H., Ünal, N., Atasoy, F., Özbeyaz, C., Aytaç, M., 2002. Karayaka ve Bafra (Sakız × Karayaka G1) Koyunlarının Lalahan Hayvancılık Araştırma Enstitüsü Şartlarına Uyum Kabiliyeti. Lalahan Hayvancılık Araştırma Enstitüsü Dergisi, 42(1): 11- 24. body height, chest depth and body length measurements. Funding This study was supported by the Scientific Research Projects Coordinatorship of Kafkas University (Project No: 2010-VF- 22) Colomer-Rocher, F., Morand-Fher, P., Kirton, A.H., Delfa, R., Sierra, I., 1988. Standard methods to study the quantitative and qualitative carcass characteristics in goat and sheep. Cuadernos INIA 17, 25. Declaration of Conflicts of Interest All authors declare that there is no conflict of interest related to this article. Aksoy, A.R., 1995. Farklı kesim ağırlıklarında morkaraman ve tuj erkek kuzularının besi performansı kesim ve karkas özellikleri. Ankara Üniversitesi Veteriner Fakültesi Dergisi. 42(1): 15- 23. All authors declare that there is no conflict of interest related to this article. Declaration of Author Contributions Declaration of Author Contributions The authors declare that they have contributed equally to the article. All authors declare that they have seen/read and approved the final version of the article ready for publication. The authors declare that they have contributed equally to the article. All authors declare that they have seen/read and approved the final version of the article ready for publication. Aksoy, A.R., Kırmızıbayrak, T., Saatcı, M., Dalcı, M.T., 2001. Tuj Irkı koyunların verim özellikleri. II. süt verimi ve yapağı verimi. Veteriner Bilimleri Dergisi, 17(2): 123-126. Declaration of Conflicts of Interest All authors declare that there is no conflict of interest related to this article. 4. Discussion On the 180th day, the body length (58.06 cm) determined for Bafra sheep was similar to the values reported at the beginning of the experiment for all three groups, while it was found to be lower in other periods. On the 90th day, the measurements of chest girth, body length, body length, chest depth (64.76, 52.34, 51.44, 23.89 cm) determined by Akçapınar et al. (2001) in Sakız × Akkaraman F1s were lower than the values obtained in different periods in all three groups in the experiment. As a result, the differences between the various parameters obtained during the experiment were not significant except for the hot carcass, thigh, arm and loin weights and front shank circumference. This is thought to be due to the high variation in live weights among lambs at the beginning of the experiment. Akçapınar, H., Atasoy, F., Ünal, N., Aytaç, M., Aylanç, A., 2000. Bafra (Sakız×KarayakaG1) Kuzularda Besi ve Karkas Özellikleri. Lalahan Hayvancılık Araştırma Enstitüsü Şartlarına Uyum Kabiliyeti. Lalahan Hayvancılık Araştırma Enstitüsü Dergisi, 42(2) 19- 28. Akçapınar, H.: Koyun Yetiştiriciliği. Yenilenmiş 2. baskı, İsmat Matbaacılık, Ankara, ISBN: 975-96978-1-5. Akçapınar, H., Özbeyaz, C., 1999. Hayvan Yetiştiriciliği Temel Bilgileri 1. baskı, Kariyer Matbaacılık, ISBN: 975-96978- 0-7, Ankara. References Akçapınar, H., Ünal, N., Özbeyaz, C., 2001. Kuzu Eti Üretimine Uygun Ana ve Baba Hatlarının Geliştirilmesinde Akkaraman, Sakız ve Kıvırcık Irklarından Yararlanma İmkanları, II. Kuzularda Bazı Vücut Ölçüleri ve Toklularda Bazı Verim Özellikleri. Lalahan Hayvancılık Araştırma Enstitüsü Dergisi, 41(1): 25- 34. Çiçek, H., Sakarya, E., 2003. Afyon ili sığır besi işletmelerinde kârlılık ve verimlilik analizleri. Lalahan Hayvancılık Araştırma Enstitüsü Dergisi, 43(2):1-13. Demir, P., Adıgüzel Işık, S., Aydın, E., Yazıcı, K., Ayvazoğlu, C., 2015. Ardahan ilinde koyun yetiştiriciliğinin sosyo-ekonomik önemi. YYU Veteriner Fakültesi Dergisi, 26(3): 141-146. 263 MAS JAPS 8(2): 256–264, 2023 Karaman lambs raised in semi-intensive conditions. Kafkas Üniversitesi, Veteriner Fakültesi Dergisi, 9: 75-78. Eliçin A., Geliyi, C., Ertuğrul, M. Cengiz, F., İlaslan, M., Aşkın, Y., 1988. Farklı yöntemlerle beslenen tuj koyunlarının besi gücü ve karkas özellikleri. A.Ü. Ziraat Fakültesi Yıllığı. 39: 323-333. Koçak, A.F., 2009. Türkiye’de yapılan kuzu besi çalışmaları. Namık Kemal Üniversitesi, Fen Bilimleri Enstitüsü, Yüksek Lisans Tezi, Tekirdağ. Elmalı Aksu, D., Demir, P., Kaya, İ., 2010. Tuj kuzularında farklı konsantre yemlerle yapılan besinin maliyet-fayda analizi. Kafkas Üniversitesi, Veteriner Fakültesi Dergisi, 16(5): 771-775. Laçin, E., Aksoy, A.R., 2003 Kars bölgesinde yetiştirilen morkaraman ve tuj kuzularının büyüme özelliklerinin karşılaştırılması. Kafkas Üniversitesi, Veteriner Fakültesi Dergisi, 9(1): 33-37. Işık, S., Kaya, İ., 2011. Vejetasyon döneminin mera kalitesi ile merada otlayan TUJ ırkı koyun ve kuzuların besi performansı üzerine etkisi. Kafkas Üniversitesi, Veteriner Fakültesi Dergisi, 17(1): 7-11. Sarı M., Aksoy .R., Tilki M., Kaya İ., Işık S., 2012 Effect of different fattening methods on slaughter and carcass characteristics of Tuj male lambs. Archiv Tierzucht, 55(5): 480-484. Kaya İ, Şahin T, Elmalı Aksu D, Ünal Y., 2011. Merada otlatma ve meraya ilave konsantre yem verilmesinin kuzularda performans ve rumen parametrelerine etkisi. Kafkas Üniversitesi, Veteriner Fakültesi Dergisi, 17(5): 693-697. Tekel, N., Şireli, H.D., Vural, M.E., 2007. Besi süresinin ivesi erkek kuzuların besi performansı ve karkas özelliklerine etkisi. Ankara Üniversitesi Ziraat Fakültesi Tarım Bilimleri Dergisi, 13(4): 372-378. İlaslan, M., Geliyi, C., 1979. Altı aylık erkek morkaraman ve TUJ kuzularının besi gücü ve bazı karkas özellikleri üzerine araştırmalar. Deneme ve Üretme İstasyonu. Yayın No:8, Kars. TÜİK (Türkiye İstatistik Kurumu), 2023. Erişim Tarihi: 04.04.2023. Hayvansal Üretim İstatistikleri, 20021. Erişim: https://data.tuik.gov.tr/Kategori/GetKat egori?p=Tarim-111 Karaoğlu, M., Macit M., Aksoy, A., 2001 Entansif besiye alınan TUJ kuzularının besi performansı üzerine bir araştırma. Turkish Journal of Veterinary & Animal Sciences, 25: 255-260. Ulusan, H.O.K., Aksoy, A.R., 1996. Kafkas Üniversitesi Veteriner Fakültesi Çiftliğinde Yetiştirilen Tuj ve Morkaraman Koyunların Verim Performansları. 2. To Cite: Adıgüzel Işık, S., Sarı, M., Tilki, M., Önk, K., 2023. The Effect of Fattening Time on Fattening Performance, Slaughter and Case Features in Tuj Male Lamb. MAS Journal of Applied Sciences, 8(2): 256–264. DOI: http://dx.doi.org/10.5281/zenodo.7933388. References Büyüme ve Beden Ölçüleri. Kafkas Üniversitesi, Veteriner Fakültesi Dergisi, 2(2): 139-146. Kırmızıbayrak, T., Saatcı, M., Aksoy, A.R., 2003. Slaughter and carcass characteristics of Tushin and Red 264
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Characteristics of morbidity and mortality conferences associated with the implementation of patient safety improvement initiatives, an observational study
BMC health services research
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© 2016 François et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. François et al. BMC Health Services Research (2016) 16:35 DOI 10.1186/s12913-016-1279-8 François et al. BMC Health Services Research (2016) 16:35 DOI 10.1186/s12913-016-1279-8 * Correspondence: pfrancois@chu-grenoble.fr 1Quality of Care Unit, University Hospital, and Research Unit, TIMC-IMAG (UMR 5525 CNRS/UJF-Grenoble 1), Grenoble F-38043, France Full list of author information is available at the end of the article Characteristics of morbidity and mortality conferences associated with the implementation of patient safety improvement initiatives, an observational study Patrice François1*, Frédéric Prate2, Gwenaëlle Vidal-Trecan3, Jean-François Quaranta2, José Labarere1 and Elodie Sellier1 Abstract Background: The aim of this study was to identify the characteristics of morbidity and mortality conferences (MMCs) associated with the implementation of patient health-care quality and safety improvement initiatives. Methods: We conducted an observational study of MMCs and followed up improvement initiatives for 1 year. Data on MMC baseline characteristics were abstracted using document analysis and observation of a meeting in three university hospitals in France (Grenoble, Nice, and Cochin [Paris] hospitals). Fifty-nine MMCs were included in medical (n = 24), surgical (n = 21), and anesthesiology and/or intensive care (n = 14) departments. An effectiveness index was computed by summing a composite score for each initiative pertaining to the MMC. Results: Overall, 282 initiatives were identified in 42 MMCs. During the follow-up period, 215 initiatives (76 %) were totally or partially implemented and the impact was evaluated for 73 (26 %). An effectiveness index higher than the median (i.e., ≥10) was associated with a standardized presentation of cases (81 % versus 29 %, p <0.001), recording of improvement initiatives (94 versus 57, p = 0.001), the existence of an annual activity report (94 % versus 68 %, p = 0.01), the prior dissemination of a meeting agenda (71 % versus 36 %, p = 0.007), longer meeting duration (109 versus 80 min, p = 0.005), anesthesiology and/or intensive care specialty (39 % versus 7 %, p = 0.02), a theme-focused MMC (29 % versus 4 %, p = 0.01), and a thorough analysis of failures (58 % versus 25 %, p = 0.01). Conclusions: This study suggests that the implementation of improvement initiatives relates to MCC characteristics. Recommendations for developing more effective patient safety-oriented MMCs can be proposed. Conclusions: This study suggests that the implementation of improvement initiatives relates to MCC characteristics. Recommendations for developing more effective patient safety-oriented MMCs can be proposed. Keywords: Morbidity and mortality conferences, Patient safety, Quality improvement, Hospital © 2016 François et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a lin Endpoint All MMCs established in the participating hospitals for more than 1 year were eligible. They were identified by researchers between September and December 2010. The purpose of the study was presented to the MMC leaders and their consent was required for participation in the study. All MMC leaders gave their informal oral consent for document analysis and requested the oral consent of MMC participants to accept the presence of two observers at a meeting. In case of refusal from the MMC leader and/or a participant, the MMC was not in- cluded in the study. Data collected on the forms con- tained no data directly or indirectly identifying patients or healthcare professionals. Ethics review board (Direction for clinical research, Grenoble university hospital) approval was not required for this observational study because no personal data was collected [19, 20]. The main endpoint of the study was an effectiveness index calculated for each department and based on the number and completion of improvement initiatives. Each single initiative was scored according to four items including designation of a person in charge of imple- mentation (yes or no), definition of a timeline (yes or no), completion (fully, partially, or not completed), and evaluation of its impact (fully, partially, or not evalu- ated). Completion was categorized as partially when a part of the action plan was not achieved or when the entire target population was not reached. The evaluation was considered as partial if it was only an informal assess- ment and was considered as complete if the impact of the action was formally assessed by an indicator or audit. The initiative score was obtained by summing the points for each item (Table 1) and ranged from 0 to 6, with a higher score denoting higher levels of completion and evaluation. Study design We conducted an observational study of MMC character- istics with a prospective follow-up of improvement initia- tives in three university hospitals in France (Grenoble, Nice, and Cochin [Paris] hospitals). In each hospital, the organization of MMCs was defined in a guideline and de- partments could obtain methodological assistance from the quality-assurance team. Background This observation may reflect the lack of explicit goals, methods, and format for MMCs [3, 4, 15]. However, it is not known whether the characteristics of MMCs are associated with effectiveness in healthcare qual- ity and safety. Previous studies have reported conflicting results regarding the impact of MMCs. Few single-center studies found significant reductions in adverse events such as ventilator-associated pneumonia rates or cardiac arrest incidence [10, 16]. Other studies failed to show any im- provement in patient clinical outcomes, [17, 18] probably due to the low incidence of adverse events [18]. Another way to assess the effectiveness of MMCs is to study their effect on care processes. Since changes in practices are mediated by the improvement initiatives that are decided on during the meetings, studying these initiatives may help assess the effectiveness of the con- ferences [8, 9, 11]. Additionally, two researchers independently observed a meeting for each identified MMC, using a structured data collection form (Additional files 3 and 4). They recorded the types of participants, the format of presentations (use of slides, chronological presentation of facts, literature re- view), and the content of the discussion (investigation of adverse events and underlying factors). Observers attended two 4-h sessions together to standardize data collection and coding, and coding instructions were written in a data collection guide. The aim of this multicenter study was to investigate the characteristics of MMCs and to find which of them were associated with the number of improvement initia- tives and their implementation. Methods Study design All improvement initiatives identified by direct obser- vation or document analysis were followed up for 1 year. They were categorized according to the International Classification for Patient Safety [21]. At the end of the study period, MMC leaders were asked whether the initia- tives had been implemented and if their impact had been evaluated. Two investigators independently reviewed the documents to ascertain whether the improvement initia- tives were actually implemented and evaluated. Background is basically an educational process and a training oppor- tunity for residents [6, 7]. Furthermore, MMCs oriented toward clinical risk management can help develop the general competencies of those involved in practice-based learning and improvement as well as a system-based practice, mandated by the Accreditation Council for Graduate Medical Education (ACGME) [4, 7–12]. Morbidity and mortality conferences (MMCs) were pri- marily established as an educational tool for surgeons in the United States [1]. Their use rapidly extended to other specialties and countries. MMCs seek to analyze medical errors and adverse events in order to improve medical practices [2–5]. Identifying and analyzing errors Evidence is lacking on whether the MMC is an effective tool for improving patient safety [12, 13]. Substantial vari- ations exist in MMCs with regard to frequency, attend- ance, case selection or presentation, analysis methods, and * Correspondence: pfrancois@chu-grenoble.fr 1Quality of Care Unit, University Hospital, and Research Unit, TIMC-IMAG (UMR 5525 CNRS/UJF-Grenoble 1), Grenoble F-38043, France Full list of author information is available at the end of the article François et al. BMC Health Services Research (2016) 16:35 Page 2 of 8 Page 2 of 8 Page 2 of 8 follow-up [13, 14]. This observation may reflect the lack of explicit goals, methods, and format for MMCs [3, 4, 15]. However, it is not known whether the characteristics of MMCs are associated with effectiveness in healthcare qual- ity and safety. Previous studies have reported conflicting results regarding the impact of MMCs. Few single-center studies found significant reductions in adverse events such as ventilator-associated pneumonia rates or cardiac arrest incidence [10, 16]. Other studies failed to show any im- provement in patient clinical outcomes, [17, 18] probably due to the low incidence of adverse events [18]. MMC written documents produced during the year before the inclusion date were analyzed. These documents included the charter or the organizational procedure, all meeting re- ports, the annual activity reports, and all documents related to improvement initiatives decided in meetings. Data col- lected included department specialty, documents tracing the activity, number of meetings, number of cases presented, and number of senior physicians, residents, nurses and other paramedics who attended the meetings during the period under study. Attendance rates were computed by dividing the number of MMC attendants by the number of eligible professionals in the department. follow-up [13, 14]. Data collection The effectiveness index of MMCs within a department was obtained by summing the initiative scores related to this department. The effectiveness index was higher In each center, data on MMC baseline characteristics were abstracted from document analysis by two researchers with the MMC leader present (Additional files 1 and 2). All François et al. BMC Health Services Research (2016) 16:35 Page 3 of 8 Page 3 of 8 Table 1 Items and scoringa system for improvement initiative completion (N = 282) Points Number Percent Designation of person in charge No 0 132 (46.8) Yes 1 150 (53.2) Definition of a timeline No 0 185 (65.6) Yes 1 97 (34.4) Completion of action None 0 67 (23.8) Partial 1 28 (9.9) Complete 2 187 (66.3) Evaluation None 0 209 (74.1) Partial 1 38 (13.5) Complete 2 35 (12.4) aFor each improvement initiative, the score ranged from 0 to 6 Table 1 Items and scoringa system for improvement initiative completion (N = 282) Table 1 Items and scoringa system for improvement initiative of four meetings per MMC (IQR, 3–7) were conducted during the study period (Table 2). A median number of 18 cases were examined (IQR, 9–47), mostly deaths or complications from a medical procedure. Senior physi- cians and residents accounted for the vast majority of MMC attendants. of four meetings per MMC (IQR, 3–7) were conducted during the study period (Table 2). A median number of 18 cases were examined (IQR, 9–47), mostly deaths or complications from a medical procedure. Senior physi- cians and residents accounted for the vast majority of MMC attendants. A meeting report was found for each meeting in 53 MMCs (90 %), whereas some meeting reports were lack- ing in five MMCs and no meeting report was found in one MMC. The improvement initiatives were recorded for 45 MMCs (76 %). Direct observation of MMCs recorded 766 case presen- tations, including 352 deaths (45.8 %), 405 complications (52.7 %), and nine near-miss events. Senior physicians ex- clusively presented the cases in 34 MMCs (58 %) (Table 3). In the vast majority of MMCs, the clinical facts were de- scribed chronologically. In 13 MMCs (22 %), the presenter reported information drawn from a literature review. The discussion was centered on clinical practice (91 %) and less frequently on organizational issues (49 %). Data collection Defects in the patient’s care were sought in 54 MMCs (91 %) and were thoroughly analyzed in 25 MMCs (42 %) with a when the initiatives were more numerous and more thoroughly planned, implemented, and evaluated. Table 2 Baseline morbidity and mortality conference characteristics abstracted from document analysis (n = 59) Table 2 Baseline morbidity and mortality conference characteristics abstracted from document analysis (n = 59) Center, n, (%) Grenoble 29 (49.2) Nice 21 (35.6) Cochin 9 (15.3) Specialty, n, (%) Medicine 24 (40.7) Surgery 21 (35.6) Anesthesiology and intensive care 14 (23.7) Documents, n, (%) Written charter 53 (89.8) Annual activity report 48 (81.4) Nominative list of attendants 50 (84.7) Meeting report for each meeting 53 (89.8) Record of decided actions 45 (76.3) Organization Number of meetings during the year, median, [IQR] 4 [3─7] Number of cases studied during the year, median, [IQR] 18 [9─47] Theme-focused MMC, n, (%) 10 (17.0) Prior dissemination of meeting agenda, n, (%) 32 (54.2) Professionals attending at least one meeting, %, [IQR] Senior physicians 80 [60─100] Residents 77 [55─100] Head nurses 67 [0─100] Nurses 8 [0─19] Statistical analysis MMC baseline characteristics were reported as numbers and percentages for categorical variables, and median and interquartile range (IQR) for continuous variables. The continuous variables, including the effectiveness index, were dichotomized according to their median. In univariate analysis, we examined the associations be- tween the dichotomized effectiveness index and MMC characteristics using the chi-square test or Fischer’s exact test, when appropriate, for categorical variables, the chi-square test for trend for ordered categorical vari- ables, and the Kruskal-Wallis test for continuous vari- ables. We performed multivariate logistic regression analysis to estimate adjusted odds ratios for the charac- teristics that were independently associated with the dichotomized effectiveness index. Covariates were re- moved from a full non-parsimonious model using a backward approach with a p-value <0.10; p-values less than 0.05 were considered statistically significant. In case of multiple comparisons, the Bonferroni correction was applied to calculate a corrected threshold αc. Analyses were performed using Stata 11.0 (Stata Corp, College Station, TX, USA). Results Organizational, equipment, and patient factors accounted for 32.3, 8.5, and 7.1 % of im- provement initiatives respectively Table 3 Baseline morbidity and mortality conference characteristics recorded by direct observation (n = 59) Characteristics Number Percent Function of the professional presenting the cases, n, (%) Senior physician 34 (57.6) Resident 4 (6.8) Both 21 (35.6) Cases presentation, n, (%) Standardized with use of slides 33 (55.9) Chronological presentation of facts 54 (91.5) Presentation of literature data 13 (22.0) Topics of discussion, n, (%) Clinical practice 54 (91.5) Communication/organizational issues 29 (49.2) Failures, n, (%) Searched 54 (91.5) Searched and thoroughly analyzed 25 (42.4) Searched and analyzed using a structured method 3 (5.1) Monitoring of previous initiatives, n, (%) 8 (13.6) Length of meeting (min), median, [IQR] 87 [60─120] Table 4 Factors that contributed to an incident and were the target of an improvement initiative decided during morbidity and mortality conferences (N = 282) Factors Number Percent Staff 111 39.4 Training 32 11.3 Orientation 2 0.7 Supervision/assistance 4 1.4 Availability of checklists/protocols/policies 72 25.5 Adequate staff numbers/quality 1 0.4 Organizational/environmental 91 32.3 Matching physical environment to needs 8 2.8 Making arrangements for access to a service 17 6.0 Performing risk assessment/root cause analyses 2 0.7 Current code/specifications/regulations being met 9 3.2 Arranging ready access to protocols/policies/ decision aids 31 11.0 Improved leadership/guidance 22 7.8 Matching of staff to tasks/skills 1 0.4 Improving safety culture 1 0.4 Other 36 12.8 Recommending a new practice 9 3.2 Literature review 14 5.0 Study of clinical cohorts 8 2.8 Improved file/traceability 3 1.1 Declaration to risk management unit 2 0.7 Agent/equipment 24 8.5 Provision of equipment 20 7.1 Regular audits 4 1.4 Patient 20 7.1 Provision of adequate care/support 7 2.5 Provision of patient education/training 6 2.1 Provision of protocols/decision aid 6 2.1 Provision of medication dispensing aid 1 0.4 Table 4 Factors that contributed to an incident and were the target of an improvement initiative decided during morbidity and mortality conferences (N = 282) Factors Number Percent Staff 111 39.4 Training 32 11.3 Orientation 2 0.7 Supervision/assistance 4 1.4 Availability of checklists/protocols/policies 72 25.5 Adequate staff numbers/quality 1 0.4 Organizational/environmental 91 32.3 Matching physical environment to needs 8 2.8 Making arrangements for access to a service 17 6.0 Performing risk assessment/root cause analyses 2 0.7 Current code/specifications/regulations being met 9 3.2 Arranging ready access to protocols/policies/ decision aids 31 11.0 Improved leadership/guidance 22 7.8 Matching of staff to tasks/skills 1 0.4 Improving safety culture 1 0.4 Other 36 12.8 Recommending a new practice 9 3.2 Literature review 14 5.0 Study of clinical cohorts 8 2.8 Improved file/traceability 3 1.1 Declaration to risk management unit 2 0.7 Agent/equipment 24 8.5 Provision of equipment 20 7.1 Regular audits 4 1.4 Patient 20 7.1 Provision of adequate care/support 7 2.5 Provision of patient education/training 6 2.1 Provision of protocols/decision aid 6 2.1 Provision of medication dispensing aid 1 0.4 search for underlying factors. Results All solicited MMC leaders and participants agreed to participate in the study. The study sample consisted of 59 MMCs, including 24 (40.7 %) in medical units, 21 (35.6 %) in surgical units, and 14 (23.7 %) in anesthesiology or intensive care units. A median number François et al. BMC Health Services Research (2016) 16:35 Page 4 of 8 Page 4 of 8 Table 3 Baseline morbidity and mortality conference characteristics recorded by direct observation (n = 59) Characteristics Number Percent Function of the professional presenting the cases, n, (%) Senior physician 34 (57.6) Resident 4 (6.8) Both 21 (35.6) Cases presentation, n, (%) Standardized with use of slides 33 (55.9) Chronological presentation of facts 54 (91.5) Presentation of literature data 13 (22.0) Topics of discussion, n, (%) Clinical practice 54 (91.5) Communication/organizational issues 29 (49.2) Failures, n, (%) Searched 54 (91.5) Searched and thoroughly analyzed 25 (42.4) Searched and analyzed using a structured method 3 (5.1) Monitoring of previous initiatives, n, (%) 8 (13.6) Length of meeting (min), median, [IQR] 87 [60─120] search for underlying factors. This cause analysis was based on a structured method in three MMCs (5 %). In eight MMCs (14 %), the previously identified initiatives were followed up at each subsequent meeting. A total of 282 improvement initiatives were identified in MMCs in 42 departments during the study period, with a median number of four initiatives per department (Table 4). Of these, 111 initiatives (39.4 %) targeted factors related to the staff, with 72 aiming at developing or amending check- lists, protocols, or policies. Results BMC Health Services Research (2016) 16:35 Page 5 of 8 Page 5 of 8 Table 5 Differences between the characteristics of morbidity and mortality conferences according to the level of the effectiveness index Table 5 Differences between the characteristics of morbidity and mortality conferences according to the level of the effectiveness d Table 5 Differences between the characteristics of morbidity and mortality conferences according to the level of the effectiveness y y g index Index <10 Index ≥10 p* N = 28 N = 31 Center, n, (%) 0.14 Grenoble 17 (60.7) 12 (38.7) Nice 9 (32.1) 12 (38.7) Paris 2 (7.1) 7 (22.6) Specialty, n, (%) 0.02 Medicine 14 (50.0) 10 (32.3) Surgery 12 (42.9) 9 (29.0) Anesthesia and intensive care 2 (7.1) 12 (38.7) Formalization characteristics, n, (%) Charter 23 (82.1) 30 (96.8) 0.08 Annual activity report 19 (67.9) 29 (93.5) 0.01 Nominative list of attendants 22 (78.6) 28 (90.3) 0.19 Meeting reports for each meeting 25 (89.3) 28 (90.3) 0.61 Record of decided actions 16 (57.1) 29 (93.5) 0.001 Organization No. of meetings during the year, median, [IQR] 4 [3–7] 4 [3–7] 0.65 No. of cases, median, [IQR] 19 [8–60] 15 [10–29] 0.63 Theme focused MCC, n (%) 1 (3.6) 9 (29.0) 0.01 Prior dissemination of meeting agenda, n (%) 10 (35.7) 22 (71.0) 0.007 Monitoring of previous actions, n, (%) 1 (3.6) 7 (22.6) 0.04 Length of meeting (min), median, [IQR] 80 [50–90] 118 [60–120] 0.005 No. Results of professionals attending, %, [IQR] Physicians, % [IQR] 82 [59–100] 80 [68–100] 0.83 Residents, % [IQR] 67 [60–100] 78 [50–100] 0.36 Head nurses, % [IQR] 60 [0–100] 75 [0–100] 0.79 Nurses, % [IQR] 2 [0–12] 9 [3–21] 0.06 Cases presentation and discussion Standardized with use of visual support, n (%) 8 (28.6) 25 (80.6) <0.001 Presentation of literature data, n (%) 1 (3.6) 12 (38.7) 0.001 Search of failures, n(%) 24 (85.7) 30 (96.8) 0.15 Thorough analysis of failure, n,(%) 7 (25.0) 18 (58.1) 0.01 Abbreviations: IQR interquartile range, MMC morbidity and mortality conference *p-values must be interpreted with respect to the threshold αc = 0.002, adjusted by the Bonferroni method Abbreviations: IQR interquartile range, MMC morbidity and mortality conference *p-values must be interpreted with respect to the threshold αc = 0.002, adjusted by the Bonferroni method interval, [1.66–5.04]) and recording of decisions for im- provement initiatives (aOR = 3.31, 95 % CI, [1.54–7.1]) remained independently associated with a high effectiveness index. We found that the effectiveness of MMCs, as reflected by a composite index, was associated with the standard- ized presentation of cases using visual aids. This finding was consistent with previous studies reporting that the use of a standard format or slides for case pre- sentations enhanced the effectiveness of MMCs in terms of participant satisfaction and production of improvement initiatives [22, 23]. Results This cause analysis was based on a structured method in three MMCs (5 %). In eight MMCs (14 %), the previously identified initiatives were followed up at each subsequent meeting. A total of 282 improvement initiatives were identified in MMCs in 42 departments during the study period, with a median number of four initiatives per department (Table 4). Of these, 111 initiatives (39.4 %) targeted factors related to the staff, with 72 aiming at developing or amending check- lists, protocols, or policies. Organizational, equipment, and patient factors accounted for 32.3, 8.5, and 7.1 % of im- provement initiatives, respectively. The median score for each improvement initiative completion was 3 (IQR, 1–4). A person in charge was designated for 150 (53.2 %) actions and a timeline was defined for 97 (34.4 %) (Table 1). Overall, 215 initiatives (76.2 %) were implemented either partially or fully and their impact was evaluated for 73 (25.9 %). previously decided actions (p = 0.04), and theme-focused MMCs (p = 0.01). The higher effectiveness index was also associated with meeting characteristics: when the presentation of cases was standardized with the use of visual aids (p < 0.001), when the presentation included literature data (p = 0.001), when failures were sought and thoroughly analyzed with the search for causes of adverse events (p = 0.01). When interpreting p-values with the threshold αc = 0.002, the only features associated with the effectiveness of MMCs were standardized presentation using visual aids and recording of decisions for improvement initiatives. The median effectiveness index per MMC was 10 (IQR, 3–43). In univariate analysis, the MMCs with an effectiveness index higher than the median were com- pared with those having a lower index than the median (Table 5). A higher effectiveness index was associated with a higher prevalence of documents, in particular with annual activity reports (p = 0.01) and with organizational issues: longer duration of meetings (p = 0.005), prior dis- semination of a meeting agenda (p = 0.007), monitoring of In multivariate analysis, a standardized presentation using visual aids (adjusted odds ratio = 2.89, 95 % confidence François et al. Discussion In MMCs attended only by physicians, the debate tends to focus on clinical questions and medical practices, whereas in multidisciplinary MMCs, organizational issues are more often discussed [27]. Eliciting input from all staff involved in patient care has been described as essential to a high-quality investiga- tion because the patient’s clinical course is thoroughly overviewed [13, 18, 28]. A multidisciplinary approach might also foster a culture of teamwork [1–3, 9, 11]. Above all, MMCs are a direct means to involve staff in quality-improvement initiatives [10]. y ) Other frequently reported changes relate to criteria for selecting cases and monitoring improvement initiatives. The number and types of cases presented during MMCs are extremely variable and affect the content of discus- sions and outcomes of the MMC [5, 27]. Some authors advocate a rapid analysis of all deaths and complications because unexamined cases are missed opportunities to identify failures [30, 31]. Others consider a detailed inves- tigation of a limited number of adverse events to be more effective to mitigating recurrent errors than a superficial investigation of a large number [6, 12, 13]. Our study is not contributive to this debate because we did not find any association between the number of cases examined by the MMC and the MMC’ index of effectiveness. In trad- itional MMCs, a large proportion of the cases presented were selected for their educational interest or potential clinical teaching value and often lack root cause analysis [11, 14, 17]. To guide MMCs toward patient safety, one study recommended a change consisting in selecting the cases on the basis of the potential for highlighting import- ant healthcare system safety issues [8]. This selection is usually made by a multidisciplinary committee or a mor- tality review task force [9–11]. Planning and monitoring the implementation of improvement initiatives are other major issues. Depending on the context, this task is usu- ally entrusted to specific working groups, an executive board, a quality-improvement committee, or a perform- ance improvement meeting [9, 11, 12, 26]. The depth of the analysis of adverse events appears to be a key issue for MMC effectiveness. The thoroughness of the analysis of root causes is contingent upon the use of a method, time availability, and the involvement of all stakeholders. This is rarely compatible with the format of the traditional MMC. We observed that only three MMCs used a structured method. Discussion This study indicates that MMCs may produce initiatives for improving the quality and safety of care and that most of these initiatives are actually implemented. How- ever, this ability to initiate improvement actions varies widely across MMCs. Other MMC baseline characteristics associated with improvement initiatives were formalization and organizational issues: production of annual activity François et al. BMC Health Services Research (2016) 16:35 Page 6 of 8 Page 6 of 8 reports, prior dissemination of a meeting agenda, recording of improvement initiatives, longer meetings, and theme- focused meetings. These characteristics imply a more for- malized organization and a higher level of traceability. This effort to formalize the meetings reflects the importance given to this activity as well as a high level of organizational culture consistent with the principles of quality improve- ment [24]. The association of anesthesiology and intensive care departments with a high effectiveness index is not sur- prising because anesthesiology is recognized as one of the safest clinical specialties and a leader in patient safety [25]. after the meeting, makes it possible to devote more time to analysis and to meet all stakeholders involved in the event who might not participate in the MMC. Associating the effectiveness index with the organization of thematic MMCs is also part of a detailed analysis. In these meet- ings, the cases selected refer to the same issues. A more focused discussion facilitates a more thorough analysis of adverse events [6]. Certain authors noted that MMCs were missed oppor- tunities for exploring systems contributing to medical errors and adverse outcomes in patient care and for implementing system changes [4, 5, 11]. System-based is- sues are rarely identified in MMCs and the time devoted to discussing interventions to improve patient care is insufficient [5]. Various experiments, usually conducted at a single hospital or department, have been designed to change the format of MMCs to move toward patient safety and enhancing residents’ ACGME competency in systems-based practice. Most of these safety-oriented MMCs include the aforementioned characteristics (i.e., multidisciplinary participation, standardized presentation, and root cause analysis). p p y This study fails to show a significant association be- tween attendance of healthcare professionals and the ef- fectiveness index of MMCs. However, many studies have found that multidisciplinary MMCs were more oriented toward the analysis of systemic causes of adverse events and were more likely to implement improvement initia- tives [9, 12, 26]. Authors’ contributions – Inviting all staff to participate in multidisciplinary meetings; PF participated in the design of the work, in data analysis and drafted the manuscript. FP: participated in the design of the work and revised the manuscript for important intellectual content. GVT participated in the design of the work and revised the manuscript for important intellectual content. JFQ participated in the design of the work and revised the manuscript for important intellectual content. JL participated in the data analysis and interpretation and revised the manuscript for important intellectual content. ES participated in the data analysis and interpretation and drafted the manuscript. All authors approved the final version to be published agreed to be accountable for all aspects of the work. – Selecting the cases presented based on their potential for systemic improvement. This study had several limitations. First, the endpoint of MMC effectiveness was not an objective measure of improvement but an ad hoc index based on decision making and completion of initiatives for improvement. Taking action does not guarantee the effectiveness of the action but taking action is a step that can lead to im- provement. We therefore considered, as other authors have, that the completion of improvement initiatives could be a reasonable surrogate endpoint for assessing the effectiveness of MMCs [8, 9, 11]. Acknowledgments We acknowledge Linda Northrup for her assistance in editing the manuscript in English. We acknowledge Linda Northrup for her assistance in editing the manuscript in English. This study was supported by the French Ministry of Health: Projet de Recherche en Qualité Hospitalière [25Preqhos10]. The French Ministry of Health did not participate in design or conduct of the study; collection, management, analysis, and interpretation of the data; or in preparation, review, or approval of the manuscript. Second, the results from our multivariable logistic regression analysis should be interpreted with caution because the relatively limited number of observations compared with the large number of independent variables may lead to overfitting. Colinearity between independent variables might explain why unadjusted associations did not remain significant in multivariable analysis. Discussion This observation was in accordance with Aboumatar et al., who reported that only one team used a structured method for incident analysis in 12 MMCs at Johns Hopkins Hospital [13]. In experiments intended to guide MMCs toward pa- tient safety, one of the main changes is to facilitate root cause analysis of events in order to promote system changes [11, 12]. Most often, this is done using a formal method of analysis derived from Ichikawa’s fishbone dia- gram [4, 11, 26] or from the protocol of the Association of Litigation and Risk Management (ALARM) [10, 12, 29]. In many cases, the investigation was conducted outside and before the meeting in which the case was discussed [4, 10, 12, 23]. Depending on the study, the case selected for analysis was assigned to a resident or fellow for in- vestigation within a framework called a “systems audit,” [4] “learning from the defect tool,” [12] “audit-based program,” [10] or “assessment tool.” [23] The time spent on this task is estimated at 35 h [4]. The externalization of adverse event investigation, before or The present study’s results, as well as published evi- dence, do not clearly identify an ideal format for MMCs. However, we can formulate a number of recommenda- tions for care safety-oriented MMCs: François et al. BMC Health Services Research (2016) 16:35 Page 7 of 8 Page 7 of 8 – Clearly defining the goals of the MMC and its functioning in a charter; References 1. Kravet SJ, Howell E, Wright SM. Morbidity and mortality conference, grand rounds, and the ACGME’s core competencies. J Gen Intern Med. 2006; 21(11):1192–4. 1. Kravet SJ, Howell E, Wright SM. Morbidity and mortality conference, grand rounds, and the ACGME’s core competencies. J Gen Intern Med. 2006; 21(11):1192–4. 2. Szekendi MK, Barnard C, Creamer J, Noskin GA. Using patient safety morbidity and mortality conferences to promote transparency and a culture of safety. Jt Comm J Qual Patient Saf. 2010;36(1):3–9. 3. Ksouri H, Balanant PY, Tadie JM, Heraud G, Abboud I, Lerolle N, et al. Impact of morbidity and mortality conferences on analysis of mortality and critical events in intensive care practice. Am J Crit Care. 2010;19(2):135–45. quiz 146. Additional files Additional file 1: Analyse documentaire. (DOC 105 kb) Additional file 2: Document analysis. (DOCX 22 kb) Additional file 3: Observation d'une réunion. (DOC 81 kb) Additional file 4: Observation of MMC meeting. (DOCX 23 kb) Additional file 1: Analyse documentaire. (DOC 105 kb) Additional file 2: Document analysis. (DOCX 22 kb) Additional file 3: Observation d'une réunion. (DOC 81 kb) Additional file 4: Observation of MMC meeting. (DOCX 23 kb) Additional file 1: Analyse documentaire. (DOC 105 kb) Additional file 2: Document analysis. (DOCX 22 kb) Additional file 3: Observation d'une réunion. (DOC 81 kb) Additional file 4: Observation of MMC meeting. (DOCX 23 kb) – Formalizing and tracking the activity of MMCs in meeting and annual reports; – Using a standardized format and visual aids for case presentation; p – Analyzing the root causes of failures, using a structured method; The authors declare that they have no competing interest. The authors declare that they have no competing interest. Author details 1 1Quality of Care Unit, University Hospital, and Research Unit, TIMC-IMAG (UMR 5525 CNRS/UJF-Grenoble 1), Grenoble F-38043, France. 2Public Health Department, University Hospital, Nice F-06003, France. 3Public Health Unit: Risk Management and Quality of Care, Paris Centre University Hospital Group, AP-HP, and Research Unit, (INSERM U738), Paris Descartes University, Sorbonne Paris cite, Paris F- 75014, France. Received: 7 January 2015 Accepted: 22 January 2016 Received: 7 January 2015 Accepted: 22 January 2016 Third, this study was conducted in three university hospitals in France wherein the development of MMCs is rather recent (i.e., dating from the 1990s) and the par- ticipation in MMCs is not required in the medical train- ing curriculum. Hence, these findings may not apply to other settings or countries. Competing interests – Organizing the follow-up of actions for improvement; Conclusions Morbidity and mortality conference: a survey of academic internal medicine departments. J Gen Intern Med. 2003;18(8):656–8. 15. Orlander JD, Barber TW, Fincke BG. The morbidity and mortality conference: the delicate nature of learning from error. Acad Med. 2002;77(10):1001–6. 16. Nolan SW, Burkard JF, Clark MJ, Davidson JE, Agan DL. Effect of morbidity and mortality peer review on nurse accountability and ventilator-associated pneumonia rates. J Nurs Adm. 2010;40(9):374–83. 17. Steiger HJ, Stummer W, Hanggi D. Can systematic analysis of morbidity and mortality reduce complication rates in neurosurgery? Acta Neurochir. 2010; 152(12):2013–9. 17. Steiger HJ, Stummer W, Hanggi D. Can systematic analysis of morbidity and mortality reduce complication rates in neurosurgery? Acta Neurochir. 2010; 152(12):2013–9. 18. Denis B, Ben Abdelghani M, Peter A, Weiss AM, Bottlaender J, Goineau J. Two years of mortality and morbidity conferences in a hospital gastrointestinal endoscopy unit. Gastroenterol Clin Biol. 2003;27(12):1100–4. 19. Claudot F, Alla F, Fresson J, Calvez T, Coudane H, Bonaiti-Pellie C. Ethics and observational studies in medical research: various rules in a common framework. Int J Epidemiol. 2009;38(4):1104–8. 20. Republic F. Loi n°2012-300 du 5 mars 2012 relative aux recherches impliquant les personnes humaines. Journal officiel de la république française. 2012;56:10–8. 21. Sherman H, Castro G, Fletcher M, Hatlie M, Hibbert P, Jakob R, et al. Towards an International Classification for Patient Safety: the conceptual framework. Int J Qual Health Care. 2009;21(1):2–8. 22. Kim MJ, Fleming FJ, Peters JH, Salloum RM, Monson JR, Eghbali ME. Improvement in educational effectiveness of morbidity and mortality conferences with structured presentation and analysis of complications. J Surg Educ. 2010;67(6):400–5. 23. Mitchell EL, Lee DY, Arora S, Kenney-Moore P, Liem TK, Landry GJ, et al. Improving the quality of the surgical morbidity and mortality conference: a prospective intervention study. Acad Med. 2013;88(6):824–30. 24. Pelieu I, Djadi-Prat J, Consoli SM, Cariou A, Guidet B, You-Harada C, et al. Impact of organizational culture on preventability assessment of selected adverse events in the ICU: evaluation of morbidity and mortality conferences. Intensive Care Med. 2013;39(7):1214–20. 25. Staender SE, Mahajan RP. Anesthesia and patient safety: have we reached our limits? Curr Opin Anaesthesiol. 2011;24(3):349–53. 26. Schwarz D, Schwarz R, Gauchan B, Andrews J, Sharma R, Karelas G, et al. Implementing a systems-oriented morbidity and mortality conference in remote rural Nepal for quality improvement. BMJ Qual Saf. 2011;20(12):1082–8 27. Sellier E, David-Tchouda S, Bal G, Francois P. François et al. BMC Health Services Research (2016) 16:35 Conclusions This study demonstrates substantial variations in MMC characteristics, which may relate to their effectiveness in improving patient safety. The framework of MMCs is highly flexible, which is a cause of MMC variability. However, this flexibility enables each team to adapt the MMC format to its objectives and constraints, which may contribute to the involvement of physicians. It is tempting to rely on MMCs to involve healthcare pro- viders in patient safety management, but this goal requires revising the functioning of MMCs to establish a more rigorous methodological framework and to guide MMCs toward the identification, analysis, and prevention of adverse events. 4. Szostek JH, Wieland ML, Loertscher LL, Nelson DR, Wittich CM, McDonald FS, et al. A systems approach to morbidity and mortality conference. Am J Med. 2010;123(7):663–8. 5. Pierluissi E, Fischer MA, Campbell AR, Landefeld CS. Discussion of medical errors in morbidity and mortality conferences. JAMA. 2003;290(21):2838–42. 6. Gore DC. National survey of surgical morbidity and mortality conferences. Am J Surg. 2006;191(5):708–14. 9. Kauffmann RM, Landman MP, Shelton J, Dmochowski RR, Bledsoe SH, Hickson GB, et al. The use of a multidisciplinary morbidity and mortality conference to incorporate ACGME general competencies. J Surg Educ. 2011; 68(4):303–8. Page 8 of 8 Page 8 of 8 François et al. BMC Health Services Research (2016) 16:35 10. Kirschenbaum L, Kurtz S, Astiz M. Improved clinical outcomes combining house staff self-assessment with an audit-based quality improvement program. J Gen Intern Med. 2010;25(10):1078–82. 11. Deis JN, Smith KM, Warren MD, Throop PG, Hickson GB, Joers BJ, et al.: Transforming the Morbidity and Mortality Conference into an Instrument for Systemwide Improvement. In: Advances in Patient Safety: New Directions and Alternative Approaches (Vol 2: Culture and Redesign). edn. Edited by Henriksen K, Battles JB, Keyes MA, Grady ML. Agency for Healthcare Research and Quality, Rockville (MD); 2008. 12. Berenholtz SM, Hartsell TL, Pronovost PJ. Learning from defects to enhance morbidity and mortality conferences. Am J Med Qual. 2009;24(3):192–5. 12. Berenholtz SM, Hartsell TL, Pronovost PJ. Learning from defects to enhance morbidity and mortality conferences. Am J Med Qual. 2009;24(3):192–5. 13. Aboumatar HJ, Blackledge CG, Dickson C, Heitmiller E, Freischlag J, Pronovost PJ. A descriptive study of morbidity and mortality conferences and their conformity to medical incident analysis models: results of the morbidity and mortality conference improvement study, phase 1. Am J Med Qual. 2007;22(4):232–8. 14. Orlander JD, Fincke BG. Conclusions Morbidity and mortality conferences: their place in quality assessments. Int J Health Care Qual Assur. 2012;25(3):189–96. 28. Kim C, Fetters MD, Gorenflo DW. Residency education through the family medicine morbidity and mortality conference. Fam Med. 2006;38(8):550–5. Submit your next manuscript to BioMed Central and we will help you at every step: Submit your next manuscript to BioMed Central and we will help you at every step: 29. Vincent C, Taylor-Adams S, Chapman EJ, Hewett D, Prior S, Strange P, et al. How to investigate and analyse clinical incidents: clinical risk unit and association of litigation and risk management protocol. BMJ. 2000;320(7237):777–81. • We accept pre-submission inquiries • Our selector tool helps you to find the most relevant journal • We provide round the clock customer support • Convenient online submission • Thorough peer review • Inclusion in PubMed and all major indexing services • Maximum visibility for your research Submit your manuscript at www.biomedcentral.com/submit a d e e p you at e e y step: 30. Murayama KM, Derossis AM, DaRosa DA, Sherman HB, Fryer JP. A critical evaluation of the morbidity and mortality conference. Am J Surg. 2002; 183(3):246–50. 31. Hutter MM, Rowell KS, Devaney LA, Sokal SM, Warshaw AL, Abbott WM, et al. Identification of surgical complications and deaths: an assessment of the traditional surgical morbidity and mortality conference compared with the American College of Surgeons-National Surgical Quality Improvement Program. J Am Coll Surg. 2006;203(5):618–24.
https://openalex.org/W4376124762
https://scipost.org/10.21468/SciPostPhys.14.5.103/pdf
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Hamiltonian structure of 2D fluid dynamics with broken parity
SciPost physics
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Gustavo Machado Monteiro1⋆, Alexander G. Abanov2,3 and Sriram Ganeshan1,4 1 Department of Physics, City College, City University of New York, New York, NY 10031, USA 2 Simons Center for Geometry and Physics, Stony Brook, NY 11794, USA 3 Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794, USA 4 CUNY Graduate Center, New York, NY 10031, USA ⋆gmachadomonteiro@ccny.cuny.edu Isotropic fluids in two spatial dimensions can break parity symmetry and sustain transverse stresses which do not lead to dissipation. Corresponding transport coeffi- cients include odd viscosity, odd torque, and odd pressure. We consider an isotropic Galilean invariant fluid dynamics in the adiabatic regime with momentum and parti- cle density conservation. We find conditions on transport coefficients that correspond to dissipationless and separately to Hamiltonian fluid dynamics. The restriction on the transport coefficients will help identify what kind of hydrodynamics can be obtained by coarse-graining a microscopic Hamiltonian system. Interestingly, not all parity-breaking transport coefficients lead to energy conservation and, generally, the fluid dynamics is energy conserving but not Hamiltonian. We show how this dynamics can be realized by imposing a nonholonomic constraint on the Hamiltonian system. Received 17-08-2021 Accepted 15-02-2023 Published 10-05-2023 Check for updates doi:10.21468/SciPostPhys.14.5.103 Copyright G. Machado Monteiro et al. This work is licensed under the Creative Commons Attribution 4.0 International License. Published by the SciPost Foundation. SciPost Phys. 14, 103 (2023) 1 Introduction In fluid dynamics, viscosities appear as transport coefficients in the first-order derivative ex- pansion of the stress tensor. Viscosity terms preserve both mass and momentum conservation laws but usually spoil the energy conservation due to their dissipative nature. For example, shear viscosity (η) introduces friction between adjacent fluid layers that do not flow with the same velocity, whereas the bulk viscosity (ζ) provides resistance to compression or expansion of the fluid. In two spatial dimensions, there exist viscosity coefficients within the first-order hydrody- namics that break parity symmetry and preserve both the fluid isotropy and energy conser- vation. Odd viscosity (ηH) is undoubtedly the most famous of the parity-breaking viscosity terms, first showing up in the study of plasma physics [1] and later on as a new quantized re- sponse in quantum Hall systems [2]. It was introduced in the hydrodynamic context by Avron in [3] and was recently experimentally observed in both electron fluids [4] and active matter systems [5]. In quantum Hall systems, the odd viscosity is associated with the intrinsic angular momen- tum density of the electron fluid [6–8]. In classical systems, the intrinsic angular momentum density (ℓ) is an independent dynamical variable with its own continuity equation. On the other hand, odd viscosity is a transport coefficient, that is, a function of density and tempera- ture. If we initialize ℓto be proportional to density, this relationship is preserved for all times since both quantities satisfy similar continuity equations (in the absence of internal torque). This class of initial conditions with ℓ∝ρ corresponds to a projected Hamiltonian system. In general, such a projection need not lead to a new Hamiltonian system. However, ℓ∝ρ does not spoil the underlying Poisson algebra as shown in Ref. [9]. Together with a velocity re- definition [8], this projection gives rise to odd viscosity terms in the momentum conservation equation. Physically, this projection (ℓ∝ρ) can be realized in systems where fluid intrinsic angular momentum equilibrates much faster than the other hydrodynamic quantities [10]. Recently, it was shown in Ref. [11] that odd viscosity could also arise in the equation of motion from a non-Hamiltonian reduction of the intrinsic angular momentum ℓ. For that, the authors introduced dissipative terms and an external drive to a Hamiltonian system. The out- of-equilibrium dynamics leads to the relaxation of the fluid intrinsic angular momentum, giving rise to the odd viscosity term in the Navier-Stokes equation. Contents 1 Introduction 2 2 Energy conservation in 2D fluid dynamics 3 3 Hamiltonian fluid dynamics in two dimensions 6 3.1 Hamiltonian structure of zeroth-order hydrodynamics 6 3.2 Modification of brackets for the first-order hydrodynamics 7 3.3 Constraints imposed by Jacobi identity 8 3.4 Conditions for Hamiltonian hydrodynamics 9 3.5 Generalized Hamiltonian hydrodynamics 10 4 Energy conservation and nonholonomic constraints 12 5 Discussion and conclusions 14 A Conditions for energy conservation 16 A.1 Case I: G′(ρ) = 0 18 A.2 Case II: G′(ρ) ̸= 0 18 1 1 Introduction 2 2 Energy conservation in 2D fluid dynamics 3 3 Hamiltonian fluid dynamics in two dimensions 6 3.1 Hamiltonian structure of zeroth-order hydrodynamics 6 3.2 Modification of brackets for the first-order hydrodynamics 7 3.3 Constraints imposed by Jacobi identity 8 3.4 Conditions for Hamiltonian hydrodynamics 9 3.5 Generalized Hamiltonian hydrodynamics 10 4 Energy conservation and nonholonomic constraints 12 5 Discussion and conclusions 14 A Conditions for energy conservation 16 A.1 Case I: G′(ρ) = 0 18 A.2 Case II: G′(ρ) ̸= 0 18 1 SciPost Phys. 14, 103 (2023) B Condition to satisfy the Jacobi identity References B Condition to satisfy the Jacobi identity 22 1 Introduction We discuss the projection of the intrinsic angular momentum to a function of mass density and the breakdown of the Hamiltonian system from the point of view of nonholonomic constraints.i ing heat transport.1 There are in total 6 independent viscosity coefficients which preserve fluid isotropy and satisfy Galilean symmetry in two dimensions. Half of these transport coefficients are even under parity symmetry, and the other half is parity odd.2 In general, parity-violating forces are transverse to the fluid motion and perform no work. Therefore, such terms are expected not to dissipate energy. However, it is not apparent whether a 2D hydrodynamical system with parity-odd coefficients possesses conserved energy in general. In addition, even if the conserved energy exists, it is not obvious that the corresponding system is Hamiltonian. This paper is organized as follows: we begin by defining our hydrodynamic system in Sec 2 and present the conditions for the fluid energy to be conserved. In Sec. 3, we derive under which conditions the aforementioned energy-conserving systems are Hamiltonian. In Sec. 4, we study the connection between dynamical intrinsic angular momentum and odd viscosity as well as its implications towards non-Hamiltonian systems with conserved energy density. We close the paper with conclusions and discussions. Some technical details are relegated to appendices. 2Throughout this paper, we denote parity-breaking terms with a subscript H. 1Adiabatic conditions are satisfied when the fluid contracts or expands so fast that there is no time to exchange heat between its adjacent layers. The adiabaticity ensures that energy conservation follows directly from mass and momentum conservation laws. 2Throughout this paper, we denote parity-breaking terms with a subscript H. 1 Introduction The non-Hamiltonian projection in Ref. [11], odd viscosity is a linear function of the mass density, but it depends explicitly on the external drive. Although Refs. [9–11] describe different physical systems, all of them obtain odd viscosity through relaxation of the intrinsic angular momentum. However, odd viscosity is not the only parity odd coefficient in two dimensions and it is not a priori clear if some or all of these other coefficients can be obtained starting from a microscopic Hamiltonian system. In fact, the identification of Hamiltonian systems provides a benchmark for idealized dissipationless systems about which the dissipative contributions can be introduced.i In this work, we start from the most general first-order hydrodynamic equations of motion and derive under which conditions the density dependent viscosity coefficients can be derived from a Hamiltonian system. Throughout the paper, we only consider adiabatic flows, neglect- 2 SciPost Phys. 14, 103 (2023) ing heat transport.1 There are in total 6 independent viscosity coefficients which preserve fluid isotropy and satisfy Galilean symmetry in two dimensions. Half of these transport coefficients are even under parity symmetry, and the other half is parity odd.2 In general, parity-violating forces are transverse to the fluid motion and perform no work. Therefore, such terms are expected not to dissipate energy. However, it is not apparent whether a 2D hydrodynamical system with parity-odd coefficients possesses conserved energy in general. In addition, even if the conserved energy exists, it is not obvious that the corresponding system is Hamiltonian. We show that not all parity-breaking transport coefficients amount to energy conservation. For a hydrodynamic system whose energy is conserved, we derive sufficient conditions on the transport coefficients for the system to be Hamiltonian. As a consequence, we obtain that an energy-conserving hydrodynamic system is Hamiltonian if there exists a conserved quan- tity, ρvi + εi j∂jηH, which satisfies the diffeomorphism algebra. This quantity is associated with the “molecular” center-of-mass momentum density, as pointed out in [11]. The energy- conserving cases that fail to be Hamiltonian systems are closely related to projections of the intrinsic angular momentum incompatible with the Poisson algebra. 2 Energy conservation in 2D fluid dynamics The relation between pressure and mass density for adiabatic flows gives us the equation of state, (4) p(ρ) = ρ ϵ′(ρ) −ϵ(ρ), (4) where ϵ(ρ) is the internal energy density of the fluid.il where ϵ(ρ) is the internal energy density of the fluid.ili In first-order hydrodynamics, the fluid velocity cannot be uniquely defined, leading to different hydrodynamic frames [12–15]. Even though hydrodynamic equations depend on the specific parametrization of momentum density in terms of the fluid velocity, the momentum conservation must not rely on any particular definition of the fluid velocity. In this work, we define the fluid velocity such that the momentum density is expressed as ρvi. Equations (1, 2) must be invariant under the Galilean symmetry, that is, t →t , xi →xi −Vi t , and vi →vi + Vi , t →t , xi →xi −Vi t , and vi →vi + Vi , for a constant boost velocity Vi. Consequently, the divergence of the stress tensor must be invariant under this Galilean symmetry; that is, the force must be independent of the boost velocity. Moreover, this also implies that the mass current can only differ from the momen- tum density by some “magnetization current”, which does not modify the equations of mo- tion (1, 2). The isotropic condition imposes that there are only 6 independent viscosity coefficients two dimensions, that is, ηi jkl = η δikδjl + δilδjk −δi jδkl  + ζδi jδkl + Γ εi jεkl + ηH εikδjl + εjlδik  + ζH δi jεkl + ΓHεi jδkl . (5) (5) Here and in the following, we suppress the dependence of all coefficients on density using the notation η(ρ) →η, etc. As previously mentioned, η, ζ, and ηH are shear, bulk, and odd viscosities, respectively. The quantity ζH is the odd pressure coefficient, Γ is the rotational viscosity, and we refer to the ΓH term as the odd torque coefficient. Rotational viscosity gives rise to torque when the fluid vorticity is non-zero, and the odd pressure coefficient generates pressure when fluid vorticity does not vanish. Finally, the odd torque coefficient ΓH generates torque when the fluid expands or compresses.3 A close inspection of Eqs. (3) and (5) shows that there is a symmetry among transport coefficients that leaves Eq. (2) invariant. 3For a hydrodynamic system without any internal torque, the stress tensor must be symmetric, which imposes that Γ = ΓH = 0. 2 Energy conservation in 2D fluid dynamics Hydrodynamic equations consist of local conservation laws for mass and momentum, assuming all other relevant quantities are equilibrated. These equations are supplemented by constitu- tive relations between the conserved quantities. The presence of a finite mean-free-path and a finite characteristic relaxation time of the interacting system modify the dynamics at small length scales and at transient times, giving rise to derivative corrections in these constitutive relations. This means that constitutive relations can be formally written as an expansion in derivatives, both in time and space, and the hydrodynamic equations are obtained by trun- cating this series at some particular order. In non-relativistic hydrodynamics, spatial and time derivatives do not scale the same way, and only terms with a single spatial derivative enter in the constitutive relations in the first-order derivative expansion. Mass (the continuity equa- tion) and momentum conservation can be written in terms of the mass density (ρ) and velocity (vi) as (vi) as ∂tρ + ∂i(ρvi) = 0, (1) ∂t vj + vi∂ivj = 1 ρ ∂iTi j . (2) (1) (2) Here, the stress tensor Ti j is of first-order in spatial gradients and is given by Ti j = −p(ρ)δi j + ηi jkl(ρ)∂kvl , (3) (3) Ti j = −p(ρ)δi j + ηi jkl(ρ)∂kvl , 1Adiabatic conditions are satisfied when the fluid contracts or expands so fast that there is no time to exchange heat between its adjacent layers. The adiabaticity ensures that energy conservation follows directly from mass and momentum conservation laws. 1Adiabatic conditions are satisfied when the fluid contracts or expands so fast that there is no time to exchange heat between its adjacent layers. The adiabaticity ensures that energy conservation follows directly from mass and momentum conservation laws. 3 SciPost Phys. 14, 103 (2023) where ηi jkl is the viscosity tensor. In principle, all transport coefficients must be functions of density and temperature, however, for adiabatic flows, temperature can be expressed in terms of fluid density. The relation between pressure and mass density for adiabatic flows gives us the equation of state, where ηi jkl is the viscosity tensor. In principle, all transport coefficients must be functions of density and temperature, however, for adiabatic flows, temperature can be expressed in terms of fluid density. 2 Energy conservation in 2D fluid dynamics Indeed, under the transformation η →η + c1 , ζ →ζ −c1 , Γ →Γ −c1 , (6) ηH →ηH + c2 , ζH →ζH −c2 , ΓH →ΓH + c2 , (7) (6) (7) (6) (7) with two arbitrary constants c1 and c2, we obtain ∂iTi j →∂i[Ti j + 2∂∗ i € c1 v∗ j + c2 vj Š ] = ∂iTi j . (8) (8) Here and in the following, we define the star operation as a∗ i ≡εi jaj. Since we are only interested in equations of motion and not in a particular form of the stress tensor, we will ignore these redundancies for the rest of this work. The particular form of the stress tensor, however, is crucial for the free surface problems for which a no-stress boundary condition is imposed [16]. 4 SciPost Phys. 14, 103 (2023) For reasons that will be clear later, it is convenient to parametrize the parity-breaking part of Eq. (5), i.e. viscosity coefficients with subscript H, as ηH i jkl = ¯ηi jkl −ρG′δi jεkl . (9) (9) Here we have introduced the tensor ¯ηi jkl = ηH εikδjl + εjlδik  + ΓH εi jδkl −δi jεkl  , (10) (10) which is anti-symmetric with respect to the interchange of following pairs of indices ¯ηi jkl = −¯ηkli j . (11) (11) Comparing (5) with (9,10), we see that the newly introduced function G(ρ) is related to ζH by omparing (5) with (9,10), we see that the newly introduced function G(ρ) is related to ζH by ζH = −ΓH −ρG′ . (12) (12) In order to study the Hamiltonian structure of Eqs. (1-3,5) the first step is to obtain under which conditions these equations allow for a third conserved quantity, namely, energy. We are looking for a conserved energy density E satisfying ∂tE + ∂iQi = 0 , (13) (13) with some local energy current Qi. To be consistent with zeroth-order hydrodynamics, that is, ηi jkl →0, the energy density should have the form E = 1 2ρv2 i + ϵ(ρ) + ... , (14) (14) where dots denote terms of higher order in spatial gradients of density and velocity fields. Here and in the following, we use v2 i instead of vivi to shorten up the notation. where dots denote terms of higher order in spatial gradients of density and velocity fields. 2 Energy conservation in 2D fluid dynamics Here and in the following, we use v2 i instead of vivi to shorten up the notation. i We now state the general condition (up to the redundancies (6-8) in the stress tensor) for the energy conservation while leaving the full details of the calculation to the Appendix A. Statement I. The energy of a hydrodynamic system described by Eqs. (1-5) is only conserved when the parity-preserving viscosity coefficients vanish, that is, η = ζ = Γ = 0, and when the parity-breaking viscosity coefficients satisfy one of the following two conditions ase 1: For ηH(ρ) and ΓH(ρ) arbitrary and Case 1: For ηH(ρ) and ΓH(ρ) arbitrary and G = 0. Case 2: For an arbitrary function G(ρ) and an arbitrary constant parameter c, along with Case 2: For an arbitrary function G(ρ) and an arbitrary constant parameter c, along with ηH = cG , ΓH = c(G −2ρG′). From Eq. (12), we obtain that ζH = −ΓH in the first case and ζH = −c(G −2ρG′) −ρG′ in the second one. The conserved energy density in both cases can be generically written as E = 1 2ρv2 i + ϵ + vi∂∗ i G + c ρ (∂iG)2 . (15) (15) Note that when G = 0 (Case 1), the energy density has the same functional form as in the inviscid case. Note that when G = 0 (Case 1), the energy density has the same functional form as in the inviscid case. 5 SciPost Phys. 14, 103 (2023) The dissipative nature of viscosities η,ζ,Γ is well known. It is not known however that an arbitrary choice of odd viscosities ηH,ζH,ΓH may not lead to dissipationless fluid dynamics. The energy density equation can be deduced from Eqs. (1-3) and can be written as ∂t ϵ + 1 2ρv2 i  + ∂i ”€ ϵ′ + 1 2 v2 j Š ρvi −ηi jkl vj∂kvl — = −ηi jkl∂ivj∂kvl . (16) (16) In Case 1, the viscosity tensor is given by ¯ηi jkl which forces the right hand side of (16) to vanish due to the antisymmetry property (11), leading to conserved energy density. The second condition of Statement I is more subtle, and we refer the reader to Appendix A for details. For the particular case of c = 0, the only nonvanishing viscosity coefficient is ζH = −ρG′. 2 Energy conservation in 2D fluid dynamics For this particular case, the corresponding stress is diagonal and can be consid- ered a modification of the pressure term in the Euler equation so that p →p −ζHω. Here ω = ∂1v2 −∂2v1 is the fluid vorticity.l In the next section, we will address when the energy-conserving fluid dynamics described in Statement I can be endowed with the Hamiltonian structure. 3 Hamiltonian fluid dynamics in two dimensions A fluid dynamic system is Hamiltonian if its hydrodynamic equations can be generated by a Hamiltonian function (total energy of the fluid) and a set of Poisson brackets. In other words, both mass and momentum conservation laws can be written as Hamilton’s equations. We often refer to the Hamiltonian function together with the Poisson algebra as the Hamil- tonian structure. In contrast to the standard textbook examples, here we have both the Hamiltonian, i.e. the integrated energy density of the fluid (Eq. (15)) and the equations of motion (Eqs. (1-3)) together with the conditions of Statement I. Our goal is to derive, when it exists, the Poisson algebra for these systems. As a result of our analysis, we show that not all cases in Statement I can possess Hamiltonian structure. It is worth to note that the Hamiltonian function need not always be the total energy of system, however we do not consider this possibility in this work. We aim to recover the ideal fluid structure, in the limit of vanishing viscosity coefficients. In addition to that, we only consider local deformations of the ideal fluid Poisson algebra here. 3.1 Hamiltonian structure of zeroth-order hydrodynamics Before we proceed to study the cases of Statement I, let us briefly review the well-known Hamiltonian formulation for the inviscid or, more precisely, the zeroth-order hydrodynam- ics [17–19]. Let us consider the set of Eqs. (1-3) with ηi jkl = 0. Here it is convenient to write the hydrodynamic equations in terms of conserved quantities since they are frame- independent. Indeed, it is straightforward to check that both equations (1) and (2), written in terms of ρ and Ji ≡ρvi, are generated by the Hamiltonian H0 = Z  J2 i 2ρ + ϵ(ρ)  d2x , (17) (17) along with the following Poisson brackets along with the following Poisson brackets along with the following Poisson brackets {ρ(x),ρ(y)} = 0, (18) {ρ(x),Ji(y)} = −ρ(y) ∂ ∂yi δ(x −y), (19) {Ji(x),Jk(y)} = • Jk(x) ∂ ∂xi −Ji(y) ∂ ∂yk ˜ δ(x −y). (20) (18) (19) (20) 6 SciPost Phys. 14, 103 (2023) The subalgebra defined in Eq. (20) is the diffeomorphism algebra so that the momentum density Ji is the generator of “local translations” (diffeomorphisms). The Lie-Poisson algebra defined in Eqs. (18-20) is a semidirect product algebra which we will refer to simply as Ex- tended Diffeomorphism Algebra (EDA) hereon. The time evolution of any quantity is defined by ∂tQ = {H,Q}.4 In particular, for the time evolution of density and momentum density fields, one proceeds as ∂tρ(x) = {H,ρ(x)} = Z • δH δρ(y){ρ(y),ρ(x)} + δH δJi(y){Ji(y),ρ(x)} ˜ d2 y , (21) ∂tJi(x) = {H,Ji(x)} = Z • δH δρ(y){ρ(y),Ji(x)} + δH δJk(y){Jk(y),Ji(x)} ˜ d2 y . (22) (21) (22) It can be checked that substituting Poisson’s brackets (18-20) into the above equations one obtains the correct evolution equations for ρ and Ji = ρvi equivalent to (1,2). It can be checked that substituting Poisson’s brackets (18-20) into the above equations one obtains the correct evolution equations for ρ and Ji = ρvi equivalent to (1,2). Using (18-20) one can compute Poisson brackets of any two functionals of ρ and Ji. Poisson brackets between two functions (or functionals) of ρ and Ji must satisfy two conditions: (1) antisymmetry {Q,R} = −{R,Q}, (23) (23) and (2) Jacobi identity J  Q,R,S ≡{{Q,R},S} + {{S,Q},R} + {{R,S},Q} = 0. (24) (24) Here J (Q,R,S), defined in the first line of (24), is referred as the Jacobiator of three function- als Q,R,S of ρ and Ji. 3.1 Hamiltonian structure of zeroth-order hydrodynamics The Jacobi identity is the statement that the Jacobiator vanishes for any three functionals.5 It can be checked that (18-20) satisfy antisymmetry condition and Jacobi identity (23,24). 5Jacobi identity is associated to the existence of local canonical coordinates. 5Jacobi identity is associated to the existence of local canonical coordinates. 4Here, we follow the notation convention in Ref. [17] The algebra presented here may differ by an overall gative sign from some other references in the literature. 5 3.3 Constraints imposed by Jacobi identity Prima facie one might think that the identification of antisymmetric brackets (26) means that all energy-conserving cases specified by Statement I are Hamiltonian. However, for the system to be Hamiltonian, brackets must also satisfy the Jacobi identity (24). We now present the main condition for which the brackets in Eqs. (18,19,26) satisfy the Jacobi identity (24). Statement II. The antisymmetric brackets from Eqs. (18,19,26) are Poisson brackets, i.e, satisfy Jacobi identity if and only if ΓH(ρ) = ηH(ρ) −ρ η′ H(ρ). (29) (29) When this condition holds, there exists a locally conserved quantity, namely Ji ≡Ji + ∂∗ i ηH(ρ), (30) (30) which satisfies the diffeomorphism algebra. 3.2 Modification of brackets for the first-order hydrodynamics The direct computation of equations of motion generated by the Hamiltonian (25) with the algebra (18,19,26) provides us the following hydrodynamic equations ∂tρ = −∂iJi , (27) ∂tJk = −∂i •JiJk ρ + p δik −ηH iklm ∂l €Jm ρ Š˜ , (28) (27) (28) with ηH i jkl defined by (9,10) with parameters specified in the Statement I. More specifically, in Case 1, both ηH and ΓH are independent functions of density in the bracket (26) and the Hamiltonian is obtained by taking G = 0 in the Eq. (25). In Case 2, we must substitute ηH = cG and ΓH = c(G −2ρG′) in the bracket (26). It is easy to see that this system of equations is equivalent to Eqs. (1,2), when the stress tensor is given by Eqs. (3-5) and the viscosity tensor satisfies one of the the cases in the Statement I. Because these equations are generated by antisymmetric brackets, the Hamiltonian (25) itself is automatically conserved, since ∂tH = {H, H} = 0. In the following, we will check if these almost Poisson brackets satisfy the Jacobi identity. 3.2 Modification of brackets for the first-order hydrodynamics Since not all dynamical systems with conserved energy are Hamiltonian systems [20–22], the scope of this section is to find under which conditions the systems defined in the Statement I are Hamiltonian. For that, we must obtain the brackets that, together with the Hamiltonian H = Z  J2 i 2ρ + ϵ + Ji ρ ∂∗ i G + c ρ (∂iG)2  d2x , (25) (25) generate Eqs. (1,2), where the stress tensor satisfy both Eqs. (3-5) and the Statement I. The Hamiltonian (25) is obtained by integrating the energy density (15). It is important to point out that this choice of Hamiltonian is not only natural, but it recovers the ideal fluid Hamilto- nian in the limit when ηi jkl →0. generate Eqs. (1,2), where the stress tensor satisfy both Eqs. (3-5) and the Statement I. The Hamiltonian (25) is obtained by integrating the energy density (15). It is important to point out that this choice of Hamiltonian is not only natural, but it recovers the ideal fluid Hamilto- nian in the limit when ηi jkl →0.i We find that the continuity equation can be generated by the brackets (18,19), while the bracket (20) must be modified in order to provide us the correct momentum conservation equation. After such deformation, the momentum density algebra becomes {Ji(x),Jk(y)} = • Jk(x) ∂ ∂xi −Ji(y) ∂ ∂yk ˜ δ(x −y) −∂ ∂x j • ¯ηjilk ρ(x)  ∂ ∂xl δ(x −y) ˜ , (26) (26) 4Here, we follow the notation convention in Ref. [17] The algebra presented here may differ by an overa negative sign from some other references in the literature. 5Jacobi identity is associated to the existence of local canonical coordinates. 5Jacobi identity is associated to the existence of local canonical coordinates. 7 SciPost Phys. 14, 103 (2023) where ¯ηi jkl is defined in (10). The antisymmetry property of ¯ηi jkl (Eq. (11)) together with the identities f (x)δ(x −y) = f (y)δ(x −y), ∂ ∂xm δ(x −y) = −∂ ∂ym δ(x −y), guarantees the antisymmetry of the bracket (26). Here, we assume that the bracket defor- mation is local and recovers the diffeomorphism algebra (20) in the limit of an ideal fluid. The algebra (18,19,26) is sometime called almost Poisson brackets [22], since it satisfies the property (23), but not necessarily the Jacobi identity (24). which satisfies the diffeomorphism algebra. To see the origin of the condition (29) let us consider the modified momentum den- sity Ji (30). It is clear that the bracket {ρ(x), Ji(y)} is not modified and coincides with (19). Using brackets (18,19,26) it is straightforward to compute y i ρ ii Using brackets (18,19,26) it is straightforward to compute ¦ Ji(x), Jk(y) © = • Jk(x) ∂ ∂x i −Ji(y) ∂ ∂yk ˜ δ(x −y) −(εjiδlk −δjiεlk) × ∂ ∂x j •ΓH −ηH + ρη′ H  (x) ∂ ∂x l δ(x −y) ˜ . (31) (31) 8 8 SciPost Phys. 14, 103 (2023) One immediately notices that the condition (29) annihilates the second term in the right hand side of Eq. (31) and the algebra of brackets of ρ and Ji becomes identical to the original diffeomorphism algebra (18-20) thereby satisfying the Jacobi identity. Throughout the rest of the paper we will use Ji to refer to the diffeomorphism generators. In Appendix B, we perform more direct computation showing that the condition (29) is also necessary for brackets (18,19,26) to satisfy the Jacobi identity. The key point of that computation is that the Jacobiator (see Eq. (24)) is given by J ¦ Ji(x),Jk(y),Jm(z) © = • εkm ∂ ∂xi ∂ ∂yl ∂ ∂zl + εik ∂ ∂xl ∂ ∂yl ∂ ∂zm + εmi ∂ ∂xl ∂ ∂yk ∂ ∂zl ˜ ” 2(ηH −ρη′ H −ΓH)δ(x −y)δ(x −z) — . (32) (32) The Jacobiator J vanishes only when (29) holds completing the proof of Statement I The Jacobiator J vanishes only when (29) holds completing the proof of Statement II. J y p g p We now discuss the physical picture behind the constraint (29). The constraint can be rewritten as ΓH/ρ + ρ(ηH/ρ)′ = 0. We consider the angular momentum per particle ℓ/ρ = ηH/ρ and notice that if it is itself ρ-independent, the constraint requires ΓH = 0. We see that if one compresses the fluid of rotating particles, no intrinsic torque is needed if the angular momentum of each particle does not depend on the particles’ density. If ηH(ρ) is nonlinear in ρ, the compression would require an additional torque applied to each parti- cle. If (29) is satisfied, this torque can be provided by the intrinsic torque ΓH of the fluid. If the condition (29) is not met, additional “constraint forces” are needed rendering the system non-Hamiltonian. 3.4 Conditions for Hamiltonian hydrodynamics [11], the authors identify the generators of diffeomorphism Ji to the “molecular” center-of-mass momentum density. For Case 2, the Hamiltonian is different from that of the inviscid case and can be writte as as H = Z  J2 i 2ρ + ϵ + Ji ρ ∂∗ i G  d2x . (33) (33) However, the Poisson brackets remain the same as in the inviscid zeroth-order hydrodynamics, i.e. EDA given by (18,19,20). In this case the full stress tensor is explicitly given by However, the Poisson brackets remain the same as in the inviscid zeroth-order hydrodynamics, i.e. EDA given by (18,19,20). In this case the full stress tensor is explicitly given by Ti j = − € p + ρG′ω Š δi j , (34) (34) which proves the Corollary III.1. 3.4 Conditions for Hamiltonian hydrodynamics For the first-order hydrodynamics defined by Eqs. (1-5) to be Hamiltonian the viscous stress coefficients in Eq. (5) must jointly satisfy Statement I and Statement II. Case 1 of Statement I defines a Hamiltonian system as long as ΓH = −ζH = ηH(ρ) −ρ η′ H(ρ). For the Case 2, the Jacobi identity constraint is incompatible with the energy conservation condition unless c = 0. We summarize these findings in the following statement. Statement III. The hydrodynamics Eqs. (1-5) is Hamiltonian only in the following cases Case 1: For arbitrary ηH(ρ), G = 0, and Case 1: For arbitrary ηH(ρ), G = 0, and ΓH(ρ) = −ζH(ρ) = ηH(ρ) −ρ η′ H(ρ). Case 2: For arbitrary G(ρ) and ζH(ρ) = −ρG′(ρ), ΓH(ρ) = ηH(ρ) = 0. Furthermore, Case 2 itself comes with a corollary. Corollary III.1. If the momentum density satisfies the diffeomorphism algebra (20) the only allowed viscosity term in the Hamiltonian is the odd pressure term ζH. In both cases, the hydrodynamic equations are obtained from the Hamiltonian (25) and the Poisson brackets (18,19) and (26), with the viscosity coefficients satisfying one of the con- ditions in the Statement III. Note that the Hamiltonian function for Case 1 has the same form as the inviscid Hamiltonian (17). In addition to that, we would like to emphasize that the Hamiltonian hydrodynamics corresponding to Case 1 could be equivalently written in terms of the diffeomorphism generator Ji defined in (30). In these new variables, the Poisson al- gebra becomes the EDA and the equation of motion for the “modified momentum density” Ji 9 SciPost Phys. 14, 103 (2023) posses higher-order derivative terms and no odd viscosity stress (only odd pressure). This was already pointed out in several references, such as [9,11,16] for the particular case of ΓH = 0. When ΓH = 0, the Jacobi identity condition (29) imposes that ηH(ρ) = νoρ, where νo is a constant kinematic odd viscosity. In fact, in the Ref. [11], the authors identify the generators of diffeomorphism Ji to the “molecular” center-of-mass momentum density. posses higher-order derivative terms and no odd viscosity stress (only odd pressure). This was already pointed out in several references, such as [9,11,16] for the particular case of ΓH = 0. When ΓH = 0, the Jacobi identity condition (29) imposes that ηH(ρ) = νoρ, where νo is a constant kinematic odd viscosity. In fact, in the Ref. 6These terms generalize the “quantum pressure” arising from the Madelung transformations in Schrödinger equation. 3.5 Generalized Hamiltonian hydrodynamics In this form the only viscous term present is the odd pressure term with ζH = −ρG ′ and primes denote derivatives with respect to ρ. Let us now shift the momentum density according to (30), i.e. Ji = Ji + ∂∗ i ηH, where ηH(ρ) is an arbitrary function of ρ. As a result, we obtain the hydrodynamic system in terms of these new variables,7 that is, ∂tρ + ∂iJi = 0, (40) ∂tJk + ∂i JiJk ρ −T H ik ‹ = 0, (41) (40) (41) where the new stress tensor T H i j is given by T H i j = ηH i jkl∂k €Jl ρ Š −A ρ ∂iρ ∂jρ −δi j ” p −B(∇ρ)2 −C∆ρ — , (42) (42) with with ζH = −ηH −ρG ′ , ΓH = ηH −ρη′ H , (43) A = K′2 −η′ H 2 , C = A+ η′ H(G ′ + η′ H), (44) B = 1 2A′ + (G ′ + η′ H)  η′′ H − η′ H ρ  . (45) (43) (44) (45) We notice that the modified stress tensor’s parity-breaking part is generally defined by two independent functions ηH(ρ) and G(ρ). An additional free function K(ρ) contributes to Madelung terms. The expressions (43-45) are the most general relations on parity-odd coefficients compatible with Hamiltonian hydrodynamics. If by some reason one requires that Madelung term vanish one obtains K = ±ηH and (G ′ + η′ H)η′ H = 0. The latter equation has two solutions G = −ηH or ηH = 0. These two solutions give Cases 1 and 2 of the Statement III, respectively.It is interesting to note that the odd viscosity term ηH appears in this construction not as a parameter of the Hamiltonian (36) but as the parameter of the momentum density shift or equivalently as a modification of Poisson’s brackets. We remark here that it is relatively straightforward to generate all Hamiltonian systems. One can start with a general local form of the Hamiltonian (36), generate equations using (18-20) and then consider redefinitions of hydrodynamic fields (30) preserving the structure of equations of motion. However, this procedure is based on the assumption that there are no non-trivial extensions of the EDA within the order in derivatives used in this work. 3.5 Generalized Hamiltonian hydrodynamics In the previous sections, we showed that the Hamiltonian structure is intimately related to the existence of hydrodynamic variables ρ and Ji, which satisfy the EDA. This way, we can easily generalize our results and propose the most general Hamiltonian hydrodynamics within an appropriate counting scheme. It is not hard to see that the Poisson algebra (18,19,20) is invariant under the scaling Ji →αJi , ∂i →α∂i , ρ →ρ . (35) (35) Hence, the diffeomorphism generators Ji, defined in Eq. (30) also scales as Ji →αJi. This new counting scheme differs from the original derivative expansion of the stress tensor. Under this scaling, first-order hydrodynamic terms, such as viscous terms in the stress tensor, show up in the same order as the following second-order hydrodynamic terms τi jkl(ρ)∂kρ ∂lρ + σi jkl(ρ)∂k∂lρ . In the following, we refer to them as Madelung terms.6 Note that Eq. (35) together with the continuity equation impose that ∂t must be of order α2. The scaling (35) is similar to the one used for energy conservation in Appendix A and gives us that the energy density of the fluid must scale in the same way as the fluid stress tensor. Thus, within this counting scheme, the most general Hamiltonian dynamics is given by the following simple prescription. Let us first take the most general Hamiltonian of the second order in α, that is, H = Z  J2 i 2ρ + ϵ + Ji ρ ∂∗ i G + 1 2ρ (∂iK)2  d2x , (36) (36) where Ji is the diffeomorphism generator, G and K are arbitrary functions of ρ. Let us as- sume conventional EDA brackets (18-20) and generate equations of motion for ρ and Ji. The equation for ρ is the standard continuity equation ∂tρ + ∂iJi = 0, (37) (37) 6These terms generalize the “quantum pressure” arising from the Madelung transformations in Schrödinger equation. 10 SciPost Phys. 14, 103 (2023) while the one for Ji is  ‹ ∂tJk + ∂i JiJk ρ −Tik ‹ = 0, (38) i ∂tJk + ∂i JiJk ρ −Tik ‹ = 0, (38) ∂tJk + ∂i JiJk ρ −Tik ‹ = 0, (38) with 1  €J∗ k Š  (38) with Ti j = −1 ρ ∂iK∂jK −  p + ρ G ′∂k €J∗ k ρ Š −K′∆K  δi j . (39) (39) Once again, pressure is given by (4). 7There is a certain ambiguity in the form of the stress tensor resulting from the freedom to add to the stre arbitrary divergenceless terms. These additions, however, do not change the equations of motion. 4 Energy conservation and nonholonomic constraints The absence of Hamiltonian structure in energy-conserving systems is one of the prominent features of so-called nonholonomic systems. These systems are described as systems with restrictions on types of motion. Typical examples include systems like rolling balls and rolling wheels as well as skates with rolling constraints and skating constraints, respectively [21,22, 24]. In these systems, the constraints imposed on velocities are not integrable and, therefore, cannot be reduced to the constraints on the configurational space of the dynamic system. Such constraints are called nonholonomic and are related to the break down of the Jacobi identity in the Hamiltonian framework [22,25].l In this section, we consider the fluid dynamics described by Case 1 of Statement I, but not satisfying the condition of Statement II. We show that it arises from Hamiltonian fluid dynamics with internal angular momentum degree of freedom subject to a nonholonomic constraint. The constraint pins the internal angular momentum density to the function of the density of the fluid, preserving energy conservation but breaking the Hamiltonian structure. Let us consider the following Hamiltonian Hλ = Z d2x  J2 i 2ρ + ϵ(ρ) + λ(ℓ+ 2ηH(ρ))2  . (46) (46) This Hamiltonian is a functional of hydrodynamic fields ρ and Ji as well as of the new field ℓ, which corresponds to the internal angular momentum density of the fluid. The numerical constant λ > 0 couples the internal angular momentum density to a function of the density of the fluid ηH(ρ). For large λ, it is energetically favorable for the system to have ℓ≈−2ηH.i Let us assume that the fields obey the Lie-Poisson algebra given by the brackets {ρ(x),ρ(y)} = {ℓ(x),ρ(y)} = {ℓ(x),ℓ(y)} = 0, (47) {ρ(x),Ji(y)} = −ρ(y) ∂ ∂yi δ(x −y), (48) {ℓ(x),Ji(y)} = ” 2ΓH(ρ(x)) ∂ ∂x i −ℓ(y) ∂ ∂yi — δ(x −y), (49)  Ji(x),Jk(y) = • Jk(x) ∂ ∂x i −Ji(y) ∂ ∂yk ˜ δ(x −y) + (εikδjl + δikεjl) ∂ ∂x j •ℓ(x) 2 ∂ ∂x l δ(x −y) ˜ −(δi jεkl −εi jδkl) ∂ ∂x j • ΓH(ρ(x)) ∂ ∂x l δ(x −y) ˜ . (50) (47) (48) (49) (50) One can check that these brackets do satisfy the Jacobi identity. In fact, this is true by construc- tion, since the brackets involving ℓwere derived from replacing ηH by the new variable −1 2ℓ in Eqs. (98, 105). 3.5 Generalized Hamiltonian hydrodynamics A priori one might have a non-trivial extension of Poisson algebra similar to the central extensions con- sidered in [23]. The authors are not aware of the theorem on the absence of such extensions, and one should consider the computations done in Appendix B as an explicit proof of such a theorem within our counting scheme. 11 SciPost Phys. 14, 103 (2023) 4 Energy conservation and nonholonomic constraints Furthermore, we can recover the conventional EDA presented in [9, 11] if we rewrite this algebra in terms of the quantities Ji,ρ, L, which are defined by Ji = Ji −1 2∂∗ i ℓ, (51) L = ℓ+ M , (52) (51) (51) (52) (51) (52) (52) L = ℓ+ M , (52) with with with with t ΓH = 1 2(M −ρM′). (53) ΓH = 1 2(M −ρM′). (53) (53) The Hamiltonian (46) with these brackets define a Hamiltonian fluid dynamics, whos The Hamiltonian (46) with these brackets define a Hamiltonian fluid dynamics, whose The Hamiltonian (46) with these brackets define a Hamiltonian fluid dynamics, whose 12 SciPost Phys. 14, 103 (2023) equations of motion are given by n are given by ∂tρ + ∂i(ρvi) = 0, (54) ∂tℓ+ ∂i (ℓvi) = −2ΓH ∂ivi , (55) ∂tJj + ∂i ρvivj + ˜p δi j  = ∂i ” ηℓ i jkl∂kvl — , (56) ηℓ i jkl = −1 2ℓ(δikεjl + δjlεik) + ΓH (δi jεkl −εi jδkl), (57) ˜p = ρϵ′ −ϵ + λ(δℓ)2 −4λ(ηH −ρη′ H −ΓH)δℓ. (58) (56) (58) Here we introduced the notation δℓ= ℓ+ 2ηH and vi = Ji/ρ. Notice that the form of the viscous tensor (57) is identical to (10) with the replacement ℓ→−2ηH. Here we introduced the notation δℓ= ℓ+ 2ηH and vi = Ji/ρ. Notice that the form of the viscous tensor (57) is identical to (10) with the replacement ℓ→−2ηH. It is important to understand that the dynamical system (54-58) is Hamiltonian for any value of the parameter λ as it is generated by the Hamiltonian (46) with the use of Poisson brackets (47-50). It is clear that, at finite energy, the intrinsic angular momentum ℓshould follow −2ηH(ρ), in the limit λ →∞. However, from (54,55) we obtain that ∂t(δℓ) + ∂i(δℓvi) = −2(ΓH −ηH + ρη′ H)∂ivi . (59) (59) If the condition (29) is satisfied, the right hand side of (59) vanishes. In this case one can start with initial conditions ℓ= −2ηH(ρ) and the dynamics (59) will preserve these conditions at all times. The constraint If the condition (29) is satisfied, the right hand side of (59) vanishes. In this case one can start with initial conditions ℓ= −2ηH(ρ) and the dynamics (59) will preserve these conditions at all times. 4 Energy conservation and nonholonomic constraints The energy equation acquires a dissipative term ∂tE + ∂iQi = −γλ2(δℓ)2 . (62) (62) This regularization procedure allows us to take the limit λ →∞without imposing the incom- pressibility condition. Solving Eq. (61) in powers of 1/λ gives us This regularization procedure allows us to take the limit λ →∞without imposing the incom- pressibility condition. Solving Eq. (61) in powers of 1/λ gives us ℓ= −2ηH −2 γλ(ΓH −ηH + ρη′ H)∂ivi + O(λ−2). (63) (63) Plugging this expression back in the Eqs. (56-58), we obtain the regularized stress tensor Ti j = (−p + ζ∂kvk)δi j + ¯ηi jkl∂kvl , (64) (64) with the bulk viscosity given by with the bulk viscosity given by ζ = 8 γ(ΓH −ηH + ρη′ H)2 . (65) (65) The intrinsic angular momentum relaxation introduces a bulk viscosity in the system and spoils the energy conservation. With the dissipative regularization (61) the limit λ →∞can be taken. The energy equation (62) in this limit becomes The intrinsic angular momentum relaxation introduces a bulk viscosity in the system and spoils the energy conservation. With the dissipative regularization (61) the limit λ →∞can be taken. The energy equation (62) in this limit becomes ∂tE + ∂iQi = −ζ(∂ivi)2 , (66) (66) where the bulk viscosity is given by Eq. (65). We observe that the limit λ →∞produced a family of hydrodynamic equations characterized by the parameter γ (compare with [27,28]). Within this family for γ →0, the bulk viscosity becomes infinite and forces the fluid to be incompressible. This way, we recover the Hamiltonian case with second-class constraints, discussed previously. In the opposite limit γ →∞, the bulk viscosity vanishes, and the system conserves energy, even though it cannot be written from a Hamiltonian principle. 4 Energy conservation and nonholonomic constraints The constraint −1 2ℓ= ηH(ρ) (60) (60) in this case is the first-class constraint [26] and the substitution of ℓ= −2ηH(ρ) in all brackets, Hamiltonian and equations is consistent and produces the Hamiltonian dynamics of ρ and Ji specified in the Statement III, Case 1. Let us assume now that (29) does not hold. In this case, imposing the constraint (60) cannot be reduced to just a choice of initial conditions. Choosing initial conditions satisfy- ing ℓ= −2ηH we find that, for large but finite λ, ℓwill deviate from −2ηH in time, due to (59). However, this deviation creates a large pressure term (58) proportional to λ which will lead the flow to be incompressible, that is, ∂ivi = 0. Consequently, the right hand side of Eq. (59) vanishes, making sure that ℓ≈−2ηH. The limiting solution at λ →∞will satisfy the constraint (60) at all times, however it constrains the flow to be incompressible. In other words, in the absence of the restriction (29), the time evolution of the constraint (60) gives rise to incompressibility, which is a second-class constraint [26]. The system with both con- straints, that is, Eq. (60) together with ∂ivi = 0, can be written from a Hamiltonian principle by working out the Dirac brackets of the system [26], which will turn out to be non-local. If, on the other hand, we insist in imposing only the constraint (60), without the incompressibility condition, i.e. neglecting Eq. (59), we end up with a nonholonomic constraint. This can be directly observed, if we substitute ℓby −2ηH(ρ) in the Poisson bracket (49). This replacement is inconsistent to Eq. (48). In the following, we explore a possible origin of energy-conserving but non-Hamiltonian fluid dynamics as coming from Hamiltonian systems with additional degrees of freedom through dynamical nonholonomic constraints. The problem of realizing nonholonomic con- straints has been considered in the context of dynamical systems. The realization of constraints is not always unique and might result in different equations of motion. We refer the reader to the original article [27] and reviews [21, 22]. The discussion here is heuristic and is closely related to the so-called vakonomic mechanics [28]. Let us introduce a relaxation term proportional to δℓon the right hand side of Eq. (55), that is, (61) ∂tℓ+ ∂i(ℓvi) = −2ΓH∂ivi −γλ(δℓ), (61) ∂tℓ+ ∂i(ℓvi) = −2ΓH∂ivi −γλ(δℓ), 13 SciPost Phys. 14, 103 (2023) with γ > 0. 5 Discussion and conclusions We considered a space of two-dimensional fluid dynamics with parity-breaking terms in the viscous stress tensor in this work. We started by identifying the subset of energy-conserving fluids within this space (Statement I). Surprisingly, not all parity-odd viscosity coefficients lead to energy conservation in first-order hydrodynamics. For example, for a hydrodynamic system with ηi jkl = ΓHεi jδkl, Eqs. (77-81) give us ∂tE + ∂iQi = −  ΓH ρ2 ‹′ ΓH(∂iρ)2 + Γ 2 H ρ2 ∆ρ  ∂jvj . The right hand side can be either positive or negative, depending on the flow and the den- sity distribution. Hydrodynamic systems which neither conserve energy nor are exclusively dissipative may be realized in active matter systems, where the driving is local. If, however, we insist on having both energy conservation and (ηH,ΓH,ζH) being independent functions, we must allow for Madelung terms in the stress tensor, which is the subject of future work. Some of the hydrodynamical systems considered in this work turn out to be energy-conserving but not Hamiltonian. An obstacle for the system to be Hamiltonian is that the brackets gen- erating equations of motion fail to satisfy the Jacobi identity. We found that this condition amounts to (29) defining what we might refer to as Hamiltonian fluids. We also observed that the bracket generating equations of Hamiltonian fluids could always be transformed to 14 SciPost Phys. 14, 103 (2023) ⌘ijkl = ⌘(δikδjl + δilδjk −δijδkl) + ⇣δijδkl + Γ ✏ij✏kl + ⌘H (✏ikδjl + ✏jlδik) + ⇣H δij✏kl + ΓH✏ijδkl ⌘ijkl = ⌘H ijkl ⌘ijkl = ¯⌘ijkl ⌘= Γ = ⇣= 0 ⇣H = −ΓH ⌘H = cG ΓH = c(G −2⇢G0) ⇣H = −c(G −2⇢G0) −⇢G0 ΓH = ⌘H −⇢⌘0 H c = 0 Energy conservation Hamiltonian Isotropic viscous tensor Parity-odd viscous tensor ⇣H = −⇢G0 Figure 1: The space of parity breaking barotropic Galilean fluids in two dimensions. In addition to the internal energy density ϵ(ρ), the space is parametrized by viscosity coefficients that are considered to be arbitrary functions of density. Figure 1: The space of parity breaking barotropic Galilean fluids in two dimensions. In addition to the internal energy density ϵ(ρ), the space is parametrized by viscosity coefficients that are considered to be arbitrary functions of density. the conventional extended diffeomorphism algebra (EDA) (18-20) by changing hydrodynamic variables (Statement II). 5 Discussion and conclusions In particular, if the momentum density satisfies the EDA, the only al- lowed viscosity term in the Hamiltonian dynamics is the odd pressure ζH. The main results supporting the described structure of the space of theories are formulated as Statements I-III with some details of derivations relegated to appendices. The study of the space of parity-violating hydrodynamic equations in 2+1 dimensions have been done before both in relativistic [13] and nonrelativistic [29,30] context. In this work, we focus on the Hamiltonian fluids. We use a nonrelativistic counting scheme, described in 3.5, to make sure that there are only a finite number of terms in the stress tensor at any given order of the counting scheme. We find the most general Hamiltonian fluid dynamics within the second- order of that counting scheme. This dynamics is characterized by three independent functions of density. The stress tensor (42) and the correspondent transport coefficients are given by Eqs (43-45).l In Section 4, we provided a possible origin of nonholonomic fluid dynamics as originating from fully Hamiltonian extended dynamics with nonholonomic constraints imposed on an ad- ditional degree of freedom. This additional degree of freedom, in our case, has a meaning of an intrinsic angular momentum density of the fluid. We introduced an energy cost term in the Hamiltonian (46), such that, in the limit of infinite rigidity (λ →∞), the intrinsic angular momentum (ℓ) is pinned to the odd viscosity, ηH(ρ). Solving for ℓ, with a particular regu- larization procedure, we obtain an effective dissipative hydrodynamic system with the stress tensor given by Eqs. (64,65). Therefore, “integrating out” the intrinsic angular momentum density provides us a one-parameter family (γ) of a dissipative hydrodynamic system. Inter- estingly enough, we can recover the energy conservation for γ →0 and γ →∞. In the former case, the hydrodynamic system is Hamiltonian and subjected to the incompressibility condi- tion, i.e. ∂ivi = 0. In the latter, we obtain an energy-conserving system, described in Case 1 of 15 SciPost Phys. 14, 103 (2023) the Statement I, yet not Hamiltonian, since it does not satisfy the condition of the Statement II. the Statement I, yet not Hamiltonian, since it does not satisfy the condition of the Statement II. To conclude, if the stress tensor contains gradient terms, there are both Hamiltonian and energy-conserving nonholonomic fluids. We note that the stability analysis is very different for Hamiltonian and nonholonomic systems [22]. Acknowledgements We want to thank Tom Lubensky, Tomer Markovich, and Boris Khesin for helpful discussions. We specially thank Boris Khesin for bringing Ref. [23] to our attention and Tomer Markovich for carefully reading and suggesting improvements to the manuscript. Funding information This work is supported by NSF CAREER Grant No. DMR-1944967 (SG) and partly from PSC-CUNY Award. GMM was supported by 21st century foundation startup award from CCNY. This research was supported by grants NSF DMR-1606591 (AGA) and US DOE DESC-0017662 (AGA). 5 Discussion and conclusions In particular, additional instabilities are expected to occur in nonholonomic systems realizable in active matter. A Conditions for energy conservation counting scheme differs from the original derivative expansion and set Madelung terms, such as γi jkl(ρ)∂kρ∂lρ +σi jkl(ρ)∂k∂lρ, to be of the same order as viscous terms.. For the inviscid case the well-known conserved energy is recovered by setting F = G = W = 0. gy y g Taking the time derivative of Eq. (69) give us gy y Taking the time derivative of Eq. (69) give us ∂tE = −∂iQi + F′(ρ)ϵ′′(ρ)(∂iρ)2 + Ai jkl ∂ivj∂kvl + Bi jkl ∂iρ ∂jρ ∂kvl + Ci jkl ∂i∂jρ ∂kvl , (70) where ∂tE = −∂iQi + F′(ρ)ϵ′′(ρ)(∂iρ)2 + Ai jkl ∂ivj∂kvl + Bi jkl ∂iρ ∂jρ ∂kvl + Ci jkl ∂i∂jρ ∂kvl , (70) (70) where Qi = E vi + Ti jvj −F δik + G εik ρ ∂jTjk + ρκW∂iρ − F′ δjm + G′ εjm ρ ηimkl ∂jρ ∂kvl , (71) Ai jkl = −ηi jkl + F 2 εi jεkl + F 2 δikδjl + δilδjk −δi jδkl  +  F 2 −ρF′ ‹ δi jδkl −ρ G′δi jεkl , (72) Bi jkl =  F′ ρ δjm + G′ ρ εjm ‹′ ηimkl + ρ W ′ 2 δi jδkl −W 2 δikδjl + δilδik −δi jδkl  , (73) Ci jkl =  F′ ρ δjm + G′ ρ εjm ‹ ηimkl + ρ W δi jδkl . (74) (71) (73) (74) The term F′ϵ′′(∂iρ)2 is velocity independent and must vanish by itself for the energy to be conserved. This means that either F′(ρ) = 0 or ϵ′′(ρ) = 0. However, the sound velocity on a fluid is given by Æ cs = Æ ρϵ′′(ρ), which implies that F′(ρ) must necessarily vanish to guarantee energy conservation. Since the energy density is only defined up to total derivatives, we obtain that which implies that F′(ρ) must necessarily vanish to guarantee energy conservation. Since the energy density is only defined up to total derivatives, we obtain that F(ρ) = 0, (75) (75) which substantially simplifies Eqs. (72-74). which substantially simplifies Eqs. (72-74). The term Ai jkl ∂ivj ∂kvl is a quadratic form and cannot be written as a total derivative unless Γ = ζ = −η = c1. However, as mentioned in the main text, we ignore this particular case, since it does not modify the equations of motion in flat space. Thus, Ai jkl ∂ivj ∂kvl must necessarily vanish to ensure energy conservation. A Conditions for energy conservation Let us consider Eqs. (1-5) and let us work out under which conditions this set of equations allows for a third conserved quantity, namely, energy conservation. One way to do so is to determine the most general form of the energy density and then match all the transport coef- ficients such that the energy density E satisfies Eq. (13). To determine the form of E, we need to study the symmetries of Eqs. (1-2). The continuity equation ∂tρ + ∂i(ρvi) = 0, ∂tρ + ∂i(ρvi) = 0, is invariant under the following scaling xi →xi/α, t →t/β , and vi →viβ/α. (67) (67) Plugging this scaling into equation ∂t vj + vi∂ivj = 1 ρ ∂iTi j = 1 ρ ∂i  −p(ρ)δi j + ηi jkl(ρ)∂kvl  , and choosing that ρ →ρ, we obtain and choosing that ρ →ρ, we obtain Ti j →(β/α)2Ti j . (68) Ti j →(β/α)2Ti j . (68) This means that all viscosity coefficients scale as β/α2. Since they are only functions of ρ, they should have no scaling, which imposes that β = α2. Here, one could argue that pressure is also only a function of the density and, thus, should not scale. However, we must note that p′(ρ) = c2 s , where cs is the sound velocity. Since cs scales as the velocity flow, we obtain that pressure must scale as (β/α)2. The scaling (67) with β = α2 fixes the form of energy density. Hence, the most general energy density of order α2, up to total derivatives, is given by E = 1 2ρv2 i + ϵ(ρ) + F(ρ)κ + G(ρ)ω + 1 2W(ρ)(∂iρ)2 , (69) (69) where ω = ∂iv∗ i is the fluid vorticity, κ = ∂ivi is the flow compressibility and the functions F(ρ), G(ρ) and W(ρ) must be determined in terms of the viscosity coefficients. Note that this where ω = ∂iv∗ i is the fluid vorticity, κ = ∂ivi is the flow compressibility and the functions F(ρ), G(ρ) and W(ρ) must be determined in terms of the viscosity coefficients. Note that this 16 SciPost Phys. 14, 103 (2023) counting scheme differs from the original derivative expansion and set Madelung terms, such as γi jkl(ρ)∂kρ∂lρ +σi jkl(ρ)∂k∂lρ, to be of the same order as viscous terms.. For the inviscid case the well-known conserved energy is recovered by setting F = G = W = 0. A Conditions for energy conservation This is obtained when Ai jkl = −Akli j and, after imposing Eq. (75), we end up with η(ρ) = ζ(ρ) = Γ(ρ) = 0, (76) ζH(ρ) + ΓH(ρ) + ρ G′(ρ) = 0. (77) (76) (77) (76) (77) Let us now turn our attention to the last two terms. They give us Let us now turn our attention to the last two terms. They give us Bi jkl ∂iρ ∂jρ ∂kvl + Ci jkl ∂i∂jρ ∂kvl = ∂i κ∂iρ −∂jρ ∂jvi ρ 2ηHG′  + ΓH −ηH ρ G′ + ρW ‹ κ∆ρ + G′ ρ ‹′ (ΓH −ηH) − η′ HG′ ρ + ρW ′ 2  κ(∂iρ)2 + η′ HG′ ρ −W 2  ∂iρ ∂jρ (∂ivj + ∂jvi −δi jκ). (78) + η′ HG′ ρ −W 2  ∂iρ ∂jρ (∂ivj + ∂jvi −δi jκ). (78) (78) In order to write the right hand side of Eq. (78) as a total derivative, we must impose that In order to write the right hand side of Eq. (78) as a total derivative, we must impose that η′ G′ W η′ HG′ ρ −W 2 = 0, (79) G′ ρ (ΓH −ηH) + ρW = 0, (80) G′ ρ ‹′ (ΓH −ηH) − η′ HG′ ρ + ρW ′ 2 = 0. (81) (79) (80) ρ G′ ρ ‹′ (ΓH −ηH) − η′ HG′ ρ + ρW ′ 2 = 0. (81) (81) 17 17 SciPost Phys. 14, 103 (2023) Equation (77) allows us to express G(ρ) in terms of ζH(ρ) and ΓH(ρ). This means that there are four variables (ηH,ζH,ΓH,W) and 3 equations. Unless Eqs. (79-81) are linearly dependent, there is no way to satisfy them for ηH(ρ), ζH(ρ) and ΓH(ρ) independent. Plugging Eq. (79) into Eq. (80), we find that ΓH −ηH + 2ρη′ H  G′ = 0. (82) ΓH −ηH + 2ρη′ H  G′ = 0. (82) This breaks into two possible cases, namely, G′(ρ) = 0 or G′(ρ) ̸= 0. This breaks into two possible cases, namely, G′(ρ) = 0 or G′(ρ) ̸= 0. A.1 Case I: G′(ρ) = 0 A.1 Case I: G′(ρ) = 0 A.1 Case I: G′(ρ) = 0 A.1 Case I: G′(ρ) = 0 Let us first consider the case when G′(ρ) = 0. Plugging this into Eq. (79) gives us W = 0, which is consistent with Eq. (81). From Eq. (77), we see that this case is simply the condition ζH(ρ) = −ΓH(ρ), (83) (83) or equivalently ηi jkl(ρ) = ¯ηi jkl(ρ), (84) (84) where ¯ηi jkl is defined in Eq. (10). A.2 Case II: G′(ρ) ̸= 0 In this case, Eq. (82) imposes that ΓH(ρ) −ηH(ρ) + 2ρη′ H(ρ) = 0, (85) (85) and Eq. (81) can be written solely in terms of G′(ρ) and ηH(ρ). Plugging Eq. (79) into Eq. (81) and expressing ΓH(ρ) in term of ηH(ρ) gives us and Eq. (81) can be written solely in terms of G′(ρ) and ηH(ρ). Plugging Eq. (79) into Eq. (81) and expressing ΓH(ρ) in term of ηH(ρ) gives us η′ H(ρ) G′′(ρ) −η′′ H(ρ) G′(ρ) = 0. (86) (86) Note that G′(ρ) ̸= 0, otherwise we recover the case I. Therefore, we can express η′ H(ρ) in terms of G′(ρ). This gives us η′ H(ρ) = c G′(ρ), (87) (87) for a constant c. Hence, we obtain for a constant c. Hence, we obtain for a constant c. Hence, we obtain ηH(ρ) = c G(ρ) + c2 , (88) ΓH(ρ) = c  G(ρ) −2ρ G′(ρ)  + c2 , (89) ζH(ρ) = −c G(ρ) + (2c −1)ρ G′(ρ) −c2 , (90) W(ρ) = 2c ρ € G′(ρ) Š2 (91) (88) (90) (91) for a generic function G(ρ) and some constant c2. However, if we focus on the stress tensor, we see that for a generic function G(ρ) and some constant c2. However, if we focus on the stress tensor, we see that Ti j = −  p(ρ) + (2c −1)ρ G′(ρ)ω  δi j −2 cρ G′(ρ)κεi j + [c G(ρ) + c2]εik ∂kvj . (92) (92) The constant c2 in the last term does not contribute to equations of motion and we can set it to zero without loss of generality. Moreover, when c = 0, only odd pressure is present and the stress tensor becomes diagonal. 18 SciPost Phys. 14, 103 (2023) B Condition to satisfy the Jacobi identity For the system to be Hamiltonian, the algebra defined through expressions (18), (19), and (26) must satisfy the Jacobi identity. Let us define FA = Z fA ρ + Ji ξi A  d2x , (93) (93) for some test functions fA, ξ1 A and ξ2 B. In this notation, Jacobi identity can be written as εABC{{FA, FB}, FC} = 0. (94) (94) Using equation (18), we find that the brackets between FA and FB is given by Using equation (18), we find that the brackets between FA and FB is given by {FA, FB} = ZZ d2x d2 y ”fA(x)ξi B(y) −fB(x)ξi A(y)  {ρ(x),Ji(y)} + ξi A(x)ξk B(y){Ji(x),Jk(y)} — , {FA, FB} = Z d2x  ρ ξi A∂i fB −ξi B∂i fA  + Ji ξk A∂kξi B −ξk B∂kξi A  + ¯ηjiℓk ∂jξi A∂ℓξk B  . (95) {FA, FB} = Z d2x  ρ ξi A∂i fB −ξi B∂i fA  + Ji ξk A∂kξi B −ξk B∂kξi A  + ¯ηjiℓk ∂jξi A∂ℓξk B  . (95 (95) Plugging the expression (95) into equation (94), we find Plugging the expression (95) into equation (94), we find εABC{{FA, FB}, FC} = εABC ZZ d2x d2 y  2  ξi C(y)ξk A(x) ∂fB ∂x k (x) −fC(x)ξk A(y) ∂ξi B ∂x k (x)  × {ρ(x),Ji(y)} + 2ξk C(x)ξℓ A(y) ∂ξi B ∂xℓ(x){Ji(x),Jk(y)} + fC(y) ∂ξi A ∂x j (x) ∂ξk B ∂xℓ (x){ ¯ηjiℓk(x),ρ(y)} + ξm C (y) ∂ξi A ∂x j (x) ∂ξk B ∂xℓ (x){ ¯ηjiℓk(x),Jm(y)}  . (96) εABC{{FA, FB}, FC} = εABC ZZ d2x d2 y  2  ξi C(y)ξk A(x) ∂fB ∂x k (x) −fC(x)ξk A(y) ∂ξi B ∂x k (x)  i εABC{{FA, FB}, FC} = εABC ZZ d2x d2 y  2  ξi C(y)ξk A(x) ∂fB ∂x k (x) −fC(x)ξk A(y) ∂ξi B ∂x k (x)  × {ρ(x),Ji(y)} + 2ξk C(x)ξℓ A(y) ∂ξi B ∂xℓ(x){Ji(x),Jk(y)} + f (y) ∂ξi A(x) ∂ξk B (x){ ¯η (x) ρ(y)} × {ρ(x),Ji(y)} + 2ξk C(x)ξℓ A(y) ∂ξi B ∂xℓ(x){Ji(x),Jk(y)} + fC(y) ∂ξi A ∂x j (x) ∂ξk B ∂xℓ (x){ ¯ηjiℓk(x),ρ(y)} + ξm C (y) ∂ξi A ∂x j (x) ∂ξk B ∂xℓ (x){ ¯ηjiℓk(x),Jm(y)}  . (96) (96) Note that there are two types of terms in equation (96), i.e. B Condition to satisfy the Jacobi identity some of them depend on 3 vectors (ξA,ξB,ξC), whereas the others depend on 2 vectors (ξA,ξB) and one function fC. Since they are independent, each type of term must vanish separately. Let us now focus on terms with 2 vectors (ξA,ξB) and one function fC. The Jacobi identity imposes that Note that there are two types of terms in equation (96), i.e. some of them depend on 3 vectors (ξA,ξB,ξC), whereas the others depend on 2 vectors (ξA,ξB) and one function fC. Since they are independent, each type of term must vanish separately. Let us now focus on terms with 2 vectors (ξA,ξB) and one function fC. The Jacobi identity imposes that εABC Z d2x ” 2ρ(x)ξi A(x)ξk B ∂2 fC ∂x i∂x k (x) − ∂ξi A ∂x j (x) ∂ξk B ∂xℓ (x) Z d2 y fC(y){ ¯ηjiℓk(x),ρ(y)} — = 0, εABC ZZ d2x d2 y ∂ξi A ∂x j (x) ∂ξk B ∂xℓ (x)fC(y){ ¯ηjiℓk(x),ρ(y)} = 0, (97) (97) where in the second line we used that εABCξi Aξk B is antisymmetric in the indices (i, k). Equa- tion (97) imposes that { ¯ηjiℓk(x),ρ(y)} = 0, (98) (98) which is automatically satisfied when the components ¯ηi jkℓare functions solely of ρ. 19 SciPost Phys. 14, 103 (2023) Let us now turn our attention to terms in equation (96) with 3 vectors (ξA,ξB,ξC), εABC Z d2x – 2 ¯ηjiℓk(x) ∂ξk C ∂xℓ (x) ∂ ∂x j  ξm A ∂ξi B ∂x m  (x) −2Ji(x)ξk A(x)ξj B(x) ∂2ξi C ∂x k∂x j (x) + Z d2 y ξm C (y) ∂ξi A ∂x j (x) ∂ξk B ∂xℓ (x){ ¯ηjiℓk(x),Jm(y)}  = 0, εABC Z d2x – ¯ηjiℓk(x) ‚ ξm A (x) ∂ ∂x m ‚ ∂ξi B ∂x j ∂ξk C ∂xℓ Œ (x) + 2 ∂ξm A ∂x j (x) ∂ξi B ∂x m (x) ∂ξk C ∂xℓ (x) Œ + Z d2 y ξm C (y) ∂ξi A ∂x j (x) ∂ξk B ∂xℓ (x){ ¯ηjiℓk(x),Jm(y)}  = 0. (99 (99) In the third line, we used one more time that εABCξk Aξj B is antisymmetric in the indices (k, j) and that εABC ¯ηjiℓk∂m ∂jξi B∂ℓξk C  = εABC( ¯ηjiℓk −¯ηi jkℓ)∂ℓξk C ∂m∂jξi B = 2εABC ¯ηjiℓk∂ℓξk C ∂m∂jξi B . B Condition to satisfy the Jacobi identity 14, 103 (2023) Plugging equation (103) into (102), we see that Plugging equation (103) into (102), we see that quation (103) into (102), we see that εABC Z d2x ΓH −ηH ∂ξm A ∂x m −ξm A ∂ηH ∂x m + Z d2 y ξm A (y){ ¯ηH(x),Jm(y)}  i k εABC Z d2x ΓH −ηH ∂ξm A ∂x m −ξm A ∂ηH ∂x m + Z d2 y ξm A (y){ ¯ηH(x),Jm(y)}  × (εjℓδik + δjℓεik) ∂ξi B ∂x j ∂ξk C ∂xℓ = 0. (104 × (εjℓδik + δjℓεik) ∂ξi B ∂x j ∂ξk C ∂xℓ = 0. (104) (104) The bracket between the odd viscosity and the momentum density is fully determined by Jacobi identity, i.e. The bracket between the odd viscosity and the momentum density is fully determined by Jacobi identity, i.e. {ηH(x),Jm(y)} = •€ ηH(x) −ΓH ρ(x) Š ∂ ∂x m + ∂ηH ∂x m (x) ˜ δ(x −y), {ηH(x),Jm(y)} = − • ηH(y) ∂ ∂ym + ΓH ρ(x)  ∂ ∂x m ˜ δ(x −y). (105) (105) So far, we have not used that ηH is a function of ρ. Imposing it into equation (104) give us us us εABC(εjℓδik + δjℓεik) Z d2x ” ΓH(ρ) −ηH(ρ) + ρ η′ H(ρ) —∂ξm A ∂x m ∂ξi B ∂x j ∂ξk C ∂xℓ = 0, (106) (106) in other words, the Jacobi identity is only satisfied when in other words, the Jacobi identity is only satisfied when in other words, the Jacobi identity is only satisfied when ΓH(ρ) = ηH(ρ) −ρ η′ H(ρ). (107) (107) In fact, equation (105) must always be valid, even when ηH cannot be expressed in terms of ρ. Therefore, equation (105) defines the brackets between the fluid intrinsic angular mo- mentum and momentum density. Equation (105) however has a deeper implication. Note that ∂ ∂x j • ¯ηjiℓk(x) ∂ ∂xℓ ˜ δ(x −y) = ∂ ∂x j •€ ηH(x) εjℓδik + εikδjℓ  + ΓH(x)(εjiδℓk −δjiεℓk) Š ∂ ∂xℓ ˜ δ(x −y), ∂ ∂x j • ¯ηjiℓk(x) ∂ ∂xℓ ˜ δ(x −y) =  εi j ∂ ∂yj  ηH(y) ∂ ∂yk ‹ −εkj ∂ ∂x j  ηH(x) ∂ ∂x i ‹ δ(x −y) −εi j ∂ ∂x j • ΓH(x) ∂ ∂x k ˜ δ(x −y) + εkj ∂ ∂yj • ΓH(x) ∂ ∂yi ˜ δ(x −y). B Condition to satisfy the Jacobi identity Integrating equation (99) by parts give us εABC Z d2x – 2 ¯ηjiℓk(x) ∂ξm A ∂x j (x) ∂ξi B ∂x m (x) ∂ξk C ∂xℓ (x) − ∂ξi B ∂x j (x) ∂ξk C ∂xℓ (x) ∂ ∂x m ξm A ¯ηjiℓk  (x) + Z d2 y ξm A (y) ∂ξi B ∂x j (x) ∂ξk C ∂xℓ (x){ ¯ηjiℓk(x),Jm(y)} ™ = 0. (100) (100) Note that equation (100) is valid for any spatial dimensions, since we still have not used the 2-dimensional form of ¯ηi jkℓ. Moreover, if the stress tensor is symmetric, ¯ηi jkℓ= ¯ηjikℓand the first term vanishes identically. Let us now focus on the first term in (100). Hence, Note that equation (100) is valid for any spatial dimensions, since we still have not used the 2-dimensional form of ¯ηi jkℓ. Moreover, if the stress tensor is symmetric, ¯ηi jkℓ= ¯ηjikℓand the first term vanishes identically. Let us now focus on the first term in (100). Hence, 2εABC ¯ηjiℓk∂jξm A ∂mξi B∂ℓξk C = εABC ¯ηjiℓkεjiεnr∂nξm A ∂mξr B∂ℓξk C = 2ΓHεjkδiℓ∂jξi A∂ℓξk B∂mξm C , and equation (100) becomes εABC Z d2x ∂ξi B ∂x j (x) ∂ξk C ∂xℓ (x) € ΓH(x)(εjkδiℓ+ δjkεiℓ) −¯ηjiℓk(x) Š∂ξm A ∂x m (x) −ξm A (x) ∂¯ηjiℓk ∂x m (x) + Z d2 y ξm A (y){ ¯ηjiℓk(x),Jm(y)}  = 0. (101) (101) However, using that εABC∂iξi A∂jξj B = 0, together with However, using that εABC∂iξi A∂jξj B = 0, together with εjkδiℓ+ δjkεiℓ= εjℓδik + δjℓεik , we obtain εABC Z d2x ∂ξi B ∂x j (x) ∂ξk C ∂xℓ (x) € εjℓδik + δjℓεik ŠΓH(x) −ηH(x) ∂ξm A ∂x m (x) −ξm A (x)∂ηH ∂x m (x)  − € εjiδℓk −δjiεℓk Š ξm A (x) ∂ΓH ∂x m (x) + Z d2 y ξm A (y){ ¯ηjiℓk(x),Jm(y)}  = 0. (102) Here is convenient to use that ΓH is a function of ρ, that is, Here is convenient to use that ΓH is a function of ρ, that is, Here is convenient to use that ΓH is a function of ρ, that is,  ΓH ρ(x)  ,Jm(y) = −Γ ′ H ρ(x)  ρ(y) ∂ ∂ym δ(x −y). (103) (103) 20 SciPost Phys. B Condition to satisfy the Jacobi identity (108) Using equation (105), we can eliminate the dependence in ΓH, since −εi j ∂ ∂x j • ΓH(x) ∂ ∂x k ˜ δ(x −y) = {∂∗ i ηH(x),Jk(y)} −ηH(y)εi j ∂2 ∂yj∂yk δ(x −y), (109) εk j ∂ ∂yj • ΓH(x) ∂ ∂yi ˜ δ(x −y) = {Ji(x),∂∗ k ηH(y)} + ηH(x)εkj ∂2 ∂x j∂x i δ(x −y). (110) Therefore, we obtain Therefore, we obtain ∂ ∂x j • ¯ηjiℓk(x) ∂ ∂xℓ ˜ δ(x −y) ={∂∗ i ηH(x),Jk(y)} + {Ji(x),∂∗ k ηH(y)} ∂ ∂x j • ¯ηjiℓk(x) ∂ ∂xℓ ˜ δ(x −y) ={∂∗ i ηH(x),Jk(y)} + {Ji(x),∂∗ k ηH(y)} + • ∂iηH(y) ∂ ∂yk −∂∗ k ηH(x) ∂ ∂x k ˜ δ(x −y). (111) + • ∂iηH(y) ∂ ∂yk −∂∗ k ηH(x) ∂ ∂x k ˜ δ(x −y). (111) (111) Combining this with equation (26), we see that the quantities Ji+∂∗ i ηH are the diffeomorphism generators, that is, they satisfy following algebra Ji + ∂∗ i ηH  (x), Jk + ∂∗ k ηH  (y) = •Ji + ∂∗ i ηH  (y) ∂ ∂yk − Jk + ∂∗ k ηH  (x) ∂ ∂x i ˜ δ(x −y). (112 Ji + ∂∗ i ηH  (x), Jk + ∂∗ k ηH  (y) = •Ji + ∂∗ i ηH  (y) ∂ ∂yk − Jk + ∂∗ k ηH  (x) ∂ ∂x i ˜ δ(x −y). (112) Ji + ∂∗ i ηH  (x), Jk + ∂∗ k ηH  (y) = •Ji + ∂∗ i ηH  (y) ∂ ∂yk − Jk + ∂∗ k ηH  (x) ∂ ∂x i ˜ δ(x −y). (112) 21 SciPost Phys. 14, 103 (2023) References [1] E. Lifshitz and L. Pitaevskii, Physical kinetics: Volume 10, Butterworth-Heinemann, Ox- ford, UK, ISBN 9780750626354 (1981). [2] J. E. Avron, R. Seiler and P. G. Zograf, Viscosity of quantum Hall fluids, Phys. Rev. Lett. 75, 697 (1995), doi:10.1103/PhysRevLett.75.697. [3] J. E. Avron, Odd viscosity, J. Stat. Phys. 92, 543 (1998), doi:10.1023/A:1023084404080. [4] A. I. Berdyugin et al., Measuring Hall viscosity of graphene’s electron fluid, Science 364, 162 (2019), doi:10.1126/science.aau0685. [5] V. Soni, E. S. Bililign, S. Magkiriadou, S. Sacanna, D. Bartolo, M. J. Shelley and W. T. M. Irvine, The odd free surface flows of a colloidal chiral fluid, Nat. Phys. 15, 1188 (2019), doi:10.1038/s41567-019-0603-8. [6] N. Read, Non-Abelian adiabatic statistics and Hall viscosity in quantum Hall states and px + ipy paired superfluids, Phys. Rev. B 79, 045308 (2009), doi:10.1103/PhysRevB.79.045308. [7] F. D. M. Haldane, Geometrical description of the fractional quantum Hall effect, Phys. Rev. Lett. 107, 116801 (2011), doi:10.1103/PhysRevLett.107.116801. [8] A. G. Abanov, On the effective hydrodynamics of the fractional quantum Hall effect, J. Phys. A: Math. Theor. 46, 292001 (2013), doi:10.1088/1751-8113/46/29/292001. [9] M. Lingam, Hall viscosity: A link between quantum Hall systems, plasmas and liquid crys- tals, Phys. Lett. A 379, 1425 (2015), doi:10.1016/j.physleta.2015.03.014. [10] D. Banerjee, A. Souslov, A. G. Abanov and V. Vitelli, Odd viscosity in chiral active fluids, Nat. Commun. 8, 1573 (2017), doi:10.1038/s41467-017-01378-7. [11] T. Markovich and T. C. Lubensky, Odd viscosity in active matter: Microscopic origin and 3D effects, Phys. Rev. Lett. 127, 048001 (2021), doi:10.1103/PhysRevLett.127.048001. [12] L. Landau and E. Lifshitz, Fluid mechanics, Elsevier, Amsterdam, Netherlands, ISBN 9780080339337 (1987), doi:10.1016/C2013-0-03799-1. [13] K. Jensen, M. Kaminski, P. Kovtun, R. Meyer, A. Ritz and A. Yarom, Parity- violating hydrodynamics in 2 + 1 dimensions, J. High Energy Phys. 05, 102 (2012), doi:10.1007/JHEP05(2012)102. [14] S. Dubovsky, L. Hui, A. Nicolis and D. T. Son, Effective field theory for hydrodynam- ics: Thermodynamics, and the derivative expansion, Phys. Rev. D 85, 085029 (2012), doi:10.1103/PhysRevD.85.085029. [15] F. M. Haehl, R. Loganayagam and M. Rangamani, Adiabatic hydrodynam- ics: The eightfold way to dissipation, J. High Energy Phys. 05, 060 (2015), doi:10.1007/JHEP05(2015)060. [16] A. G. Abanov, T. Can, S. Ganeshan and G. M. Monteiro, Hydrodynamics of two- dimensional compressible fluid with broken parity: Variational principle and free sur- face dynamics in the absence of dissipation, Phys. Rev. Fluids 5, 104802 (2020), doi:10.1103/PhysRevFluids.5.104802. 22 SciPost Phys. 14, 103 (2023) [17] V. Zakharov, Hamiltonian formalism for hydrodynamic plasma models, Sov. References Phys. J. Exp. Theor. Phys. 33, 927 (1971). [18] V. E. Zakharov and E. A. Kuznetsov, Hamiltonian formalism for nonlinear waves, Phys.- Uspekhi 40, 1087 (1997), doi:10.1070/PU1997v040n11ABEH000304. [19] P. J. Morrison, Hamiltonian description of the ideal fluid, Rev. Mod. Phys. 70, 467 (1998), doi:10.1103/RevModPhys.70.467. [20] V. I. Arnold, Mathematical methods of classical mechanics, Springer, New York, USA, ISBN 9781475716955 (1978), doi:10.1007/978-1-4757-1693-1. [21] V. I. Arnold, V. V. Kozlov and A. I. Neishtadt, Mathematical aspects of classical and ce- lestial mechanics, Springer, Berlin, Heidelberg, Germany, ISBN 9783540282464 (2006), doi:10.1007/978-3-540-48926-9. [22] A. M. Bloch, Nonholonomic mechanics, Springer, New York, USA, ISBN 9781441930439 (2003), doi:10.1007/b97376_5. [23] B. Janssens and C. Vizman, Central extensions of Lie algebras of symplectic and divergence free vector fields, Banach Center Publ. 110, 105 (2016), doi:10.4064/bc110-0-7. [24] H. Goldstein, C. Poole and J. Safko, Classical mechanics, Pearson, London, UK, ISBN 9780201657029 (2001). [25] A. J. Van Der Schaft and B. M. Maschke, On the Hamiltonian formulation of non- holonomic mechanical systems, Rep. Math. Phys. 34, 225 (1994), doi:10.1016/0034- 4877(94)90038-8. [26] P. A. M. Dirac, Lectures on quantum mechanics, Courier Corporation, North Chelmsford, USA, ISBN 9780486417134 (2001). [27] V. V. Kozlov, The problem of realizing constraints in dynamics, J. Appl. Math. Mech. 56, 594 (1992), doi:10.1016/0021-8928(92)90017-3. [28] V. Kozlov, Realization of nonintegrable constraints in classical mechanics, Proc. USSR Acad. Sci. 272, 550 (1983). [29] M. Kaminski and S. Moroz, Nonrelativistic parity-violating hydrodynamics in two spatial dimensions, Phys. Rev. B 89, 115418 (2014), doi:10.1103/PhysRevB.89.115418. [30] A. Lucas and P. Surówka, Phenomenology of nonrelativistic parity-violating hydrodynamics in 2+1 dimensions, Phys. Rev. E 90, 063005 (2014), doi:10.1103/PhysRevE.90.063005. 23
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Súvislosti konceptu spoločensky zodpovedného podnikania
Pošta, telekomunikácie a elektronický obchod
2,010
cc-by
2,477
Pošta, Telekomunikácie a Elektronický obchod ISSN 1336-8281 SÚVISLOSTI KONCEPTU SPOLOČENSKY ZODPOVEDNÉHO PODNIKANIA Vladimíra Žiačková∗ Úvod Spoločensky zodpovedné podnikanie (CSR) je konceptom, ktorý pozitívnym vplyvom na spoločnosť na mikroúrovni ovplyvňuje zároveň celú spoločnosť a úzko súvisí s naliehavou snahou nájsť prostriedky riešenia globálnych problémov dnešného sveta. Tlak na podniky, aby sa začali správať spoločensky zodpovedne, je odpoveďou na sociálne a ekonomické výzvy, ktorým čelia komunity všade na svete, a je dôkazom, že ani samotné vlády, ani predstavitelia občianskej spoločnosti nedokážu nájsť dlhodobo udržateľné riešenia bez zapojenia súkromného sektora. V súčasnom období zvyšujúcej sa konkurencie, ako aj zvyšujúcich sa požiadaviek zákazníkov, ktoré spôsobujú komplexné zmeny okolia, je samozrejmé, že šancu uspieť majú len podniky, ktoré sú dostatočne flexibilné. Preto sa počas uplynulých desiatich rokov spoločensky zodpovedné podnikanie stalo rozhodujúcim nástrojom podnikovej politiky. Podniky nie sú uzatvorené jednotky, ktoré nie sú nezávislé od prostredia, v ktorom pôsobia. Práve naopak – ich aktivity vedú k tomu, že sú závislé od stálej výmeny s vonkajším prostredím a formujú globálny systém, ktorý má ekologickú, ekonomickú a sociálnu stránku. Podniky vytvárajú vzájomný vzťah s prostredím, keďže vplyvy na spoločnosť vyvolané činnosťou podnikov pôsobia spätne na samotné podniky. Táto súvislosť je známa ako princíp kontextuálnej relativity. Na základe tohto princípu podniky neexistujú izolovane a preto je v ich záujme brať do úvahy ekologickú, či sociálnu stránku svojich podnikateľských aktivít. CSR vs. trvalo udržateľný rozvoj a podnikateľská etika Trvalo udržateľný rozvoj predstavuje koncept, ktorý bol prijatý Svetovou konferenciou OSN pre životné prostredie a rozvoj a neskôr aj Svetovou bankou. Tento koncept vychádza z myšlienky zladiť rast blahobytu žijúcich generácií s ochranou životného prostredia. Kľúčovou ideou je nelimitovať možnosti budúcich generácií. Pojem trvalo udržateľný rozvoj (sustainable development) sa prvýkrát objavil v správe Svetovej komisie pre životné prostredie a rozvoj zo summitu v Rio de Janeiru. Spôsob podnikania založený na trvalo udržateľnom rozvoji hľadá rovnováhu medzi individuálnymi právami a slobodami a vymedzením zodpovednosti za svoje správanie so zreteľom na dôsledky svojho konania vo vzťahu ku všetkým zainteresovaným stranám. [1] Národná stratégia trvalo udržateľného rozvoja SR hovorí, že „trvalo udržateľným rozvojom sa rozumie cielený, dlhodobý, komplexný a synergický proces, ovplyvňujúci podmienky a všetky aspekty života, na všetkých ∗ Ing. Vladimíra Žiačková, Žilinská univerzita v Žiline, Fakulta Prevádzky a ekonomiky dopravy a spojov, Katedra spojov, Univerzitná 1, 010 26 Žilina, tel. č.: 041/513 3144, e-mail: vladimira.ziackova@fpedas.uniza.sk IV/2010 52 Pošta, Telekomunikácie a Elektronický obchod ISSN 1336-8281 úrovniach a smerujúci k takému funkčnému modelu určitého spoločenstva, ktorý kvalitne uspokojuje biologické, materiálne, duchovné a sociálne potreby a záujmy ľudí, pričom eliminuje alebo výrazne obmedzuje zásahy ohrozujúce, poškodzujúce alebo ničiace podmienky a formy života, nezaťažuje krajinu nad únosnú mieru, rozumne využíva jej zdroje a chráni kultúrne a prírodné dedičstvo.“ Podnikateľská etika je normatívna etika, ktorá sa zaoberá pôsobením morálnych noriem a princípov na všetkých úrovniach ekonomiky. Predmetom podnikateľskej etiky je oblasť konfliktu medzi ekonomickou a etickou racionalitou, medzi individuálnymi a všeobecnými záujmami, medzi princípom maximalizácie zisku a dobrom, resp. princípom spravodlivosti. [2] Vzťah medzi podnikaním a spoločenskou zodpovednosťou je jednou z najaktuálnejších tém podnikateľskej etiky. [3] Všetky uvedené teórie vychádzajú zo zodpovednosti voči spoločnosti, sú však viditeľné určité rozdiely. Koncept zodpovedného podnikania je zameraný najmä na externé prostredie a prvotne vychádza z marketingu, trvalo udržateľný rozvoj sa zaoberá životným prostredím a podnikateľská etika vychádza z princípu etiky samotnej, aplikovanej v podnikateľskom prostredí. Dodržiavanie princípov zodpovedného podnikania je kľúčom k trvalo udržateľnému rozvoju. Ak sa však podnik hlási k princípom podnikateľskej etiky, tým sa hlási aj k ekologickému a sociálne orientovanému podnikaniu. Jednoznačne môžeme konštatovať, že medzi týmito teóriami je veľmi tenká línia a často medzi nimi dochádza k názorovým nezrovnalostiam a prelínaniu obsahových vymedzení. Prelínanie týchto konceptov reflektuje Reidenbachov a Robinov model, v rámci ktorého môžeme určiť niekoľko vývojových stupňov morálneho rozvoja podnikov, ktoré sú znázornené na obrázku 1. ETICKÝ ETICKY SA RODIACI SPOLOČENSKY ZODPOVEDNÝ FORMÁLNE PRÁVNY AMORÁLNY Obrázok 1. Reidenbachov a Robinov model morálneho rozvoja podniku Zdroj: ROLNÝ, I. - LACINA, L.: Globalizace, etika, ekonomika. 3. vyd. Ostrava: Key Publishing, s.r.o., 2008. 281 s. ISBN 978-80-87071-62-5. s. 65. Z obrázku vyplýva, že autori rozlišujú z etického hľadiska celkom 5 vývojových typov podnikov podľa proporcií ich záujmu o zisk a podnikateľskú etiku. Adekvátne charakteristikám jednotlivých stupňov môžeme prisúdiť i mieru spoločenskej zodpovednosti podniku. IV/2010 53 Pošta, Telekomunikácie a Elektronický obchod ISSN 1336-8281 1. stupeň – amorálny: V tejto fáze sa podnik riadi zásadou, že jeho správanie je etické, pokiaľ jeho nečisté praktiky nie sú odhalené. Nijaký etický kódex, príp. iná norma tu neexistujú, všetko je podriadené maximalizácii zisku. 2. stupeň – formálne právny: Podnik dbá o to, aby jeho činnosť bola po formálnej právnej stránke v poriadku. Pohybuje sa výhradne na pôde legálnosti, i keď maximálne využíva legislatívne nedostatky vo svoj prospech. Ak sa objavia spoločenské problémy, na škody, ktoré spôsobí reaguje ex-post. Ak existuje podnikový etický kódex, či iné verejne prezentované zásady, sú zamerané výhradne na požiadavky lojality zamestnancov voči podniku. 3. stupeň – spoločensky zodpovedný: Manažment podniku si uvedomuje, že fungovať len na právnej rovine nestačí, preto vzrastá jeho záujem o podnikateľskú etiku. Podniková kultúra odráža zodpovedný občiansky postoj, nezameriava sa výhradne na akcionárov, ale berie ohľad i na širšiu verejnosť. Zvyšuje sa vyváženosť záujmu o zisk s etickou stránkou spôsobu jeho dosiahnutia. Chýbajú však konkrétne systémové a organizačné opatrenia. 4. stupeň – eticky sa rodiaci: Etické hodnoty sa stávajú súčasťou podnikovej kultúry. Najvyššími hodnotami podnikového manažmentu sa stávajú vytýčené kľúčové hodnoty podniku, ktoré sú deklarované verejnosti. Na tomto stupni sa objavuje aktívna snaha vedenia reagovať na vznikajúce spoločenské problémy a prihlásiť sa verejne ku spoločenskej zodpovednosti. Pri ekonomických rozhodnutiach manažment prihliada k morálnym hodnotám. I napriek tomu na tomto stupni nie sú spracované etické princípy a zásady do celej organizačnej štruktúry podniku. Etika ešte nie je súčasťou strategického plánovania, i keď je na ňu kladený zreteľ pri praktickej podnikateľskej činnosti. 4. stupeň – etický: Tento stupeň je charakteristický rovnovážnym záujmom podniku o etické a ekonomické výsledky. Etická analýza ekonomickej činnosti je integrovanou súčasťou podnikateľských zámerov podniku a jeho strategického plánu a využíva ju na predvídanie možných problémov. Dôraz na etické normy a princípy je súčasťou všetkých dokumentov a materiálov podniku. V jeho organizačnej štruktúre existujú články vedenia, ktoré sa priamo etickými problémami a ich predchádzaním zaoberajú. [4] Stakeholderská teória „Stakeholderská teória identifikuje najdôležitejšie skupiny, ktoré podnik ovplyvňujú, alebo ktoré ovplyvňuje samotný podnik. Teória pomohla manažérom, ktorí chceli aplikovať spoločensky zodpovedné podnikanie v praxi, určiť, kam majú zacieliť svoju pozornosť a upresnila voči komu majú byť zodpovední.“ Uvedená teória predstavuje formuláciu stakeholderskej koncepce vytvorenú Fremanom v roku 1984. [4] Práve od tohto roku sa začínajú objavovať namiesto všeobecných definícií, ktorých objektom je osoba manažéra, definície reagujúce na stakeholderský prístup. Najlepšie je tento posun viditeľný v definíciách Johnsona, ktorý tvrdí, že zodpovedný podnik je ten, ktorý berie do úvahy okrem záujmov shareholderov tiež záujmy zamestnancov, dodávateľov, lokálnych komunít a spoločnosti. [5] Táto teória vyjadruje, že podnik vystupuje ako subjekt zodpovednosti za svoje konanie a za dôsledky svojho konania vo vzťahu k rozličným skupinám. [1] Pre tieto skupiny sa IV/2010 54 Pošta, Telekomunikácie a Elektronický obchod ISSN 1336-8281 používa pojem stakeholderi, ktorý nemá úplne presný jednoslovný preklad do slovenčiny, kde sa zaužíval preklad „záujmové skupiny“, príp. „zainteresované subjekty“. [6] S rozvojom stakeholderskej teórie sú odhaľované ďalšie skupiny, ktoré sú vo vzájomnej interakcii s podnikom a teda voči ktorým by mal byť podnik zodpovedný. Tým stakeholderská teória, ktorá v 90. rokoch minulého storočia pomohla spresniť šírku podnikového záberu voči stakeholderom, začína vďaka svojmu neustálemu rozvoju strácať hranice, čo spôsobuje, že sa stáva pre zodpovedné podnikanie nepoužiteľnou, resp. použiteľnou len pri určitom obmedzení a za cenu určitého skreslenia. [4] Aj napriek tomu má stakeholderská teória stále nezanedbateľný význam. Možným pozitívnym výsledkom dialógu so zainteresovanými skupinami je napr. šírenie dobrých praktík, vzájomná inšpirácia a motivácia. Veľmi zreteľne sa tento aspekt prejavuje v dodávateľsko-odberateľských vzťahoch, napr. ak je odberateľom podnik s vysokým profilom spoločenskej zodpovednosti a ak bude rovnaké štandardy vyžadovať od svojich dodávateľov. Dialóg so zainteresovanými subjektmi je zložitý, a to predovšetkým s tými, ktoré podniky nie vždy považujú za svoje zainteresované subjekty (napr. nevládne ekologické organizácie). Má byť vedený včas, transparentne, efektívne, racionálne a s obojstrannou dobrou vôľou. Takto vedený dialóg, môže prinajmenšom pomôcť prekonávať vzájomnú nedôveru a zaisťovať vzájomné pochopenie. Dialóg potom v ideálnych prípadoch môže vyústiť až v dlhodobé partnerstvo medzi jednotlivými sektormi spoločnosti - súkromným a verejným (tzv. cross-sector partnership). [7] Šírku záberu stakeholderskej koncepcie najvýstižnejšie zobrazuje prehľad uvedený v Prílohe A. Podnik potrebuje vedieť, ktorí stakeholderi sú najdôležitejší. Preto by mal pred zahájením spoločensky zodpovedných aktivít vytvoriť tzv. analýzu zúčastnených strán. [8] Pomocou analýzy podnik určí kľúčových stakeholderov, ktorí majú najväčší vplyv na jeho prosperitu a najvyššie očakávania od jeho zodpovedného podnikania. Pri analýze je možné použiť maticu zobrazenú na obrázku 2. miera očakávania vysoká nízka priebežne informovať viesť dialóg odpovedať na otázky zaistiť spokojnosť nízka vysoká miera vplyvu Obrázok 2. Matica analýzy stakeholderov Zdroj: STEINEROVÁ, M., VÁCLAVÍKOVÁ, A., MERVART, R. (Business Leaders Forum): Společenská odpovědnost firem. Praha: TOP Partners, s.r.o., 2008, s. 17. Jednotlivým kvadrantom matice podnik priradí stakeholderov podľa miery ich vplyvu a očakávaní. Tým zároveň získa predstavu o ďalšom postupe voči jednotlivým skupinám. Riadenie spolupráce so stakeholdermi vedie k ich poznaniu, porozumeniu ich záujmov a k následnému dialógu, ktorého výsledkom je obojstranná spokojnosť – tzv. win – win situácia. Ideálnym stavom je rovnováha medzi aktivitami, ktoré uprednostňuje vedenie podniku a tými, o ktoré prejavia záujem stakeholderi. [9] IV/2010 55 Pošta, Telekomunikácie a Elektronický obchod ISSN 1336-8281 Pyramída spoločensky zodpovedného podnikania Archie B. Carroll bol prvým teoretikom, ktorý rozlíšil viac druhov podnikovej zodpovednosti. Pyramída CSR, zobrazená na obrázku 3, by mala manažérom pomôcť systematicky uvažovať o očakávaniach rozličných skupín stakeholderov. Vymedzenie dimenzií v pyramíde je pragmatické, pretože akceptuje tiež požiadavky na ziskovosť a legálnosť činnosti podnikov. Nerieši však situácie, keď sa dostanú niektoré zodpovednosti do konfliktu. [5] filantropická zodpovednosť etická zodpovednosť právna zodpovednosť ekonomická zodpovednosť Obrázok 3. Pyramída spoločenskej zodpovednosti Zdroj: WERTHER, W., CHANDLER, D.: Strategic Corporate Social. Sage Publications, Inc., California, 2006. ISBN 978-1-4129-1373- 7, p. 9. Podrobnejšia konštrukcia pyramídy spoločenskej zodpovednosti je zameraná na rozlíšenie podnikovej filantropie a zodpovedného podnikania. Toto rozlíšenie reflektuje obrázok 4. podniková filantropia Charitatívne dary Spoločenské investície Komerčné aktivity v spoločnosti Nezištná podpora verejne prospešných projektov a potrebných oblastí prostredníctvom darov a služieb. Strategická angažovanosť podnikov, ktorá má pozitívny vplyv na reputáciu. Spojenie komerčných a filantropických aktivít spoločnosti, propagácia značky. Mandatórne výdavky Výdavky, ktoré sú dôsledkom zákona, smernice alebo zmluvy, napr. použitie podielu zaplatenej dane na osobitné účely. Poslanie firmy – komerčná činnosť Podnik úspešne realizuje svoju komerčnú činnosť s cieľom dosiahnuť max. zisk, zároveň dodržiava etické, spoločenské a environmentálne normy. spoločensky zodpovedné podnikanie Obrázok 4. Rozšírená pyramída spoločenskej zodpovednosti Zdroj: HORÁKOVÁ, I., et al.: Strategie firemní komunikace. Praha: Management Press, 2008. 233 s. ISBN 978-80-7261-178-2, s. 93. IV/2010 56 Pošta, Telekomunikácie a Elektronický obchod ISSN 1336-8281 Obrázok popisuje štruktúru rôznych foriem podnikovej angažovanosti a je štandardom, ktorý definuje náklady vynaložené na spoločensky zodpovedné aktivity. Tento štandard známy pod názvom „Štandard zodpovedný podnik“ v roku 2005 zaviedlo české Fórum darcov. [10] Trojitá výsledovka Spoločenská zodpovednosť podniku sa prejavuje integráciou pozitívnych postojov, praktík, či programov do stratégie podniku. Vyžaduje posun pohľadu na vlastnú spoločenskú rolu z úrovne „profit only“ k širšiemu pohľadu v kontexte 3P – „people, planet, profit“ (ľudia, planéta, prínos) ako znázorňuje obrázok 5. PRÍNOS triple bottom line PLANÉTA ĽUDIA Obrázok 5. Trojitá výsledovka, Zdroj: vlastné spracovanie Kontext troch prvkov, ktoré tvoria základ pyramídy CSR, znamená fungovanie s ohľadom na tzv. triple – bottom – line, kedy sa podnik sústreďuje nielen na ekonomický rast, ale aj na environmentálne, či sociálne aspekty svojej činnosti [11] Porterova konkurenčná výhoda Porter definuje, že konkurenčná výhoda je jadrom výkonnosti podniku na tých trhoch, kde je konkurencia. Vzniká z hodnoty, ktorú je podnik schopný vytvoriť pre kupujúcich, a ktorá prevyšuje náklady podniku na jej vytvorenie. [12] Podnik má konkurenčnú výhodu, ak implementuje stratégiu, ktorú konkurenti nie sú schopní napodobniť, prípadne by to pre nich bolo príliš nákladné. Práve takou stratégiou je stratégia zodpovedného podnikania. Záver Kým v minulosti pojem spoločensky zodpovedné podnikanie zosobňovali najmä filantropi, v súčasnosti sa stáva neoddeliteľnou súčasťou bežnej praxe. Túto skutočnosť výstižne vyjadruje výrok bývalého britského premiéra Gordona Browna: „Spoločenská zodpovednosť podnikov dnes smeruje ďaleko za hranice filantropie minulosti a stáva sa z nej celoročná zodpovednosť, ktorú podniky prijímajú s ohľadom na životné prostredie, ktoré ich obklopuje, na zacielenie do miestnych komunít a s vedomím, že meno značky závisí nielen na kvalite, cene a nezameniteľnosti, ale rovnako na celkovom spolupôsobení so zamestnancami, s komunitou a životným prostredím. Požiadavka spoločensky zodpovedného podnikania stojí stále naliehavejšie v popredí všetkých podnikateľských aktivít. Vzťahuje sa vždy na konkrétne prostredie, jeho charakter a špecifiká. Subjekt tak vždy stojí v prostredí určitých spoločenských hodnôt, preferencií a IV/2010 57 Pošta, Telekomunikácie a Elektronický obchod ISSN 1336-8281 záujmov, ku ktorým sa vzťahuje a ktoré ovplyvňujú proces jeho rozhodovania o prevzatí vlastnej zodpovednosti. V súčasnosti sa stále viac presadzuje tendencia chápania zodpovednosti nie ako osobnej zodpovednosti pred určitou konkrétnou situáciou, ale ako zodpovednosť vo vzťahu k spoločnosti, ľudstvu a prírode. Preto je teória spoločensky zodpovedného podnikania vysoko aktuálna. Nehovorí sa už ani tak o tom, či sa majú podniky správať spoločensky zodpovedne, ale skôr o tom, čo to presne znamená a ako túto ideu podporiť. Ťažiskom by mala zostať prax - realizácia konkrétnych aktivít a opatrení, jasne definované, transparentné a dodržiavané pravidlá, vytváranie a implementácia uznávaných štandardov. Literatúra [1] REMIŠOVÁ, A.: Etika a ekonomika. 2. vyd. Bratislava: Ekonomická univerzita v Bratislave, Vydavateľstvo Ekonóm, 2004. 238 s. ISBN 80-225-1820-4. [2] REMIŠOVÁ, A.: Podnikateľská etika v praxi. Vydavateľstvo EPOS, Bratislava. 1999. 272 s. ISBN 80-8057-106-6. [3] ROLNÝ, I. - LACINA, L.: Globalizace, etika, ekonomika. 3. vyd. Ostrava: Key Publishing, s.r.o., 2008. 281 s. ISBN 978-80-87071-62-5. [4] BLAŽEK, L. - DOLEŽALOVÁ, K. - KLAPALOVÁ, A.: Společenská odpovědnosť podniku. In: WORKING PAPER č. 9/2005, Centrum výzkumu konkurenční schopnosti české ekonomiky. Brno, 2005. ISSN 1801-4496. [5] CAROLL, A. B. - BUCHHOLTZ, A. K.: Business and Society - Ethics and Stakeholders Management. 7. vyd. Ohio: SouthWestern Publishing Co., 1999. 970 s. ISBN 978-0-32456939-1. [6] BUSSARD, A. – BUNČÁK, M. – MARČEK, E. – MAZURKIEWICZ, P. – MARKUŠ, M.: Spoločensky zodpovedné podnikanie. [online]. Bratislava: Nadácia Integra, 2005. [2010-06-06]. Dostupné na: <http://www.nadaciapontis.sk/tmp/asset_cache/link/ 0000013632/Publikacia_SZP.pdf>. [7] FRANC, P. - NEZHYBA, J. - HEYDENREICH, C: Když se bere společenská odpovědnost vážně. 1. vyd. Brno: Ekologický právní servis, 2006. 72 s. ISBN 80-8654408-7. [8] MAJTÁN, M., et al.: Manažment. Bratislava: SPRINT, 2008. 424 s. ISBN 978-80-8908572-9. [9] STEINEROVÁ, M. - VÁCLAVIKOVÁ, A. - MERVART, R.: Společenská odpovědnost firem, průvodce nejen pro malé a střední podniky. Praha: TOP Partners, s.r.o., 2008. [10] HORÁKOVÁ, I., et al.: Strategie firemní komunikace. Praha: Management Press, 2008. 233 s. ISBN 978-80-7261-178-2. [11] TRNKOVÁ, J.: Společenská odpovědnost firem - kompletní průvodce tématem & závěry z průzkumu v ČR. Praha: Business Leaders Forum, 2004. 56 s. [12] ZICH, R.: Strategický rozvoj konkurenčních výhod v koncepci úspěchuschopnosti ve vztahu k pojetí založeném na zdrojích a základních kompetencích. In Ekonomika a management. [online]. Vydanie 3/2009. [Citované 2010-08-01]. Dostupné na: http://www.ekonomikaamanagement.cz/cz/clanek-strategicky-rozvoj-konkurencnichvyhod-v-koncepci-uspechuschopnosti-ve-vztahu-k-pojeti-zalozenem-na-zdrojich-azakladnich-kompetencich.html. ISSN 1802-8934. IV/2010 58
https://openalex.org/W2985439094
https://ojs.cvut.cz/ojs/index.php/ap/article/download/5017/5247
English
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TUNNEL PORTAL INSTABILITY IN LANDSLIDE AREA AND REMEDIAL SOLUTION: A CASE STUDY
Acta Polytechnica
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cc-by
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∗corresponding author: farhadfarhadi18964@gmail.com Abstract. The construction of tunnel portals in mountainous or slope areas often involves problems, which are closely related to factors, such as slope topography, geology, geotechnics, construction geometry and the tunnel excavation method. The activation of landslides or the acceleration of these events is one of the main challenges faced in the construction of tunnel portals. In this paper, we address the instability problem in Sabzkuh tunnel portal that has been excavated with a complex geological profile and high seismicity in Iran’s High Zagros region. The complexity and intense heterogeneity in geological formations, land acquisition problems and the lack of appropriate monitoring programs led to the instability of the tunnel portal. The excavation process started without applying appropriate techniques for a ground stabilization. The use of inappropriate tunnel excavation methods for this unstable geological structure resulted in an activation of an old Solaghan fault and several collapses in the tunnel. Crossing the collapsed areas and reinforcing the tunnel portal took about 7 months and imposed heavy costs on the project. This case study deals with the importance of the choice of the site location, ground and underground monitoring, analysing and summarizing the collected data in order to prepare a geological model before and during the construction process. Keywords: Slope instability, collapse, landslide, Sabzkuh Tunnel, remedial solution DOI:10.14311/AP.2019.59.0435 Acta Polytechnica 59(5):435–447, 2019 DOI:10.14311/AP.2019.59.0435 Acta Polytechnica 59(5):435–447, 2019 © Czech Technical University in Prague, 2019 available online at https://ojs.cvut.cz/ojs/index.php/ap TUNNEL PORTAL INSTABILITY IN LANDSLIDE AREA AND REMEDIAL SOLUTION: A CASE STUDY rhad Farhadi Ayoubloua,∗, Majid Taromib, Abbas Eftekharic Farhad Farhadi Ayoubloua,∗, Majid Taromib, Abbas Eftekharic a Amirkabir University of Technology, Faculty of Engineering, Department of Civil Engineering, Hafez Street, No 350, 4413-15875 - Tehran, Iran b Islamic Azad University of South Tehran Branch, Faculty of Engineering, Department of Civil Engin Karimkhan-e-Zand Street, No. 223, 1584743311 - Tehran, Iran Islamic Azad University of South Tehran Branch, Faculty of Engineering, Department of Civil Engineer Karimkhan-e-Zand Street, No. 223, 1584743311 - Tehran, Iran c Kashan University, Faculty of Engineering, Department of Mining Engineering, 6th kilometer from Ghotbe Ravandi Boulevard, 8731753153 - Kashan, Iran Kashan University, Faculty of Engineering, Department of Mining Engineering, 6th kilometer from Gho Ravandi Boulevard, 8731753153 - Kashan, Iran c Kashan University, Faculty of Engineering, Department of Mining Engineering, 6th kilometer from Ghotbe Ravandi Boulevard, 8731753153 - Kashan, Iran ∗corresponding author: farhadfarhadi18964@gmail.com ∗corresponding author: farhadfarhadi18964@gmail.com 1. Introduction characteristics of soil layers, old landslide activation, poor drainage, and the use of unfavourable tunnel excavation methods caused a funnel like collapse in tunnel in such a way that the cave-in measured about 22 meters in diameter on the ground level. Crossing through the collapsing area took about seven months to complete and it imposed high costs on the project and consequently its schedule [1, 2]. Sabzkuh water conveyance tunnel with a length of 10,617 meters is being excavated using both conven- tional and mechanized techniques in Chaharmahal and Bakhtiari Province across the Iran’s central zone and Zagros and with a close distance from the Za- gros Fault in the High Zagros region. The Naghan earthquake on 7 May 1997 with a 6 magnitude on the Richter scale and the resulting landslide in the rural areas of Saki-Abad and at the southern tunnel entrance in the southern part of Choghakhor Lake caused a structural failure in the region under the study. This paper presents a case study of the instability at Sabzkuh tunnel portal, which is located in an area with a high potential for landslides, faults and the complex geological structures that were not known before starting the tunnelling operations. After de- scribing the geological characteristics and geotechnical conditions of the study area, the importance of mon- itoring systems to identify landslide and instability potentials before and during the tunnel excavation was estimated using various methods. Afterwards, the slope instability and tunnel collapse mechanisms were investigated. Then, the collected data were accumu- lated in a database in order to analyse the landslide profile, find slope improvement strategies, and con- tinue the excavation operation. Due to geological complexities, high groundwater levels in the region, and the inability of the project employer to acquire enough land to build the tunnel en- trance in an appropriate location, the slope stability in the Sabzkuh tunnel entrance faced a challenge. After constructing tranches and before starting the tunnel excavation, signs of slope instability were observed. However, as these signs were not taken seriously and there were no proper monitoring programs as well as guidelines and appropriate measures for stabilization, the instability level was intensified. After excava- tion of 35 meters from the tunnel using conventional methods, the steep slope of layers, poor geotechnical 435 Acta Polytechnica F. F. Ayoublou, M. Taromi, A. Eftekhari Figure 1. Map of geological zone in Iran [3]. Figure 1. 2.1. Geology of study area The study region, Solaghan Fault is located along northeast Sabzkuh syncline at N130 and a dip di- rection to the southwest in the southwestern part of Choghakhor Lake. This fault has caused Paleozoic units and clastic-rock units on the fault path, have been placed on recent sediments. There are many springs such as Saki Abad spring running along this fault. The fault zone is not visible across the tunnel, but Solaghan fault can be detected on the satellite images because of the height differences caused by the fault and the border that is placed between the vegetation and mountains. Solaghan Fault is placed 2. General geology on a rupture structure with a dip of 40 to 65 degree and the fault zone is located in a distance of 0 + 380 (10 + 237) meters from the tunnel portal. This fault has branches that spread from the high depths to the surface and are called the STF. In the footwall and headwall of the fault, two thrust faults have also been detected and are regarded as the footwall and headwall of the Solaghan fault zone. The function of the fault caused the disturbance and complexity of geological layers in the region, which is displayed in Figure 2. The STF1 fault is the first fault in the tunnel portal and is regarded as one of the branches of footwalls of Solaghan Fault. There is no external evidence for the existence of the fault in the area of the tunnel portal. This fault has been discovered based on the geological log of boreholes and the data from the geophysical study. These data show that the fault has a dip close to Solaghan Fault and in the same direction. The fault zone is located in a distance of 0 + 235 meters from the northern tunnel portal. The fault is located on a rupture structure with a dip of about 25 to 60 degrees (Figure 2). The studied region is located in the southeastern part of Chaharmahal and Bakhtiari Province in Iran. The water transfer route from Sabzkuh to Choghakhor is located in wrinkled mountain belts of Zagros, which is located in the middle part of the Alpine orogeny belt and is considered as one of the youngest Cenozoic orogenies. In addition, the tunnel portal is located in the southern part of the lake of Choghakhor Dam and the north of Kalar Mountain Range. Zagros thrust encompasses the highest Zagros Mountains (Zardkuh 4 400 ˜meters, Oshtorankuh 4 170 meters, and Dena 4 000 meters) and thus it is called High Zagros (Figure 1). 1. Introduction Map of geological zone in Iran [3]. 4.3. Slope stability analysis results A comparison of the slope stability safety factors in the limit equilibrium analysis and the numerical analysis shows that the safety factor obtained in the numerical analysis is lower than that obtained through the limit equilibrium analysis. In addition, the complex geome- try slope, the presence of water in the slope and the inclusion of the earthquake effects in both methods can reduce the slope stability safety factor [6]. The safety factor calculated from the limit equilibrium and numerical analysis are shown in Table 2. Stability analysis (Flac/Slope) Due to the advantages of the slope analysis using numerical analysis compared to the limit equilibrium analysis, the slope stability analysis was performed using Flac/Slope Software [5], which is a numerical software that works based on finite difference method. This software is capable of calculating the safety factor of slopes by reducing soil shear strength at different stages to the slope failure. The stability analysis for the cross-section in question was performed for static and pseudo-static conditions and in the presence of water. Table 1 shows the calculated safety factor. 4.2. Numerical analysis and the position of drilled boreholes indicate that the geological structure in the flood plain is different from that of the hillsides, and the geological structure of the entrance area consists of the units mixed with sand, clay, and silt. In addition, the boreholes and the surface monitoring results show that the groundwater is at a high level. 3. Geotechnical study The local evidence and the data from the boreholes indicate that the geology of the area is composed of alluvium and debris-flow deposits in the vicinity of the heights. The results obtained from the observations 436 Tunnel portal instability in landslide area and remedial solution vol. 59 no. 5/2019 Figure 2. The plan of the study area. Figure 2. The plan of the study area. 4. Slope stability analysis To perform the slope stability analysis of Sabzkuh tun- nel entrance, a limit equilibrium method was employed using Slide 5.0 Software (2010) [4] and the numerical analysis using FLAC/Slope [5] and the safety factor of the slope stability was measured in both static and pseudo-static conditions. The input parameters of the soil for these applications are shown in Table 1. The slope was designed with berms of 4 meter in width and 8 meters in height each. The slope for the two lower steps was set as 1 : 1 and for the two higher steps was set as 1 : 2 (horizontal). Stability analysis (Slide 5.0 Software) The tunnel entrance cross-section was estimated using Slide 5.0 [4] by including the effects of groundwater and the pseudo-static seismic analysis. Given the high seismicity potential of the studied region, the horizontal seismic coefficient was set as 0.5 and the minimum safety factor was set as 1. The critical circular cutting surface was automatically created and the safety factor was calculated under different conditions. As it can be seen, the quasi-static slope safety is generally smaller than that of the static condition. Also, the presence of the underground water in the slope can reduce the safety factor by almost 30 %. 4.1. Limit equilibrium analysis Given the geological conditions of the region un- der study, which was made of heterogeneous soils, Morgenestern-Price Method (Half-sine function) was used to perform the stability analysis of the Sabzkuh tunnel entrance. However, both methods are disadvantageous as they do not consider the effects of the tunnel excavation on the slope stability. Therefore, it can be concluded that the slope stability calculations, taking into account the tunnel structure in slope, is a full three-dimensional problem and using two-dimensional analysis methods makes the slope stability calculations unreliable. 6. Tunnel collapse and slope failure Since the gravity component in steep slopes increases the shear stress, the slope topography and angle is the main feature of slopes in terms of sensitivity to land- slide and risk assessment. Therefore, slopes with lower angles are less likely to undergo failure [7]. Changes in the slope geometry reduce the shear stress in the soil yielding and intensify the slope instability. The problem of land acquisition by the employer affected slope geometry, so that the tunnel portal was designed with steep slopes and high altitude. This reduced the safety factor of the slope stability. The excavation operation of the T1 part of Sabzkuh tunnel was generally performed below the groundwa- ter levels. Because of the excavation operation in the saturated ground, the pore water seeped into the created cavity. On the one hand, the flow of the groundwater reduced the quality of geotechnical pa- rameters of the soil mass around the tunnel, but, on the other hand, reduced the effective stress around the tunnel. This problem along with facing the old land- slide surface with complex geological stratification, and inappropriate excavation pace, led to the insta- bility on the tunnel crown. Encountering these areas at a distance of 35 m along the tunnel simultaneously led to local collapses in the forefront of the excavation operation and the rapid development of collapses in less than 8 hours towards the tunnel crown, creating a chimney-like cavity at the top of the tunnel and 5. Slope instability monitoring Safety, reliability, the optimization of the design, and the evaluation of its effectiveness, the calibration of the employed model, the evaluation of the maintenance system, the prediction of failure and displacement are among the main objectives of the monitoring of geotechnical structures. One of the most primitive methods of slope monitoring is a visual inspection 437 Acta Polytechnica F. F. Ayoublou, M. Taromi, A. Eftekhari Construction materials γ (ton/m3) (deg.) C (kPa) ML 1.96 17 28 SC-SM 1.99 29 5 CH-CL 1.80 17 0.00 Table 1. Physical and mechanical features of the slope soil. analysis safety factor limit equilibrium analysis static without groundwater 1.68 static with groundwater 1.39 pseudo-static without groundwater 1.22 pseudo-static with groundwater 1.03 numerical analysis static without groundwater 1.64 static with groundwater 1.22 pseudo-static without groundwater 1.13 Table 2. The safety factor calculated from the limit equilibrium and numerical analysis. Construction materials γ (ton/m3) (deg.) C (kPa) ML 1.96 17 28 SC-SM 1.99 29 5 CH-CL 1.80 17 0.00 Table 1. Physical and mechanical features of the slope soil. eventually leading to the slope failure. In addition, the activation of the old landslide surface caused the mass smoothening of about 1000 cubic meters of soil from the collapsing area into the tunnel exterior and the development of the cavity into the entrance slope (Figure 4). by geotechnical engineers and geologists. The imple- mentation of reinforced concrete slabs covering the surfaces of the slopes and berms led to the inaccu- racy of visual inspections and observations. Upon the completion of the excavation and concrete slope cover and before starting the tunnel excavation, some cracks were observed on the surface of concrete slab covers and in the slope surface water sewage channel, which indicated the displacement in the slopes. 7. The survey phase After the tunnel collapse, given the size and complex- ities of continuing the excavation process, a working group of experts consisting of geological, geotechnical, and structural engineers was formed to investigate the possible causes of the collapse and how to pass through the collapsing zone. They also analysed factors af- fecting the slope stability and the tunnel collapse by conducting surface and subsurface studies and back analysis. The following sections addressed the reasons for the tunnel collapse. This caused the alarm for geotechnical engineers to design a monitoring system using mapping points for monitoring slopes. For this purpose, nine settlement markers were installed on the surface along the tunnel and the berms and the monitoring of them was car- ried out by surveying (Figure 3). Readings of those markers were taken at regular intervals to check for any signs of settlement or heave. The results of the monitoring showed some displacements in both Z and Y directions. 7.2. Geology Placing geological units with different permeability and strength together and providing a poor surface with steep slope and improper orientation of the soil layers are among factors affecting the slope instability and the collapse in the tunnel. Stratified steep soils are prone to landslides and displacement along the 438 Tunnel portal instability in landslide area and remedial solution 8. Remedial solution The results of ground surface and subsurface studies show that the axis of Sabzkuh tunnel has an angle of about 30 degrees with the old sliding surface. Given that the tunnel axis is parallel to the slope direction, the shear deformation occurs along the linear profile. In addition, the angle between the sliding surface and the tunnel axis resulted in the development of the shear zone. However, the effects of the tunnel excavation were not considered in the slope stability analysis. The results of numerical analyses and limit equilibrium show that the sliding wedge is located across the tunnel route and there is a possibility of the slope instability as a result of the tunnel excavation. In landslides, in which the used materials are mainly debris and hillside alluvia, the collapsing area is not generally reinforced under the alluvial deposits and a shell is located in substances, such as silt and materials with low adhesion to rock fragments in different sizes. Given the negative effects of the slope materials and sliding areas in the alluvial slopes and hillside debris, the slope stability is vulnerable to many different factors. Therefore, the procedure taken to stabilize the landslide is of a high importance [8]. 7.3. Hydrology Water is always considered as an important factor in the slope instability. Climatological studies, periodic explorations of boreholes and springs in the studied region and the observation of aquifers when excavating the tunnel entrance, all of them showed the high groundwater levels in the region. A nonstop rainfall just one week before the collapse resulted in the water infiltration into the pores of the soil masses. On the one hand, this increased the pore water pressure and reduced the effective tension among the soil grains and, on the other hand, the additional weight of the slope ingredients, due to the saturation, increased the shear stress between the slope layers. Ultimately, the water infiltration into the faults increased the hydrostatic pressure so that the gravity drainage system alone could not meet the water discharge requirements inside the slope. Geoelectrical explorations that were performed in this study used combined resistivity profiling (CRP). This technique is able to detect heterogeneities and discontinuities, such as fault zones and intersections, in the studied area. In order to evaluate the variation in the resistance of alluvial layers and detecting them based on their resistivity and their possible rupture to a distance of 350 meters from the entrance of the tunnel, a total number of 82 CRP stations were used on four main exploration lines called lines 1 to 4 with a north-south orientation. In addition, a total of 12 offset lines, termed as X1 to X12, were marked on the location map (Figure 6). Seismography In order to perform a low-depth reflective survey across the survey lines in the site of Sabzkuh wa- ter tunnel, the following operating parameters were defined as shown in figure 9. 7.5. Geophysical studies 7.5. Geophysical studies weak layers. Thus, special attention must be paid to the geological aspects when performing the slope stability assessment. In Figure 5, the geological char- acteristics of the soil layers, the slope of the layers, the groundwater level, and the different levels of over- burden of the tunnel are displayed at a distance of 350 meters from the tunnel entrance (Figure 5). The present study used geoelectrical techniques in conjunction with seismography to analyse the slope instability and identify sites with landslide and fault potentials. Geoelectrics Electrical resistivity methods are among the most widely used conventional methods of geophysical ex- plorations that are highly effective in both engineering studies and exploring various geological features. Elec- trical resistivity methods are also frequently used to explore landslides due to their accuracy and speed. The main rationale behind the use of geoelectircal techniques is their high resolution power to identify aquifers across the collapse areas as these aquifers accelerate the slide of instable masses. 7.4. History of landslides and tunnel excavation To avoid the adverse effects of landslides during the tunnel excavation, a distance between the tunnel axis and the sliding area was studied. This requires a good understanding of the interaction between the landslide and tunnel excavation, which must be investigated in terms of controlling displacements and the effects of stress through long-term monitoring and numerical analyses. Tunnel portal instability in landslide area and remedial solution vol. 59 no. 5/2019 Figure 3. The location of monitoring points in the tunnel portal. Figure 4. The development of the collapse and slope failur. Figure 3. The location of monitoring points in the tunnel portal. Figure 3. The location of monitoring points in the tunnel portal. Figure 4. The development of the collapse and slope failur. Figure 5. The geological characteristics of the soil layers of tunnel portal. Figure 3. The location of monitoring points in the tunnel portal. Figure 4. The development of the collapse and slope failur. Figure 4. The development of the collapse and slope failur. Figure 4. The development of the collapse and slope failur. Figure 4. The development of the collapse and slope failur. Figure 5. The geological characteristics of the soil layers of tunnel portal. Figure 5. The geological characteristics of the soil layers of tunnel portal. 439 F. F. Ayoublou, M. Taromi, A. Eftekhari Acta Polytechnica 8.3. Debris flows In April 2013, coinciding with the implementation of the drainage system in the slopes and before the start of the tunnel excavation, after heavy rainfall and rapid melting of snow because of a spike in temperature in the surrounding mountains, signs of the increased stress imposed on the pre-support systems and the arch support technique were observed (Figure 10). In order to validate and verify the results of the numerical analysis, a convergence station was installed in the centre of the tunnel crown in the collapsing area and the displacement of the support system during the filling process was monitored and recorded. The maximum displacement recorded in the tunnel crown was 8 mm. The results of the monitoring are shown in Figure 14. Following this, just one day after the heavy rain- fall, the second event occurred. Within 35 meters of the tunnel entrance, about 500 cubic meters of soil in the form of debris flows started to move from the tunnel crown toward the entrance of the tunnel in 8 hours (Figure 11). The samples taken for the materials showed that more than 50 percent of the materials included gravels, sand, and silt and only a small percentage of clay. These materials started to flow down under the influence of the steep slope of lay- ers, the gravity, and gravitational forces accompanied by the increased leakage force. In addition, another reason for the occurrence of debris flow was the pres- ence of an old landslide in this area, which placed unstable soil masses on steep slopes. The infiltration of water flow over the old landslide lubricated and smoothed the sliding materials. Besides, the impacts and shocks from the arch support system stimulated sliding masses in the slope followed by decreased re- sistance forces, which resulted in debris flows inside the tunnel. 8.5. The tunnel excavation method The cross-excavation method resulted in the develop- ment of the plastic zone around the tunnel and the tunnel stability was deteriorated after confronting the old sliding surface, leading to the slope failure. The forefront displacement was controlled by changing the cross-excavation method into Sequential Excavation Method (SEM) and performing the reinforcement mea- sures in the forefront including the use of fiberglass nails, traditional cement injection around the tunnel, an early installation of the apron wall, the improve- ment of the drainage system, and regular monitoring inside the tunnel. This resulted in the expansion of the cavity devel- oped in the entrance and intensified the slope insta- bility. Besides, the implemented pre-support system moved down about 60 cm, but it was not broken due 8.2. Slope improvement To fill the cavity developed in the slope by meeting the slope stability requirements and minimizing stresses applied to the pre-support system, three options were proposed, (Table 3) and the three-dimensional mod- elling was performed using FLAC-3D Software [10]. The input parameters of the soil for the modelling are shown in Table 1. Given the high groundwater levels and annual rainfalls in the region as well as the water seepage through the irrigation of farming lands, two types of drainage systems were proposed: (1) installing drainage sys- tems with a long length in the entrance (2) installing drainage systems inside the tunnel to lower groundwa- ter levels. A pumping system was used in the route of Section T1 to lower groundwater levels and to re- duce risks during the tunnel excavation. The surface water collection system in the tunnel entrance was also repaired and improved. Besides, the irrigation of gardens around the tunnel entrance came to a halt to reduce the effects of water leakage in this area. Finally, micro-piles and nailing were also employed to stabilize the slope. In order to model the filling conditions of the col- lapsing cavity, it was divided into two parts: The first part started from the tunnel crown to a height of 5 me- ters and the second parts included areas from a height of 5 meters to a height of 11.8 meters (Figure 12). In the next stage, the properties of filling materials were studied and the displacement and maximum stress on the crown were calculated. The technical and economic results indicated that the first option is not favourable because of the displacement and high stress imposed on the support system. From the second and third options, the second option was selected due to lower displacement and stresses applied to the tunnel crown and its economic advantages. As shown in Fig. 13, the maximum calculated displacement in the tunnel crown after filling the collapsing cavity with soil and lightweight aggregate concrete (LWAC) is about 20 mm. 8.1. Passing through the collapsing area of the tunnel After summarizing the data from identification and survey stages, the three-dimensional slope stability analysis was performed by considering the sliding sur- face, the new geological model, and the effects of the tunnel excavation on the slope stability. The results of this analysis predicted the tunnel collapse [2]. There- fore, as indicated by the complex geological model, conducting complementary studies and revising the excavation method was deemed necessary. In order to pass the collapsing area, the causes and mechanism of similar collapses were studied by taking into account technical and economic considerations. For this purpose, the results of second stage excavation of Istanbul Metro between Unkapani and Yenikapi were studied. Given the almost similar excavation method and geological conditions in both projects, and also the efficiency of umbrella arch method (UAM) 440 Tunnel portal instability in landslide area and remedial solution vol. 59 no. 5/2019 Figure 6. Profile plan of geoelectrical explorations. Figure 6. Profile plan of geoelectrical explorations. Figure 7. The cross-section of geoelectrical explorations. Figure 7. The cross-section of geoelectrical explorations. 441 F. F. Ayoublou, M. Taromi, A. Eftekhari Acta Polytechnica blou, M. Taromi, A. Eftekhari Acta Pol Figure 8. Profile plan of geoelectrical cross-sections. Figure 9. Seismic reflection survey profile. Figure 8. Profile plan of geoelectrical cross-sections. Figure 8. Profile plan of geoelectrical cross-sections. Figure 9. Seismic reflection survey profile. Figure 9. Seismic reflection survey profile. 442 Tunnel portal instability in landslide area and remedial solution vol. 59 no. 5/2019 in sensitive regions, this method was proposed by the designers [9]. Then, in the implementation phase of this method in the collapsing area in Section T1 of Sabzkuh tunnel, IPE180 with 15 cm spacing and a length of 9 meter was used based on the design re- quirements, implementing the arch support technique and results of the finite element analysis [2]. to its high rigidity. After the discharge of sliding mate- rials inside the tunnel, so as to prevent re-occurrence of the problem and reduce the pressure from the exca- vation, the forefront was plugged with plastic concrete with a thickness of 10 m before resuming the excava- tion. 8.6. Monitoring stages In order to evaluate the performance and control the optimal progress of the project based on the rein- 443 F. F. Ayoublou, M. Taromi, A. Eftekhari Acta Polytechnica Figure 10. Cracking in the pre-support system. Figure 10. Cracking in the pre-support system. Options Materials Special weight (KN/m3) First phase materials Second phase materials 1 Soil 18 2 Soil and lightweight aggregate concrete (LWAC) 13 18 3 Controlled low-strength concrete materials (CLSM) and soil 10 18 Table 3. Properties of the proposed options. Figure 11. The mud flow running into the tunnel. rcement procedure, the slope monitoring continued hrough visual visits and geodetic surveying to make ure that the instability would not be further devel- ped in the long run. As it is shown in figure 14, efore the start of the reinforcement operations, the splacement rate was on the rise. The displacement th Y i t th l th d Figure 12. Two stages of filling the collapsing cavity above the tunnel crown. of the stage excavation, displacement rates becam almost stagnant (Figure 15). Figure 10. Cracking in the pre-support system. Figure 10. Cracking in the pre-support system. Options Materials Special weight (KN/m3) First phase materials Second phase materials 1 Soil 18 2 Soil and lightweight aggregate concrete (LWAC) 13 18 3 Controlled low-strength concrete materials (CLSM) and soil 10 18 Table 3. Properties of the proposed options. Table 3. Properties of the proposed options. Figure 12. Two stages of filling the collapsing cavity above the tunnel crown. Figure 11. The mud flow running into the tunnel. Figure 11. The mud flow running into the tunnel. Figure 11. The mud flow running into the tunnel. Figure 12. Two stages of filling the collapsing cavity above the tunnel crown. forcement procedure, the slope monitoring continued through visual visits and geodetic surveying to make sure that the instability would not be further devel- oped in the long run. As it is shown in figure 14, before the start of the reinforcement operations, the displacement rate was on the rise. The displacement along the Y axis was greater than along other axes due to a higher sliding potential. The maximum displace- ment was observed in Pin No.1, which was caused by a high pore-water pressure in this area of aquifers that were observed during the slope excavation. 8.6. Monitoring stages After per- forming each step of the improvement in the tunnels and the slope, displacements slowed down. After the completion of the improvements and with the start of the stage excavation, displacement rates became almost stagnant (Figure 15). of the stage excavation, displacement rates became almost stagnant (Figure 15). 9. Discussion and conclusion This article presents a case study of the activation of a landslide resulting from the tunnel excavation in an area with complex geological conditions and active tectonics that were not identified before starting the tunnelling operation. The excavation of the tunnel portal in problematic areas has always been associated 444 Tunnel portal instability in landslide area and remedial solution vol. 59 no. 5/2019 Figure 13. The displacement changes around the tunnel after filling the collapsing cavity with the second option. The displacement changes around the tunnel after filling the collapsing cavity with the second option. Figure 13. The displacement changes around the tunnel after filling the collapsing cavity with the sec Figure 14. The displacement curve of the convergence station in the centre of the tunnel crown in collapsing area. Figure 14. The displacement curve of the convergence station in the centre of the tunnel crown in collapsing area. with some challenges, which implies the necessity of the slope management and planning. Accordingly, the following points must be taken into account for the tunnel excavation: • Monitoring and controlling displacement in complex and problematic areas are of high significance for exploring and predicting necessary actions and de- tecting the causes of abnormalities in the slope and the tunnel support system through measuring sur- face topography, visual and inspections, piezometer, convergence-meter inside the tunnel, geotechnical laboratory studies, and geological mapping. • Monitoring and controlling displacement in complex and problematic areas are of high significance for exploring and predicting necessary actions and de- tecting the causes of abnormalities in the slope and the tunnel support system through measuring sur- face topography, visual and inspections, piezometer, convergence-meter inside the tunnel, geotechnical laboratory studies, and geological mapping. • Two boreholes A and B had been drilled for the design of the Sabzkuh tunnel portal to identify underground excavation layers. Given that the ex- cavation data were collected from sporadic points, they were not helpful in estimating the changes in the underground layers between these two borehole points. Therefore, integrating the results of ground and underground studies is necessary in regions with complex geological conditions in order to pan an appropriate geological model. • The excavation and maintenance techniques can affect the stability of the slope. As such, the inter- action between the excavation method and the slope stability should be considered in the modelling. 9. Discussion and conclusion • The tunnel excavation resulted in the redistribution of stress in the earth surrounding the tunnel excava- tion and the activation of an old landslide. There- fore, the effects of the tunnel excavation should be considered in the slope stability analysis. • In mountainous areas, detailed studies need to be conducted in order to identify old landslides, find the optimal route for the tunnel axis, and observe the needed distance from these areas. 445 F. F. Ayoublou, M. Taromi, A. Eftekhari Acta Polytechnica y , , Figure 15. The slope monitoring stages. Figure 15. The slope monitoring stages. Figure 15. The slope monitoring stages. Figure 15. The slope monitoring stages. Acknowledgements [3] M. Mannani, M. Yazdi. Late triassic and early cretaceous sedimentary sequences of the northern Isfahan province Central Iran): Stratigraphy and paleoenvironments. Boletín de la Sociedad Geológica Mexicana 61:367–374, 2009. doi:10.18268/BSGM2009v61n3a6. The authors are thankful to the Project Manager of Sabzkuh water supply system, Mr. A. Izadi of F.T.R Engineering Ins. for sharing his vast experience and his guidance. The authors are thankful to the Project Manager of Sabzkuh water supply system, Mr. A. Izadi of F.T.R Engineering Ins. for sharing his vast experience and his guidance. [4] R. Geomechanics Software Solutions. Slide software - Stability analysis for soil and rock slopes, 2010. [9] I. Ocak. Control of surface settlements with umbrella arch method in second stage excavations of Istanbul metro. Tunnelling and Underground Space Technology 23:674–681, 2008. doi:10.1016/j.tust.2007.12.005. References [1] A. Eftekhari, M. Taromi, M. Saeidi. Uncertainties and complexities of the geological model in slope stability: A case study of Sabzkuh tunnel. International Journal of Mining and Geo-Engineering 48(1):69–79, 2014. doi:10.22059/IJMGE.2014.51807. [5] Itasca Consulting Group. Flac Slope Manual, 2002. [6] M. Cała, J. Flisiak. Slope stability analysis with numerical and limit equilibrium methods. In Conference of Computer Methods in Mechanics (CMM 2003). Gliwice, Poland, 2003. [2] M. Taremi, A. Eftekhari, M. Saeedi. A study of the reinforcement effect of IPE arc support technique (IAST): A case study of Sabzkuh tunnel. Journal of Engineering Geology 9:2559–2574, 2015. doi:10.18869/acadpub.jeg.9.1.2559. [7] T. Kritikos, T. Davies. Assessment of rainfall- generated shallow landslide/debris-flow susceptibility and runout using a GIS-based approach: Application to western Southern Alps of New Zealand. Landslides 12:1051–1075, 2015. doi:10.1007/s10346-014-0533-6. 446 Tunnel portal instability in landslide area and remedial solution vol. 59 no. 5/2019 [10] M. Itasca Consulting Group. FLAC3D - Fast Lagrangian Analysis of Continua in 3 Dimensions, 2005. [8] J. Du, K. Yin, S. Lacasse. Displacement prediction in colluvial landslides, three Gorges reservoir, China. Landslides 10:203–218, 2013. doi:10.1007/s10346-012-0326-8. Tunnel portal instability in landslide area and remedial solution [8] J. Du, K. Yin, S. Lacasse. Displacement prediction in colluvial landslides, three Gorges reservoir, China. Landslides 10:203–218, 2013. doi:10.1007/s10346-012-0326-8. [10] M. Itasca Consulting Group. FLAC3D - Fast Lagrangian Analysis of Continua in 3 Dimensions, 2005. 447
https://openalex.org/W3137497233
https://link.springer.com/content/pdf/10.1007/s10096-021-04211-8.pdf
English
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A decade of neonatal sepsis caused by gram-negative bacilli—a retrospective matched cohort study
European journal of clinical microbiology & infectious diseases
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ERROR: type should be string, got "https://doi.org/10.1007/s10096-021-04211-8\nEuropean Journal of Clinical Microbiology & Infectious Diseases (2021) 40:1803–1813 https://doi.org/10.1007/s10096-021-04211-8\nEuropean Journal of Clinical Microbiology & Infectious Diseases (2021) 40:1803–1813 https://doi.org/10.1007/s10096-021-04211-8\nEuropean Journal of Clinical Microbiology & Infectious Diseases (2021) 40:1803–1813 ORIGINAL ARTICLE Abstract This study is to determine the incidence and outcome of neonatal gram-negative bacilli (GNB) sepsis in Stockholm, Sweden, and\ndescribe bacterial characteristics. This is a retrospective cohort study. All infants with GNB-sepsis between 2006 and 2016 were\nincluded and matched with two control groups, with suspected sepsis and uninfected neonates, respectively. Outcome was death\nbefore discharge, risk of death within 5 days after sepsis onset, and morbidity. The resistance pattern from all GNB was collected,\nand all available isolates were subjected to genome typing. All neonates with GNB-sepsis (n = 107) were included, and the\ncumulative GNB-sepsis incidence was 0.35/1000 live born. The in-hospital mortality was 30/107 (28%). GNB late-onset sepsis\n(LOS) was associated with an increase in mortality before discharge compared to uninfected controls (OR = 3.9; CI 1.6–9.4) but\nnot versus suspected sepsis. The suspected LOS cases did not statistically differ significantly from uninfected controls. The case\nfatality rate (CFR) at 5 days was 5/33 (15%) in GNB early-onset sepsis (EOS) and 25/74 (34%) in GNB-LOS. The adjusted\nhazard for 5 days CFR was higher in GNB-LOS versus uninfected controls (HR = 3.7; CI 1.2–11.2), but no significant difference\nwas seen in GNB-LOS versus suspected sepsis or in suspected sepsis versus controls. ESBL production was seen in 7/107 (6.5%)\nof the GNB isolates. GNB-LOS was associated with a higher 5 days CFR and in-hospital mortality compared to uninfected\ncontrols but not versus suspect sepsis. The incidence of both GNB-EOS and GNB-LOS was lower than previously reported from\ncomparable high-income settings. The occurrence of antibiotic resistance was low. Keywords Gram-negative bacilli . Sepsis . Neonatal . Antibiotic resistance . Mortality Viveka Nordberg1,2\n& Aina Iversen3,4 & Annika Tidell5 & Karolina Ininbergs3,4 & Christian G. Giske3,4 & Lars Navér1,2 Received: 20 September 2020 /Accepted: 23 February 2021\n# The Author(s) 2021\n/ Published online: 24 March 2021 Received: 20 September 2020 /Accepted: 23 February 2021\n# The Author(s) 2021\n/ Published online: 24 March 2021 * Viveka Nordberg\nviveka.nordberg@ki.se Keywords Gram-negative bacilli . Sepsis . Neonatal . Antibiotic resistance . Mortality A decade of neonatal sepsis caused by gram-negative\nbacilli—a retrospective matched cohort study Viveka Nordberg1,2\n& Aina Iversen3,4 & Annika Tidell5 & Karolina Ininbergs3,4 & Christian G. G Materials and methods There was no variability of GA in the matching groups, but\nthere was variability in closest birth date in the controls de-\npending on GA. The variability in closest birth date between\ncases in the three matching groups was 10 years, but on aver-\nage below 24 months. Identifying the cases and the controls To identify the sepsis cases, we used the ICD-10 codes for\nGNB-sepsis in the electronic medical record systems Take\nCare and Clinisoft and merged them with the Swedish\nNeonatal Quality Register (SNQ). Patient characteristics from\nthe total NICU-stay were collected. The two groups of controls, manually collected from the\nsame registries, were neonates with suspected sepsis and those\nuninfected during their NICU-stay. We chose controls with the\nsame gestational age (GA) and closest birth date. Suspected\nsepsis was defined as the ICD-10 code P36.9, clinical symp-\ntoms, a negative blood culture, and subsequent antibiotic ther-\napy for at least 5 days. Uninfected infants, alive at 72 h of age,\nwere defined as not fulfilling the ICD-10 criteria for sepsis or\nsuspect sepsis during the NICU-stay. The proportion of the case\nvs suspected sepsis vs uninfected was planned to be 1:1:3. The\nnumber of uninfected neonates in the same gestational ages as\nthe cases during 2006–2016 was insufficient; hence, the pro-\nportion of the cases to controls was 1:1:2.6. We aimed to analyze the incidence of neonatal GNB-\nsepsis and associated mortality and morbidity in neonates\nin our setting. We also wanted to determine whether there\nwere differences in outcome between patients with culture\nproven sepsis, suspected sepsis (negative blood culture)\nand uninfected patients. We characterized the invasive\nbacterial isolates as to clonality and presence of AMR\ngenes. Patients and study design deaths/year globally [13]. A reduction in inappropriate use of\nantibiotics would be the most important step to decrease AMR. The challenge is to reduce the use of antibiotics without an\nincrease in fatal outcome [14, 15]. A matched cohort study was undertaken where all neonates\nwith GNB-sepsis at Stockholm’s four NICUs between\nJanuary 2006 and December 2016 were included. We identi-\nfied all patients with a positive GNB blood culture, at least two\nclinical signs (fatigue, respiratory instability, temperature insta-\nbility, poor feeding, vomiting, cyanosis) and antibiotic therapy\nfor > 5 days. Patients with GPB-sepsis were not analyzed. EOS\nand LOS were defined according to age at onset of sepsis\nsymptoms before or after 72 h of age. Early diagnosis and treatment of neonatal sepsis are dif-\nficult, and the fact that a consensus definition of neonatal\nsepsis is lacking makes it even more challenging [16–18]. The neonatal immune defense, clinical symptoms, and\npathophysiologic responses to bacterial infection differ in\nterm and preterm neonates due to age-dependent maturity. Sepsis onset is most rapid in preterm neonates [19–21]. The\ncharacteristics of the infecting bacteria, such as virulence\nand resistance factors, play a role in the dynamics of\nthe infection. A positive blood culture is the gold stan-\ndard definition of sepsis. However, the difficulties in\ngetting adequate blood volumes for culture and bio-\nmarkers with low sensitivity and specificity complicate\nthe sepsis diagnosis [22]. The intestinal dysbiosis, fol-\nlowing antibiotic treatment, is associated with a higher\nrisk of LOS, necrotizing enterocolitis (NEC) and other\nlong-term morbidities [23–28]. Study population and setting There are six delivery units and four NICUs in the\nStockholm region. A total of 29,553 infants were born alive\nat these delivery units during 2016. The NICUs are\nKarolinska Danderyd (level 2), Karolinska Solna (level\n3), Karolinska Huddinge (level 3), and Södersjukhuset\n(level 2). From March 2014 to May 2016, a seventh small\ndelivery unit and levels 1–2 neonatal unit, BB Sophia,\noperated. Introduction neonatal mortality and accounts for more than one million\ndeaths/year worldwide [1, 2]. In high-income settings, the inci-\ndence of neonatal sepsis is reported to be 1–4/1000 live births\n[1, 3]. Among very low birth weight (VLBW) neonates, ap-\nproximately 30–40% suffer from late-onset sepsis (LOS) with a\nmortality rate between 10 and 36% depending on the infecting\norganism [4–6]. Infants with gram-negative bacilli (GNB)-LOS\nare associated with a higher mortality compared to gram-\npositive bacteria (GPB)-LOS [7, 8]. Studies from Sweden in\nthe last decade report an incidence of early-onset sepsis (EOS)\nof 0.9/1000 live births with a case fatality rate (CFR) of 7% and\nthe GNB-EOS incidence of 0.25/1000 live born with a CFR of\n13% [9]. There are no previous studies on the incidence or the\nCFR of neonatal GNB-LOS in Sweden. Neonatal infections account for more than one-third (36%) of\nall neonatal deaths globally. Sepsis is the leading cause of * Viveka Nordberg\nviveka.nordberg@ki.se * Viveka Nordberg\nviveka.nordberg@ki.se 1\nDepartment of Neonatology, Karolinska University Hospital,\nStockholm, Sweden 2\nDepartment of Clinical Science, Intervention and Technology\n(CLINTEC), Division of Paediatrics, Karolinska Institutet,\nStockholm, Sweden The growing challenge of antimicrobial resistance (AMR) in\nneonatal intensive care units (NICUs), especially with resistant\nGNB, is associated with a high mortality and poor long-term\noutcome [7, 10–12]. The spread of antibiotic resistant bacteria\nhas been a persisting clinical problem during the last decades\nand has resulted in approximately 214,000 attributable neonatal 3\nDepartment of Clinical Microbiology, Karolinska University\nHospital, Stockholm, Sweden 4\nDepartment of Laboratory Medicine, Division of Clinical\nMicrobiology, Karolinska Institutet, Stockholm, Sweden 5\nDepartment of Neonatology, Sachs’ Children’s Youth Hospital,\nSödersjukhuset, Stockholm, Sweden Eur J Clin Microbiol Infect Dis (2021) 40:1803–1813 1804 Outcomes and definition of sepsis-related mortality The primary outcome was death before discharge from NICU. The secondary outcomes were sepsis mortality 5 days after\nonset of GNB-LOS and major morbidities, such as retinopa-\nthy of prematurity (ROP), intraventricular hemorrhage (IVH),\nand bronchopulmonary dysplasia (BPD). The all-cause neonatal mortality before 28 days of life in\nthe Stockholm region was 0.7–1.8/1000 live born (mean 1.4/\n1000) (2006–2016). The recommended empiric antibiotic\ntherapy for unknown EOS was since 2012 benzylpenicillin/\namikacin and for LOS cloxacillin/amikacin or cefotaxime/\namikacin [29]. Between 2006-2012 the empiric aminoglyco-\nside was gentamicin or netilmicin, which during 2012 was\nchanged to amikacin due to local outbreaks with gentamicin\nresistant E.coli. Infection control routines were similar in\nall included hospitals. Death 5 days following a positive blood culture is present-\ned in the study as 5 days case fatality rate (CFR). The\nsuspected sepsis CFR was death 5 days after onset of therapy\nfor suspected sepsis. Repeated episodes of sepsis were docu-\nmented in a few numbers of patients, but survival was ana-\nlyzed from the first invasive GNB episode. Proportions of\nmultidrug-resistant GNB strains and the burden of AMR in\nclinical samples were determined. Eur J Clin Microbiol Infect Dis (2021) 40:1803–1813 1805 Statistical methods This was an open cohort design with varying lengths of time\nfrom onset of sepsis to discharge. Comparisons of continuous\nvariables were made with Wilcoxon rank-sum or two sample\nt-test and summarized using means and SDs if unimodal, sym-\nmetrically distributed variables. If the distribution was\nskewed, they were shown with median values and ranges. Pearson’s Chi-squared test was used to compare categorical\nvariables. Statistical significance was defined as p values <\n0.05, and confidence intervals of 95% were used. Selection of bacterial isolates steroid treatment. In the LOS group, we adjusted for gesta-\ntional age, gender, prenatal steroid treatment, mechanical ven-\ntilation, and necrotizing enterocolitis (NEC). We chose these\nvariables since mechanical ventilation is associated with a\nhigher mortality and prenatal steroids with a lower mortality\ngenerally. We also adjusted for NEC since we considered\nNEC to be a confounder in the association between GNB-\nsepsis and death. Because of the strong correlation between\nbirth weight (BW) and GA, the risk factor BW was excluded\nfrom the analysis. In the logistic regression for morbidities\n(ROP, IVH, BPD), we used composite binary variables for\ndeath and the specific morbidity. GNB in the study refers to the following species: Escherichia\ncoli, Klebsiella pneumoniae, K. oxytoca, K. aerogenes,\nEnterobacter cloacae, Citrobacter koseri, Serratia\nmarcescens, Proteus mirabilis, Pseudomonas aeruginosa,\nAcinetobacter baumannii, and Haemophilus influenzae. The\nNeisseria species were considered to be contaminants. Blood\ncultures with contaminants were not included. All isolates\nwere susceptibility tested for the following: gentamicin,\namikacin, trimethoprim-sulfamethoxazole, cefotaxime, cef-\ntazidime, ciprofloxacin, imipenem, meropenem, ertapenem,\nand piperacillin-tazobactam. We analyzed EOS and LOS separately in the survival anal-\nysis. The Kaplan-Meier method was used to visualize survival\nover time. In the survival analysis for 5-day mortality after\nindex day (GNB-sepsis date of the respective case), Cox pro-\nportional hazard regression was performed to measure the\nhazard ratio (HR) for dying between the cases and their\nmatched controls. The HR gives the time-dependent instanta-\nneous rate ratio of dying, but is in this study interpreted as a\nratio of risks of death occurring within 5 days, similar to the\ninterpretation of ORs in logistic regression. Results During the study period, 310,091 infants were born alive at the\nincluded delivery units. Of these, 31,878 (10.2%) neonates\nwere admitted to the neonatal units of Karolinska Danderyd\n(n = 10,418), Karolinska Solna (n = 5828), Karolinska\nHuddinge (n = 6904), and Södersjukhuset (n = 8728). These\nfour units are levels 2–3 NICUs with a total of 75–80in-patient\ncots. Characterization of gram-negative bacilli All GNB isolates were cultured, isolated, and identified ac-\ncording to routine validated clinical methods and guidelines\nused during the study period. Antibiotic susceptibility testing\nwas performed by the disk diffusion method and interpreted\naccording to the guidelines of the Swedish Reference Group\nof Antibiotics before 2011 and between 2011 and 2016 ac-\ncording to guidelines from the European Committee on\nAntimicrobial Susceptibility Testing (www.eucast.org). MDR was defined as resistance to at least one antibiotic\nagent in three or more antibiotic groups [30]. Covariates adjusted for in the Cox-regression model in the\nEOS and LOS cohort were the same as in the logistic regres-\nsion model. Stata Statistical Software version 16.0, StataCorp,\nTX, USA, and JMP 15.1.0. SAS Institute Inc., Cary, USA,\nwere used. Due to the retrospective design of the study, only 33/107\nisolates were available for the genetic analyzes. Whole ge-\nnome sequencing (WGS) was performed at the Science for\nLife Laboratory (SciLife, Solna, Sweden). Multi-locus se-\nquencing (MLST) was performed in silico as described previ-\nously [31]. All Enterobacterales were assigned to sequence\ntypes except S. marcescens. The isolates that were closely\nrelated in the MLST analysis were further analyzed with sin-\ngle nucleotide polymorphism (SNP) analysis in CLC\nWorkbench [31]. Mortality Among neonates with invasive GNB-sepsis (n = 111),\nmedical records were retrievable in 107 patients, of which\n33 were GNB-EOS and 74 were GNB-LOS. These cases were\nmatched with 107 patients with suspected sepsis (culture-\nnegative) and 295 uninfected controls. In total, data from\n509 patients were analyzed. The clinical characteristics of in-\ncluded patients are presented in Table 1. Thirty (30/107) neonates with GNB-sepsis died before dis-\ncharge (5/33 EOS and 25/74 LOS), with a case fatality rate\nof 28%. The median age at death was 28 days (IQR 14–52)\namong the infants with GNB-LOS that died during hospital\nstay. The mortality in the EOS group was too small to make\nunivariate comparisons between the groups relevant. Comparing GNB-LOS with the suspected sepsis and uninfect-\ned control groups, the proportion of deaths before discharge\nwas 33.7% (25/74), 18.9% (14/74), and 7.6% (15/196), re-\nspectively. The CFR of GNB-LOS in different gestational\nages were in GA ≤28 (18/52, 35 %), GA 29–32 (6/17,\n35%), GA 33–36 (1/3, 33%), and GA ≥37 (0/2, 0%). Proportions of deaths of GNB-EOS and GNB-LOS in differ-\nent gestational ages are presented in Online Resource 1. More than one LOS episode was seen in 35/107 (33%)\ncases where the causative pathogens were GNB and GPB,\nand 57% (20/35) of them had a GPB-sepsis episode before a\nGNB-sepsis. The 33 GNB-EOS cases were distributed as 4, 4,\n1, 3, 2, 4, 4, 5, 1, 2, and 3 per year during the years 2006–\n2016. There was no statistical difference in the trend of EOS\ncases per year during the study period. The 74 GNB-LOS\ncases were distributed as 4, 9, 12, 5, 11, 8, 5, 3, 4, 5, and 8\nwhich indicate a slight but not statistically significant decrease\nover the period. In the logistic regression of the relation between GNB-LOS\nand death, there was a 2.2 times higher odds (crude OR) of\ndying before discharge at NICU in the GNB-sepsis group\n(EOS and LOS combined) compared to the suspected sepsis\ngroup and 4.8 times higher odds compared to uninfected\ncases. There was no statistically significant difference in mor-\ntality before discharge between patients with GNB-EOS,\nsuspected EOS, and controls. Gestational age was the only\nfactor associated with death in GNB-EOS(Table 2). Mortality The pairwise analysis between groups showed that the me-\ndian age at diagnosis was 1 day for GNB-EOS, 0 for suspected\nEOS (p = 0.023), 19 days for GNB-LOS, and 9 for suspected\nLOS (p < 0.001). The administration of prenatal steroids did not differ be-\ntween culture proven GNB-EOS and suspected sepsis. The\nGNB-EOS group did not differ from the suspected EOS group\nregarding administration of antibiotics to mothers prenatally\n(p = 0.11), but the GNB-EOS group had a significantly higher\nuse compared to the uninfected group (52% vs 33 %). Similar\nresults were found in GNB-LOS (49%) where use of antenatal\nantibiotics differed from their uninfected control group (40%)\n(p < 0.01).’ Neonates with GNB-LOS were 6.5 (crude OR) and 3.9 (CI:\n1.6–9.4) (adjusted OR) more likely to die during hospital stay\ncompared to the uninfected matched control group. A higher\ngestational age was protective. The comparison between\nGNB-LOS and suspected LOS showed no significant differ-\nence in the odds of dying before discharge (OR 2.0; CI: 0.8–\n4.6) (Table 2). There were 43/74GNB-LOS cases vs 41/74 suspected LOS\ncases that received prophylactic antibiotics before the sepsis/\nsuspected sepsis episodes. Mode of delivery did not differ\nbetween the groups in the GNB-EOS analysis, but caesarean\nsection was significantly more common in GNB-LOS (42%)\ncompared to suspected LOS (15%) and uninfected controls\n(22%) (Table 1). The 5 days CFR was 15% (5/33) in GNB-EOS. All neo-\nnates with GNB-EOS that died died before 5 days after GNB-\nEOS onset. The 5 days CFR of GNB-LOS was 17.6% (13/74). The crude 5 days CFR differed significantly between GNB-\nLOS and the uninfected controls (p < 0.001) and between\nGNB-LOS and the suspected sepsis group (p = 0.039) but\nnot between the suspected sepsis group and uninfected con-\ntrols (p = 0.37). In a Cox-regression model, the adjusted haz-\nard ratio (HR) of dying 5 days after GNB-LOS onset vs unin-\nfected controls was 3.7 (CI: 1.2–11.2), but no increased hazard\nwas seen in GNB-LOS versus suspected LOS (Table 3). The\ncumulative survival rate, shown in the Kaplan-Meier curves\nfor 5 days survival, is illustrated in Fig. 2. Intensive care interventions The median days of mechanical ventilation differed between\nGNB-EOS cases (median 1 day, IQR 0–7 days) and uninfect-\ned cases (median 0, IQR 0–0 days). The days of total parental\nnutrition (TPN) in the GNB-EOS (median 8 days, IQR 2–13)\ndays were higher and differed significantly from the uninfect-\ned group (median 1 day, IQR 0–8 days). Incidence of GNB-sepsis and baseline characteristics A flowchart of included patients is depicted in Fig. 1 during\nthe period, a total of 804 admitted infants had a culture-\nconfirmed neonatal sepsis, which corresponds to a total inci-\ndence of 2.6/1,000 live born. GNB-sepsis counted for 111/804\n(14%) of all culture-confirmed sepsis cases. The proportion of GNB-sepsis for all admitted neonates\nwas 111/31,878 (0.36%), with a cumulative incidence of\n0.35 cases per 1000 live born during the study period. Among the infants admitted to the neonatal unit,\n1026/31,878 (3.2%) had suspected but not culture-verified\nsepsis with a cumulative incidence of 3.3/1,000 live born. We used logistic regression to measure odds ratios (OR) of\ndying, separately for EOS and LOS, and adjusted for different\nvariables in the regression model of EOS and LOS. Variables\nadjusted for in the EOS group were as follows: gestational\nage, gender, perinatal antibiotics, birth mode, and prenatal Eur J Clin Microbiol Infect Dis (2021) 40:1803–1813 1806 Flow chart of all included patients in the study Fig. 1 A Flow chart of all included patients in the study Eur J Clin Microbiol Infect Dis (2021) 40:1803–1813 1807 Mortality Morbidity GNB-LOS and suspected LOS had significantly more days\nof ventilatory support, umbilical artery catheter (UAC), pe-\nripheral central venous catheter (pCVC), and TPN than the\nuninfected group. Days of TPN and total days with pCVC\nwere significantly higher in the GNB-LOS group compared\nto the suspected sepsis and the uninfected group (Table 1). The GNB-EOS group differed in univariate analysis from the\nuninfected controls with a higher proportion of IVH grades 3–\n4 (15% vs 2%, p = 0.004) and ROP 3–4 (12% vs 1%, p =\n0.01). No difference was seen regarding BPD. Morbidity Verified\nGNB-LOS differed from uninfected controls regarding ROP 1808 Eur J Clin Microbiol Infect Dis (2021) 40:1803–1813 Table 1\nCharacteristics of 107 GNB cases (EOS and LOS) and pair-wise comparisons with suspected sepsis controls and uninfected controls\nGNB-EOS (n=33) Susp EOS (n=33)\nNo inf control (n=99) P*\nEOS\nP**\nEOS\nP***\nEOS\nGNB-LOS (n=74) Susp LOS (n=74)\nNo inf control (n=196) P*\nLOS\nP**\nLOS\nP***\nLOS\nGest age (w)\n34 (26–38)\n34 (26–38)\n34 (26–38)\n0.94\n0.97\n0.91\n27 (25–29)\n27 (25–29)\n27 (25–29)\n0.98\n0.60\n0.58\nGender, male\n16 (48)\n21 (64)\n57 (58)\n0.16\n0.36\n0.42\n45 (61)\n53 (72)\n99 (51)\n0.16\n0.13\n0.002\nBW (g)\n2225 (994–2950)\n2013 (686–3500)\n2087 (995–3325)\n0.88\n0.81\n0.89\n885 (750–1395)\n812 (627–1259)\n960 (747–1315)\n0.17\n0.69\n0.04\nApgar at 5 min<7\n13 (39)\n5 (15)\n26 (26)\n0.027\n0.16\n0.18\n23 (31)\n29 (39)\n63 (32)\n0.33\n0.83\n0.33\nCaesarean section\n16 (48)\n16 (48)\n50 (22)\n0.90\n0.96\n0.84\n31 (42)\n11 (15)\n44 (22)\n<0.001 <0.001\n0.17\nPrenatal steroids\n11 (33)\n14 (42)\n34 (34)\n0.72\n0.72\n0.40\n52 (70)\n64 (87)\n146 (75)\n0.17\n0.61\n0.034\nAntenatal antibiotics\n17 (52)\n11 (33)\n16 (16)\n0.11\n<0.001\n0.037\n36 (49)\n31 (42)\n79 (40)\n0.048 <0.01\n0.81\nOnset sepsis (d)\n1 (0–1)\n0 (0)\n0.023\n19 (11–31)\n9 (4–17)\n<0.001\nDays of MV\n1 (0–7)\n0 (0–6)\n0 (0)\n0.77\n<0.001\n0.57\n8 (2–24)\n9 (2–16)\n0 (0–7)\n0.43\n<0.001\n<0.001\nDays of CPAP\n2 (0–8)\n1 (0–4)\n3 (0–20)\n0.31\n0.048\n0.24\n16 (3–36)\n18 (2–38)\n6 (1–25)\n0.77\n0.003\n0.03\nDays of TPN\n8 (2–13)\n2 (0–10)\n1 (0–8)\n0.06\n0.001\n0.001\n22 (11–37)\n13 (8–24)\n9 (5–14)\n0.001 <0.001\n<0.001\nDays of UAC\n1 (0–6)\n0 (0–2)\n0 (0–4)\n0.038\n0.046\nNA\n6 (3–8)\n5 (0–7)\n3 (0–6)\n0.43\n<0.001\n0.036\nDays of UVC\n1 (0–5)\n0 (0–1)\n0 (0–0)\n0.062\n0.015\nNA\n1 (0–4)\n2 (0–5)\n0 (0–5)\n0.40\n0.72\n0.20\nDays of pCVC\n0 (0–9)\n0 (0–9)\n0 (0–0)\n0.39\n<0.001\n0.55\n15(8–28)\n7 (1–20)\n2 (0–8)\n0.009 <0.001\n<0.001\nBPD discharge\n4 (12)\n6 (18)\n13 (13)\n0.64\n0.67\n0.78\n32 (43)\n35 (47)\n64 (33)\n0.48\n0.12\n0.083\nROP 1–2 discharge\n4 (12)\n6 (18)\n2 (2)\n0.48\n0.004\n0.059\n9 (12)\n20 (27)\n26 (13)\n0.11\n0.99\n0.017\nROP 3–4 discharge\n4 (12)\n0 (0)\n1 (1)\n0.095\n0.01\n0.85\n10 (14)\n4 (5)\n9 (5)\n0.18\n0.019\n0.83\nIVH 1–2 discharge\n7 (21)\n4 (12)\n5 (5)\n0.32\n0.005\n0.059\n16 (22)\n14 (19)\n19 (10)\n0.55\n0.008\n0.039\nIVH 3–4 discharge\n5 (15)\n3 (9)\n2 (2)\n0.48\n0.004\n0.059\n6(8)\n6 (8)\n11 (6)\n0.60\n0.20\n0.45\nAll NEC\n27 (36)\n15 (20)\n5 (3)\n0.09\n0.059\n0.39\nSurgical NEC\n11 (15)\n5 (7)\n0 (0)\n0.11\n0.003\n0.78\nMortality\n5 (15)\n3 (9)\n7 (7)\n0.46\n0.24\n0.86\n25 (34)\n12 (16)\n15 (7.6)\n0.04\n<0.001\n0.008\n*Comparison between case and suspect sepsis, **comparison between case and uninfected control, ***comparison between suspected case and uninfected control. Discussion For GNB-LOS, the OR for the composite variable death/\nBPD was 3.8 (CI: 1.68–8.67) compared to uninfected con-\ntrols, but no difference was seen compared to suspect LOS. Gram-negative sepsis is an uncommon but serious disorder in\nthe neonate, especially in the premature born [4–6, 8, 32]. In\nthis 11-year retrospective study, we sought to describe GNB-\nsepsis by reporting the incidence, subsequent mortality, and\nmorbidity and to compare it to suspected sepsis and uninfected\ncontrols in neonates in our region. Morbidity Of all GNB strains, 7/107 were resistant\nto at least two groups of antimicrobials, and all were suscep-\ntible to carbapenems. 3–4 (14% vs 5%, p = 0.019), but not regarding IVH 3–4 and\nBPD (Table 1). Morbidity analyses with logistic regression for\nGNB-EOS showed an OR for the composite outcome mea-\nsure death/IVH3–4 of 7.5 (CI: 1.29–43.4) compared to sus-\npect EOS and 5.2 (CI: 1.17–23.4) compared to uninfected\ncontrols. For GNB-LOS OR was 3.0 (CI: 1.30–6.76) for\ndeath/ROP3–4 compared to suspect LOS and 6.3 (CI: 2.79–\n14.0) compared to uninfected controls. Morbidity Continuous variables are presented with\nmeans, SD, medians, and interquartile range. Categorical variables are presented with proportions and %. BW birth weight, MV mechanical ventilation, CPAP continuous positive airway pressure, TPN total\nparental nutrition, pCVC peripheral central venous catheter, UVC umbilical venous catheter, UAC umbilical arterial catheter, BPD bronchopulmonary dysplasia, ROP retinopathy of the newborn, IVH\nintraventricular hemorrhage *Comparison between case and suspect sepsis, **comparison between case and uninfected control, ***comparison between suspected case and uninfected control. Continuous variables are presented with\nmeans, SD, medians, and interquartile range. Categorical variables are presented with proportions and %. BW birth weight, MV mechanical ventilation, CPAP continuous positive airway pressure, TPN total\nparental nutrition, pCVC peripheral central venous catheter, UVC umbilical venous catheter, UAC umbilical arterial catheter, BPD bronchopulmonary dysplasia, ROP retinopathy of the newborn, IVH\nintraventricular hemorrhage Eur J Clin Microbiol Infect Dis (2021) 40:1803–1813 1809 Table 2\nLogistic regression with adjusted odds ratio of neonatal death after GNB-sepsis before discharge from NICU\nEOS\nAdjusted OR\n95% CI\np Value\nLOS\nAdjusted OR\n95% CI\np Value\nGNB-EOS: uninfected*\n2.5\n0.53–11.4\n0.25\nGNB-LOS: uninfected*\n3.9\n1.61–9.36\n0.003\nSuspected EOS: uninfected*\n0.92\n0.18–4.74\n0.92\nSuspected LOS: uninfected*\n2.0\n0.78–5.05\n0.15\nGNB-EOS: suspected EOS*\n2.7\n0.49–14.7\n0.26\nGNB-LOS: suspected LOS*\n2.0\n0.82–4.65\n0.13\nGestational week\n0.8\n0.67–0.95\n0.01\nGestational week\n0.8\n0.67–0.92\n0.002\nGender (male)\n0.9\n0.26–2.84\n0.81\nGender (male)\n1.8\n0.87–3.62\n0.12\nPrenatal steroids\n0.7\n0.13–3.79\n0.67\nMechanical ventilation\n3.8\n1.00–14.1\n0.049\nPrenatal antibiotics\n2.1\n0.50–8.56\n0.32\nPrenatal steroids\n0.4\n0.16–0.89\n0.26\nBirth mode (CS)\n1.4\n0.37–5.50\n0.60\nNecrotizing enterocolitis\n3.0\n1.34–6.48\n0.007\nAdjusted odds ratio of the comparisons between the sepsis group and the reference groups. GNB-EOS and GNB-LOS are reported separately. *Reference group ogistic regression with adjusted odds ratio of neonatal death after GNB-sepsis before discharge from NICU Adjusted odds ratio of the comparisons between the sepsis group and the reference groups. GNB-EOS and GNB-LOS are reported separately. *Reference group Table 4. The genomic characterization of the invasive isolates\nthat infected one-third of the neonates in the study can be seen\nin Online Resource 4. Of all GNB strains, 7/107 were resistant\nto at least two groups of antimicrobials, and all were suscep-\ntible to carbapenems. Table 4. The genomic characterization of the invasive isolates\nthat infected one-third of the neonates in the study can be seen\nin Online Resource 4. Bacterial characteristics and antibiotic resistance All 107 GNB from confirmed positive blood cultures are pre-\nsented in Online Resource 2. The majority belonged to the\norder Enterobacterales, comprising E. coli, K. pneumoniae,\nEnterobacter spp., and S. marcescens. Three other gram-\nnegative species were represented: A. baumannii,\nP. aeruginosa, and H. influenzae. Proportions of deaths from\nGNB-EOS and GNB-LOS and the causing pathogen can be\nseen in Online Resource 3. Multidrug resistance was observed\nin 3/47E. coli and 2/20K. pneumoniae and 2/14E. cloacae. The antibiotic resistance pattern of all isolates is presented in The incidence of neonatal GNB-sepsis in the region was\n0.35/1000 live born neonates and remained unchanged during\nthe study period. The incidence of GNB-EOS was 0.11/1000\nlive births which is about half of what recently has been re-\nported from the western part of Sweden, where the incidence\nof GNB-EOS was 0.25/1000 live births [9]. The difference is\nsubstantial but might be influenced by methodological differ-\nences. The incidence of GNB-LOS was 0.24/1000 live births\nand has not been previously described in a Swedish context. Table 3\nCox-regression survival analysis of hazard rate (HR) at 5 days after onset of LOS symptoms\nCase—uninfected*\nCase—suspected*\nSuspect—uninfected*\nGroup\nHR\n95% CI\np Value\nHR\n95% CI\np Value\nHR\n95% CI\np Value\n5 days ALL crude\n5.5\n2.4–12.8\n<0.001\n4.5\n1.9–10.7\n0.001\n1.2\n0.3–4.9\n0.76\n5 days LOS crude\n5.8\n2.2–15.2\n<0.001\n3.2\n1.0–10.0\n0.039\n1.8\n0.5–6.3\n0.37\n5 days LOS adjusted#\n3.7\n1.2–11.2\n0.019\n2.7\n0.8–8.8\n0.095\n1.4\n0.4–5.4\n0.65\n*Reference group\n# The analyses are adjusted for gestational age, gender, prenatal steroids, mechanical ventilation, and necrotizing enterocolitis (NEC)\nThe uninfected group is matched to the same days of life when the GNB-sepsis case was diagnosed Table 3\nCox-regression survival analysis of hazard rate (HR) at 5 days after onset of LOS symptoms g\np\n# The analyses are adjusted for gestational age, gender, prenatal steroids, mechanical ventilation, and necrotizing enterocolitis (NEC)\nThe uninfected group is matched to the same days of life when the GNB-sepsis case was diagnosed Eur J Clin Microbiol Infect Dis (2021) 40:1803–1813 1810 Fig. 2 The Kaplan-Meier method visualizes survival over time in GNB-\nLOS. The figure depicts survival 5 days after sepsis onset parenteral nutrition, and central catheters, than the uninfected\ncontrols. Bacterial characteristics and antibiotic resistance The antenatal factors delivery by caesarean section and\nexposure to prenatal antibiotics occurred more frequently in\ninfants with GNB-LOS than in infants with suspected sepsis\nor in uninfected controls. A dysbiotic neonatal intestinal mi-\ncrobiota due to C-sectionand/or use of antibiotics has previ-\nously been associated as a risk factor for neonatal LOS. The\nsuggested biological rationale is that an altered first-\ncolonizing microbiota cannot confer protection against bacte-\nrial translocation in the neonatal intestine [33, 34]. We found GNB-sepsis to be a great risk factor for\nmortality and show the in-hospital mortality rate to be\n28% of all GNB-sepsis cases. The in-hospital mortality\nrate was more than 2.3 times higher among the infants\nwith GNB-LOS compared to those with GNB-EOS,\nwhich possibly reflects the fact that the LOS group\nwere more premature, had lower BW, had more co-\nmorbidities and a longer duration of hospital care. Prenatal steroids have been shown to be protective\nagainst a number of morbidities in preterm infants\n[35], and in this study it was protective against death\nfrom GNB-LOS but not from GNB-EOS. Fig. 2 The Kaplan-Meier method visualizes survival over time in GNB-\nLOS. The figure depicts survival 5 days after sepsis onset The incidence of 1.4 E.coli-LOS per 1000 NICU admissions\nwas about half that reported in studies from other high-income\ncountries [3, 5, 8]. We found that the need for intensive care interventions\ndiffered between the groups. The GNB-LOS group had sig-\nnificantly more days of supportive intensive care compared to\nuninfected controls, but not to suspected-LOS. These invasive\nmeasures could be risk factors for LOS but also the conse-\nquences of infection. As well neonates with suspected sepsis\nneeded more intensive care in terms of mechanical ventilation, When adjusted for confounders, the GNB-LOS group’s in-\nhospital mortality was 3.9 times higher compared to uninfect-\ned controls. We found no statistical differences in in-hospital\nmortality between the other control groups. Gram-negative bacteria\nNumber of isolates\nRatio of resistant isolates\nEnterobacterales\nE.coli\n47\n2/47 GEN\n3/47 TSU, CTX, CFZ\n7/47 TSU\nK. pneumoniae\n20\n2/20 TSU, CTX, CTZ, GEN, CIP\nK. aerogenes\n2\n1/2 TSU\nK. oxytoca\n4\n0\nE. cloacae\n14\n1/14 GEN\n2/14 CTX, CFZ\nS. marcescens\n10\n0\nC. koseri\n1\n0\nNon-Enterobacterales genera\nAcinetobacter\nA. baumannii\n3\n0\nPseudomonas\nP. aeruginosa\n4\n0\nHaemophilus\nH. Table 4 Summary of antibiogram\nof the 107 Gram-negative isolates\nfrom all neonates included in the\nstudy All isolates were susceptibility tested for the following: GEN gentamicin, AMI amikacin, TSU trimethoprim-\nsulfamethoxazole, CTX cefotaxime, CFZ ceftazidime, CIP ciprofloxacin, IMI imipenem, MER meropenem, ERT\nertapenem, and PT piperacillin-tazobactam Bacterial characteristics and antibiotic resistance influenzae\n2\n0\nAll isolates were susceptibility tested for the following: GEN gentamicin, AMI amikacin, TSU trimethoprim-\nsulfamethoxazole, CTX cefotaxime, CFZ ceftazidime, CIP ciprofloxacin, IMI imipenem, MER meropenem, ERT\nertapenem, and PT piperacillin-tazobactam 1811 Eur J Clin Microbiol Infect Dis (2021) 40:1803–1813 Many studies on neonatal sepsis present crude mortality after\na positive blood culture. However, autopsy completion is infre-\nquently performed. We have tried to relate the sepsis episode\nwith sepsis-related mortality and calculated the 5 days CFR. The 5 days CFR for GNB-EOS was 15% and for GNB-LOS\n17%. GNB-LOS was most common (70%) in the lower GA (≤\n28 weeks), and the CFR was as high as 35% in this group. repeatedly small outbreaks of gentamicin-resistantE.coli in the\nregion. After that, we could not see any high rates resistance to\namikacin or third generation cephalosporins that would lead to\nany change in the empiric therapy. One strength of the study is its population-based approach as\nit covers almost all 310,091 infants born in the Stockholm region\nduring the study period. Another strength of the study is that all\nmedical records from the patients with GNB-sepsis, suspected\nsepsis, and controls were validated against medical records. All\ndata was validated against medical records because between\n2006 and 2010, there were no predefined sepsis criteria and data\ncompleteness in SNQ regarding causative agents was low in the\nstudy region. Sepsis criteria have in later years been standardized,\nand reporting to SNQ has been changed from retrospective sum-\nmaries to web-based uploads on a daily basis. In later years, SNQ\nhas been shown to exhibit similar or higher completeness for\nneonatal sepsis as the Swedish Medical Birth register which is\nconsidered to be very high [41] . From the survival analysis, we concluded that the adjusted\nhazard for dying within 5 days from the GNB-LOS onset was\nfour times greater than if the neonate was uninfected. There\nwas no statistical significance in the adjusted Cox-regression\nanalysis in comparing the other groups with each other, which\npossibly might reflect a type II error and the small number of\nobservations. The Kaplan-Meier curve gives us the indication\nthat suspected-LOS is associated with a greater hazard of sur-\nviving than in uninfected, but we could not show that statisti-\ncally. Bacterial characteristics and antibiotic resistance Causal data on reasons for death in the suspected sepsis\nand uninfected group were not analyzed but could be ex-\nplained by the most common non-infectious causes of death\nin the NICU such as respiratory failure, asphyxia, IVH, met-\nabolic disease, and lethal genetic syndromes. The limitations of the study are related to the retrospective\ndesign and, despite covering all cases during an 11-year peri-\nod in an area with more than 2 million inhabitants, the small\nsample size. The procedure of matching the controls to each\nsepsis case has been done as accurately as possible. The phys-\niological vulnerability of the neonate in different gestational\nages is the most important variable for matching. The size of\nthe cohort makes it impossible to match for more morbidities\nand is therefore a limitation of the study. Without doubt, culture proven GNB-LOS is related to an\nincreased risk of mortality and morbidity, as previously reported\n[3, 6, 8, 32]. However, the power of this study is not sufficient to\nfind out whether suspect sepsis is an entity of its own or just\nsepsis not possible to detect by culture. Studies conducted in\nhigh-income countries report suspected sepsis to be 6–16 times\nas more common than culture proven sepsis [14, 18]. We could not draw conclusions about the association between\nGNB-sepsis and severe complications of preterm birth such as\nBPD and ROP 3–4, as the most severely ill patients died before\nthey could be validated for these conditions. IVH occurs early\nduring the same time frame as GNB-EOS and was also overrep-\nresented in GNB-EOS compared to neonates with suspected\nsepsis and the uninfected. As IVH often occurs before the onset\nof GNB-LOS, we did not analyze it in this context. Both ROP 3–\n4 and BPD was associated with GNB-LOS. Data availability The dataset is available on your request. 8. Stoll BJ, Hansen N, Fanaroff AA, Wright LL, Carlo WA,\nEhrenkranz RA, Lemons JA, Donovan EF, Stark AR, Tyson JE,\nOh W, Bauer CR, Korones SB, Shankaran S, Laptook AR,\nStevenson DK, Papile LA, Poole WK (2002)Late-onset sepsis in\nvery low birth weight neonates: the experience of the NICHD\nNeonatal Research Network. Pediatrics 110(2 Pt 1):285–291 Conflict of interest\nThe authors declare no competing interests. Open Access This article is licensed under a Creative Commons\nAttribution 4.0 International License, which permits use, sharing, adap-\ntation, distribution and reproduction in any medium or format, as long as\nyou give appropriate credit to the original author(s) and the source, pro-\nvide a link to the Creative Commons licence, and indicate if changes were\nmade. The images or other third party material in this article are included\nin the article's Creative Commons licence, unless indicated otherwise in a\ncredit line to the material. If material is not included in the article's\nCreative Commons licence and your intended use is not permitted by\nstatutory regulation or exceeds the permitted use, you will need to obtain\npermission directly from the copyright holder. To view a copy of this\nlicence, visit http://creativecommons.org/licenses/by/4.0/. 11. World Health Organisation (2014) Antimicrobial resistance: global\nreport on surveillance. www.who.int 12. Ting JY, Synnes A, Roberts A, Deshpandey A, Dow K, Yoon EW,\nLee KS, Dobson S, Lee SK, Shah PS, Canadian Neonatal Network\nI (2016) Association between antibiotic use and neonatal mortality\nand morbidities in very low-birth-weight infants without culture-\nproven sepsis or necrotizing enterocolitis. JAMA Pediatr 170(12):\n1181–1187. https://doi.org/10.1001/jamapediatrics.2016.2132 13. Laxminarayan R, Matsoso P, Pant S, Brower C, Rottingen JA,\nKlugman K, Davies S (2016) Access to effective antimicrobials: a\nworldwide challenge. Lancet 387(10014):168–175. https://doi.org/\n10.1016/S0140-6736(15)00474-2 Conclusion We conclude that GNB-sepsis is rare but it remains a serious\nthreat to neonatal patients in the region. GNB-sepsis is a risk\nfactor for neonatal mortality compared to suspect sepsis and\nuninfected controls. We found a lower incidence of GNB-\nEOS than previously described in Sweden and other high-\nincome settings, and for the first time, we present the inci-\ndence of GNB-LOS in Sweden. The GNB-EOS or GNB-\nLOS incidence did not change during the study period. The\nincidence of AMR was low, the AMR pattern did not reveal\nany highly resistant strains, and the incidence did not change\nover time. This is reassuring as the current empiric therapy\nagainst bacterial sepsis of unknown origin appears to be rele-\nvant despite its use over a long period of time. E.coli was the most common pathogen causing GNB-LOS\nwith a 5 days CFR of 9%. The highest 5 days CFR (33%) was\ncaused by the Enterobacter spp. We could not statistically\nrelate specific pathogens to mortality which is an important\nissue for the clinician. The rate of antibiotic resistant bacteria in our study was low\ncompared to studies from other settings [36, 37]. In a recent\nretrospective study between 2009 and 2017 from the USA, a\nmean of 5% ESBL-producingE.coli was seen in a large cohort\n(n = 733) of neonatal E-coli sepsis [38]. The proportion of all\nESBL-producingEnterobacterales in our study, with a smaller\nsample size, was 7/107 (6.5%) and is still considered low. The\nlow incidence of GNB-LOS and AMR could be the result of\nlong-standing efforts in infection control and antimicrobial\nstewardship [39, 40]. In 2012, we changed our empiric ami-\nnoglycoside from gentamicin or netilmicin to amikacin due to Supplementary Information The online version contains supplementary\nmaterial available at https://doi.org/10.1007/s10096-021-04211-8. Acknowledgements We like to thank Jessica Stenquist, Gabriella Lang,\nand Mikaela Winderud for their contribution to the data collection. Code availability\n“Not applicable.” Eur J Clin Microbiol Infect Dis (2021) 40:1803–1813 1812 5. Tsai MH, Hsu JF, Chu SM, Lien R, Huang HR, Chiang MC, Fu\nRH, Lee CW, Huang YC (2014) Incidence, clinical characteristics\nand risk factors for adverse outcome in neonates with late-onset\nsepsis. Pediatr Infect Dis J 33(1):e7–e13. https://doi.org/10.1097/\nINF.0b013e3182a72ee0 Authors’ contributions VN, LN, AI, and CG planned and designed the\nstudy. VN and AT acquired the data. VN, AI, KI, and CG performed the\nmicrobiological analyses. Declarations Ethics approval\nThe study is approved by the Regional Ethics Review\nboard in Stockholm (Dnr:2016/202-31/2). Ethics approval\nThe study is approved by the Regional Ethics Review\nboard in Stockholm (Dnr:2016/202-31/2). 9. Johansson Gudjonsdottir M, Elfvin A, Hentz E, Adlerberth I,\nTessin I, Trollfors B (2019) Changes in incidence and etiology of\nearly-onset neonatal infections 1997-2017 - a retrospective cohort\nstudy in western Sweden. BMC Pediatr 19(1):490. https://doi.org/\n10.1186/s12887-019-1866-z Consent to participate\n“Not applicable.” Consent for publication\nThis study has not been submitted for publica-\ntion or consideration in any other journal. Consent for publication\nThis study has not been submitted for publica-\ntion or consideration in any other journal. 10. Stoll BJ, Hansen NI, Adams-Chapman I, Fanaroff AA, Hintz SR,\nVohr B, Higgins RD, National Institute of Child H, Human\nDevelopment Neonatal Research N (2004) Neurodevelopmental\nand growth impairment among extremely low-birth-weight infants\nwith neonatal infection. Jama 292(19):2357–2365. https://doi.org/\n10.1001/jama.292.19.2357 Conflict of interest\nThe authors declare no competing interests. Conclusion VN and LN drafted the manuscript and the data\nanalysis. VN, LN, AI, CG, AT, and KI participated in the interpretation of\nthe data and critically revised the manuscript. All authors have read and\napproved the final manuscript. 6. Tsai MH, Chu SM, Lee CW, Hsu JF, Huang HR, Chiang MC, Fu\nRH, Lien R, Huang YC (2014) Recurrent late-onset sepsis in the\nneonatal intensive care unit: incidence, clinical characteristics and\nrisk factors. Clin Microbiol Infect 20(11):O928–O935. https://doi. org/10.1111/1469-0691.12661 Funding Open access funding provided by Karolinska Institute. The\nstudy was supported by grants from the Samariten Foundation for\nPediatric Research, Mjölkdroppen Foundation, Kronprinsessan Lovisas\nFoundation for pediatric healthcare, and Karolinska University Hospital\nresearch fund. 7. Benjamin DK, DeLong E, Cotten CM, Garges HP, Steinbach WJ,\nClark RH (2004) Mortality following blood culture in premature\ninfants: increased with Gram-negative bacteremia and candidemia,\nbut not gram-positive bacteremia. J Perinatol 24(3):175–180. https://doi.org/10.1038/sj.jp.7211068 Data availability The dataset is available on your request. References 14. Cantey JB, Wozniak PS, Pruszynski JE, Sanchez PJ (2016)\nReducing unnecessary antibiotic use in the neonatal intensive care\nunit (SCOUT): a prospective interrupted time-series study. Lancet\nInfect Dis 16(10):1178–1184. https://doi.org/10.1016/S1473-\n3099(16)30205-5 1. Shane AL, Sanchez PJ, Stoll BJ (2017) Neonatal sepsis. Lancet\n390(10104):1770–1780. https://doi.org/10.1016/S0140-6736(17)\n31002-4 15. Bion J, Richardson A, Hibbert P, Beer J, Abrusci T, McCutcheon\nM, Cassidy J, Eddleston J, Gunning K, Bellingan G, Patten M,\nHarrison D, Matching Michigan C, Writing C (2013) 'Matching\nMichigan': a 2-year stepped interventional programme to minimise\ncentral venous catheter-blood stream infections in intensive care\nunits in England. BMJ Qual Saf 22(2):110–123. https://doi.org/\n10.1136/bmjqs-2012-001325 2. UNICEF (2019,; https://data.unicef.org/topic/child-survival/\nneonatal-mortality/.) Neonatal mortality. UNICEF Data:\nMonitoring the situation of children and women. 3. Hornik CP, Fort P, Clark RH, Watt K, Benjamin DK Jr, Smith PB,\nManzoni P, Jacqz-Aigrain E, Kaguelidou F, Cohen-Wolkowiez M\n(2012) Early and late onset sepsis in very-low-birth-weight infants\nfrom a large group of neonatal intensive care units. Early Hum Dev\n88(Suppl 2):S69–S74. https://doi.org/10.1016/S0378-3782(12)\n70019-1 16. Newman TB, Puopolo KM, Wi S, Draper D, Escobar GJ (2010)\nInterpreting complete blood counts soon after birth in newborns at\nrisk for sepsis. Pediatrics 126(5):903–909. https://doi.org/10.1542/\npeds.2010-0935 4. Auriti C, Ronchetti MP, Pezzotti P, Marrocco G, Quondamcarlo A,\nSeganti G, Bagnoli F, De Felice C, Buonocore G, Arioni C, Serra\nG, Bacolla G, Corso G, Mastropasqua S, Mari A, Corchia C, Di\nLallo D, Rava L, Orzalesi M, Di Ciommo V (2010) Determinants of\nnosocomial infection in 6 neonatal intensive care units: an Italian\nmulticenter prospective cohort study. Infect Control Hosp\nEpidemiol 31(9):926–933. https://doi.org/10.1086/655461 17. Wynn JL, Polin RA (2018) Progress in the management of neonatal\nsepsis: the importance of a consensus definition. Pediatr Res 83(1-\n1):13–15. https://doi.org/10.1038/pr.2017.224 18. Klingenberg C, Kornelisse RF, Buonocore G, Maier RF, Stocker M\n(2018)Culture-negative early-onset neonatal sepsis - at the 1813 Eur J Clin Microbiol Infect Dis (2021) 40:1803–1813 crossroad between efficient sepsis care and antimicrobial steward-\nship. Front Pediatr 6:285. https://doi.org/10.3389/fped.2018.00285 infection: the association of bacterial clones and virulence genes\nwith septic shock, source of infection and recurrencies. Antimicrob Agents Chemother. https://doi.org/10.1128/AAC. 02351-19 19. Wynn JL, Wong HR (2010) Pathophysiology and treatment of\nseptic shock in neonates. Clin Perinatol 37(2):439–479. https://\ndoi.org/10.1016/j.clp.2010.04.002 32. 32. References Greenberg RG, Kandefer S, Do BT SPB, Stoll BJ, Bell EF, Carlo\nWA, Laptook AR, Sanchez PJ, Shankaran S, Van Meurs KP, Ball\nMB, Hale EC, Newman NS, Das A, Higgins RD, Cotten CM,\nEunice Kennedy Shriver National Institute of Child H, Human\nDevelopment Neonatal Research N (2017)Late-onset sepsis in ex-\ntremely premature infants: 2000-2011. Pediatr Infect Dis J 36(8):\n774–779. https://doi.org/10.1097/INF.0000000000001570 20. Adkins B, Leclerc C, Marshall-Clarke S (2004) Neonatal adaptive\nimmunity comes of age. Nat Rev Immunol 4(7):553–564. https://\ndoi.org/10.1038/nri1394 21. Olin A, Henckel E, Chen Y, Lakshmikanth T, Pou C, Mikes J,\nGustafsson A, Bernhardsson AK, Zhang C, Bohlin K, Brodin P\n(2018) Stereotypic immune system development in newborn chil-\ndren. Cell 174(5):1277–1292 e1214. https://doi.org/10.1016/j.cell. 2018.06.045 33. Aloisio I, Quagliariello A, De Fanti S, Luiselli D, De Filippo C,\nAlbanese D, Corvaglia LT, Faldella G, Di Gioia D (2016)\nEvaluation of the effects of intrapartum antibiotic prophylaxis on\nnewborn intestinal microbiota using a sequencing approach\ntargeted to multi hypervariable 16S rDNA regions. Appl\nMicrobiol Biotechnol 100 (12):5537-5546. doi:https://doi.org/10. 1007/s00253-016-7410-2 22. Schelonka RL, Chai MK, Yoder BA, Hensley D, Brockett RM,\nAscher DP (1996) Volume of blood required to detect common\nneonatal pathogens. J Pediatr 129(2):275–278 23. Cotten CM, Smith PB (2013) Duration of empirical antibiotic ther-\napy for infants suspected of early-onset sepsis. Curr Opin Pediatr\n25(2):167–171. https://doi.org/10.1097/MOP.0b013e32835e01f6 34. Singer JR, Blosser EG, Zindl CL, Silberger DJ, Conlan S, Laufer\nVA, DiToro D, Deming C, Kumar R, Morrow CD, Segre JA, Gray\nMJ, Randolph DA, Weaver CT (2019) Preventing dysbiosis of the\nneonatal mouse intestinal microbiome protects against late-onset\nsepsis. Nat Med 25(11):1772–1782. https://doi.org/10.1038/\ns41591-019-0640-y 24. Greenwood C, Morrow AL, Lagomarcino AJ, Altaye M, Taft DH,\nYu Z, Newburg DS, Ward DV, Schibler KR (2014) Early empiric\nantibiotic use in preterm infants is associated with lower bacterial\ndiversity and higher relative abundance of Enterobacter. J Pediatr\n165(1):23–29. https://doi.org/10.1016/j.jpeds.2014.01.010 25. Alexander VN, Northrup V, Bizzarro MJ (2011) Antibiotic expo-\nsure in the newborn intensive care unit and the risk of necrotizing\nenterocolitis. J Pediatr 159(3):392–397. https://doi.org/10.1016/j. jpeds.2011.02.035 35. Been JV, Degraeuwe PL, Kramer BW, Zimmermann LJ (2011)\nAntenatal steroids and neonatal outcome after chorioamnionitis: a\nmeta-analysis. BJOG 118(2):113–122. https://doi.org/10.1111/j. 1471-0528.2010.02751.x 26. References Arrieta MC, Stiemsma LT, Dimitriu PA, Thorson L, Russell S,\nYurist-Doutsch S, Kuzeljevic B, Gold MJ, Britton HM, Lefebvre\nDL, Subbarao P, Mandhane P, Becker A, McNagny KM, Sears\nMR, Kollmann T, Investigators CS, Mohn WW, Turvey SE,\nFinlay BB (2015) Early infancy microbial and metabolic alterations\naffect risk of childhood asthma. Sci Transl Med 7(307):307ra152. https://doi.org/10.1126/scitranslmed.aab2271 36. Dramowski A, Madide A, Bekker A (2015) Neonatal nosocomial\nbloodstream infections at a referral hospital in a middle-income\ncountry: burden, pathogens, antimicrobial resistance and mortality. Paediatr Int Child Health:2046905515Y0000000029. https://doi. org/10.1179/2046905515Y.0000000029 37. Sharma D, Kumar C, Pandita A, Pratap OT, Dasi T, Murki S (2015)\nBacteriological profile and clinical predictors of ESBL neonatal\nsepsis. J Matern Fetal Neonatal Med:1–4. https://doi.org/10.3109/\n14767058.2015.1011118 27. Dedrick S, Sundaresh B, Huang Q, Brady C, Yoo T, Cronin C,\nRudnicki C, Flood M, Momeni B, Ludvigsson J, Altindis E\n(2020) The role of gut microbiota and environmental factors in type\n1 diabetes pathogenesis. Front Endocrinol (Lausanne) 11:78. https://doi.org/10.3389/fendo.2020.00078 38. Flannery DD, Akinboyo IC, Mukhopadhyay S, Tribble AC, Song\nL, Chen F, Li Y, Gerber JS, Puopolo KM (2020) Antibiotic suscep-\ntibility of Escherichia coli among infants admitted to neonatal in-\ntensive care units across the US from 2009 to 2017. JAMA Pediatr. https://doi.org/10.1001/jamapediatrics.2020.4719 p\ng\n28. Marild K, Ye W, Lebwohl B, Green PH, Blaser MJ, Card T,\nLudvigsson JF (2013) Antibiotic exposure and the development\nof coeliac disease: a nationwide case-control study. BMC\nGastroenterol 13:109. https://doi.org/10.1186/1471-230X-13-109 39. Bjorkman L, Ohlin A (2015) Scrubbing the hub of intravenous\ncatheters with an alcohol wipe for 15 sec reduced neonatal sepsis. Acta Paediatr 104(3):232–236. https://doi.org/10.1111/apa.12866 p\ng\n29. http://www.lakemedelsverket.se/ SMPa Neonatal sepsis- back-\nground information (Swedish) 40. Gray JW, Ubhi H, Milner P (2014) Antimicrobial treatment of\nserious gram-negative infections in newborns. Curr Infect Dis\nRep 16(2):400. https://doi.org/10.1007/s11908-014-0400-6 30. Magiorakos AP, Srinivasan A, Carey RB, Carmeli Y, Falagas ME,\nGiske CG, Harbarth S, Hindler JF, Kahlmeter G, Olsson-Liljequist\nB, Paterson DL, Rice LB, Stelling J, Struelens MJ, Vatopoulos A,\nWeber JT, Monnet DL (2012) Multidrug-resistant, extensively\ndrug-resistant and pandrug-resistant bacteria: an international ex-\npert proposal for interim standard definitions for acquired resis-\ntance. Clin Microbiol Infect 18(3):268–281. https://doi.org/10. 1111/j.1469-0691.2011.03570.x 41. Norman M, Kallen K, Wahlstrom E, Hakansson S, Collaboration\nSNQ (2019) The Swedish Neonatal Quality Register - contents,\ncompleteness and validity. Acta Paediatr 108(8):1411–1418. https://doi.org/10.1111/apa.14823 31. References Froding I, Hasan B, Sylvin I, Coorens M, Naucler P, Giske CG\n(2020)Extended-Spectrumbeta-Lactamase- and plasmid AmpC-\nproducing Escherichia coli causing community-onset bloodstream Publisher’s note Springer Nature remains neutral with regard to jurisdic-\ntional claims in published maps and institutional affiliations."
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Long memory estimation for complex-valued time series
Statistics and computing
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This is a repository copy of Long memory estimation for complex-valued time series. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/132566/ Version: Published Version Version: Published Version Article: Knight, Marina Iuliana orcid.org/0000-0001-9926-6092 and Nunes, Matthew A. (2018) Long memory estimation for complex-valued time series. Statistics and computing. pp. 1- 20. ISSN 0960-3174 https://doi.org/10.1007/s11222-018-9820-8 Reuse This article is distributed under the terms of the Creative Commons Attribution (CC BY) licence. This licence allows you to distribute, remix, tweak, and build upon the work, even commercially, as long as you credit the authors for the original work. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Abstract Long memory has been observed for time series across a multitude of fields, and the accurate estimation of such dependence, for example via the Hurst exponent, is crucial for the modelling and prediction of many dynamic systems of interest. Many physical processes (such as wind data) are more naturally expressed as a complex-valued time series to represent magnitude and phase information (wind speed and direction). With data collection ubiquitously unreliable, irregular sampling or missingness is also commonplace and can cause bias in a range of analysis tasks, including Hurst estimation. This article proposes a new Hurst exponent estimation technique for complex-valued persistent data sampled with potential irregularity. Our approach is justified through establishing attractive theoretical properties of a new complex-valued wavelet lifting transform, also introduced in this paper. We demonstrate the accuracy of the proposed estimation method through simulations across a range of sampling scenarios and complex- and real-valued persistent processes. For wind data, our method highlights that inclusion of the intrinsic correlations between the real and imaginary data, inherent in our complex-valued approach, can produce different persistence estimates than when using real-valued analysis. Such analysis could then support alternative modelling or policy decisions compared with conclusions based on real-valued estimation. Keywords Complex-valued time series · Hurst exponent · Irregular sampling · Long-range dependence · Wavelets Keywords Complex-valued time series · Hurst exponent · Irregular sampling · Long-range depen Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing eprints@whiterose.ac.uk including the URL of the record and the reason for the withdrawal request. eprints@whiterose.ac.uk https://eprints.whiterose.ac.uk/ eprints@whiterose.ac.uk https://eprints.whiterose.ac.uk/ eprints@whiterose.ac.uk https://eprints.whiterose.ac.uk/ Statistics and Computing https://doi.org/10.1007/s11222-018-9820-8 Marina I. Knight1 · Matthew A. Nunes2 Marina I. Knight1 · Matthew A. Nunes2 Received: 22 December 2017 / Accepted: 22 June 2018 © The Author(s) 2018 Received: 22 December 2017 / Accepted: 22 June 2018 © The Author(s) 2018 Received: 22 December 2017 / Accepted: 22 June 2018 © The Author(s) 2018 2 Department of Mathematics and Statistics, Fylde College, Lancaster University, Lancaster LA1 4YF, UK 1 Department of Mathematics, University of York, Heslington, York YO10 5DD, UK 1.1 Persistence in wind series Our motivating data example in this article arises from cli- matology. More specifically, wind series have been analysed extensively in the literature for modelling local weather pat- terns and spread of pollutants, as well as global climate dynamics. Long memory in wind series has been established by a number of authors; see, for example, Haslett and Raftery (1989), Chang et al. (2012) and Piacquadio and de la Barra (2014) and references therein. Specifically, Hurst exponent estimates for wind speed series on a range of sampling reso- lutions, including the 5min scale considered here, have been showntobeintherange0.7–0.9,indicatingstronglong-range dependence; see, for example, Fortuna et al. (2014). Accurate Hurst exponent estimation is used for accurate forecasting of wind speed, for example to assess future power yields (Haslett and Raftery 1989; Bakker and van den Hurk 2012). Our motivating data example in this article arises from cli- matology. More specifically, wind series have been analysed extensively in the literature for modelling local weather pat- terns and spread of pollutants, as well as global climate dynamics. Long memory in wind series has been established by a number of authors; see, for example, Haslett and Raftery (1989), Chang et al. (2012) and Piacquadio and de la Barra (2014) and references therein. Specifically, Hurst exponent estimates for wind speed series on a range of sampling reso- lutions, including the 5min scale considered here, have been showntobeintherange0.7–0.9,indicatingstronglong-range dependence; see, for example, Fortuna et al. (2014). Accurate Hurst exponent estimation is used for accurate forecasting of wind speed, for example to assess future power yields (Haslett and Raftery 1989; Bakker and van den Hurk 2012). Wind speed analysis in the literature is predominantly per- formed using real-valued data, such as (magnitude) wind speed series. However, more recently, a number of authors have advocated modelling wind measurements as complex- valued, developing analysis tools which exploit both speed and directional information of wind time series; see, for example, Goh et al. (2006) and Tanaka and Mandic (2007). These complex-valued modelling approaches have resulted in methodology for improved prediction for series such as those considered in this article (Mandic et al. 2009; Dowell et al. 2014). To our knowledge, long memory estimation for stationary time series is exclusively performed using real- valued time series. In this article, we analyse the degree of persistence (long memory intensity) exhibited by complex- valued wind measurements, i.e. 1 Introduction 2013; Rehman and Siddiqi 2009; Knight et al. 2017). The wind series we consider in this article consists of two datasets measured at a 5min resolution from the Iowa Depart- ment of Transport’s Automated Weather Observing System (AWOS). The (speed and angular) measurements for both datasets are available at http://mesonet.agron.iastate.edu/ AWOS/. We firstly analyse data obtained from the Atlantic Municipal Airport (AIO) monitoring site over a period from 15 April 2017 until 30 April 2017. Whilst the sampling inter- valforthemeasurementsisreportedas5min,duetoanumber of reasons, for example faulty recording devices, the data in fact feature missingness which results in a mix of sampling intervals—our first dataset has intervals ranging from 5 to 15min. Complex-valued processes, both proper (circular) and improper (noncircular), are relevant across fields such as oceanography and geophysics (Adali et al. 2011; Sykulski et al. 2017), where data are typically difficult to acquire and will frequently suffer from omissions/ missingness or be irregularly sampled (see, e.g. Fig. 1). In the next section, we describe datasets arising in environmental science that feature missing observations, which can be examined for long memory with a complex-valued representation. How- ever, we note here that data from other scientific areas may benefit from analysis with our proposed methodology; see Sect. 6 for further discussion. Since we have both speed and directional information for the dataset, we shall view the series using a complex-valued representation. The real and imaginary components of the series are shown in Fig. 1a, b, together with the locations of the missing data (depicted by triangles). The length of the first series is n = 3131 with an overall rate of miss- ingness of 12%. Similar datasets from the Iowa monitoring system have been previously studied in the literature for the non-missing case but not in the context of Hurst estimation; see, for example, Tanaka and Mandic (2007) and Adali et al. (2011). 1 Introduction aspect which has received recent attention is the property of impropriety or noncircularity, describing series whose statis- tics are not rotationally invariant in the complex plane [for a precise definition, the reader is directed to Sykulski and Percival (2016)]. Such models of improper processes have seen growing interest in the statistics community; see, for example, Schreier and Scharf (2003), Rubin-Delanchy and Walden (2008) and Mohammadi and Plataniotis (2015). Fur- thermore, complex-valued analysis of real-valued data has been shown to be beneficial in a number of settings; see, for example, Olhede and Walden (2005) and Hamilton et al. (2017). For a comprehensive introduction to complex-valued signals, we refer the reader to Schreier and Scharf (2010); see Adali et al. (2011) and Walden (2013) for recent advances in modelling complex-valued signals. Complex-valued time series arise in many scientific fields of interest, for example digital communication and signal processing (Curtis 1985; Martin 2004), environmental series (Gonella 1972; Lilly and Gascard 2006; Adali et al. 2011) and physiology (Rowe 2005). Modelling and analysis of such series in the complex domain is not only natural, but also convenient. In addition, complex-valued time series mod- els are often able to represent more realistic behaviour in observed physical processes; see, for example, Mandic and Goh(2009) andSykulski et al. (2017). Aparticular modelling Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11222-018-9820-8) contains supplementary material, which is available to authorized users. Recently, there has been an increased interest in models for complex-valued stochastic processes exhibiting long- range dependence (i.e. persistent) behaviour, which has seen extensions of real-valued process modelling frameworks for the complex-valued fractional Brownian motion (fBM) and Matérn processes, see, respectively, Coeurjolly and Porcu (2017) and Lilly et al. (2017), as well as for (improper) frac- tional Gaussian noise (Sykulski and Percival 2016). For these B Matthew A. Nunes m.nunes@lancaster.ac.uk Marina I. Knight Marina.Knight@york.ac.uk B Matthew A. Nunes m.nunes@lancaster.ac.uk Marina I. Knight Marina.Knight@york.ac.uk 12 3 3 Statistics and Computing speed and direction, using new complex-valued Hurst esti- mation methodology we propose here. constructions, just as for real-valued processes (Hurst 1951; Mandelbrot and Ness 1968), the degree of memory can still be quantified by means of a single parameter, the Hurst expo- nent parameter (Amblard et al. 2012; Sykulski and Percival 2016). Accurate estimation of the Hurst parameter offers valuable insight into a multitude of modelling and analysis tasks, such as model calibration and prediction (Beran et al. 1.1 Persistence in wind series series which have both wind To explore the potential persistence in wind series, we examine the autocorrelation in the real and imaginary parts of the series, shown in Fig. 2a, b for the Wind A series. For these data, both components show highly significant auto- correlation over a range of lags, indicating long memory. To further illustrate potential benefits of a more considered analysis approach for such data, we also investigate a dataset from the same monitoring site but for a different time peri- ods, specifically, 30 April 2017 until 14 May 2017. For this dataset, the majority of the data are observed at a spacing of 5min, but a significant amount have intra-measurement sampling between 10 and 20min resulting from a missing- ness proportion of 20%; the series is of length n = 2942. We have specifically chosen to examine this second time period due to its high degree of missingness. The two components of the complex-valued series can be seen in Fig. 1c, d (triangles indicate missing series values). Wind speed analysis in the literature is predominantly per- formed using real-valued data, such as (magnitude) wind speed series. However, more recently, a number of authors have advocated modelling wind measurements as complex- valued, developing analysis tools which exploit both speed and directional information of wind time series; see, for example, Goh et al. (2006) and Tanaka and Mandic (2007). These complex-valued modelling approaches have resulted in methodology for improved prediction for series such as those considered in this article (Mandic et al. 2009; Dowell et al. 2014). To our knowledge, long memory estimation for stationary time series is exclusively performed using real- valued time series. In this article, we analyse the degree of persistence (long memory intensity) exhibited by complex- valued wind measurements, i.e. series which have both wind Similar observations about potential long memory char- acteristics can be made for the second complex-valued wind series. In particular, both real and imaginary components of the series show considerable autocorrelation over a large range of lags (Fig. 2c, d). In addition, plotting the series in the complex plane, we see that both datasets exhibit a rotational behaviour, due to the angular component of the series (Fig. 3). 1.1 Persistence in wind series The series are not symmetric, exhibiting clear noncircularity, suggesting a model which allows for impropriety is appropriate for analy- 12 123 Statistics and Computing Statistics and Computing (a) (b) (c) (d) Apr 19 Apr 24 Apr 29 10 20 Time Wind Series (Real component) Apr 19 Apr 24 Apr 29 0 10 20 Time Wind Series (Imag. component) May 04 May 09 May 14 Time Wind Series (Real component) May 04 May 09 May 14 −30 −20 −10 0 −20 −10 −30 −20 −10 0 −30 −20 −10 0 10 20 10 20 Time Wind Series (Imag. component) Fig. 1 a Real component of the Wind A data series; b imaginary component of the Wind A data series; c real component of the Wind B data series; d imaginary component of the Wind B data series. Red triangles indicate missing data locations. (Color figure online) (b) Apr 19 Apr 24 Apr 29 0 10 20 Time Wind Series (Imag. component) −20 −10 (a) Apr 19 Apr 24 Apr 29 10 20 Time Wind Series (Real component) −30 −20 −10 0 (c) May 04 May 09 May 14 Time Wind Series (Real component) −30 −20 −10 0 10 20 (d) May 04 May 09 May 14 −30 −20 −10 0 10 20 Time Wind Series (Imag. component) (d) (c) Fig. 1 a Real component of the Wind A data series; b imaginary component of the Wind A data series; c real component of the Wind B data series; d imaginary component of the Wind B data series. Red triangles indicate missing data locations. (Color figure online) sis [for an in-depth discussion of these properties, the reader is directed to e.g. Sykulski and Percival (2016)]. This reflects similar observations on impropriety shown for other Iowa AWOS data in Adali et al. (2011), as well as other wind series (Mandic and Goh 2009). of information into a single, complex-valued series and anal- yse its properties (Mandic and Goh 2009). Adopting this approach thus calls for analysis techniques capable of dealing with complex-valued data. Additionally, for many applica- tions the process sampling structure is inherently irregular, as the two components may be measured at irregular times, or the data may be blighted by missingness due to measurement device failures. 1.1 Persistence in wind series In the real-valued case, the common prac- tice of preprocessing the data to mitigate against irregular or missing observations results in inaccuracies in long memory estimation by traditional methods. More specifically, there is now well-documented evidence that preprocessing by impu- tation or interpolation as well as data aggregation leads to 1.2 Aim and structure of the paper A feature of many geophysical series, such as described in Sect. 1.1, is that there is a need to jointly analyse both com- ponents of a bivariate signal in order to reveal a common behaviour. Due to the natural representation in the complex plane,onemathematicalsolutionistocombinethetwopieces 12 3 3 Statistics and Computing Statistics and Computing 0 20 40 60 80 100 0.0 0.2 0.4 0.6 0.8 1.0 Lag ACF (a) 0 20 40 60 80 100 0.0 0.2 0.4 0.6 0.8 1.0 Lag ACF (b) 0 20 40 60 80 100 0.0 0.2 0.4 0.6 0.8 1.0 Lag ACF (c) 0 20 40 60 80 100 0.0 0.2 0.4 0.6 0.8 1.0 Lag ACF (d) Fig. 2 a Autocorrelation for (a) the real component of the Wind A series from Fig. 1; b the imaginary component of the Wind A series; c the real component of the Wind B series from Fig. 1; and d the imagi- nary component of the Wind B series (all treated as regularly spaced). Both components of the two datasets show autocorrelation at large lags, indicating persistent behaviour 0 20 40 60 80 100 0.0 0.2 0.4 0.6 0.8 1.0 Lag ACF (a) 0 20 40 60 80 100 0.0 0.2 0.4 0.6 0.8 1.0 Lag ACF (b) 0 20 40 60 80 100 0.0 0.2 0.4 0.6 0.8 1.0 Lag ACF (c) 0 20 40 60 80 100 0.0 0.2 0.4 0.6 0.8 1.0 Lag ACF (d) (d) (c) Fig. 2 a Autocorrelation for (a) the real component of the Wind A series from Fig. 1; b the imaginary component of the Wind A series; c the real component of the Wind B series from Fig. 1; and d the imagi- nary component of the Wind B series (all treated as regularly spaced). Both components of the two datasets show autocorrelation at large lags, indicating persistent behaviour processes featuring regular or irregular sampling (including missingness). overestimation of persistence; see, for example, Beran et al. (2013), Zhang et al. (2014) or Knight et al. (2017). In practice, to the authors’ best knowledge, the only tech- nique that permits Hurst exponent estimation for complex- valuedprocessesisthatofCoeurjollyandPorcu(2017)which tackles the setting of regularly sampled (proper) complex- valued fractional Brownian motion. 1.2 Aim and structure of the paper Motivated by the serious implications of inaccurate estimation in the real-valued setting, in this work we propose the first methodologi- cal approach that answers the timely challenge of accurate assessment of long memory persistence for complex-valued At the heart of our methodology is a second generation wavelet-based approach. The reasoning behind this choice is twofold: (1) (classical) wavelets have proved to be very successful in the context of regularly sampled (real-valued) time series with long memory and are considered the ‘right domain’ of analysis (Flandrin 1998), and (2) for irregularly sampled (real-valued) processes, or those featuring missing- ness, the wavelet lifting algorithm of Knight et al. (2017) has provided a first long memory estimation solution and was 12 3 3 Statistics and Computing −20 −10 0 10 20 −10 0 10 20 Real component Imaginary component (a) −20 −10 0 10 20 −20 −15 −10 −5 0 5 10 Real component Imaginary component (b) Fig. 3 Scatter plot of real and imaginary series values for a the Wind A data and b the Wind B series shown in Fig. 1. Both series exhibit noncircular (improper) characteristics −20 −10 0 10 20 −20 −15 −10 −5 0 5 10 Real component Imaginary component (b) −20 −10 0 10 20 −10 0 10 20 Real component Imaginary component (a) (b) (a) Fig. 3 Scatter plot of real and imaginary series values for a the Wind A data and b the Wind B series shown in Fig. 1. Both series exhibit noncircular (improper) characteristics 2 Review of complex-valued processes, long-range dependence and wavelet lifting shown to yield competitive results even for regularly sam- pled data. The main contributions of the work in this paper are as follows. We propose (1) a novel lifting algorithm designed to work on complex-valued data with a potentially irregular sampling structure and (2) a Hurst parameter estimator for complex-valued processes sampled with a regular or irreg- ular structure. Our method will be shown to improve on real-valued Hurst estimation results, including for regularly spaced data. 2.1 Complex-valued processes Let us denote a (complex-valued) second-order stationary time series by {Xt} and its autocovariance function as γX(ti − t j) = E(Xti Xt j ), under the assumption that E(Xt) = 0 and denoting by ·p complex conjugation. As the autoco- variance function γX does not completely characterize a complex-valued time series, we also make use of its com- plementary or pseudo-covariance, rX(ti −t j) = E(Xti Xt j ), again assuming E(Xt) = 0. In general, both autocovariances are complex-valued and have the properties of Hermitian symmetry and symmetry, respectively [see, e.g. Sykulski and Percival (2016)]. The remainder of this article is organized as follows. We begin, in Sect. 2, by reviewing (complex-valued) long memory processes and giving an overview of wavelet lifting transforms. Section 3 introduces our novel complex-valued lifting transform, establishes its iterative bases construction and theoretical results on its decorrelation properties. Sec- tion 4 demonstrates how these properties can be exploited to design our proposed lifting-based Hurst exponent esti- mation procedure for complex-valued data sampled with irregularity/ missingness. Section 5.1 contains a simulation study evaluating the performance of our new method using synthetic data. In Sect. 5.2, we consider the application of our approach to the wind series datasets introduced in Sect. 1.1, discussing the potential consequences of our anal- ysis. Finally, Sect. 6 outlines some avenues of future work and discusses other potential applications. In many applications, such as radar and communications, processes are assumed to have the property that rX(·p) = 0 (Neeser and Massey 1993; Picinbono 1994; Adali et al. 2011); such processes are known as proper or circularly symmetric and are completely determined by their autoco- variance γX. In contrast, applications such as those described in Schreier and Scharf (2010), Adali et al. (2011) and Chandna and Walden (2017) deal with improper processes, whereby there exists a lag τ such that rX(τ) ̸= 0. Another often encountered property is that of time reversibility; for complex-valued processes, Didier and Pipiras (2011) have shown that time reversibility results in complex-valued pro- cesses with real-valued autocovariances, which is precisely the setting under which Sykulski and Percival (2016) develop 12 3 3 Statistics and Computing has long memory (−β = 2δ−3 = 2H −2 ∈(−1, 0); hence, 1/2 < H < 1). their exact simulation method for improper stationary Gaus- sian processes. 2.2 Long memory and its estimation Classical literature for long-range behaviour of real-valued processes shows that persistence is often characterized by a parameter, such as the Hurst exponent, H, introduced to the literature by Hurst (1951) in hydrology and its estima- tion is treated across a large body of established literature, for example Beran et al. (2013). Mandelbrot and Ness (1968) introduced self-similar and related processes with long memory, along with the associated statistical inference. Extensions of fractional Brownian motion to the complex- valued case, defined as a self-similar Gaussian process with stationary increments, are dealt with in, for example, Coeur- jolly and Porcu (2017) and Lilly et al. (2017). Put simply, the property of self-similarity amounts to the preservation of the process’ statistical properties in the face of rescaling, thus naturally fostering the definition of the Hurst exponent. Just as in the real-valued case, a complex-valued self- similar process {Xt} with parameter H satisfies X(at) d= aH X(t) for a > 0, H ∈(0, 1) and where d= means equal in distribution (Coeurjolly and Porcu 2017). Note that the self-similarity definition implies that both the real and imaginary strands of the complex-valued process {Xt} evolve according to the same exponent H. The property of self-similarity results into the fBM spectrum to behave as fX(ω) = A2|ω|−2δ for frequencies ω, a constant A and δ ∈(1/2, 3/2). The spectral slope parameter δ is linked to the aspect ratio of process rescaling for self-similar behaviour as H = δ −1/2 ∈(0, 1) and also determines the degree of persistence in the differenced version of the process, the frac- tional Gaussian noise (Lilly et al. 2017). An example of such a process is the improper fractional Gaussian noise with the pseudo-covariance proportional to the autocovariance (both real-valued), both proportional to τ 2δ−3 (Sykulski and Per- cival 2016; Lilly et al. 2017). 2.1 Complex-valued processes For real-valued time series, estimation of the Hurst expo- nent H traditionally takes place in the time domain (Mandel- brot and Taqqu 1979; Bhattacharya et al. 1983; Taqqu et al. 1995; Giraitis et al. 1999; Higuchi 1990; Peng et al. 1994) and/ or in the frequency domain by means of connections to Fourier or wavelet spectrum decay, for example Lobato and Robinson (1996), McCoy and Walden (1996), Whitcher and Jensen (2000) and Abry et al. (2013). Recent works that deal with long memory estimation in various settings are Vidakovic et al. (2000), Shi et al. (2005), Hsu (2006), Jung et al. (2010) and Coeurjolly et al. (2014). Some authors have recently considered Hurst estimation using complex- valued wavelets in the regularly spaced real-valued image context; see Nelson and Kingsbury (2010), Jeon et al. (2014) and Nafornita et al. (2014). Reviews comparing several tech- niques for Hurst exponent estimation (for real-valued series) can be found in, for example, Taqqu et al. (1995). Even when only considering real-valued data, Knight et al. (2017) show that methods designed for regularly spaced data often fail to deliver a robust estimate if the time series is subject to miss- ing observations or has been sampled irregularly, and in this context they propose a lifting-based approach for Hurst esti- mation. Whilst this approach serves well when the process is real-valued, it cannot cope with complex-valued processes. Coeurjolly and Porcu (2017) propose a method of estima- tion in the setting of (circular) complex-valued fractional Brownian motion assuming a regular sampling structure, but cannot readily cope with sampling irregularity or measure- ment dropout/ missingness. 2.3 Wavelet lifting paradigm for irregularly sampled real-valued data The lifting algorithm, first introduced by Sweldens (1995), constructs ‘second-generation’ wavelets adapted for non- standard data settings, such as intervals, surfaces, as well as irregularly spaced data. Lifting has since been used successfully for a variety of statistical problems dealing withreal-valuedsignals,includingnonparametricregression, spectral estimation and long memory estimation; see, for example, Trappe and Liu (2000), Nunes et al. (2006), Knight et al. (2012), Knight et al. (2017) and Hamilton et al. (2017). For a recent review of lifting, the reader is directed to Jansen and Oonincx (2005). Definition 1 (Lilly et al. 2017) A stationary (finite variance) complex-valued process {Xt} with real-valued autocovari- ance γX is said to have long memory if γX(τ) ∼cγ |τ|−β as |τ| →∞and β ∈(0, 1), where ∼means asymptotic equality. In other words, the process autocovariance displays long-term decay. Equivalently, the autocovariance Fourier pair, namely the spectral density, has the property that fX(ω) ∼c f |ω|−α for frequencies ω →0 and α ∈(0, 1) with α = 1−β = 2H −1. In general, if 0.5 < H < 1 the process exhibits long mem- ory, with higher H values indicating stronger dependence, whilst if 0 < H < 0.5 the process has short memory. An improper fractional Gaussian noise constructed as outlined above (Sykulski and Percival 2016) with 1 < δ < 3/2 thus As our proposed lifting transform and subsequent long memory estimation method both make use of a recently developed lifting transform, the lifting one coefficient at a time (LOCAAT) transform of Jansen et al. (2001), Jansen et al. (2009), we shall briefly introduce it next. Suppose a real-valued function f (·p) is observed at a set of n, possibly irregular, locations or time points, x = 123 123 Statistics and Computing (x1, . . . , xn) and is represented by {(xi, f (xi) = fi)}n i=1. The lifting algorithm of Jansen et al. (2001) begins with the f = ( f1, . . . , fn) values, known as scaling function val- ues, together with an interval associated with each location, xi, which represents the ‘span’ of that point. By performing LOCAAT, we aim to transform the initial f into a set of, say, L coarser scaling coefficients and (n −L) wavelet or detail coefficients, where L is a desired ‘primary resolution’ scale. This is achieved by repeating three steps: split, predict and update. In the algorithm of Jansen et al. 2.3 Wavelet lifting paradigm for irregularly sampled real-valued data (2001), the split step is performed by choosing a point to be removed (‘lifted’), jn, say. We denote this point by (x jn, f jn) and identify its set of neighbouring observations, In. The predict step estimates f jn by using regression over the neighbouring locations In. The prediction error (the difference between the true and predicted function values), d jn or detail coefficient, is then computed by An attractive feature of lifting schemes, including the LOCAAT algorithm, is that the transform can be inverted easily by reversing the split, predict and update steps. The current scarcity of Hurst estimation techniques for complex-valued processes, in a uniform, but even more so in a non-uniform sampling setting, and the effectiveness of the lifting transform in representing irregularly sampled infor- mation, jointly motivate our proposed approach to tackle this analysis problem: firstly we propose a novel lifting transform able to cope with irregularly sampled complex- valued processes, and secondly we construct a long memory estimator using the corresponding complex-valued lifting coefficients. Notably, the proposed method is suitable for regularly or irregularly sampled processes, both real- and complex-valued; in particular, Hurst estimation is addressed for improper complex-valued processes that have real-valued covariances, as introduced in Sykulski and Percival (2016), as well as for proper complex-valued series, as described in Coeurjolly and Porcu (2017). d jn = f jn −  i∈In an i fi, (1) (1) 3 A new lifting algorithm for complex-valued signals and its properties where (an i )i∈In are the weights resulting from the regres- sion procedure. For points with only one neighbour, the prediction is simply d jn = f jn −fi. This prediction via regression can of course be carried out using a variety of weights. Notably, Hamilton et al. (2017) proposed to use two (rather than just one) prediction filters and encompassed the detail information into complex-valued wavelet coeffi- cients. As more information was extracted from the signal, this approach was shown to improve results for nonparamet- ric regression and spectral/ coherence estimation settings, but nevertheless is limited to real-valued signals. The update step consists of updating the f -values of the neighbours of jn used in the predict step using a weighted proportion of the detail coefficient: In this section, we introduce our proposed lifting algorithm for a complex-valued function and establish its decorrelation properties. neighbours {sn,i} are updated according to filter L: removed first, but other predefined removal choices are also possible, as we shall discuss below. We shall often refer to the removal order as a trajectory, following Knight and Nason (2009). cn−1,i = cn,i + bn i λ jn, sn−1,i = sn,i + ln i sn, jn ∀i ∈Jn, (7) (7) Predict The set of neighbours (Jn) of the point jn is iden- tified. Note that the set of neighbours is indexed by n as the choice will depend on the removal stage (via the points remaining at that stage). The predict step estimates cn, jn = f jn by using regression over the neighbouring loca- tions Jn andtwopredictionschemes,astrategyfirstsuggested by Hamilton et al. (2017) for real-valued signals. Each pre- diction scheme is defined by its respective filter, L and M, orthogonal on each other. The filter L corresponds to the (possibly) linear regression choice as is usual in LOCAAT. The filter M is linked to L through a specific set of properties, discussed in detail in Hamilton et al. (2017) and described in step 2 of Algorithm 1. Both filters are constructed such that the corresponding wavelet coefficients of any constant poly- nomial are 0 (known in the wavelet literature, as possessing (at least) one vanishing moment). where bn i = (sn, jnsn−1,i)/( i∈Jn s2 n−1,i) are the update weights, again computed so that the mean of the signal is pre- served (Jansen et al. 2009). Updating the neighbours’ spans accounts for the modification to the sampling grid induced by removing one of the observations, and using just one filter for update [akin to the approach of Hamilton et al. (2017)] ensures the use of a common scale across both d(1) and d(2). The observation jn is then removed from the set of smooth coefficients; hence, after the first algorithm iteration, the index set of smooth coefficients is Sn−1 = {1, ..., n}\{ jn} and the index set of detail coefficients is Dn−1 = { jn}. The algorithm is then reiterated until the desired primary reso- lution level R has been achieved. In practice, the choice of the primary level R in LOCAAT lifting schemes is not cru- cial provided it is sufficiently low (Jansen et al. 2009), with R = 2 recommended by Nunes et al. (2006). neighbours {sn,i} are updated according to filter L: The prediction residuals following the use of each filter are given by The three steps are then repeated on the updated signal, and each repetition yields two new wavelet coefficients. After points jn, jn−1, . . . , jR+1 have been removed, the function can be represented as a set of 2 × (n −R) detail coefficients, {d(1) jk }k∈Dn−R and {d(2) jk }k∈Dn−R, and R smooth coefficients, {cr−1,i}i∈Sn−R, thus resulting in a redundant transform. An algorithmic description of C2-LOCAAT appears in Algo- rithm 1. λ jn = ln jncn, jn −  i∈Jn ln i cn,i, (3) μ jn = mn jncn, jn −  i∈Jn mn i cn,i, (4) (3) (4) where {ln i }i∈Jn∪{ jn} and {mn i }i∈Jn∪{ jn} are the prediction weights associated with filters L and M; as is typical in LOCAAT, we take ln jn = 1. The proposed algorithm can then be easily inverted by recursively ‘undoing’ the update, predict and split steps described above for the first filter (L). More specifically, the inverse transform can be performed by the steps jn Our proposal is to obtain two complex-valued detail (wavelet) coefficients by combining the two prediction resid- uals as follows: Undo Update cn,i = cn−1,i −bn i λ jn, ∀i ∈Jn te cn,i = cn−1,i −bn i λ jn, ∀i ∈Jn Undo Update cn,i = cn−1,i −bn i λ jn, ∀i ∈Jn d(1) jn = λ jn + i μ jn, (5) d(2) jn = λ jn −i μ jn. (6) (5) 3.1 Proposed C2-LOCAAT algorithm for complex-valued signals Suppose now a complex-valued function f (·p) is observed at a set of n, possibly irregular, locations or time points, x = (x1, . . . , xn) and is represented by {(xi, f (xi) = fi)}n i=1. Our proposed algorithm builds a redundant transform that starts with the complex-valued signal f = ( f1, . . . , fn) ∈ Cn and transforms it into a set of, say, R coarse (complex- valued) scaling coefficients and 2×(n−R) (complex-valued) detail coefficients, where R is the desired primary resolution scale. As is usual in lifting, our algorithm reiterates the three steps—split, predict and update—in a modified version, as described below. f (updated) i := fi + bn i d jn, i ∈In, (2) (2) where the weights (bn i )i∈In are subject to the constraint that the algorithm preserves the signal mean value (Jansen et al. 2001, 2009). The interval lengths associated with the neigh- bouring points are also updated to account for the effect of the removal of jn. In effect, this attributes a portion of the interval associated with the removed point to each neighbour. At the first stage (n) of the algorithm, denote the smooth coefficients as cn,k = fk, the set of indices of smooth coef- ficients by Sn = {1, . . . , n} and the set of indices of detail coefficients by Dn = ∅. The sampling structure is accounted for using the distance between neighbouring observations, and at stage n we define the span of xk as sn,k = xk+1−xk−1 2 . These split, predict and update steps are then repeated on the updated signal, and after each iteration a new wavelet coefficient is produced. Hence, after say (n −L) removals, the original data are transformed into L scaling and (n −L) wavelet coefficients. This is similar in spirit to the classical discrete wavelet transform (DWT) step which takes a signal vector of length 2ℓand through filtering operations produces 2ℓ−1 scaling and 2ℓ−1 wavelet coefficients. At the next stage (n−1), the proposed algorithm proceeds as follows: Split Choose a point to be removed and denote its index by jn. Typically, points from the densest sampled regions are 123 12 3 Statistics and Computing neighbours {sn,i} are updated according to filter L: neighbours {sn,i} are updated according to filter L: neighbours {sn,i} are updated according to filter L: Proposed C2-LOCAAT using two symmetrical neighbours: By construction, M is orthogonal on L, has at least one vanishing moment and ∥L∥= ∥M∥. Using M, obtain a new prediction residual, μ jn (see Eq. (4)). (b) Construct a new filter M = (Am, (1+ A)m, m) with A = l1−2 l1+1 and m = l1+1 √ 3 . By construction, M is orthogonal on L, has at least one vanishing moment and ∥L∥= ∥M∥. Using M, obtain a new prediction residual, μ jn (see Eq. (4)). p μjn q (c) The complex-valued wavelet (detail) coefficients at jn are d(1) jn = λ jn + i μ jn and d(2) jn = λ jn −i μ jn. jn (c) The complex-valued wavelet (detail) coefficients at jn are d(1) jn = λ jn + i μ jn and d(2) jn = λ jn −i μ jn. jn (c) The complex-valued wavelet (detail) coefficients at jn are d(1) jn = λ jn + i μ jn and d(2) jn = λ jn −i μ jn. 3. Update: the smooth coefficients and their associated scales using the filter L (see Eq. (7)). Update the index sets of smooth and detail coefficients as Sn−1 = Sn\{ jn} and Dn−1 = { jn}, respectively. 3. Update: the smooth coefficients and their associated scales using the filter L (see Eq. (7)). Update the index sets of smooth and detail coefficients as Sn−1 = Sn\{ jn} and Dn−1 = { jn}, respectively. 3. Update: the smooth coefficients and their associated scales using the filter L (see Eq. (7)). Update the index sets of smooth and detail coefficients as Sn−1 = Sn\{ jn} and Dn−1 = { jn}, respectively. 4. Iterate steps 1–3 for jn−1, . . . , jR+1 with a typical primary reso- lution level R = 2, hence obtain a set of complex-valued wavelet coefficients indexed by DR = { jn, ..., jR+1}. Alg. 1 The complex-valued lifting scheme (C2-LOCAAT) on a complex-valued signal matrix with complex-valued entries. When expressed as a matrix transform, our proposed C2-LOCAAT algorithm for a complex-valued process ( f ) can be expressed as Proposed C2-LOCAAT using two symmetrical neighbours: Proposed C2-LOCAAT using two symmetrical neighbours: Choose a removal order (trajectory), either dictated by the sampling sequence or following a random permutation. 1. Split: Choose the first/next point to be removed from the set of smooth coefficients Sn = {1, ..., n} and denote its index by jn. (a) Determine the set of neighbours Jn (one each side of jn) and use linear regression over the neighbourhood in order obtain a prediction at jn. Calculatethepredictionresidual,λ jn,asthedifferencebetween the observed and predicted values at jn (see Eq. (3)). This coupled with the requirement of achieving at least one vanish- ing moment amounts to obtaining a filter L = (l1, 1,l3) with l1 + l3 = 1. l 2 (a) Determine the set of neighbours Jn (one each side of jn) and use linear regression over the neighbourhood in order obtain a prediction at jn. Calculatethepredictionresidual,λ jn,asthedifferencebetween the observed and predicted values at jn (see Eq. (3)). This coupled with the requirement of achieving at least one vanish- ing moment amounts to obtaining a filter L = (l1, 1,l3) with l1 + l3 = 1. Choice of removal order The lifting algorithms in Sects. 2.3 and 3.1 are inherently dependent on the order in which points are removed as the algorithm progresses. Jansen et al. (2009) remove points in order from the finest continuous scale to the coarsest, to mimic the DWT, which produces coefficients at the finest scale first, then at progressively coarser scales. However, in our proposed C2-LOCAAT scheme, we can choose to remove points according to a predefined path (or trajectory) T = (xo1, . . . , xon), where (o1, o2, . . . , on) is a permutation of the set {1, . . . , n}. Knight and Nason (2009) introduced the nondecimated lifting transform, which pro- poses examining data using P bootstrapped paths from the space of n! possible trajectories. Aggregating the informa- tion obtained via this approach typically improves estimator variance and accuracy, not only in the long memory estima- tion context (Knight et al. 2017), but also for, for example nonparametric regression (Knight and Nason 2009). This strategy will be embedded in our proposed methodology in Sect. 4. (b) Construct a new filter M = (Am, (1+ A)m, m) with A = l1−2 l1+1 and m = l1+1 √ 3 . Undo Predict (6) cn, jn = λ jn − i∈Jn ln i cn,i ln jn or (8) cn, jn = μ jn − i∈Jn mn i cn,i mn jn . (9) (8) Note that if the original signal is real-valued, then d(2) = d(1) and all we need is d(1). However, when the process is complex-valued as is the case here, d(2) ̸= d(1) and we need bothd(1) andd(2).ThisisincontrasttoHamiltonetal.(2017), where the information from the two prediction schemes is corroborated into just one complex-valued wavelet coeffi- cient, and although its naive implementation on the real and imaginary process strands would yield two sets of complex- valued wavelet coefficients, it would not be obvious how to best combine their information. (9) Undoing either predict (8) or (9) step is sufficient for inver- sion. A few remarks on our proposed C2-LOCAAT lifting algo- rithm are now in order. Transform matrix representation As with any linear trans- form, the algorithm that determines one set of detail coef- ficients, say d(1), can also be represented using a matrix transform, i.e. d(1) = W (c) f , where W (c) is a n × n Update In the update step, both the (complex-valued) smooth coefficients {cn,i} and (real-valued) spans of the 123 Statistics and Computing the complex-valued wavelet coefficients produced using our C2-LOCAAT algorithm. An alternative is to group the coef- ficients via their interval lengths into ranges (2 j−1α0, 2 jα0], where j ≥1 and α0 is the minimum scale. This construc- tion more closely resembles classical wavelet dyadic scales, but both produce similar results. Note that by construction, the C2-LOCAAT transform crucially uses a common scale for both real and imaginary parts, and it is this feature that ensures that information is obtained on the same scale at every step. Proposed C2-LOCAAT using two symmetrical neighbours: 3.3 Decorrelation properties of the C2-LOCAAT algorithm with d(i) ℓ =< f , ˜ψ(i) ℓ > and c(i) r,k =< f , ˜ϕ(i) r,k > for both bases i = 1, 2, where the inner product is as usual defined on L2(C). As the update step is the same for both bases, it fol- lows that c(1) r,k = c(2) r,k. Hence, denote cr,k =< f , ˜ϕ(1) r,k >=< f , ˜ϕ(2) r,k >, for all r, k and thus the dual scaling functions coincide under both bases. In what follows, we shall denote these by ˜ϕr,k. with d(i) ℓ =< f , ˜ψ(i) ℓ > and c(i) r,k =< f , ˜ϕ(i) r,k > for both bases i = 1, 2, where the inner product is as usual defined on L2(C). As the update step is the same for both bases, it fol- lows that c(1) r,k = c(2) r,k. Hence, denote cr,k =< f , ˜ϕ(1) r,k >=< f , ˜ϕ(2) r,k >, for all r, k and thus the dual scaling functions coincide under both bases. In what follows, we shall denote these by ˜ϕr,k. Wavelet transforms are known to possess good decorrela- tion properties; see in the context of long memory processes, for example, Abry et al. (2000), Jensen (1999), Craigmile et al. (2001) for classical wavelets, and Knight et al. (2017) for lifting wavelets constructed by means of LOCAAT. The decorrelation property amounts to the consequent removal of the long memory in the wavelet domain, and thus esti- mation of the Hurst exponent can be carried out in this simplified context. Therefore, we next provide mathematical evidence for the decorrelation properties of the C2-LOCAAT algorithm and these will subsequently benefit our proposed long memory estimation procedure (see Sect. 4). The state- ment of Proposition 2 (next) aims to establish decorrelation results similar to earlier ones concerning regular wavelets (see, e.g. Abry et al (2000, p. 51) for fractional Gaussian noise, Jensen (1999, Theorem 2) for fractionally integrated processes or Theorem 5.1 of Craigmile and Percival (2005) for fractionally differenced processes) and lifting wavelets [see Proposition 1 in Knight et al. (2017)]. In what follows, we establish the decorrelation properties for the proposed complex-valued lifting transform C2-LOCAAT in a more general data setting than previously considered for lift- ing wavelets, involving complex-valued stationary processes with real-valued autocovariances that may be proper or improper in nature. where ˜ψ L denotes the dual wavelet function corresponding to the L-filter only. In our proposed construction, let us denote the two scaling function and wavelet biorthogonal bases by  ϕ(1), ˜ϕ(1), ψ(1), ˜ψ (1) and  ϕ(2), ˜ϕ(2), ψ(2), ˜ψ (2) , respectively. We now explore their relationships and recur- sive construction. The proof can be found in ‘Appendix A, Section A.1’. The proof can be found in ‘Appendix A, Section A.1’. Summarizing, the two bases can be represented as {ϕ(1), ˜ϕ, ψ(1), ˜ψ (1)} and {ϕ(1), ˜ϕ, ψ(1), ˜ψ (2)} and their recursive construction established above will be used in obtaining the formal properties required to justify our pro- posed long memory estimation approach. At stage r, the complex-valued signal f can be decom- posed on each basis as f (x) =  ℓ∈Dr d(i) ℓψ(i) ℓ(x)+  k∈Sr c(i) r,kϕ(i) r,k(x), i = 1, 2, (12) 3.3 Decorrelation properties of the C2-LOCAAT algorithm Proposition 1 Suppose we are at stage r −1 of the C2- LOCAAT algorithm. The recursive construction of the primal scaling and wavelet functions corresponding to the coeffi- cients d(1), in terms of the functions at the previous stage r, is given by ϕ(1) r−1, j(x) = ϕ(1) r, j(x) + ˜ar jϕ(1) r, jr (x), if j ∈Jr, (13) ϕ(1) r−1, j(x) = ϕ(1) r, j(x), if j /∈Jr, (14) ψ(1) jr (x) = ar jr |ar jr |2 ϕ(1) r, jr (x) −  j∈Jr br jϕ(1) r−1, j(x), (15) (13) (14) (15) where ar j = ℓr j + i mr j and ˜ar j = ar jr ar j |ar jr |2 . jr Similarly, the recursive construction for the primal scaling and wavelet functions corresponding to the coefficients d(2), in terms of the functions at the previous stage r, is given by ϕ(2) r−1, j(x) = ϕ(2) r, j(x) + ˜a r jϕ(2) r, jr (x), if j ∈Jr, (16) ϕ(2) r−1, j(x) = ϕ(2) r, j(x), if j /∈Jr, (17) ψ(2) jr (x) = ar jr |ar jr |2 ϕ(2) r, jr (x) −  j∈Jr br jϕ(2) r−1, j(x). (18) (16) (16) Proposition 2 Let X = {Xti }N−1 i=0 denote a (zero-mean) stationary long memory complex-valued time series with Lipschitz continuous spectral density fX. Assume the pro- cess is observed at irregularly spaced times {ti}N−1 i=0 , and let {{cR,i}i∈{0,...,N−1}\{ jN−1,..., jR−1}, {d jr }N−1 r=R−1} be the C2- LOCAAT transform of X, where d jr = d(1) jr d(2) jr T . Then, both sets of detail coefficients {d(1) jr }r and {d(2) jr }r have auto- correlation and pseudo-autocorrelation whose magnitudes decay at a faster rate than for the original process. Proposition 2 Let X = {Xti }N−1 i=0 denote a (zero-mean) stationary long memory complex-valued time series with Lipschitz continuous spectral density fX. Assume the pro- cess is observed at irregularly spaced times {ti}N−1 i=0 , and let {{cR,i}i∈{0,...,N−1}\{ jN−1,..., jR−1}, {d jr }N−1 r=R−1} be the C2- LOCAAT transform of X, where d jr = d(1) jr d(2) jr T . Then, both sets of detail coefficients {d(1) jr }r and {d(2) jr }r have auto- correlation and pseudo-autocorrelation whose magnitudes decay at a faster rate than for the original process. 3.2 Refinement equations for the scaling and wavelet functions under C2-LOCAAT d =  W (c) W (c)  f (10) =  d(1) d(2)  , (11) with d(1) = W (c) f and d(2) = W (c) f . d =  W (c) W (c)  f (10) =  d(1) d(2)  , (11) Although not explicitly apparent, the wavelet lifting con- struction induces a biorthogonal (second generation) wavelet basis construction; see, for example Sweldens (1995). In the real-valued lifting one coefficient at a time paradigm, as the algorithm progresses, scaling and wavelet functions decomposing the frequency content of the signal are built recursively according to the predict and update Eqs. (1) and (2) (Jansen et al. 2009). Also, the (dual) scaling func- tions are defined recursively as linear combinations of (dual) scaling functions at the previous stage. (10) (11) with d(1) = W (c) f and d(2) = W (c) f . with d(1) = W (c) f and d(2) = W (c) f . with d(1) = W (c) f and d(2) = W (c) f . Wavelet lifting scales and artificial levels The (log2) span associated with an observation at the last stage before its removal, say log2(sk, jk) for the detail coefficient d jk obtained at stage k, is used as a (continuous) measure of scale—this indirectly stems from the fact the wavelets are not dyad- ically scaled versions of a single mother wavelet. As the notion of scale of lifting wavelets is continuous, Jansen et al. (2009) group wavelet functions of similar (continu- ous) scales into ‘artificial’ levels, to mimic the dyadic levels of classical wavelets [see Jansen et al. (2001), Jansen et al. (2009) for more details]. We also adopt this strategy to group Let us now investigate the basis decomposition afforded by our proposed C2-LOCAAT transform, as a result of performing the split, predict and update steps. As our con- struction involves two prediction filters, we decompose f on two biorthogonal bases. Our construction is reminiscent of the dual-tree complex wavelet transform (CWT) (Kingsbury 2001;Selesnicketal.2005)whichemploystwoseparateclas- sical wavelet transforms, but fundamentally differs through the construction of linked orthogonal filters. 123 12 3 3 Statistics and Computing where ˜ψ L denotes the dual wavelet function corresponding to the L-filter only. where ˜ψ L denotes the dual wavelet function corresponding to the L-filter only. 4 Long memory parameter estimation using complex wavelet lifting (CLoMPE) j jr jr 2. Normalize both sets of (complex-valued) detail coefficients by their corresponding C-modulus: divide each squared (C) modulus by the corresponding diagonal entry of W (c)W (c),T , where W (c) is the complex-valued lifting transform matrix corresponding to d(1). j jr jr 2. Normalize both sets of (complex-valued) detail coefficients by their corresponding C-modulus: divide each squared (C) modulus by the corresponding diagonal entry of W (c)W (c),T , where W (c) is the complex-valued lifting transform matrix corresponding to d(1). As the newly constructed wavelet domain through C2- LOCAAT displays small magnitude autocorrelations, we now focus on the wavelet coefficient variance and show that the log2-variance of each of the complex-valued lifting coef- ficients d(1) and d(2) is linearly related to their corresponding artificial scale level, a result paralleling classical and real- valued lifting wavelet results. This result suggests a Hurst parameter estimation method for potentially irregularly sam- pled long memory processes that take values in the complex (C) domain. 3. Group the coefficients into a set of artificial scales as described in Sect. 2.3. Estimate the wavelet energy within the artificial level j⋆ by 3. Group the coefficients into a set of artificial scales as described in Sect. 2.3. Estimate the wavelet energy within the artificial level j⋆ by ˆσ (ℓ) j⋆ 2 := (n j⋆−1)−1 n j⋆  r=1 |d(ℓ) jr |2, for each ℓ= 1, 2, (24) (24) where n j⋆is the number of observations in artificial level j⋆. Note that the C2-LOCAAT construction, by its use of an unique update step, ensures that the number of observations in each j⋆artificial level coincides for both ℓ= 1 and ℓ= 2. 2 4. Fit a weighted linear regression to all points log2 ˆσ (ℓ) j⋆ 2 with ℓ= 1, 2 versus j⋆; use its slope to estimate α as suggested by the results in Proposition 3. Note that Eq. (23) allows us to pull the information across both d(1) and d(2). Proposition 3 next establishes a result similar to that in Proposition 2 of Knight et al. (2017) by taking into account the specific C2-LOCAAT construction and thus extends the scope of Hurst estimation methodology to irregularly sam- pled complex-valued processes. 5. Iterate steps A-1 to A-4 for P bootstrapped trajectories, obtaining an estimate ˆαp for each trajectory p ∈1, P. 3.3 Decorrelation properties of the C2-LOCAAT algorithm (17) (18) For the corresponding dual bases, the recursive construc- tions are given by ˜ϕr−1, j(x) = ˜ϕr, j(x) + br j ˜ψ L jr (x), ∀j ∈Jr, (19) ˜ϕr−1, j(x) = ˜ϕr, j(x), ∀j /∈Jr, (20) ˜ψ(1) jr (x) = ar jr ˜ϕr, jr (x) −  j∈Jr ar j ˜ϕr, j(x), (21) ˜ψ(2) jr (x) = ar jr ˜ϕr, jr (x) −  j∈Jr ar j ˜ϕr, j(x), (22) ˜ϕr−1, j(x) = ˜ϕr, j(x) + br j ˜ψ L jr (x), ∀j ∈Jr, (19) ˜ϕr−1, j(x) = ˜ϕr, j(x), ∀j /∈Jr, (20) ˜ψ(1) jr (x) = ar jr ˜ϕr, jr (x) −  j∈Jr ar j ˜ϕr, j(x), (21) ˜ψ(2) jr (x) = ar jr ˜ϕr, jr (x) −  j∈Jr ar j ˜ϕr, j(x), (22) Theproofcanbefoundin‘AppendixA,SectionA.2’anduses similar arguments to the proof of Proposition 1 in Knight et al. (2017), adapted for the C2-LOCAAT algorithm and complex-valuedsettingweaddresshere.JustasforLOCAAT Statistics and Computing (Knight et al. 2017), Proposition 2 above assumes no spe- cific lifting wavelet and we conjecture that if smoother lifting wavelets were employed, it might be possible to obtain even better rates of decay. Assume that {Xti }N−1 i=0 is as in Proposition 3. We estimate α as follows. 1. Apply C2-LOCAAT to the complex-valued observed process {Xti }N−1 i=0 using a particular lifting trajectory to obtain the coef- ficients {d jr = d(1) jr d(2) jr T }r; see Eq. (10). 4 Long memory parameter estimation using complex wavelet lifting (CLoMPE) The final estimator is ˆα = P−1 P p=1 ˆαp, from which an appropriate estimate for H can be obtained. Proposition 3 Let X = {Xti }N−1 i=0 denote a (zero-mean) complex-valued long memory stationary time series with finite variance and spectral density fX(ω) ∼c f |ω|−α as ω →0, for some α ∈(0, 1). Assume the series is observed at irregularly spaced times {ti}N−1 i=0 , and transform the observed data X into a collection of lifting coefficients, {d(1) jr }r and {d(2) jr }r, via application of C2-LOCAAT from Sect. 3.1. be obtained. Alg. 2 The long memory parameter estimation procedure (CLoMPE) for a complex-valued process {Xti }N−1 i=0 , sampled at potentially irregu- larly spaced times Alg. 2 The long memory parameter estimation procedure (CLoMPE) for a complex-valued process {Xti }N−1 i=0 , sampled at potentially irregu- larly spaced times 1 We would like to thank Adam Sykulski for supplying the Matlab code to simulate the improper complex fractional Gaussian noise pro- cesses. 5 Simulated performance of CLoMPE and real data analysis j Let r denote the stage of C2-LOCAAT at which we obtain the wavelet coefficients d(ℓ) jr (with ℓ= 1, 2), and let its cor- responding artificial level be j⋆. Then, denoting by | · p| the C-modulus, we have for some constant K Alg. 2 The long memory parameter estimation procedure (CLoMPE) for a complex-valued process {Xti }N−1 i=0 , sampled at potentially irregu- larly spaced times 5.1 Simulated performance of CLoMPE In what follows, we investigate the performance of our Hurst parameter estimation technique for complex-valued series. We simulated realizations of two types of long memory processes, namely circularly symmetric complex fractional Brownian motion, as introduced in Coeurjolly and Porcu (2018), and improper complex fractional Gaussian noise (with real-valued covariances) as described in Sykulski and Percival (2016),1 investigating series of lengths of 256, 512 and 1024. These lengths were chosen to reflect realistic data collection scenarios—long enough for the Hurst parameter (a low-frequency asymptotic quantity) to be reasonably esti- (σ (ℓ) j⋆)2 = E |d(ℓ) jr |2 ∼2 j⋆(α−1) × K. (23) (23) (23) The proof can be found in ‘Appendix A, Section A.3’. This result suggests a long memory parameter estimation method for an irregularly sampled, complex-valued time series, described in Algorithm 2, which we shall refer to as CLoMPE (Complex-valued Long Memory Parameter Esti- mation Algorithm). Section 5.1, next, will show that our proposed CLoMPE methodology below not only adds a new much needed tool in the estimation of long memory for complex-valued processes, but also improves Hurst exponent estimation for real-valued processes, sampled both regularly and irregularly. The proof can be found in ‘Appendix A, Section A.3’. This result suggests a long memory parameter estimation method for an irregularly sampled, complex-valued time series, described in Algorithm 2, which we shall refer to as CLoMPE (Complex-valued Long Memory Parameter Esti- mation Algorithm). Section 5.1, next, will show that our proposed CLoMPE methodology below not only adds a new much needed tool in the estimation of long memory for complex-valued processes, but also improves Hurst exponent estimation for real-valued processes, sampled both regularly and irregularly. 12 3 Statistics and Computing performs only slightly worse in terms of bias when compared to the ‘CP’ method. performs only slightly worse in terms of bias when compared to the ‘CP’ method. mated, whilst reflecting lengths of datasets encountered in practice. To investigate the effect of sampling irregularity on the performance of our method, we simulated datasets with dif- ferent levels of random missingness (5–20%), which are representative of degrees of missingness reported in many application areas, for example in paleoclimatology and envi- ronmental series (Broersen 2007; Junger and Ponce de Leon 2015). Real-valued processes To assess whether our complex- valued approach achieves performance gains for real-valued processes, we repeated the simulation study from Knight et al. (2017) for a number of long memory processes. In particular, we studied the performance of our estimator for real-valued fractional Brownian motion, fractional Gaussian noise and fractionally integrated series, for a range of Hurst parameters and levels of missingness. The processes were simulated via the fArma add-on package (Wuertz et al. 2013). We compare our method with the real-valued lifting tech- nique of Knight et al. (2017), shown to perform well in a number of settings. Again, for brevity, we do not report these bias results here, but they can be found in Appendix B in the supplementary material. 2 The authors would like to thank Jean-François Coeurjolly for provid- ing the R code for simulating the circular fractional Brownian motion series, as well as for the implementation of the estimation technique of Coeurjolly and Porcu (2017). (23) The results show that our method is competitive with the real-valued estimation method in Knight et al. (2017), achieving better results (in terms of MSE and bias) in the majority of cases for fractional Gaus- sian noise and fractionally integrated series. For fractional Brownian motion, we observe that our method achieves gains in mean square error, albeit at a cost of a decrease in bias performance. These results agree with other studies using complex-valued wavelet methodology, which is shown to outperform its real-valued counterpart in a variety of appli- cations, from denoising (Barber and Nason 2004 to Hurst estimation in the (real-valued) image context (Nelson and Kingsbury 2010; Jeon et al. 2014; Nafornita et al. 2014). This is due to the use of two rather than just one filter, thus eliciting more information from the signal under analysis. We compared results across the range of Hurst parameters H = 0.6, . . . , 0.9. Each set of results is taken over K = 100 realizations and P = 50 lifting trajectories. Our CLoMPE technique was implemented using modifications to the code fromthe liftLRD package(Knight andNunes2016) andCNL- Treg package (Nunes and Knight 2017) for the R statistical programming language (R Core Team 2013), both available on CRAN. The measure we use to assess the performance of the methods is the mean squared error (MSE) defined by MSE = K −1 K  k=1 (H −ˆHk)2. (25) (25) In the case of regularly spaced circularly symmetric frac- tional Brownian motion (i.e. 0% missingness), we compare our CLoMPE estimation technique with the recent estima- tion method in Coeurjolly and Porcu (2017) (denoted ‘CP’).2 Table 1 reports the mean squared error for our CLoMPE estimator on the complex-valued fractional Brownian motion series for different degrees of missingness (0% up to 20%). In the case of regularly spaced series, our estimation method works well when compared to the ‘CP’ method. This is pleas- ing since the “CP” method is designed for regularly spaced series, whereas CLoMPE is specifically designed for irreg- ularly spaced series. The tables also show that the CLoMPE technique is robust to the presence of missingness, attain- ing good performance even for high degrees of missingness (20%). 5.2 Analysis of complex-valued wind series with CLoMPE Boxed num- H n = 256 n = 512 n = 1024 Missingness proportion, p Missingness proportion, p Missingness proportion, p CP CLoMPE CP CLoMPE CP CLoMPE 0% 0% 5% 10% 20% 0% 0% 5% 10% 20% 0% 0% 5% 10% 20% 0.6 2 (3) 1 (2) 1 (2) 1 (1) 2 (3) 1 (2) 1 (1) 0 (0) 0 (1) 1 (1) 1 (1) 1 (1) 0 (0) 0 (0) 0 (0) 0.7 2 (3) 1 (2) 1 (1) 1 (2) 2 (3) 1 (1) 1 (1) 1 (1) 1 (1) 1 (1) 0 (1) 2 (1) 1 (1) 1 (1) 0 (0) 0.8 3 (3) 2 (2) 2 (2) 1 (2) 2 (2) 1 (2) 2 (2) 1 (2) 1 (2) 1 (2) 1 (1) 3 (2) 2 (2) 2 (1) 1 (1) 0.9 2 (3) 3 (4) 2 (3) 2 (3) 2 (2) 1 (2) 2 (2) 2 (3) 2 (2) 2 (2) 2 (2) 2 (2) 3 (2) 3 (2) 2 (2) Table 2 Mean squared error (×103) for fractional Gaussian noise featuring different degrees of missing observations for a range of Hurst parameters for the CLoMPE estimation procedure. Numbers in brackets are the estimation errors’ standard deviation H n = 256 n = 512 n = 1024 Missingness proportion, p Missingness proportion, p Missingness proportion, p 0% 5% 10% 20% 0% 5% 10% 20% 0% 5% 10% 20% 0.6 1 (2) 1 (2) 1 (2) 2 (2) 1 (1) 1 (1) 1 (1) 1 (1) 1 (1) 1 (1) 1 (1) 1 (1) 0.7 1 (2) 2 (2) 2 (2) 2 (3) 1 (1) 2 (2) 2 (2) 3 (2) 2 (1) 2 (1) 2 (1) 3 (2) 0.8 2 (2) 2 (3) 2 (3) 3 (5) 2 (2) 3 (3) 3 (3) 4 (4) 2 (2) 3 (2) 3 (2) 5 (3) 0.9 3 (4) 3 (3) 3 (3) 3 (5) 2 (2) 2 (3) 3 (3) 3 (3) 2 (2) 3 (2) 3 (2) 4 (3) ory parameter for this series is more reliable than that in the currently existing literature, as our proposed algorithm nat- urally encompasses both the complex-valued and improper features of wind series. A complex-valued analysis using our approach could hence provide more accurate long memory information, reducing miscalibration of predictive climate models. 5.2 Analysis of complex-valued wind series with CLoMPE In this section, we provide a more detailed long memory anal- ysis of the complex-valued wind series described in Sect. 1.1. More specifically, we applied our CLoMPE Hurst estimation method to the (detrended) irregularly sampled wind series to assess its persistence properties. The estimated Hurst param- eter was ˆHC = 0.86 for the Wind A series and ˆHC = 0.8 for the Wind B series, based on P = 50 lifting trajectories. Both of these estimates indicate moderate long memory. For the complex-valued fractional Gaussian noise, Table 2 demonstrates that our CLoMPE estimation technique per- formswellforregularandirregularsettings,withonlyaslight degradation in performance for increasing missingness. We also studied the empirical bias of our estimator for both types of long memory process. For reasons of brevity, we do not report these results here, but these can be found in Appendix B in the supplementary material. As for the mean squared error results above, there is a small drop in performance with increasing missingness, and our estimator To highlight potential differences with other approaches, we also performed the LoMPE technique of Knight et al. (2017) to each of the real and imaginary components of the two series. In addition, we also estimated the Hurst exponent using the Knight et al. (2017) method for the two magnitude series, since such series (i.e. data without directional infor- mation) are most commonly analysed in the literature. The Hurst exponent estimates are denoted by ˆHR and ˆHI for the real and imaginary component series, and ˆHMod for the magnitude series. The estimates are summarized in Table 3. 12 3 Statistics and Computing bers indicate best result for the regularly spaced setting. Numbers in brackets are the estimation errors’ standard deviation Table 1 Mean squared error (×103) for fractional Brownian motion series featuring different degrees of missing observations for a range of Hurst parameters for the CLoMPE estimation procedure. 5.2 Analysis of complex-valued wind series with CLoMPE We further suggest that this precision would provide more certainty when assessing renewable energy resource potential, as discussed in, for example, Bakker and van den Hurk (2012). Table 3 Hurst parameter estimates for the Wind A and Wind B data from complex-valued series using CLoMPE and from real-valued com- ponent and magnitude series using LoMPE Table 3 Hurst parameter estimates for the Wind A and Wind B data from complex-valued series using CLoMPE and from real-valued com- ponent and magnitude series using LoMPE Dataset R I Mod C Wind A 0.90 0.82 0.80 0.86 Wind B 0.85 0.75 0.80 0.80 For the Wind A dataset, our CLoMPE technique esti- mates the persistence as between those of the real and imaginary components, and higher than that of the magnitude series. In contrast, for the Wind B dataset, the estimate from our complex-valued approach coincides with the result for the series derived from the C-modulus. This analysis high- lights that ignoring the dependence structure between the real and imaginary components of the series may result in mis- estimation. Hence, we recommend an approach that uses the complex-valued structure of the data, thus accounting for its intrinsic rotary structure and dependence, not visible by only using the traditional magnitude series or individual real and imaginary strands. 6 Discussion 2 (b) (a) The dependence structure is markedly different to that shown for the real and imaginary series components shown in Fig. 2 Fig. 4 a Autocorrelation for the magnitude wind series for the Wind A series from Fig. 1 (treated as regularly spaced); b autocorrelation for the magnitude Wind B dataset from Fig. 1 (treated as regularly spaced). sition and data richness; see, for example, Aston and Kirch (2012) for an accessible introduction to the area from the sta- tistical perspective. In particular, fMRI studies often measure information on blood flow in the brain; these voxel-level data are used to investigate neuronal activity of participants dur- ing task-based experiments, and many authors have asserted that such time courses possess fractional noise structure, see, for example, Bullmore et al. (2003). Evaluation of the Hurst exponent in this context has been shown to be important in characterizingbrainactivityunderarangeofconditions,indi- cating different levels of cognitive effort (Park et al. 2010; Ciuciu et al. 2012; Churchill et al. 2016). Despite data col- lection being performed in a controlled set-up, recent work has highlighted the need for tailored statistical methodology to cope with both unbalanced designs, as well as miss- ingness, which can feature in fMRI data for a number of reasons (Lindquist 2008; Ferdowsi and Abolghasemi 2018). In actuality, fMRI scanners record both phase and magni- tudeinformation,thoughmoststudiesonlyusethemagnitude image for analysis. As a result, there has been a recent body of work dedicated to complex-valued analysis of fMRI data, most notably by Rowe and collaborators [see, e.g. Rowe (2005) and Rowe (2009) and Adrian et al. (2018)]. Such an approach has shown improvements over real-valued methods for a range of analysis tasks; see also the work by Adali and collaborators (Calhoun et al. 2002; Li et al. 2011; Rodriguez et al. 2012). Thus, our methodology has the potential of tak- ing advantage of the full complex-valued image information whilst also coping with the inherent non-uniform sampling. methods have not been able to exploit the wealth of signal information in such data, whilst also coping with irregular sampling regimes. Our CLoMPE wavelet lifting methodol- ogy was shown to give accurate Hurst estimation for a variety of complex-valued fractional processes and is suitable for both proper and improper complex-valued processes. Simu- lations demonstrate that the technique is robust to estimation with significant degrees of missingness, as well as in the non-missing (regular) setting. 6 Discussion Hurst exponent estimation is a recurrent topic in many scientific applications, with significant implications for mod- elling and data analysis. One important aspect of real-world datasets is that their collection and monitoring are often not straightforward, leading to missingness, or to the use of prox- ies with naturally irregular sampling structures. In parallel, in many applications of interest there is a natural complex- valued representation of data. To this end, this article has proposed the first Hurst estimation technique for complex- valued processes with sampling missingness or irregularity, and in doing so it has also constructed a novel lifting algo- rithm able to work on complex-valued data sampled with irregularity. Until the work in this article, Hurst estimation It could also be argued that these differences in esti- mates are unsurprising, since the dependence structure for the magnitude series, shown in Fig. 4, is visibly different to that of the real and imaginary component series shown in Fig. 2. We argue that our estimation of the long mem- 12 3 Statistics and Computing 0 20 40 60 80 100 0.0 0.2 0.4 0.6 0.8 1.0 Lag ACF (a) Fig. 4 a Autocorrelation for the magnitude wind series for the Wind A series from Fig. 1 (treated as regularly spaced); b autocorrelation for the magnitude Wind B dataset from Fig. 1 (treated as regularly spaced). 0 20 40 60 80 100 0.0 0.2 0.4 0.6 0.8 1.0 Lag ACF (a) 0 20 40 60 80 100 −0.2 0.0 0.2 0.4 0.6 0.8 1.0 Lag ACF (b) Fig. 4 a Autocorrelation for the magnitude wind series for the Wind A series from Fig. 1 (treated as regularly spaced); b autocorrelation for the magnitude Wind B dataset from Fig. 1 (treated as regularly spaced). The dependence structure is markedly different to that shown for the real and imaginary series components shown in Fig. 2 0 20 40 60 80 100 −0.2 0.0 0.2 0.4 0.6 0.8 1.0 Lag ACF (b) The dependence structure is markedly different to that shown for the real and imaginary series components shown in Fig. 2 0 20 40 60 80 100 0.0 0.2 0.4 0.6 0.8 1.0 Lag ACF (a) 0 20 40 60 80 100 −0.2 0.0 0.2 0.4 0.6 0.8 1.0 Lag ACF (b) The dependence structure is markedly different to that shown for the real and imaginary series components shown in Fig. 123 6 Discussion We have demonstrated the use of our CLoMPE tech- nique in an application arising in environmental science. Through our analysis of wind speed data, we have shown that embedding directional wind information in the analysis can lead to significantly different Hurst exponent estimates when compared to only considering real-valued information, such as magnitude series. This highlights that not exploiting a complex-valued data representation in this setting can poten- tially result in misleading conclusions being drawn about wind persistence. This in turn has a subsequent impact on parameters in climate models and inefficiencies in resource management decisions. Whilst the development of our proposed complex-valued Hurst estimator was motivated by an application in climatol- ogy, we believe that the work in this article has sufficient generality to have appeal in other settings. We thus con- clude this article with outlining some example applications in which our methodology is potentially beneficial. Data from neuroimaging studies Functional magnetic reso- nance imaging (fMRI) data continue to enjoy popularity in the neuroscience community due to their non-invasive acqui- 123 Statistics and Computing  k∈Sn cn,kϕ(1) n,k(x) with ϕ(1) n,k(x) = χIn,k(x) as proposed in the LOCAAT construction (Jansen et al. 2009). (1) (1) Ocean surface measurement devices There is a long-standing history of studying ocean circulation using GPS-tracked oceanbuoydrifters,seee.g.Osborneetal.(1989).Sincethese trajectories are measured in the longitude-latitude plane, they are often converted to complex-valued vector series; see, for example, Sykulski et al. (2017). It has long been observed that due to the buffeting motion of ocean currents, posi- tional drifter trajectories often exhibit fBM-like behaviour, whilst their velocity over time resembles fGn characteris- tics (Sanderson and Booth 1991; Summers 2002; Qu and Addison 2010; Lilly et al. 2017). In this context, accurate Hurst exponent estimation is useful in indicating the inten- sity of ocean turbulence, giving evidence towards particular theorized dynamical regimes (Osborne et al. 1989). These in turn can provide insight into initial conditions and origin of ocean circulation. Moreover, the trajectories often display rotary characteristics (Elipot and Lumpkin 2008; Elipot et al. 2016). Due to the interrupted nature of satellite coverage and thepossibilityofmeasurementsfrommultiplesatelliteorbits, the temporal sampling of the trajectories are typically highly non-uniform. In addition, due to the irregular sampling struc- ture, the data are often interpolated prior to analysis (Elipot et al. 2016). 6 Discussion (28) (27) (28) For the primal wavelet function construction, we can sim- ilarly take f (x) := ψ(1) jn (x) and obtain the corresponding wavelet decomposition with coefficients d(1) jn = 1 (thus λ jn = 1 and μ jn = 0) and cn−1,k = 0, ∀k ̸= jn. From the update equations, we have cn, j = −bn j, ∀j ∈Jn and cn, j = 0, ∀j /∈Jn. For the primal wavelet function construction, we can sim- ilarly take f (x) := ψ(1) jn (x) and obtain the corresponding wavelet decomposition with coefficients d(1) jn = 1 (thus λ jn = 1 and μ jn = 0) and cn−1,k = 0, ∀k ̸= jn. From the update equations, we have cn, j = −bn j, ∀j ∈Jn and cn, j = 0, ∀j /∈Jn. Using d(1) jn = cn, jnan jn − j∈Jn an j cn, j (as above) and d(1) jn = 1, we have cn, jnan jn = 1 − j∈Jn an j bn j and cn, jn = an jn |an jn |2 1 − j∈Jn an j bn j . Since f (x) := ψ(1) jn (x), we then have Using d(1) jn = cn, jnan jn − j∈Jn an j cn, j (as above) and d(1) jn = 1, we have cn, jnan jn = 1 − j∈Jn an j bn j and cn, jn = an jn |an jn |2 1 − j∈Jn an j bn j . Since f (x) := ψ(1) jn (x), we then have Acknowledgements The R package CliftLRD implementing the CLoMPE technique will be released via CRAN in due course. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecomm ons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. ψ(1) jn (x) = an jn |an jn|2 ⎛ ⎝1 −  j∈Jn an j bn j ⎞ ⎠ϕ(1) n, jn(x) −  j∈Jn bn j ϕ(1) n, j(x) = an jn |an jn|2 ϕ(1) n, jn(x) −  j∈Jn bn j ϕ(1) n, j(x) + ˜an j ϕ(1) n, jn(x) . A Proofs and theoretical results Using the primal scaling function construction in Eq. (27), we obtain an expression for the primal wavelet function This appendix gives the theoretical justification of the results from Sects. 3 and 4, following the notation outlined in the text. ψ(1) jn (x) = an jn |an jn|2 ϕ(1) n, jn(x) −  j∈Jn bn jϕ(1) n−1, j(x), 6 Discussion One aspect of exploration in this setting could be to contrast Hurst estimation using our proposed methodol- ogy with/without data interpolation to investigate its effect, since previous work substantiates that such processing can produce bias (in the context of Hurst exponent estimation) for real-valued series (Knight et al. 2017). It would also be interesting to investigate modifications to our technique to parameter estimation for Matérn processes discussed in Lilly et al. (2017). Let us now suppose f (x) := ϕ(1) n−1, j(x), thus ϕ(1) n−1, j(x) = d(1) jn ψ(1) jn (x) +  k∈Sn−1 cn−1,kϕ(1) n−1,k(x). Hence, d(1) jn = 0, cn−1,k = 0, ∀k ̸= j and cn−1, j = 1. From the update relationship cn−1,k = cn,k + bn kλ jn from (7), we have cn−1,k = cn,k, ∀k ∈Jn (as λ jn = 0 from d(1) jn = 0) and also cn−1,k = cn,k, ∀k /∈Jn. n ,k n,k / n From Eq. (5), we have From Eq. (5), we have d(1) jn = λ jn + i μ jn = cn, jn ℓn jn + i mn jn +  k∈Jn cn,k ℓn k + i mn k . (26) By denoting an k = ℓn k + i mn k, we obtain d(1) jn = cn, jnan jn −  k∈Jn an k cn,k. Using also the fact that d(1) jn = 0, we have cn, jn = an jn |an jn |2  k∈Jn an k cn,k. If j ∈Jn then cn, j = 1 and all others are zero, so cn, jn = an jn an j |an jn |2 := ˜an j . Thus By denoting an k = ℓn k + i mn k, we obtain d(1) jn = cn, jnan jn −  k∈Jn an k cn,k. Using also the fact that d(1) jn = 0, we have cn, jn = an jn |an jn |2  k∈Jn an k cn,k. If j ∈Jn then cn, j = 1 and all others are zero, so cn, jn = an jn an j |an jn |2 := ˜an j . Thus ϕ(1) n−1, j(x) = ϕ(1) n, j(x) + ˜an j ϕ(1) n, jn(x), if j ∈Jn, (27) ϕ(1) n−1, j(x) = ϕ(1) n, j(x), if j /∈Jn. A.2 Proof of Proposition 2 continuous scale) of detail d jr by Ir, jr . These steps are subsequently reiterated, and hence the same also holds for stage r. Since from (15) and (22), regardless of whether we work with the basis indexed by ℓ= 1 or ℓ= 2, the (dual) wavelet functions are linear combinations of the (same) dual scaling functions, hence Eq. (29) can be rewritten as In order to obtain the primal scaling function recursive construction corresponding to the second basis, we proceed in the same way as for the first basis and similarly obtain ϕ(2) n−1, j(x) = ϕ(2) n, j(x) + ˜a n jϕ(2) n, jn(x), if j ∈Jn, ϕ(2) n−1, j(x) = ϕ(2) n, j(x), if j /∈Jn. E(d jr d jk ) =  R ⎧ ⎨ ⎩˜ϕr, jr (t) −  i∈Jr Ar i ˜ϕr,i(t) ⎫ ⎬ ⎭ ×  R ⎧ ⎨ ⎩˜ϕk, jk (s) −  j∈Jk Ak j ˜ϕk, j(s) ⎫ ⎬ ⎭γX(t −s) ds dt, (30) We obtain the primal wavelet equations in a similar manner to the previous development (30) ψ(2) jn (x) = an jn |an jn|2 ϕ(2) n, jn(x) −  j∈Jn bn jϕ(2) n−1, j(x). where A generically denotes the appropriate coefficient that corresponds to basis ℓ= 1 or ℓ= 2, but ˜ϕ is the same for both bases. The above equations show that the primal scaling and wavelet functions corresponding to the second basis are the con- jugates of the corresponding primal and wavelet functions under the first basis, respectively. The above equations show that the primal scaling and wavelet functions corresponding to the second basis are the con- jugates of the corresponding primal and wavelet functions under the first basis, respectively. As C2-LOCAAT progresses, the (dual) scaling functions are defined recursively as linear combinations of (dual) scal- ing functions at the previous stage, see, for example, Eq. (19). Hence, the scaling functions in the above equation can be written as linear combinations of scaling functions at the first stage (i.e. r = n). A.2 Proof of Proposition 2 For the dual scaling functions, we use the update equations and the fact that cr, j =< f , ˜ϕr, j > for any r, hence we have, at stage n, Let {Xt} be a zero-mean complex-valued stationary long memory series with autocovariance γX(τ) ∼cγ |τ|−β. We noteherethatforimproperprocessesofthetypeconsideredin Sykulski and Percival (2016), the pseudo-autocovariance has the same decay rate as the autocovariance (rX(τ) ∼cr|τ|−β) whilst for proper processes, rX(τ) = 0, ∀τ, hence we shall concentrate on the lifting decorrelation properties for improper processes. < f , ˜ϕn−1, j > = < f , ˜ϕn, j > +bn j < f , ˜ψ L n, j >, ∀j ∈Jn < f , ˜ϕn−1, j > = < f , ˜ϕn, j > ∀j /∈Jn, where ˜ψ L denotes the dual wavelet function corresponding to the L-filter only. Thus, the recursive relations for the dual scaling functions are The autocovariance of {Xt} can be written as γX(ti −t j) = E(Xti Xt j ) and rX(ti −t j) = E(Xti Xt j ), assuming E(Xt) = 0, where 0 is to be understood as the complex number 0 = 0+i 0. Hence, E(d(ℓ) j ) = 0 for ℓ= 1, 2. In what follows, we drop the superscript (ℓ) in order to avoid notational clutter. ˜ϕn−1, j(x) = ˜ϕn, j(x) + bn j ˜ψ L n, j(x), ∀j ∈Jn ˜ϕn−1, j(x) = ˜ϕn, j(x), ∀j /∈Jn. Using the assumption that E(d j) = 0, it follows that Similarly, since d(1) jn = cn, jnan jn − j∈Jn an j cn, j, we have < f , ˜ψ(1) jn >=< f , an jn ˜ϕn, jn − j∈Jn an j ˜ϕn, j > and we obtain the dual wavelet construction Similarly, since d(1) jn = cn, jnan jn − j∈Jn an j cn, j, we have < f , ˜ψ(1) jn >=< f , an jn ˜ϕn, jn − j∈Jn an j ˜ϕn, j > and we obtain the dual wavelet construction E(d jr d jk) =  R ˜ψ jr (t)  R ˜ψ jk(s)γX(t −s) ds  dt, (29) (29) ˜ψ(1) jn = an jn ˜ϕn, jn(x) −  j∈Jn an j ˜ϕn, j(x). where we have used d jr =< X, ˜ψ jr >, and the timepoints jr and jk are distinct. In what follows, denote the interval length (i.e. A.1 Proof of Proposition 1 which demonstrates the recursive construction from stage n to n −1 and concludes the proof for the primal wavelet and scaling function construction. To obtain the recursive construction for each basis, we start with the basis indexed by i = 1. At stage n, we have f (x) = 12 3 Statistics and Computing A.3 Proof of Proposition 3 where ⋆is the convolution operator, and i and j refer to time locations that were involved in obtaining d jr and d jk. Note that at this stage we do not use complex conjugation as the (dual) scaling functions are initially defined (at stage r = n) as scaled characteristic functions of the intervals associated with the observed times, i.e. ˜ϕn,i(t) = I −1 n,i χIn,i (t) (thus real- valued). As Cov(Xti , Xt j ) = γX(ti −t j) and d jr =< X, ˜ψ jr >, it follows that d jr has mean zero (as the original process is zero-mean) and in a similar manner to (29) we have E(|d jr |2) =  R ˜ψ jr (t)  R ˜ψ jr (s)γX(t −s) ds  dt, (35) (35) Using Parseval’s theorem in Eq. (31) gives where again we have dropped the basis index ℓ= 1, 2 for notational brevity and we remind the reader that |· p| denotes the C-modulus. As before, we denote the associated interval length of the detail d jr by Ir, jr . Bn,i, j = (2π)−1  R ˆ˜ϕn,i(ω)   ˜ϕn, j⋆γX  (ω) dω = (2π)−1  R ˆ˜ϕn,i(ω)ˆ˜ϕn, j(ω) fX(ω) dω, (32) (32) Using the recursiveness in the dual wavelet construction (Eqs. (15) and (22)), it follows that the (dual) wavelet func- tions are linear combinations of the (same) scaling functions. For the first basis, Eq. (35) can be rewritten as where in general ˆg denotes the Fourier transform of g. As the Fourier transform of an initial (dual) scaling function (scaled characteristic function on an interval, (b −a)−1χ[a,b]) is E(|d(1) jr |2) =  R ⎧ ⎨ ⎩ar jr ˜ϕr, jr (t) −  j∈Jr ar j ˜ϕr, j(t) ⎫ ⎬ ⎭ ×  R ⎧ ⎨ ⎩ar jr ˜ϕr, jr (s) −  j′∈Jr ar j′ ˜ϕr, j′(s) ⎫ ⎬ ⎭γX(t −s) ds dt. A.3 Proof of Proposition 3 (36)   (b −a)−1χ[a,b]  (ω) = sinc {ω(b −a)/2} exp {−i ω(b + a)/2} , where sinc(x) = x−1 sin(x) for x ̸= 0 and sinc(0) = 1 is the (unnormalized) sinc function, we can write (32) as (36) This can be expanded as  R sinc ωIn,i/2 sinc ωIn, j/2 exp  −i ωδ(In,i, In, j)  fX(ω)dω, (33) E(|d(1) jr |2) =  R  R ar jr ar jr ˜ϕr, jr (t) ˜ϕr, jr (s)γX(t −s) ds dt −  j∈Jr  R  R ar jar jr ˜ϕr, j(t) ˜ϕr, jr (s)γX(t −s) ds dt −  j′∈Jr  R  R ar jr ar j′ ˜ϕr, jr (t) ˜ϕr, j′(s)γX(t −s) ds dt +  j∈Jr  j′∈Jr  R  R ar jar j′ ˜ϕr, j(t) ˜ϕr, j′(s)γX(t −s) ds dt. (37) where δ(In,i, In, j) is the distance between the midpoints of intervals In,i and In, j at the initial stage n. j Equation (33) can be interpreted as the Fourier transform of u(x) = fX(x) sinc x In,i/2 sinc x In, j/2 evaluated at δ(In,i, In, j). (37) Since the sinc function is infinitely differentiable and the spectrum is Lipschitz continuous, results on the decay properties of Fourier transforms (Shibata and Shimizu 2001, Theorem 2.2) imply that, for i ̸= j, terms of the form Bn,i, j decay as O  δ(In,i, In, j)−1 . Hence, as in Knight et al. (2017), the further away the time points are, the less autocor- relation is present in the detail coefficients and as the rate of autocorrelation decay is of reciprocal order, it is faster than that of the original process assumed to have long memory (hence O(|τ|−β) with β ∈(0, 1)). A.2 Proof of Proposition 2 Due to the linearity of the integral operator, (30) can be written as a linear combination with complex-valued coefficients of terms like As already explained, the update step is the same for both bases and cr,k =< f , ˜ϕ(1) r,k >=< f , ˜ϕ(2) r,k >, for all r, k thus the dual scaling functions coincide under both bases ( ˜ϕ(1) r,k = ˜ϕ(2) r,k). , , Forthedualwaveletfunction,followingthesameapproach as above, we obtain Bn,i, j :=  R ˜ϕn,i(t)  R ˜ϕn, j(s)γX(t −s) ds  dt =  R ˜ϕn,i(t) ˜ϕn, j⋆γX (t) dt, Bn,i, j :=  R ˜ϕn,i(t)  R ˜ϕn, j(s)γX(t −s) ds  dt  ˜ ( ) ˜ ( ) d ˜ψ(2) jn (x) = an jn ˜ϕn, jn(x) −  j∈Jn an j ˜ϕn, j(x). =  R ˜ϕn,i(t) ˜ϕn, j⋆γX (t) dt, (31) (31) This concludes the proof for the second basis. ⊓⊔ 123 Statistics and Computing References where Δ ∈{−1 + log2(α0), log2(α0)} for some α0, thus Ir, jr = R2 j⋆for some constant R > 0. Abry, P., Flandrin, P., Taqqu, M.S., Veitch, D.: Wavelets for the analysis, estimation and synthesis of scaling data. In: Park, K., Willinger, W. (eds.) Self-similar Network Traffic and Performance Evaluation, pp. 39–88. Wiley, Chichester (2000) Now suppose i = j and both points belong to the j⋆th artificial level. In Eq. (38), we make a change of variable η = ωR2 j⋆to obtain Abry, P., Goncalves, P., Véhel, J.L.: Scaling, Fractals and Wavelets. Wiley, New York (2013) Adali, T., Schreier, P.J., Scharf, L.L.: Complex-valued signal process- ing: the proper way to deal with impropriety. IEEE Trans. Signal Proc. 59(11), 5101–5125 (2011) Br,i,i =  R sinc2(η/2) fX(η/R2 j⋆) R2 j⋆ −1 dη ∼  R sinc2(η/2)c f |η|−α R2 j⋆ α−1 dη, ( j⋆→∞) = 2 j⋆(α−1)  R c f Rα−1 sinc2(η/2)|η|−αdη = 2 j⋆(α−1)Rα−14c f Γ (−1 −α) sin(πα/2) (39) = 2 j⋆(α−1)Rα−1M, (40) Adrian, D.W., Maitra, R., Rowe, D.B.: Complex-valued time series modeling for improved activation detection in fMRI studies. Ann. Appl. Stat. 12(2) (2018) (to appear) Appl. Stat. 12(2) (2018) (to appear) Amblard, P.O., Coeurjolly, J.F., Lavancier, F., Philippe, A.: Basic prop- erties of the multivariate fractional Brownian motion. Sém. Congr. 28, 65–87 (2012) Aston, J.A.D., Kirch, C.: Evaluating stationarity via change-point alter- natives with applications to fMRI data. Ann. Appl. Stat. 6(4), 1906–1948 (2012) where α ∈(0, 1), Γ is the Gamma function and M = 4c f Γ (−1 −α) sin(πα/2). Bakker, A.M.R., van den Hurk, B.J.J.M.: Estimation of persistence and trends in geostrophic wind speed for the assessment of wind energy yields in Northwest Europe. Clim. Dyn. 39(3–4), 767–782 (2012) f If i ̸= j are points from the same neighbourhood Jr and both belong to the same artificial level j⋆, then their artificial scale measure will be the same. Performing the same change of variable as above, we obtain (as ( j⋆→∞) Barber, S., Nason, G.P.: Real nonparametric regression using complex wavelets. J. R. Stat. Soc. B 66(4), 927–939 (2004) Beran, J., Feng, Y., Ghosh, S., Kulik, R.: Long-Memory Processes. Springer, New York (2013) Bhattacharya, R.N., Gupta, V.K., Waymire, E.: The Hurst effect under trends. J. Appl. Prob. 20, 649–662 (1983) Broersen, P.M.T.: Time series models for spectral analysis of irregular data far beyond the mean data rate. Meas. Sci. Technol. A.3 Proof of Proposition 3 As in Proposition 1, using Parseval’s theorem we obtain that the above is a linear combination of terms of the form As in Proposition 1, using Parseval’s theorem we obtain that the above is a linear combination of terms of the form Br,i, j =  R ˜χr,i(t)  R ˜χr, j(s)γX(t −s)ds  dt =  R sinc(ωIr,i/2) sinc(ωIr, j/2)e−i ωδ(Ir,i ,Ir, j ) fX(ω)dω, (38) (38) A similar argument as above applies for the pseudo- covariance rX(ti −t j) = E(Xti Xt j ), as where recall that the hat notation denotes the Fourier trans- form of a function and δ(Ir,i, Ir, j) denotes the distance between the midpoints of intervals Ir,i and Ir, j. E(d jr d jk) =  R ˜ψ jr (t)  R ˜ψ jk(s)rX(t −s) ds  dt, (34) j Due to the artificial-level construction, the sequence of lifting integrals is approximately log-linear in the artificial level [see Knight et al. (2017) for details], i.e. for those points jr in the j⋆th artificial level, we have log2 Ir, jr = j⋆+ Δ and concludes the proof. ⊓⊔ 12 Statistics and Computing References 19(1), 1–13 (2007) Br,i, j ∼  R sinc2(η/2)e−i η R2 j⋆ −1 c f |η|−α R2 j⋆ α dη, = 2 j⋆(α−1)c f Rα−1  R sinc2(η/2)e−i η|η|−αdη = 2 j⋆(α−1)Rα−14c f (2α −1) sin(πα/2)Γ (1 −α) (41) = 2 j⋆(α−1)Rα−1N, (42) Bullmore, E., Fadili, J., Breakspear, M., Salvador, R., Suckling, J., Brammer, M.: Wavelets and statistical analysis of functional mag- netic resonance images of the human brain. Stat. Methods Med. Res. 12(5), 375–399 (2003) (41) (42) Calhoun, V.D., Adalı, T., Pearlson, G.D., Van Zijl, P.C.M., Pekar, J.J.: Independent component analysis of fMRI data in the complex domain. Magn. Reson. Med. 48(1), 180–192 (2002) Chandna, S., Walden, A.T.: A frequency domain test for propriety of complex-valuedvectortime series.IEEE Trans.Signal Proc.65(6), 1425–1436 (2017) where N = 4c f (2α −1) sin(πα/2)Γ (1 −α). 23(4), 439–464 (2008) Goh, S.L., Chen, M., Popovi´c, D.H., Aihara, K., Obradovic, D., Mandic, D.P.: Complex-valued forecasting of wind profile. Renew. Energy 31(11), 1733–1750 (2006) Lobato, I., Robinson, P.M.: Averaged periodogram estimation of long memory. J. Econom. 73(1), 303–324 (1996) Gonella, J.: A rotary-component method for analysing meteorological and oceanographic vector time series. Deep Sea Res. Oceanogr. Abstr. 19, 833–846 (1972) Mandelbrot, B.B., Taqqu, M.S.: Robust R/S analysis of long-run serial correlation. Bull. Int. Stat. Inst. 48(2), 59–104 (1979) Mandelbrot, B.B., Van Ness, J.W.: Fractional Brownian motions, frac- tional noises and applications. SIAM Rev. 10(4), 422–437 (1968) Hamilton, J., Nunes, M.A., Knight, M.I., Fryzlewicz, P.: Complex- valued wavelet lifting and applications. Technometrics 60(1), 46–60 (2017) Mandic, D.P., Goh, V.S.L.: Complex Valued Nonlinear Adaptive Filters: Noncircularity, Widely Linear and Neural Models, vol. 59. Wiley, Hoboken (2009) Haslett, J., Raftery, A.E.: Space-time modelling with long-memory dependence: assessing Ireland’s wind power resource. Appl. Stat. 38(1), 1–50 (1989) Mandic, D.P., Javidi, S., Goh, S.L., Kuh, A., Aihara, K.: Complex- valued prediction of wind profile using augmented complex statistics. Renew. Energy 34(1), 196–201 (2009) Higuchi, T.: Relationship between the fractal dimension and the power law index for a time series: a numerical investigation. Physica D 46(2), 254–264 (1990) Martin, K.W.: Complex signal processing is not complex. IEEE Trans. Circ. Syst. I Reg. Pap. 51(9), 1823–1836 (2004) Hsu, N.J.: Long-memory wavelet models. Stat. Sin. 16, 1255–1271 (2006) McCoy, E.J., Walden, A.T.: Wavelet analysis and synthesis of stationary long-memory processes. J. Gr. Comput. Stat. 5(1), 26–56 (1996) Mohammadi, A., Plataniotis, K.N.: Improper complex-valued multiple- model adaptive estimation. IEEE Trans. Signal Proc. 63(6), 1528– 1542 (2015) Hurst, H.E.: Long-term storage capacity of reservoirs. Trans. Am. Soc. Civ. Eng. 116, 770–808 (1951) Jansen, M., Oonincx, P.: Second Generation Wavelets and Applications. Springer, Berlin (2005) Nafornita, C., Isar, A., Nelson, J.D.B: Regularised, semi-local hurst estimation via generalised lasso and dual-tree complex wavelets. In: IEEE International Conference on Image Processing (ICIP) 2014, pp 2689–2693. IEEE (2014) Jansen, M., Nason, G.P., Silverman, B.W.: Scattered data smoothing by empirical Bayesian shrinkage of second generation wavelet coef- ficients. In: Unser, M., Aldroubi, A. (eds.) Wavelet Applications in Signal and Image Processing IX, vol. 4478, pp. 87–97. SPIE, Bellingham (2001) Neeser, F.D., Massey, J.L.: Proper complex random processes with applications to information theory. IEEE Trans. Inf. where N = 4c f (2α −1) sin(πα/2)Γ (1 −α). Atmos. Environ. 102, 96–104 (2015) Curtis, T.E.: Digital signal processing for sonar. In: Urban, H.S. (ed.) Adaptive Methods in Underwater Acoustics, pp. 583–605. Springer, Netherlands (1985) Kingsbury, N.: Complex wavelets for shift invariant analysis and fil- tering of signals. Appl. Comput. Harmon. Anal. 10(3), 234–253 (2001) Didier, G., Pipiras, V.: Integral representations and properties of oper- ator fractional Brownian motions. Bernoulli 17(1), 1–33 (2011) Knight, M.I., Nason, G.P.: A nondecimated lifting transform. Stat. Com- put. 19(1), 1–16 (2009) Dowell, J., Weiss, S., Infield, D., Chandna, S.: A widely linear multi- channel wiener filter for wind prediction. In: IEEE Workshop on Statistical Signal Processing (SSP) 2014, pp 29–32. IEEE (2014) Knight, M.I., Nunes, M.A.: liftLRD: Wavelet lifting estimators for the Hurst exponent for regular and irregular time series. R package version 1.0-5 (2016) Elipot, S., Lumpkin, R.: Spectral description of oceanic near-surface variability. Geophys. Res. Lett. 35(5), L05606 (2008) Knight, M.I., Nunes, M.A., Nason, G.P.: Spectral estimation for locally stationary time series with missing observations. Stat. Comput. 22(4), 877–8951 (2012) Elipot, S., Lumpkin, R., Perez, R.C., Lilly, J.M., Early, J.J., Sykulski, A.M.: A global surface drifter data set at hourly resolution. J. Geo- phys. Res. Oceans 121(5), 2937–2966 (2016) Knight, M.I., Nason, G.P., Nunes, M.A.: A wavelet lifting approach to long-memory estimation. Stat. Comput. 27(6), 1453–1471 (2017) Ferdowsi, S., Abolghasemi, V.: Simultaneous BOLD detection and incomplete fMRI data reconstruction. Med. Biol. Eng. Comput. 56(4), 599–610 (2018) Li, H., Correa, N.M., Rodriguez, P.A., Calhoun, V.D., Adali, T.: Appli- cation of independent component analysis with adaptive density model to complex-valued fMRI data. IEEE Trans. Biomed. Eng. 58(10), 2794–2803 (2011) Flandrin, P.: Time–Frequency/Time-Scale Analysis. Academic Press, San Diego (1998) Lilly, J.M., Gascard, J.C.: Wavelet ridge diagnosis of time-varying ellip- tical signals with application to an oceanic eddy. Nonlinear Proc. Geophys. 23(4), 467 (2006) Fortuna, L., Nunnari, S., Guariso, G.: Fractal order evidences in wind speed time series. In: International Conference on Fractional Dif- ferentiation and Its Applications (ICFDA) 2014, pp 1–6. IEEE (2014) Lilly, J.M., Sykulski, A.M., Early, J.J., Olhede, S.C.: Fractional Brow- nian motion, the Matérn process, and stochastic modeling of tur- bulent dispersion. Nonlinear Proc. Geophys. 24, 481–514 (2017) Giraitis, L., Robinson, P.M., Surgailis, D.: Variance-type estimation of long memory. Stoch. Proc. Appl. 80(1), 1–24 (1999) Lindquist, M.A.: The statistical analysis of fMRI data. Stat. Sci. where N = 4c f (2α −1) sin(πα/2)Γ (1 −α). where N = 4c f (2α −1) sin(πα/2)Γ (1 −α). f All terms in (37) involve points from the same neighbour- hood Jr, and thus using (40), (41) together with the linearity of the integral operator, we have that Chang, T.P., Ko, H.H., Liu, F.J., Chen, P.H., Chang, Y.P., Liang, Y.H., Jang, H.Y., Lin, T.C., Chen, Y.H.: Fractal dimension of wind speed time series. Appl. Energy 93, 742–749 (2012) Churchill, N.W., Spring, R., Grady, C., Cimprich, B., Askren, M.K., Reuter-Lorenz, P.A., Jung, M.S., Peltier, S., Strother, S.C., Berman, M.G.: The suppression of scale-free fMRI brain dynam- ics across three different sources of effort: aging, task novelty and task difficulty. Nat. Sci. Rep. 6(30), 895 (2016) E(|d(1) jr |2) ∼2 j⋆(α−1)Rα−1 × ⎛ ⎝M2|ar jr |2+N 2  j  j′ ar jar j′ −M N  j ar jar jr −M N  j′ ar jr ar j′ ⎞ ⎠ = 2 j⋆(α−1)Rα−1|M ar jr −N  j∈Jr ar j|2 = C 2 j⋆(α−1), Ciuciu, P., Varoquaux, G., Abry, P., Sadaghiani, S., Kleinschmidt, A.: Scale-free and multifractal time dynamics of fMRI signals during rest and task. Front. Physiol. 3, 186 (2012) Coeurjolly, J.F., Porcu, E.: Properties and Hurst exponent estimation of the circularly-symmetric fractional Brownian motion. Stat. Prob. Lett. 128, 21–27 (2017) Coeurjolly, J.F., Porcu, E.: Fast and exact simulation of complex- valued stationary Gaussian processes through embedding circulant matrix. J. Comput. Gr. Stat. 27(2), 278–290 (2018) matrix. J. Comput. Gr. Stat. 27(2), 278–290 (2018) Coeurjolly, J.F., Lee, K., Vidakovic, B.: Variance estimation for frac- tional Brownian motions with fixed Hurst parameters. Commun. Stat. Theory Methods 43(8), 1845–1858 (2014) where C is a constant depending on c f , R and α. Craigmile, P.F., Percival, D.B.: Asymptotic decorrelation of between- scale wavelet coefficients. Trans. Im. Proc. 51(3), 1039–1048 (2005) A similar argument applies to the second basis and com- pletes the proof. ⊓⊔ 123 Statistics and Computing Craigmile, P.F., Percival, D.B., Guttorp, P.: The impact of wavelet coefficient correlations on fractionally differenced process estima- tion. In: Casacuberta, C., Miró-Roig, R.M., Verdera, J., Xambó- Descamps, S. (eds.) European Congress of Mathematics, pp. 591–599. Birkhäuser, Basel (2001) Jung, Y.Y., Park, Y., Jones, D.P., Ziegler, T.R., Vidakovic, B.: Self- similarity in NMR spectra: an application in assessing the level of cysteine. J. Data Sci. 8(1), 1 (2010) Junger, W.L., Ponce de Leon, A.: Imputation of missing data in time series for air pollutants. where N = 4c f (2α −1) sin(πα/2)Γ (1 −α). Theory 39(4), 1293–1302 (1993) Jansen, M., Nason, G.P., Silverman, B.W.: Multiscale methods for data on graphs and irregular multidimensional situations. J. R. Stat. Soc. B 71(1), 97–125 (2009) Nelson, J.D.B., Kingsbury, N.G.: Dual-tree wavelets for estimation of locally varying and anisotropic fractal dimension. In: 17th IEEE International Conference on Image Processing (ICIP) 2010, pp 341–344, IEEE (2010) Jensen, M.J.: Using wavelets to obtain a consistent ordinary least squares estimator of the long-memory parameter. J. Forecast. 18(1), 17–32 (1999) Nunes, M.A., Knight, M.I.: CNLTreg: Complex-Valued Wavelet Lifting for Signal Denoising. R package version 1 (2017) Jeon, S., Nicolis, O., Vidakovic, B.: Mammogram diagnostics via 2- D complex wavelet-based self-similarity measures. São Paulo J. Math. Sci. 8(2), 265–284 (2014) Nunes, M.A., Knight, M.I., Nason, G.P.: Adaptive lifting for nonpara- metric regression. Stat. Comput. 16(2), 143–159 (2006) Olhede, S.C., Walden, A.T.: Local directional denoising. IEEE Trans. Signal Proc. 53(12), 4725–4730 (2005) 12 3 3 Statistics and Computing Osborne, A.R., Kirwan Jr., A.D., Provenzale, A., Bergamasco, L.: Frac- tal drifter trajectories in the Kuroshio extension. Tellus A Dyn. Meteorol. Oceangr. 41(5), 416–435 (1989) Shibata, Y., Shimizu, S.: A decay property of the Fourier transform and its application to the Stokes problem. J. Math. Fluid Mech. 3(3), 213–230 (2001) Park, C., Lazar, N.A., Ahn, J., Sornborger, A.: A multiscale analysis of the temporal characteristics of resting-state fMRI data. J. Neurosci. Methods 193(2), 334–342 (2010) Summers, D.M.: Impulse exchange at the surface of the ocean and the fractal dimension of drifter trajectories. Nonlinear Proc. Geophys. 9(1), 11–23 (2002) Peng, C.K., Buldyrev, S.V., Havlin, S., Simons, M., Stanley, H.E., Gold- berger, A.L.: Mosaic organization of DNA nucleotides. Phys. Rev. E 49(2), 1685 (1994) Sweldens, W.: The lifting scheme: a new philosophy in biorthogonal wavelet construction. In: Laine A., Unser M. (eds.) Wavelet Appli- cations in Signal and Image Processing III, Proceedings of SPIE, vol. 2569, pp. 68–79 (1995) Piacquadio, M., de la Barra, A.: Multifractal analysis of wind velocity data. Energy Sustain. Dev. 22, 48–56 (2014) Sykulski, A.M., Percival, D.B.: Exact simulation of noncircular or improper complex-valued stationary Gaussian processes using circulant embedding. In: IEEE 26th International Workshop on Machine Learning for Signal Processing (MLSP) 2016, pp. 1–6 (2016) Picinbono, B.: On circularity. IEEE Trans. Signal Proc. 42(12), 3473– 3482 (1994) Qu, B., Addison, P.S.: Modelling flow trajectories using fractional brownian motion. In: International Workshop on Chaos-Fractals Theories and Applications (IWCFTA), 2010, pp 420–424. where N = 4c f (2α −1) sin(πα/2)Γ (1 −α). IEEE (2010) Sykulski, A.M., Olhede, S.C., Lilly, J.M., Early, J.J.: Frequency-domain stochastic modeling of stationary bivariate or complex-valued sig- nals. IEEE Trans. Signal Proc. 65(12), 3136–3151 (2017) R Core Team: R: A Language and Environment for Statistical Comput- ing. R Foundation for Statistical Computing, Vienna. http://www. R-project.org (2013) Tanaka, T., Mandic, D.P.: Complex empirical mode decomposition. IEEE Signal Proc. Lett. 14(2), 101–104 (2007) Rehman, S., Siddiqi, A.H.: Wavelet based Hurst exponent and fractal dimensional analysis of Saudi climatic dynamics. Chaos Solitons Fractals 40(3), 1081–1090 (2009) Taqqu, M.S., Teverovsky, V., Willinger, W.: Estimators for long-range dependence: an empirical study. Fractals 3(04), 785–798 (1995) Trappe, W., Liu, K.: Denoising via adaptive lifting schemes. In: Aldroubi A., Laine M.A., Unser M.A. (eds.) Wavelet applications in signal and image processing VIII, Proceedings of SPIE, vol. 4119, pp. 302–312 (2000) Rodriguez, P.A., Calhoun, V.D., Adalı, T.: De-noising, phase ambiguity correction and visualization techniques for complex-valued ICA of group fMRI data. Pattern Recognit. 45(6), 2050–2063 (2012) Rowe,D.B.:Modelingboththemagnitudeandphaseofcomplex-valued fMRI data. Neuroimage 25(4), 1310–1324 (2005) Vidakovic, B.D., Katul, G.G., Albertson, J.D.: Multiscale denoising of self-similar processes. J. Geophys. Res. 105(D22), 27,049–27,058 (2000) Rowe, D.B.: Magnitude and phase signal detection in complex-valued fMRI data. Magn. Reson. Med. 62(5), 1356–1357 (2009) Walden, A.T.: Rotary components, random ellipses and polarization: a statistical perspective. Philos. Trans. R. Soc. A 371(1984), 20110554 (2013) Rubin-Delanchy, P., Walden, A.T.: Kinematics of complex-valued time series. IEEE Trans. Signal Proc. 56(9), 4189–4198 (2008) Sanderson, B.G., Booth, D.A.: The fractal dimension of drifter trajec- tories and estimates of horizontal eddy-diffusivity. Tellus A Dyn. Meteorol. Oceangr. 43(5), 334–349 (1991) Whitcher, B., Jensen, M.J.: Wavelet estimation of a local long memory parameter. Explor. Geophys. 31, 94–103 (2000) Wuertz,D.etal.:fARMA:ARMATimeseriesmodelling.http://CRAN. R-project.org/package=fArma, R package version 3010.79 (2013) Schreier, P.J., Scharf, L.L.: Second-order analysis of improper complex random vectors and processes. IEEE Trans. Signal Proc. 51(3), 714–725 (2003) Zhang, Q., Harman, C.J., Ball, W.P.: Evaluation of methods for estimat- ing long-range dependence (LRD) in water quality time series with missing data and irregular sampling. In: Proceedings of American Geophysical Union Fall Meeting 2014, San Francisco (2014) Schreier, P.J., Scharf, L.L.: Statistical Signal Processing of Complex- Valued Data: The Theory of Improper and Noncircular Signals. Cambridge University Press, Cambridge (2010) Selesnick, I., Baraniuk, R., Kingsbury, N.: The dual-tree complex wavelet transform. IEEE Signal Proc. Mag. where N = 4c f (2α −1) sin(πα/2)Γ (1 −α). 22(6), 123–151 (2005) Publisher’s Note Springer Nature remains neutral with regard to juris- dictional claims in published maps and institutional affiliations. Shi, B., Vidakovic, B., Katul, G.G., Albertson, J.D.: Assessing the effects of atmospheric stability on the fine structure of surface layer turbulence using local and global multiscale approaches. Phys. Fluids 17(5), 055,104 (2005) 123 123
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Non-equilibrium steady state formation in 3+1 dimensions
SciPost physics
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Christian Ecker1⋆, Johanna Erdmenger2 and Wilke van der Schee3 1 Institut für Theoretische Physik, Goethe Universität, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany 2 Institut für Theoretische Physik und Astrophysik, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany 3 Theoretical Physics Department, CERN, CH-1211 Genève 23, Switzerland 1 Institut für Theoretische Physik, Goethe Universität, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany 2 Institut für Theoretische Physik und Astrophysik, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany 3 Theoretical Physics Department, CERN, CH-1211 Genève 23, Switzerland ⋆ecker@itp.uni-frankfurt.de Abstract We present the first holographic simulations of non-equilibrium steady state formation in strongly coupled N = 4 SYM theory in 3+1 dimensions. We initially join together two thermal baths at different temperatures and chemical potentials and compare the sub- sequent evolution of the combined system to analytical solutions of the corresponding Riemann problem and to numerical solutions of ideal and viscous hydrodynamics. The time evolution of the energy density that we obtain holographically is consistent with the combination of a shock and a rarefaction wave: A shock wave moves towards the cold bath, and a smooth broadening wave towards the hot bath. Between the two waves emerges a steady state with constant temperature and flow velocity, both of which are accurately described by a shock+rarefaction wave solution of the Riemann problem. In the steady state region, a smooth crossover develops between two regions of different charge density. This is reminiscent of a contact discontinuity in the Riemann problem. We also obtain results for the entanglement entropy of regions crossed by shock and rarefaction waves and find both of them to closely follow the evolution of the energy density. Copyright C. Ecker et al. This work is licensed under the Creative Commons Attribution 4.0 International License. Published by the SciPost Foundation. Received 12-04-2021 Accepted 16-08-2021 Published 01-09-2021 Check for updates doi:10.21468/SciPostPhys.11.3.047 Contents 1 Introduction 2 2 Riemann problem in ideal hydrodynamics 4 2.1 Double shock solution 4 2.2 Shock + rarefaction wave solution 7 3 Riemann problem in holography 9 3.1 Holographic model 9 3.2 Holographic steady states 10 4 Holographic entanglement entropy 13 1 Copyright C. Ecker et al. This work is licensed under the Creative Commons Attribution 4.0 International License. Published by the SciPost Foundation. Received 12-04-2021 Accepted 16-08-2021 Published 01-09-2021 Check for updates doi:10.21468/SciPostPhys.11.3.047 Received 12-04-2021 Accepted 16-08-2021 Published 01-09-2021 Check for updates doi:10.21468/SciPostPhys.11.3.047 SciPost Phys. 11, 047 (2021) Contents 1 Introduction 2 2 Riemann problem in ideal hydrodynamics 4 2.1 Double shock solution 4 2.2 Shock + rarefaction wave solution 7 3 Riemann problem in holography 9 3.1 Holographic model 9 3.2 Holographic steady states 10 4 Holographic entanglement entropy 13 1 SciPost Phys. 11, 047 (2021) 5 Results 16 5.1 Energy and charge density 16 5.2 Shock evolution and entropy production 22 5.3 Extremal surfaces and entanglement entropy 24 6 Discussion 28 A Rankine–Hugoniot jump conditions 29 B Sensitivity to initial conditions 30 References 30 5 Results 16 5.1 Energy and charge density 16 5.2 Shock evolution and entropy production 22 5.3 Extremal surfaces and entanglement entropy 24 6 Discussion 28 A Rankine–Hugoniot jump conditions 29 B Sensitivity to initial conditions 30 References 30 5 Results 16 5.1 Energy and charge density 16 5.2 Shock evolution and entropy production 22 5.3 Extremal surfaces and entanglement entropy 24 6 Discussion 28 A Rankine–Hugoniot jump conditions 29 B Sensitivity to initial conditions 30 References 30 30 1 Introduction Describing the far-from-equilibrium dynamics of strongly coupled quantum systems is ex- tremely challenging. Gauge/gravity duality [1–3] provides important insights by mapping the dynamics of certain strongly coupled non-Abelian gauge theories to the dynamics of classical gravity in higher dimensions. This approach has been successfully applied to study the dy- namics of the strongly coupled quark-gluon plasma in relativistic heavy ion collisions [4] and strongly correlated condensed matter systems [5,6]. The picture arises that strongly coupled far-form-equilibrium states typically evolve extremely fast towards a hydrodynamic regime before reaching a state of thermal equilibrium after a sufficiently long time. An important exception to this rule are quantum states on dynamical backgrounds that arise for example in the context of cosmology [7,8]. Another exception are systems driven by external sources that therefore never reach ther- mal equilibrium, but instead evolve towards a steady-state with non-vanishing fluxes, but time independent thermodynamic properties. An important example, which is the subject of this work, is a cold-hot interface of two identical copies of a quantum critical system at differ- ent temperatures and chemical potentials from which a Non-Equilibrium Steady State (NESS) emerges between two outgoing waves. The properties and formation process of NESSs have been studied extensively using various different approaches. In 1+1 dimensional conformal field theories (CFT2), the heat and charge flows of the system considered show universal behaviour [9–13]. The appearance of the NESS as well as its properties are insensitive to the details of the initial state and depend only on fundamental parameters, the central charge and current algebra level, of the CFT2, as well as on the initial temperatures and chemical potentials of the two copies. More recently, exact results have also been obtained in T ¯T-deformed CFT2 [14]. In [15] it was shown that the NESSs in holographic CFT2 are dual to Lorentz boosted black brane geometries in the bulk. The Einstein equations for the gravity dual determine the geometry such that even far-from-equilibrium solutions such as propagating shockwaves are related by large coordinate transformations to static AdS3. The holographic entanglement entropy has been studied for the two-dimensional case in [16] using the Hubeny-Rangamani- Takayanagi prescription [17,18]. One might ask if these NESSs are a curiosity of integrable CFT2 or if they also exist in more general theories and dimensions higher than two? 1 Introduction This question was addressed in sev- eral studies by constructing solutions of the Riemann problem in relativistic hydrodynamics 2 SciPost Phys. 11, 047 (2021) [15,19–22], in holographic CFT3 [23], in theories with gravity duals in the limit of large number of dimensions [24] and in non-relativistic theories with Lifshitz scale symmetry [25]. This led to the insight that the formation of NESSs does not rely on conformal symmetry or integrability, but rather is a universal feature of the hydrodynamic description of any fluid, independent of the underlying equation of state. However, the details on how a NESS dynamically emerges from the interface depend cru- cially on the number of dimensions in which the system lives. In 1+1 dimensions, the NESS region emerges between two planar shockwaves travelling at the speed of light outwards from the interface. In higher dimensions however, this is not the case any more: For entropic rea- sons, the wave front moving towards the hot side is a smoothly broadening rarefaction wave, while the wave front moving towards the cold side is still given by a shockwave [20,21]. g g y One goal of this work is to sharpen the picture of the formation process of NESSs at strong coupling in four spacetime dimensions. First, we compare the evolution of both the stress tensor and the charge density in the strongly coupled field theory to analytical solutions and numerical approximations of the Riemann problem in ideal and viscous hydrodynamics, re- spectively. We consider double-shock solutions, that are known to violate the second law of thermodynamics in dimensions larger that two [20, 21], physically sound combinations of shock and rarefaction waves. Also, as we discuss both for the case of two shock waves as well as for the shock+rarefaction wave combination, the charge density displays a discontinuity within the NESS region, for which we plot examples. Then, moving on to the gravity dual in five dimensions, we numerically evolve the dual gravity problem to obtain the fully far- from-equilibrium quantum dynamics in principle also beyond the hydrodynamic regime. In particular, we numerically establish and analyse the gravity dual of the rarefaction wave. While being entirely smooth, our holographic solutions agree to very good numerical accuracy with the shock+rarefaction wave scenario. Importantly, our results are in line with the proposal of [20] that a NESS forms also for the shock+rarefaction case, i.e. 1 Introduction the spreading of the rar- efaction wave is not so large as to impede the NESS formation. We present a quantitative study of the deviations between the shock+shock and shock+rarefaction cases, the hydrodynamic simulation and our holographic solutions. We find them to be generically small. Nevertheless, our holographic solutions favour the shock+rarefaction scenario. A further goal is to generalise the holographic entanglement entropy (HEE) calculation of [16] to four spacetime dimensions. In [16], where two 1+1-dimensional shockwaves and their gravity dual were considered, the time dependence of the HEE for a strip entangling region was shown to display universal behaviour and to satisfy a velocity bound. In contrast to CFT2, where the dual Riemann problem has a closed solution [26], in dimensions larger than two it is necessary to solve the extremal surface problem for the HEE numerically [27]. We perform a numerical analysis of the HEE for infinite strip regions of different width. In particular for the shock+rarefaction case, we find that a convenient way to make physical statements about the HEE time evolution is to compare it to the time evolution of the energy density. We compare the time evolution of both HEE and energy density during the passing of the shock and rarefaction waves. We find the time evolution of HEE and energy density to be very similar, the main difference being that the HEE trails the energy density by a small amount. This effect is more pronounced in the rarefaction case, where the wave takes a relatively long time to move through the entangling region. The paper is structured as follows. Sec. 2 is a review of the Riemann problem in ideal hydrodynamics. In particular, we recall the derivation of analytical solutions with two shock waves and solutions with one shock and one rarefaction wave. In Sec. 3 we introduce the holographic model which is Einstein-Maxwell gravity in five dimensions. In Sec. 4 we discuss our setup of the HEE computation. In Sec. 5 we present the time evolution of the stress tensor and charge density obtained from the holographic model and compare them to analytical and 3 SciPost Phys. 11, 047 (2021) numerical solutions of the corresponding Riemann problem in ideal and viscous hydrodynam- ics. We then analyse the holographic entanglement entropy for shock and rarefaction waves. In Sec. 6 we conclude and point towards a number of interesting future directions. 1 Introduction In two appendices we derive the Rankine-Hugoniot jump conditions and provide numerical evidence that our results are independent on how we approximate the initial interface of the Riemann problem on the gravity side. 2 Riemann problem in ideal hydrodynamics We can now state the Riemann problem which is an initial value problem for (3) with piecewise constant initial conditions at time t = 0 for the energy and charge density with a planar discontinuity at x = 0, E(0, x) = ¨ EC ∀x < 0 EH ∀x > 0 , n(0, x) = ¨ nC ∀x < 0 nH ∀x > 0 . (5) (5) In the following we assume, without loss of generality, EC < EH, where subscripts C and H denote the “cold” and the “hot” side of the system, respectively. 2 Riemann problem in ideal hydrodynamics Prior to discussing the holographic calculation, it is useful to review the Riemann problem in ideal hydrodynamics. A standard reference on the Riemann problem is [28]. Here we consider it in presence of a conserved U(1) charge. We start by defining the stress tensor and charge current of a relativistic fluid, T µν = (E + P)uµuν + Pηµν , Jµ = nuµ , (1) (1) where E, P, n and η denote energy density, pressure, charge density and the mostly plus Minkowski metric, respectively. We are interested in one dimensional relativistic flows for which the normalised velocity can be written as uµ = γ(1, v, ⃗0), u2 = uµuνηµν = −1. (2) (2) The Lorentz factor γ = 1/ p 1 −v2 is expressed in terms of the local fluid velocity v. The equations of motion of the fluid are the conservation laws for the stress tensor and the charge current The Lorentz factor γ = 1/ p 1 −v2 is expressed in terms of the local fluid velocity v. The equations of motion of the fluid are the conservation laws for the stress tensor and the charge current ∂µT µν = 0, ∂µJµ = 0. (3) (3) These equations need to be closed by an equation of state (EoS) relating pressure to energy and charge density. In what follows we neglect the dependence of the pressure on the charge density and assume the fluid to be conformally invariant, These equations need to be closed by an equation of state (EoS) relating pressure to energy and charge density. In what follows we neglect the dependence of the pressure on the charge density and assume the fluid to be conformally invariant, P(E) = c2 s E , c2 s = 1 d , (4) (4) where cs is the speed of sound and d the number of spatial dimensions. We can now state the Riemann problem which is an initial value problem for (3) with piecewise constant initial conditions at time t = 0 for the energy and charge density with a planar discontinuity at x = 0, where cs is the speed of sound and d the number of spatial dimensions. 2.1 Double shock solution (10) (10) vC(J t C −J t 1) = J x C −J x 1 , vH(J t 2 −J t H) = J x 2 −J x H . (10) These conditions determine the charge densities n1 and n2, the shock velocities vC and vH, as well as the boost velocity vS and energy density ES of the NESS region in terms of the boundary conditions nC, nH, EC and EH, vS = − cs(1 −χ) Æ (1 + c2 s χ)(c2 s + χ) , vC = −cs v u t1 + c2 s χ c2 s + χ , vH =cs v u t c2 s + χ 1 + c2 s χ , ES = p ECEH , n1 =nC v u t 1 + c2 s χ χ(c2 s + χ) , n2 =nH v u tχ(c2 s + χ) 1 + c2 s χ , (11) ES = p ECEH , (11) where χ = p EC/EH. In Fig. 1 we plot the energy and charge density for different values of χ for d = 3. In Fig. 2 (left) we show the velocities as a function of χ for d = 3, whereby we note that 1 > vH > cs and cs > vC. We express the solutions as functions of the ratio of the x-coordinate in which the shocks propagate and time t, x/t. Note that on the right of both plots, the value of the quantities shown is one since E = EH. For special ratios of the initial charge and energy densities nC nH = χ(c2 s + χ) 1 + c2 s χ , (12) (12) the contact discontinuity of the charge is absent, implying n1 = n2. For d = 3 spatial dimen- sions and nC/nH = 1/2, this is the case for χ = ( p 73 −1)/12, as also shown in Fig. 1. For smaller values of χ the charge density becomes non-monotonic: the difference in the energy densities generates such a strong flow of charge that charge builds up next to the cold bath. 2.1 Double shock solution One possible solution of the Riemann problem consists of two shock discontinuities moving in opposite directions. In this case, there are three different regions, for which the stress tensor is given by T µν C =  EC 0 0 c2 s EC  , T µν S = c2 s ES (1 + 1/c2 s )uµuν + ηµν , T µν H =  EH 0 0 c2 s EH  , (6) (6) 4 SciPost Phys. 11, 047 (2021) respectively. In this subsection we suppress the d −1 transverse coordinates for clarity. The middle region, labelled by subscript S for steady state, is described by a fluid with local rest- frame energy density ES moving with velocity vS, respectively. In this subsection we suppress the d −1 transverse coordinates for clarity. The middle region, labelled by subscript S for steady state, is described by a fluid with local rest- frame energy density ES moving with velocity vS, uµ = γ(1, vS), γ = 1/ q 1 −v2 S . (7) (7) The charge density can in addition develop a so-called contact discontinuity in the central region where the pressure and the velocity are continuous. This means that the solution for the charge density consists of four different regions in general, with local charge densities of nC, n1, n2 and nH such that Jµ C = nC  1 0  , Jµ 1 = n1γ  1 vS  , Jµ 2 = n2γ  1 vS  , Jµ H = nH  1 0  . (8) (8) omentum and charge conservation then imply the Rankine-Hugoniot jump condi- details see Appendix A) for the stress tensor at the left and right moving shock, vC(T tt C −T tt S ) = T x t C −T x t S , vC(T t x C −T t x S ) = T x x C −T x x S , vH(T tt S −T tt H ) = T x t S −T x t H , vH(T t x S −T t x H ) = T x x S −T x x H , (9) (9) and correspondingly for the charge densities vC(J t C −J t 1) = J x C −J x 1 , vH(J t 2 −J t H) = J x 2 −J x H . 2.1 Double shock solution As noted in [20, 24], a shock wave moving into a region of higher energy density an pressure locally violates the entropy condition ∂µsµ ≥0, (13) (13) where sµ = E+P T uµ = kE 1 1+c2s uµ is the entropy density current and k a constant that depends on the microscopic properties of the theory. To discuss this in the present context, we first evaluate where sµ = E+P T uµ = kE 1 1+c2s uµ is the entropy density current and k a constant that depends on the microscopic properties of the theory. To discuss this in the present context, we first evaluate 5 SciPost Phys. 11, 047 (202 χ=1/4 χ=1/2 χ=3/4 -1.0 -0.5 0.0 0.5 1.0 0.0 0.2 0.4 0.6 0.8 1.0 x/t ℰ/ℰH χ=1/4 χ= 73 -1 12 χ=3/4 -1.0 -0.5 0.0 0.5 1.0 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 x/t n /nH Figure 1: Energy density (left) and charge density (right) of the double shock solu- tion. The energy plot on the left shows the two heat baths and the NESS region. The charge plot displays the additional contact discontinuity that is absent for the middle value of χ given. SciPost Phys. 11, 047 (2021) χ=1/4 χ=1/2 χ=3/4 -1.0 -0.5 0.0 0.5 1.0 0.0 0.2 0.4 0.6 0.8 1.0 x/t ℰ/ℰH χ=1/4 χ= 73 -1 12 χ=3/4 -1.0 -0.5 0.0 0.5 1.0 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 x/t n /nH Figure 1: Energy density (left) and charge density (right) of the double shock solu- tion. The energy plot on the left shows the two heat baths and the NESS region. The charge plot displays the additional contact discontinuity that is absent for the middle value of χ given. the jump conditions for the entropy current across the shock waves. 2.1 Double shock solution Using the entropy currents in the left, central and right regions sµ C = kE 1 1+c2s C  1 0  , sµ S = kE 1 1+c2s S γ  1 vS  , sµ H = kE 1 1+c2s H  1 0  , (14) (14) we find the jump conditions for the entropy current across the shock waves to be ∆sC = vC st C −st S  − sx C −sx S  = kcsE 1 1+c2s H χ 3 2(1+c2s ) −χ 2 1+c2s v u t1 + c2 s χ c2 s + χ ! , (15) ∆sH = vH st S −st H  − sx S −sx H  = kcsE 1 1+c2s H χ 1−c2s 2(1+c2s ) − v u t c2 s + χ 1 + c2 s χ ! . (16) (15) (16) For the number of spatial dimensions d > 1, these expressions reveal that both shocks violate the jump condition for the entropy current, i.e. ∆sC/H ̸= 0. However, as shown in Fig. 2 (right), the right-moving shock (orange curve) gives ∆sH < 0. This shock, moving in the direction of the hot bath, hence violates the local second law of thermodynamics. Recently, [29] (based on [30–34]) managed to proof the local second law of thermodynamics (see also [35–37] for a statistical physics point of view) under the very general assumptions of unitarity and hence we have to regard this right-moving shock as an unphysical solution. In fact, in the next subsection we show how this problem can be resolved by replacing the unphysical shock with a physical rarefaction wave. The entropy flow across the right-moving shock is negative and monotonic. In the limit χ →0, it is bounded by lim χ→0∆sH = −k c2 s (EH) 1 1+c2s . (17) (17) The flow across the left-moving shock is completely suppressed in this limit, i.e. limχ→0 ∆sC = 0. Interestingly, for each dimension d the entropy flow across the left mover has a local maximum at some χ∗ d for which the shock produces a maximum amount of entropy. For d = 2,3,4, the corresponding value of χd is given by χ∗ 2 ≈0.1301, χ∗ 3 ≈0.1397, χ∗ 4 ≈0.1428, ... . (18) (18) 6 SciPost Phys. 2.1 Double shock solution 11, 047 (2021) vS vC vH cs 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 χ Cold Hot 0.0 0.2 0.4 0.6 0.8 1.0 -0.04 -0.03 -0.02 -0.01 0.00 0.01 χ Δs ℰH - 1 1+cs 2 /(k cs) Figure 2: (left) The velocities of the steady state flow (vS), and the left- and right- moving shock velocities vC and vH in comparison to the sound velocity cs for d = 3 according to Eqn. (11). (right) Change in entropy across the left and right moving shock waves, as function of χ = p EC/EH. ‘Cold’ refers to the left-moving and ‘Hot’ to the right-moving shock. The normalisation factor is motivated by (15). SciPost Phys. 11, 047 (2021) vS vC vH cs 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 χ - 1 Cold Hot 0.0 0.2 0.4 0.6 0.8 1.0 -0.04 -0.03 -0.02 -0.01 0.00 0.01 χ Δs ℰH /(k cs) χ χ Figure 2: (left) The velocities of the steady state flow (vS), and the left- and right- Figure 2: (left) The velocities of the steady state flow (vS), and the left- and right- moving shock velocities vC and vH in comparison to the sound velocity cs for d = 3 according to Eqn. (11). (right) Change in entropy across the left and right moving shock waves, as function of χ = p EC/EH. ‘Cold’ refers to the left-moving and ‘Hot’ to the right-moving shock. The normalisation factor is motivated by (15). 2.2 Shock + rarefaction wave solution As is well known in the literature on the Riemann problem for some time already, [38], a phys- ical solution that - unlike the shock solution discussed above - is locally in thermal equilibrium and respects the second law of thermodynamics is the rarefaction wave. For the setup consid- ered here, this was discussed for instance in [20]. A rarefaction wave is a smooth, self-similar solution that by construction saturates the entropy condition (13) and depends on x and t only via ξ = x/t. In the ξ coordinate, the conservation equations for the stress tensor become ξ d dξ  E 1 + c2 s v2 1 −v2  = d dξ  Ev 1 + c2 s 1 −v2  , ξ d dξ  Ev 1 + c2 s 1 −v2  = d dξ  E c2 s + v2 1 −v2  , (19) (19) which can be rearranged to  0 0  = M  d dξE d dξ v  . (20) (20) his system of ordinary differential equations has solutions different from E = v = 0 if and nly if This system of ordinary differential equations has solutions different from E = v = 0 if and only if This system of ordinary differential equations has solutions different from E = v = 0 if and only if d 2ξ2  (ξ)2 2  ξ (ξ) 2 ξ2 detM = c2 s ξ2 −1  v(ξ)2 −2 c2 s −1  ξv(ξ) + c2 s −ξ2 = 0, (21) (21) which gives a relation for the local velocity in terms of ξ, v(ξ) = ξ ± cs 1 ± csξ , (22) v(ξ) = ξ ± cs 1 ± csξ , (22) (22) where the plus (minus) sign corresponds to a left (right) moving wave. Next we demand local entropy conservation ∂µsµ = 0 for the right-moving wave, where the plus (minus) sign corresponds to a left (right) moving wave. Next we demand local entropy conservation ∂µsµ = 0 for the right-moving wave, ξ d dξ  E 1 1+c2s p 1 −v2  = d dξ  vE 1 1+c2s p 1 −v2  . 2.2 Shock + rarefaction wave solution (23) (23) From this we can express the energy density of the rarefaction wave as E = EH (cs −1)(ξ + 1) (cs + 1)(ξ −1) ‹ 1−c2s 2cs , (24) (24) 7 SciPost Phys. 11, 047 (2021) where we fixed the integration constant by E(ξ = cs) = EH. Similarly the conservation law for the charge current ξ d dξ  n p 1 −v2 ‹ = d dξ  nv p 1 −v2 ‹ , (25) (25) can be solved for the charge density in the rarefaction region can be solved for the charge density in the rarefaction region n(ξ) = nH (1 + ξ)(1 −cs) (1 −ξ)(1 + cs) ‹cs/2 , (26) (26) where we used (22) to express the local velocity and n(ξ = cs) = nH to fix the integration constant. By combining (22) and (24) we can express the energy density in the central region in terms of the flow velocity 1 2 where we used (22) to express the local velocity and n(ξ = cs) = nH to fix the integration constant. By combining (22) and (24) we can express the energy density in the central region in terms of the flow velocity 2 ES = EH 1 + vS 1 −vS ‹ 1−c2s 2cs . (27) (27) An analogous expression can be derived from the Rankine-Hugoniot jump conditions (9) for the left moving shock wave An analogous expression can be derived from the Rankine-Hugoniot jump conditions (9) for the left moving shock wave vC  EC −ES 1 + c2 s v2 S 1 −v2 S  = − ES(1 + c2 s )vS 1 −v2 S , −vC ES(1 + c2 s )vS 1 −v2 S = c2 s EC − ES(v2 S + c2 S) 1 −v2 S , (28) (28) from which we obtain ES = EC 2c2 s + v2 S + c4 s v2 S ± vS(1 + c2 s ) q 4c2 s + (c2 s −1)2v2 S 2c2 s (1 −v2 S) , (29) vC = v2 S + c2 s ‚ 1 −(1 −v2 S) € 1−vS 1+vS Š 1+c2s 2cs χ2 Œ vS(1 + c2 s ) , (30) (29) (30) where the solution with the minus (plus) sign corresponds to a right (left) moving rarefaction wave. 2.2 Shock + rarefaction wave solution Combining (27) and (29) fixes a unique value for vS which we are only able to determine numerically. With this in mind, we express the charge densities in terms of vS, n1 = nC (v2 S −1)χ2 € 1−vS 1+vS Š c2s +1 2cs + 1 + v2 S c2 s q 1 −v2 S ‚ 1 −χ2 € 1+vS 1+vS Š c2s +1 2cs Œ , n2 = nH (1 + vS)(1 −cs) (1 −vS)(1 + cs) ‹cs/2 . (31) (31) In Fig. 3 we plot some examples for energy and charge density. In contrast to the shock+shock case the rarefaction wave provides a continuous solution near the hot bath. From the figure it seems that χ = ( p 73 −1)/12 again provides a solution without a contact discontinuity, but in fact a careful numerical comparison shows that n1 −n2 ≈0.001092. We also note that the direction the rarefaction wave travels is solely determined by the presence of the hot bath, and does not depend on nH being higher or smaller than nC, which is clear from Fig. 3 (right). Similarly, the contact discontinuity does not get replaced by a rarefaction wave, as in the steady state rest frame it is just a connection between two baths of different charge densities. In practice charge will diffuse from the higher to the lower charge density, but this is a process that is parametrically slower than the shock and rarefaction waves (see also Section 5). All these solutions are now potential physical solutions that satisfy the second law. In the remainder of this work, we will investigate these further from a microscopic perspective. In Fig. 3 we plot some examples for energy and charge density. In contrast to the shock+shock case the rarefaction wave provides a continuous solution near the hot bath. From the figure it seems that χ = ( p 73 −1)/12 again provides a solution without a contact discontinuity, but in fact a careful numerical comparison shows that n1 −n2 ≈0.001092. We also note that the direction the rarefaction wave travels is solely determined by the presence of the hot bath, and does not depend on nH being higher or smaller than nC, which is clear from Fig. 3 (right). 2.2 Shock + rarefaction wave solution Similarly, the contact discontinuity does not get replaced by a rarefaction wave, as in the steady state rest frame it is just a connection between two baths of different charge densities. In practice charge will diffuse from the higher to the lower charge density, but this is a process that is parametrically slower than the shock and rarefaction waves (see also Section 5). All these solutions are now potential physical solutions that satisfy the second law. In the remainder of this work, we will investigate these further from a microscopic perspective. 8 SciPost Phys. 11, 047 (2021) χ=1/4 χ=1/2 χ=3/4 -1.0 -0.5 0.0 0.5 1.0 0.0 0.2 0.4 0.6 0.8 1.0 x/t ℰ/ℰH χ=1/4 χ= 73 -1 12 χ=3/4 -1.0 -0.5 0.0 0.5 1.0 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 x/t n /nH χ=1/4 χ= 73 -1 12 χ=3/4 -1.0 -0.5 0.0 0.5 1.0 0 1 2 3 4 5 x/t n /nH Figure 3: Energy density (left) and charge density (middle and right) for the shock+rarefaction wave solution. The rarefaction wave moving to the hot bath ap- pears on the right. This figure is to be compared to the two-shock solution displayed in Fig. 1. χ=1/4 χ=1/2 χ=3/4 -1.0 -0.5 0.0 0.5 1.0 0.0 0.2 0.4 0.6 0.8 1.0 x/t ℰ/ℰH χ=1/4 χ= 73 -1 12 χ=3/4 -1.0 -0.5 0.0 0.5 1.0 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 x/t n /nH χ=1/4 χ= 73 -1 12 χ=3/4 -1.0 -0.5 0.0 0.5 1.0 0 1 2 3 4 5 x/t n /nH Figure 3: Energy density (left) and charge density (middle and right) for the shock+rarefaction wave solution. The rarefaction wave moving to the hot bath ap- pears on the right. This figure is to be compared to the two-shock solution displayed in Fig. 1. 1The full five-dimensional action for this truncation would include a Chern-Simons term (see e.g. [41]), b this will play no role in our analysis and we have therefore omitted it. 3.1 Holographic model The holographic dual model that we use is five-dimensional Einstein-Maxwell gravity with negative cosmological constant. This allows us to study the dynamics of the stress tensor and a conserved U(1) current in the dual field theory. The action of the gravity system is given by S = 1 16πGN Z M d5x p −g  R + 12 L2 −e2L2 4 FMN F MN  + 1 8πGN Z ∂Mε d4x p −γK + Sct , (32) where GN is Newton’s constant, L is the asymptotic AdS radius, R is the Ricci scalar of the bulk geometry on a manifold M with flat boundary ∂M and bulk metric gMN, FMN ≡∂[MAN] is the electromagnetic field strength with AM the U(1) gauge field in the bulk and the coupling con- stant e controls the strength of the electromagnetic field. The trace of the extrinsic curvature K of the induced metric γµν and the counter-term [39,40] are to be evaluated at a radial slice ∂Mε close to the boundary and are necessary to render the variational principle well-defined and the on-shell action finite. The action (32) can be viewed as a consistent truncation of the dimensional reduction of type IIB supergravity on S5. In this case the dual gauge theory is N = 4 Super Yang-Mills and the U(1) current arises from the R-symmetry of this theory.1 In the context of this work we see (32) simply as bottom-up model that incorporates the dynamics of the stress tensor and a conserved U(1) current in the dual gauge theory. The equations of motion that follow from (32) are RMN + 4 L2 gMN = e2L2 2  FM P F P N −1 6 gMN F2 ‹ , (33a) ∇M FMN = 0. (33b) (33a) (33b) The ground state of the theory is given by a constant gauge field configuration on AdS5, ds2 = L2 u2 du2 + ηµνdxµdxν , AM = const. (34) (34) A general solution of the Maxwell equations near the AdS boundary takes in axial gauge (Au = 0) the form A general solution of the Maxwell equations near the AdS boundary takes in axial gauge (Au = 0) the form (Au = 0) the form Aµ(u, xµ) = a(0) µ (xµ) + u2 € a(1) µ (xµ) + ˜a(1) µ (xµ)logu Š + ... 3.1 Holographic model , (35) (35) 1The full five-dimensional action for this truncation would include a Chern-Simons term (see e.g. [41]), but this will play no role in our analysis and we have therefore omitted it. 9 SciPost Phys. 11, 047 (2021) where the coefficient a(0) µ (xµ) is identified as coupling of the global U(1) current Jµ(xµ) in the quantum field theory. A constant a(1) µ (xµ) is then, by the holographic dictionary (see e.g. [42]), identified as chemical potential µ for a global charge density ρ µ ≡a(0) t , 〈J t〉= ρ ≡−e2L4 8πGN a(1) t . (36) (36) In the following we will be interested in solutions dual to field theory states in the grand canonical ensemble, i.e., thermodynamic states characterised by fixed chemical potential and temperature. Such states are dual to Reissner–Nordström (RN) black branes, In the following we will be interested in solutions dual to field theory states in the grand canonical ensemble, i.e., thermodynamic states characterised by fixed chemical potential and temperature. Such states are dual to Reissner–Nordström (RN) black branes, ds2 RN = L2 u2 −f (u)dt2 + f (u)−1du2 + d⃗x2 , At(u) = µ  1 −u2 u2 h  (37a) f (u) = 1 −M u4 u4 h + Q2 u6 u6 h , M = 1 + Q2 , Q2 = µ2u2 h e2 3L2 , (37b) (37a) (37b) where u = uh is the radial location of the horizon defined by f (uh) = 0 and f (0) = 1 fixes the boundary metric to Minkowski. The temperature of the field theory state dual to the geometry (37) is given by the Hawking temperature of the horizon. It can be derived by demanding periodicity β of time circles in the Euclidean continuation of the line element, T = 1 β = −f ′(uh) 4π = 2 −Q2 2πuh . (38) (38) By the Bekenstein–Hawking formula [43,44], the entropy density is proportional to the horizon area, 3 s = L3 4G u3 h . (39) (39) The charge density then follows from using (37a) in (36), The charge density then follows from using (37a) in (36), he charge density then follows from using (37a) in (36), ρ = e2L2µ 8πGNu2 h . 3.1 Holographic model (40) (40) RN-geometries (37) with different T and µ will serve as initial conditions to the left and to the right of the interface in the Riemann problem and at the same time provide the necessary boundary conditions at spatial infinity to solve the initial value problem. In the next section we explain that NESSs emerging from the interface are dual to Lorentz transformed (boosted) versions of (37) and present the method we use to simulate their formation. 3.2 Holographic steady states The holographic duality maps NESSs in the field theory to boosted black brane geometries on the gravity side [15], ds2 NESS = L2 u2  du2 f (u)−1 −f (u)(dt coshη −dz sinhη)2 + (dz coshη −dt sinhη)2 + dx2 ⊥  , (41 ⊥  (41) 1 where the rapidity η is related to the fluid velocity vs in the steady state by η = tanh−1 vs. In contrast to Sec. 2, where we denote the spatial coordinate in which the waves propagate by x, we denote the corresponding coordinate here and in the following by z. At this point it is important to emphasise that explicit relations between the temperature, fluid velocity, etc. of the holographic steady state and the properties of the hot and cold reservoirs are only 10 SciPost Phys. 11, 047 (2021) known in d = 2 [20]. The temperatures of the cold and the hot reservoir (TC,H) depend on the corresponding chemical potentials by (38) (µC,H) and radial horizon positions (uh(C,H)), known in d = 2 [20]. The temperatures of the cold and the hot reservoir (TC,H) depend on the corresponding chemical potentials by (38) (µC,H) and radial horizon positions (uh(C,H)), TC,H = 2 −Q2 C,H 2πuh(C,H) = 1 πuh(C,H) − µ2 C,Huh(C,H) 6π e2 L2 . (42) (42) The dual geometry for the steady state regime can be approximated as ds2 =      ds2 RN,C if z ≲vC t , ds2 NESS if vC t ≲z ≲vH t , ds2 RN,H if z ≳vH t , (43) (43) where ds2 RN,C (ds2 RN,H) is (37) for T = TC(TH) and µ = µC(µH). In the hydrodynamic limit, the left (vC) and right (vH) moving wave velocities are well approximated by (28) with (22) evaluated for ξ = cs. It is important to note that if χ is not close to unity we expect more complicated solutions that in particular include the rarefaction waves introduced in Sec. 2.2. Similarly we can arrive at approximate expressions for the gauge field using the formulae in Sec. 2.2. This is only an approximate solution, because the precise form of the metric in the vicinity of the left and right moving waves is not available in closed form. In Sec. 3 we present numerical evidence that the expressions for temperature, fluid velocity and charge density derived for the shock+rarefaction solution in Sec. 3.2 Holographic steady states 2 are, at sufficiently late time, in excellent agreement with the results of the holographic simulation. To study the Riemann problem in full detail we construct the solution numerically. This will allow us to analyse the precise shapes of the propagating waves, how they change in time and how they compare to the analytically constructed shock and rarefaction wave solution in ideal hydrodynamics. For this we make the simplifying assumption that the strength of the electromagnetic field is small, i.e. e L ≪1. In this limit the backreaction of the gauge field to the metric is subleading and the right hand side of (33a) vanishes. This means our charged results are leading order results in a small e L expansion. g p For the metric and the gauge field we follow [45–48] and use the ansätze ds2 EF = −Cdt2 + 2drdt + 2Gdzdt + S2 eBdx2 ⊥+ e−2Bdz2 , (44a) AM = Atdt + Azdz , (44b) (44a) (44b) (44b) where all functions depend on the Eddington–Finkelstein like time coordinate t, the longitu- dinal coordinate z and the AdS bulk coordinate r, but not on the two transverse coordinates x⊥. The explicit form of the corresponding equations of motion for the metric can for example be found in [45,49]. 2We note that in this section we switched to the z-coordinate to describe the boundary direction, to make it explicit that we work in a 3+1D boundary field theory. Also note that in Section 2 E referred to the energy density in the local restframe, whereas to be consistent with previous literature we here use E for the energy density in the lab frame. For the hot and cold bath the lab frame is the local restframe, but for the steady state and rarefaction waves it is necessary to compare to T tt in (1). 3.2 Holographic steady states The Maxwell equations with (44b) as ansatz for the gauge field can be written as S3F′ rt = −e2B Frz S 2˜B −G′ + ˜S  + S ˜Frz  −3S2FrtS′ , (45a) S3F′ tz =1 4S2−2S ˜Frt + Frz CB′ + 2˙B + C′ + 2B′ (GFrt + Ftz) + CF′ rz + FrtG′ + S′ (−CFrz + 10GFrt −2Ftz) −2˙SFrz  + e2BG Frz S 2˜B −G′ + ˜S  + S ˜Frz  , (45b) (45a) (45b) 4S ˙Frz = −2S −˜Frt + Frz CB′ + 2˙B + C′ + 2B′ (GFrt + Ftz) + FrtG′ −S′ (CFrz + 2GFrt + 2Ftz) −2˙SFrz , (45c) 4S ˙Frz = −2S −˜Frt + Frz CB′ + 2˙B + C′ + 2B′ (GFrt + Ftz) + FrtG′ −S′ (CFrz + 2GFrt + 2Ftz) −2˙SFrz , (45c) 2S3 ˙Frt =e2B€ S 2G 2˜BFrt + ˜Frt  + 4˜BFtz + C ˜Frz + 2 ˜GFrt + 2˜Ftz  + Frz 2S C ˜B + ˜C + ˙G  + C ˜S  + 2˜S (GFrt + Ftz) Š −6S2˙SFrt , (45d) (45c) 2S3 ˙Frt =e2B€ S 2G 2˜BFrt + ˜Frt  + 4˜BFtz + C ˜Frz + 2 ˜GFrt + 2˜Ftz  + Frz 2S C ˜B + ˜C + ˙G  + C ˜S  + 2˜S (GFrt + Ftz) Š −6S2˙SFrt , (45d) 2S3 ˙Frt =e2B€ S 2G 2˜BFrt + ˜Frt  + 4˜BFtz + C ˜Frz + 2 ˜GFrt + 2˜Ftz  + Frz 2S C ˜B + ˜C + ˙G  + C ˜S  + 2˜S (GFrt + Ftz) Š −6S2˙SFrt , (45d) 11 SciPost Phys. 11, 047 (2021) where ˙h = ∂th + 1 2Ch′ and ˜h = ∂zh −Gh′. Once Frz is specified the first three equations can be used to respectively solve for Frt, Ftz and ˙Frz, after which it is possible to obtain the time derivative of Frz. The last equation is a constraint equation and can be used to monitor the accuracy of the numerical evolution. Close to the boundary, the solution for the metric and the gauge field can be expressed as power series in the radial coordinate, where ˙h = ∂th + 1 2Ch′ and ˜h = ∂zh −Gh′. Once Frz is specified the first three equations can be used to respectively solve for Frt, Ftz and ˙Frz, after which it is possible to obtain the time derivative of Frz. 3.2 Holographic steady states The last equation is a constraint equation and can be used to monitor the accuracy of the numerical evolution. Close to the boundary, the solution for the metric and the gauge field can be expressed as power series in the radial coordinate, C(r, t, z) = (r + α)2 −2∂tα + c4 r2 + ∂tc4 −4αc4 2r3 + O r−4 , (46a) B(r, t, z) = b4 r4 + 15∂t b4 + 2∂z f4 −60αb4 15r5 + O r−6 , (46b) S(r, t, z) = r + α −4∂z g4 + 3∂tc4 60r4 + O(r−5), (46c) G(r, t, z) = ∂zα + g4 r2 + 4∂t g4 + ∂zc4 −10αg4 5r3 + O(r−4), (46d) At(r, t, z) = at,2 r2 + 2 3∂zaz,2 −2αat,2 r3 + O(r−4), (46e) Az(r, t, z) = az,2 r2 + −6αaz,2 −∂zat,2 + 3∂taz,2 3r3 + O(r−4), (46f) (46a) (46b) (46f) where the function α(t,z) is a residual gauge freedom of the ansatz (44a) which we used to fix the horizon at r = 1. The functions c4(t,z), b4(t,z), g4(t,z), at,2(t,z) and az,2(t,z) are not determined by the near boundary analysis, but need to be extracted from a full bulk solution. The charge density and the holographic stress tensor in the field theory are then given by [47,49,50] where the function α(t,z) is a residual gauge freedom of the ansatz (44a) which we used to fix the horizon at r = 1. The functions c4(t,z), b4(t,z), g4(t,z), at,2(t,z) and az,2(t,z) are not determined by the near boundary analysis, but need to be extracted from a full bulk solution. The charge density and the holographic stress tensor in the field theory are then given by [47,49,50] 〈Jµ〉= e2L4 4πGN    ρ σ 0 0   , 〈T µν〉= 1 4πGN    E S 0 0 S P∥ 0 0 0 0 P⊥ 0 0 0 0 P⊥   , (47) (47) where we defined the reduced variables for charge density (ρ), charge flow (σ), energy density (E), pressure in longitudinal (P∥) and transverse (P⊥) directions and momentum flux (S). 2 These quantities are related to the expansion coefficients as follows ρ = 1 2at,2 , σ = 1 2az,2 , E = −3 4a4 , P∥= −1 4a4 −2b4 , P⊥= −1 4a4 + b4 , S = −f4 . 3.2 Holographic steady states (48) (48) (48) For N = 4 SU(Nc) SYM we have GN = π/2N 2. For N = 4 SU(Nc) SYM we have GN = π/2N 2 c . For the metric ansatz (44a) consistent initial conditions can be obtained by specifying B(r, 0, z), as well as the functions a4(0, z), f4(0, z) and α(z) that determine the stress-energy tensor at initial time t = 0. The initial conditions for the electromagnetic field strength can be parametrised by Fr y(r, 0, z) = ∂rAy and the normalisable mode of At, which we call at,2(t, z). The initial conditions B(r, 0, z) and Fr y(r, 0, z) can be used to start with a far-from-equilibrium state, which then relaxes in a time of order 1/T, where T is the local temperature at the moment at which hydrodynamics becomes a good description (hydrodynamisation) [51]. In this work, however, we are interested in much longer time scales and we therefore set the initial values of these two functions to zero, i.e., their values in thermal equilibrium. The 12 SciPost Phys. 11, 047 (2021) initial conditions for the cold and hot bath are then solely determined by the corresponding energy and charge densities, for which we choose initial conditions for the cold and hot bath are then solely determined by the corresponding energy and charge densities, for which we choose E(z) = EC + (EH −EC)θ z −1 4zmax  θ 3 4zmax −z  , (49a) ρ(z) = ρC + (ρH −ρC)θ z −1 4zmax  θ 3 4zmax −z  , (49b) (49a) (49a) (49b) (49b) where we define θ(x) = 1 2 1 + tanh 3 2 x  to be a smooth step function and zmax denotes the size of the computational domain in z-direction. Since we neglect the back-reaction of the gauge field to the geometry our results are conformally invariant and the ratio of the energy densities of the hot and cold baths simply equals the fourth root of the ratio of the correspond- ing temperatures EH EC = 4Ç TH TC . To make the scale invariance of our results manifest we multiply axis labels and legends by appropriate powers of m = πTC, with TC = ( 4 3EC)1/4/π being the temperature of the cold bath. 3.2 Holographic steady states We close this section with some comments on the numerical scheme we use to solve the dual gravity problem. We impose periodic boundary conditions at z = 0 = zmax. In the longi- tudinal direction we use a Fourier decomposition with 1500 grid points, whereas in the holo- graphic direction we use a pseudo-spectral representation with 28 grid points. Our longest simulations use zmax = 80π and run from t = 0 till t = 80 with a time step of δt = 0.0012. In all our plots we shift one of the hot/cold transitions to the origin and make sure to only show times where the periodic boundary conditions do not yet affect the results. At every time step we apply low-pass filters to the time derivatives, whereby for the holographic direction we interpolate on a grid with 2/3 of the original grid points and subsequently interpolate back to main grid (see [47]). For the longitudinal direction we keep the lowest 30% of the Fourier modes used. Using Mathematica 11 with the scheme presented in [49] this gives a runtime on a standard laptop of about one week for each of the runs presented. 4 Holographic entanglement entropy We consider entanglement entropy as a measure for the entanglement of states associated to different spatial subregions R in quantum field theory [52], SR = −TrR ˆρR log ˆρR , (50) (50) where ˆρR = Tr ¯R ˆρ denotes the reduced density matrix obtained by performing on the full density matrix ˆρ a partial trace over the degrees of freedom outside R. For simplicity we will assume spatial subregions that are adapted to the symmetries of the Riemann problem. This means we choose for R at every constant time-slice (t = t0) spatial stripes of finite width ℓin z-direction and assume very large extend ℓ⊥≫ℓin the two other spatial directions x1 ⊥and x2 ⊥, (51) R± = {t = t0, −ℓ/2 ≤z ∓∆z ≤ℓ/2, |x1 ⊥| = |x2 ⊥| ≤ℓ⊥}. (51) In practice we assume ℓ⊥→∞and define two different regions R± centered at a distance ±∆z to the left and to the right of the initial location z = 0 of the interface in the Riemann problem. In Fig. 4 we show a typical arrangement of entangling regions that we use in our numerical simulations. The two entangling regions with ℓ= 1, shown in blue and red, are centered at ∆z = ±4. We also show a typical initial (solid black) and late time (dashed black) profile of the energy density. Our motivation for this specific placement of the two regions is that both regions reside initially entirely within either the cold or the hot bath, whereas at late time they both reside entirely within the NESS region. This will allow us to independently monitor the propagation of entanglement by the shock wave in the left region 13 SciPost Phys. 11, 047 (202 m t =2 m t =40 -30 -20 -10 0 10 20 30 0.0 0.5 1.0 1.5 2.0 2.5 3.0 m z ℰ/m4 Figure 4: Entangling regions: blue and red stripes are typical arrangements of en- tangling regions of size ℓ= 1 that initially reside entirely within the cold and hot bath, respectively. Black solid and black dashed lines are the spatial distributions of the energy density at early (t = 2) and late (t = 40) time in units of m = πTC. SciPost Phys. 4 Holographic entanglement entropy 11, 047 (2021) m t =2 m t =40 -30 -20 -10 0 10 20 30 0.0 0.5 1.0 1.5 2.0 2.5 3.0 m z ℰ/m4 Figure 4: Entangling regions: blue and red stripes are typical arrangements of en- tangling regions of size ℓ= 1 that initially reside entirely within the cold and hot bath, respectively. Black solid and black dashed lines are the spatial distributions of the energy density at early (t = 2) and late (t = 40) time in units of m = πTC. and the propagation of entanglement by the rarefaction wave in the right region and compare the results. In the limit ℓ→∞the entangling region (51) covers an entire spacelike slice of Minkowski space and for thermal equilibrium states (50) equals the von Neumann entropy of the full den- sity matrix ˆρR = ˆρ, i.e., the thermodynamic entropy of a quantum state in thermal equilib- rium. For the NESS system the situation is more subtle since at finite t the NESS is still of finite size. The expectation, however, is that after taking t →∞first it is possible to take the large size limit ℓ→∞with the region falling entirely in the NESS regime. In that case it should be possible to identify the entanglement entropy with the thermal entropy of the boosted thermal state. Explicit solutions for entanglement entropy are only available in exceptional cases such as free QFTs [53] or for 1+1 dimenstional CFTs in time-independent [54] and time dependent settings [55]. The holographic duality replaces the field theory computation of entanglement entropy by a much simpler extremisation problem for the area AR of a codimension two surface in the bulk [18], A SR = AR 4GN . (52) (52) We emphasise that this was originally proposed in a static setting [17], where the extremisation reduces to a minimal surface problem, but was later extended to the time-dependent setting we use here. The relevant surface shares its boundary with the entangling region R in the field theory and extremises the area functional in the bulk theory AR[X] = Z d3σ Æ Det(∂aX M∂bX N gMN), s.t. ∂X = ∂R. (53) (53) In general the surface embedding X M = X M(σa) is parametrised by three intrinsic coordinates σa. 4 Holographic entanglement entropy In our context, it is convenient to switch from (44a) to the inverse radial coordinate u = 1/r for which the boundary is located at u = 0, ds2 = gMNdx Mdx N = −Cdt2 −2dudt u2 + 2Gdzdt + S2 eBdx2 ⊥+ e−2Bdz2 , (54) (54) with {C, G,S, B} depend on {u, t,z}. The entangling regions (51) do not break translation symmetry in x1,2 ⊥-directions of the line element (54), hence also not of the Riemann problem in the boundary theory. Since we neglect the backreaction of the gauge field to the geometry, 14 SciPost Phys. 11, 047 (2021) it does not enter in the calculation of the entanglement entropy. Analogously to [56] we can parametrise the bulk surface as follows, X M(σ, x1 ⊥, x2 ⊥) = {X α(σ), x1 ⊥, x2 ⊥}, X α(σ) = {U(σ), T(σ), Z(σ)}. (55) X M(σ, x1 ⊥, x2 ⊥) = {X α(σ), x1 ⊥, x2 ⊥}, X α(σ) = {U(σ), T(σ), Z(σ)}. (55) (55) This choice simplifies the area functional considerably, because the integration over the per- pendicular directions x1,2 ⊥ can be performed explicitly and gives an overall factor ℓ⊥/2 ZZ −ℓ⊥/2 d⃗x⊥= ℓ2 ⊥. (56) (56) The remaining expression takes the form of a geodesic action, The remaining expression takes the form of a geodesic action, The remaining expression takes the form of a geodesic action, AR[X] = ℓ2 ⊥ Z dσ v t ¯gαβ(U(σ), T(σ), Z(σ))dX α dσ dX β dσ s.t. X α(0) = {0, t0,±ℓ/2}, (57) (57) where the metric ¯gαβ is related by a conformal factor to a three dimensional subspace (α,β = {u, t,z}) of the bulk metric (44a) ¯ds 2 = ¯gαβdxαdxβ = S(u, t,z)4e2B(u,t,z)gαβdxαdxβ . (58) (58) motion that follow from δAR = 0 are given by the geodesic equation d2X α dr2 + Γ α βγ dX β dr dX γ dr = J dX α dr , (59) (59) where Γ α βγ is the Levi-Cività connection associated to ¯gαβ and is meant to be evaluated at the location of the surface X α(σ); the friction term on the right hand side includes the Jacobian J = d2τ(σ) dσ2 / dτ(σ) dσ that originates from transforming from the affine parameter τ defined by dX α(τ) dτ dX β(τ) dτ ¯gαβ = 1 to the non-affine parameter σ. 4 Holographic entanglement entropy For numerical convenience, we choose a parametrisation that leads to the following Jacobian (for details see [57]) J(σ) = −51σ + 145σ3 −205σ5 + 159σ7 −65σ9 + 11σ11 (2 −σ2)(1 −σ2)(3 −3σ2 + σ4)(1 −σ2 + σ4) . (60) (60) The area functional (53) for the stripe region (51) suffers from two kinds of infinities. The first one is due to the infinite overall factor ℓ2 ⊥due to the infinitely long sides of the stripe in transverse direction. Since this factor contains no dynamical information we tame this infinity by considering in practice the entanglement entropy per transverse area SR/ℓ2 ⊥. The second one is less trivial and due to the fact that extremal surfaces in the HRT-prescription of the holographic entanglement entropy (HEE) extend all the way to the asymptotic boundary, which has infinite distance from any point in the interior. To regularise the entanglement entropy we subtract the vacuum value, i.e., the area of surfaces in Poincaré patch AdSd+1 with appropriate conformal pre-factor, ¯ds 2 0 = ¯g(0) αβ dxαdxβ = 1 u2(d−2) dt2 −2dtdu + dz2 . (61) (61) The solution for the extremal surface embedding of stripe regions can be expressed in closed form U0(σ) = u∗(1 −σ2), (62a) Z0(σ) = sgn(σ)  −ℓ 2 + U0(σ)4 dud−1 ∗ 2F2  1 2, d 2(d−1), 3d−8 2d−6; U(σ) u∗ ‹2(d−1) , (62b) T0(σ) = t0 −U0(σ), (62c) U0(σ) = u∗(1 −σ2), (62a) Z0(σ) = sgn(σ)  −ℓ 2 + U0(σ)4 dud−1 ∗ 2F2  1 2, d 2(d−1), 3d−8 2d−6; U(σ) u∗ ‹2(d−1) , (62b) T0(σ) = t0 −U0(σ), (62c) (62a) (62c) 15 SciPost Phys. 11, 047 (2021) where the u∗= 2ℓ pπΓ € 1 d(d−1) Š /Γ € d 2(d−1) Š is the location of the turning point of the surface in radial direction. The corresponding cut-off regularised surface area is given by Acut 0 = ℓd−2 ⊥ Z σ+ σ− dσ 1 Ud−1 0 q −˙T 2 0 −2 ˙U0 ˙T0 + ˙Z2 0 , (63) (63) where the cutoff at fixed radial location u = ucut is realized by the following bounds on the non-affine parameter v σ± = ± v t 1 −ucut u∗ . 4 Holographic entanglement entropy (64) (64) Together with the cut-off regularised expression for the gravity dual of the Riemann problem Together with the cut-off regularised expression for the gravity dual of the Riemann problem Acut = ℓ2 ⊥ Z σ+ σ− dσS2eB v t −A˙T 2 −2 U2 ˙U ˙T + 2F ˙T ˙Z + S2e−2B ˙Z2 , (65) (65) we can express the finite vacuum subtracted entanglement entropy per transverse area as Sren = Acut −Acut 0 4GNℓ2 ⊥ . (66) (66) In practice, we solve (59) using a relaxation algorithm [27, 57] using a cut-off ucut = 0.075 and verified this value is small enough to not affect the results presented. In practice, we solve (59) using a relaxation algorithm [27, 57] using a cut-off ucut = 0.075 and verified this value is small enough to not affect the results presented. 5.1 Energy and charge density The shapes of the shock and the rarefaction wave in the ideal hydro simulation depend on the initial details of the transition region. However, we have checked that the energy density in the steady state region is insensitive to this choice. In Appendix B we verify that also the properties of the NESS region in the holographic system do not depend on how the initial conditions are set up. The factor 20 in the denominator of (67) is a convenient numerical choice for realizing the initial conditions such that the evolution resembles the holographic result at t = 20. The shapes of the shock and the rarefaction wave in the ideal hydro simulation depend on the initial details of the transition region. However, we have checked that the energy density in the steady state region is insensitive to this choice. In Appendix B we verify that also the properties of the NESS region in the holographic system do not depend on how the initial conditions are set up. Although the initial conditions of the hydrodynamic simulation are perfectly smooth, the wave travelling towards the cold side steepens significantly as time progresses until the ap- plicability of ideal hydrodynamics and eventually also the numerical evolution breaks down. Shock+shock Shock+rarefaction -60 -40 -20 0 20 40 60 0.0 0.5 1.0 1.5 2.0 2.5 m z ρ/m3, m t ={0, 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60, 64, 68, 72, 76, 80} Figure 6: Evolution of the energy density (top) and charge density (bottom). Coloured lines are snapshots at various different times of the holographic simulation. For comparison we show in the upper panel results of the analytical shock+shock (black dotted, at t = 40 and 80) and shock+rarefaction (black dashed) solution as well as a numerical solution of the ideal hydrodynamics equations with smooth initial data (black solid, at t = 20,40 and 60). Shock+shock Shock+rarefaction -60 -40 -20 0 20 40 60 0.0 0.5 1.0 1.5 2.0 2.5 m z ρ/m3, m t ={0, 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60, 64, 68, 72, 76, 80} Figure 6: Evolution of the energy density (top) and charge density (bottom). Coloured lines are snapshots at various different times of the holographic simulation. 5.1 Energy and charge density In this section we present our results for the evolution of energy and charge density obtained from the holographic calculation. The global features of the evolution are similar to those of the analyticalal shock+rarefaction wave solution of the Riemann problem obtained in Sec. 2.2. In Fig. 5 we plot the time evolution of the energy and charge density for an initial cold/hot ratio of χ = p EC/EH = p nC/nH = 9/16 for both the energy and charge density. In the plot for the energy density (left) we clearly see a NESS region emerging briefly after t = 0 between two wave fronts that propagate from z = 0 towards z = ±∞. In the plot on the right we show Figure 5: Time evolution of the energy density (left) and charge density (right) for χ = 9/16 and nC/nH = χ2. A steady state region forms between the shock (moving towards the cold bath) and the rarefaction wave (moving towards the hot bath). Two regions with constant charge density can be identified within the steady state region. Figure 5: Time evolution of the energy density (left) and charge density (right) for χ = 9/16 and nC/nH = χ2. A steady state region forms between the shock (moving towards the cold bath) and the rarefaction wave (moving towards the hot bath). Two regions with constant charge density can be identified within the steady state region. 16 SciPost Phys. 11, 047 (2021) the evolution of the charge density. Two regions with constant but different charge densities emerge inside the NESS region, which indicates the formation of a contact discontinuity. It is interesting to compare the result of the holographic simulation to the solution of the corresponding Riemann problem in ideal hydrodynamics. For this we show in Fig. 6 profiles of the energy density and charge density of the holographic result at various times together with the (unphysical) shock+shock and (physical) shock+rarefaction solutions presented in Sec. 2. In addition we include a numerical solution obtained from an ideal hydrodynamic simulation with smooth initial conditions for the energy density E(z) = EC + EH 2 + EH −EC 2 tanh zmax 20 sin 2πz zmax ‹ . (67) (67) The factor 20 in the denominator of (67) is a convenient numerical choice for realizing the initial conditions such that the evolution resembles the holographic result at t = 20. 5.1 Energy and charge density For comparison we show in the upper panel results of the analytical shock+shock (black dotted, at t = 40 and 80) and shock+rarefaction (black dashed) solution as well as a numerical solution of the ideal hydrodynamics equations with smooth initial data (black solid, at t = 20,40 and 60). 17 SciPost Phys. 11, 047 (2021) Figure 7: Snapshots of the local fluid velocity (solid) and charge velocity (dashed) at four different times for the same evolution as in Fig. 5. The bottom panel shows a magnification of the upper panel, where the velocity profile of the charge diffusion at the contact discontinuity of the two charge plateaus is clearly visible. Figure 7: Snapshots of the local fluid velocity (solid) and charge velocity (dashed) at four different times for the same evolution as in Fig. 5. The bottom panel shows a magnification of the upper panel, where the velocity profile of the charge diffusion at the contact discontinuity of the two charge plateaus is clearly visible. The formation of shocks from smooth initial data is a well known phenomenon in non-viscous hydrodynamics and faithful simulations require shock-capturing methods which we did not attempt to implement. The wave that moves towards the hot side on the other hand re- mains smooth and becomes wider with time. Coloured lines present snapshots of the holo- graphic result, which at early times resemble the hydrodynamic solution, but at late times become closer to the shock+rarefaction solution. The energy density in the NESS steady state region agrees accurately with the result from the ideal hydrodynamic calculation, but dif- fers slightly from the analytical shock+shock (dotted) solution. To be precise, using (27) we find ES = 625/432 ≈1.44676, ES ≈1.4450 and ES ≈1.446 for the shock+shock, shock+rarefaction and ideal hydrodynamics case respectively and ES ≈1.4435 in the holo- graphic simulation. By varying the z-location of the probe point we estimate the numerical accuracy of the holographic result to be 0.001, which means that within numerical accuracy the holographic result agrees with the shock+rarefaction solution as presented in Section 2. The formation of shocks from smooth initial data is a well known phenomenon in non-viscous hydrodynamics and faithful simulations require shock-capturing methods which we did not attempt to implement. The wave that moves towards the hot side on the other hand re- mains smooth and becomes wider with time. 5.1 Energy and charge density -15 -10 -5 0 5 10 15 0.0 0.5 1.0 1.5 2.0 2.5 m z ρ/m3, m t ={0, 4, 8, 12, 16, 20, 24, 28, 32, 36, 40} 1.363 m t 1 5 10 2 4 6 8 m t Δdiff Figure 9: Left: Diffusion of the charge density in a heat bath with constant temper- ature. Right: Evolution of the charge diffusion width ∆diff(t). The blue line is the result extracted form the numerical simulation and the black line the analytical fit. Figure 8: Time evolution of the energy density (left) and charge density (right) as a function of ξ = z/t. At the latest time we managed to obtain (mt = 80) the solution closely resembles the shock+rarefaction solution found in Section 2. -15 -10 -5 0 5 10 15 0.0 0.5 1.0 1.5 2.0 2.5 m z ρ/m3, m t ={0, 4, 8, 12, 16, 20, 24, 28, 32, 36, 40} 1.363 m t 1 5 10 2 4 6 8 m t Δdiff Figure 9: Left: Diffusion of the charge density in a heat bath with constant temper- ature. Right: Evolution of the charge diffusion width ∆diff(t). The blue line is the result extracted form the numerical simulation and the black line the analytical fit. -15 -10 -5 0 5 10 15 0.0 0.5 1.0 1.5 2.0 2.5 m z ρ/m3, m t ={0, 4, 8, 12, 16, 20, 24, 28, 32, 36, 40} 1.363 m t 1 5 10 2 4 6 8 m t Δdiff Figure 9: Left: Diffusion of the charge density in a heat bath with constant temper- ature. Right: Evolution of the charge diffusion width ∆diff(t). The blue line is the result extracted form the numerical simulation and the black line the analytical fit. -15 -10 -5 0 5 10 15 0.0 0.5 1.0 1.5 2.0 2.5 m z ρ/m3, m t ={0, 4, 8, 12, 16, 20, 24, 28, 32, 36, 40} 1.363 m t 1 5 10 2 4 6 8 m t Δdiff Figure 9: Left: Diffusion of the charge density in a heat bath with constant temper- ature. Right: Evolution of the charge diffusion width ∆diff(t). The blue line is the result extracted form the numerical simulation and the black line the analytical fit. expected from a solution that is locally in equilibrium the two velocities are virtually indis- tinguishable. 5.1 Energy and charge density Coloured lines present snapshots of the holo- graphic result, which at early times resemble the hydrodynamic solution, but at late times become closer to the shock+rarefaction solution. The energy density in the NESS steady state region agrees accurately with the result from the ideal hydrodynamic calculation, but dif- fers slightly from the analytical shock+shock (dotted) solution. To be precise, using (27) we find ES = 625/432 ≈1.44676, ES ≈1.4450 and ES ≈1.446 for the shock+shock, shock+rarefaction and ideal hydrodynamics case respectively and ES ≈1.4435 in the holo- graphic simulation. By varying the z-location of the probe point we estimate the numerical accuracy of the holographic result to be 0.001, which means that within numerical accuracy the holographic result agrees with the shock+rarefaction solution as presented in Section 2. In the bottom panel of Fig. 6, we plot profiles of the charge density in the holographic result (solid coloured lines) at various times together with two dashed lines for times t = 40 and 80, which have ¯ρ1 = 19/16 = 1.1875 and ¯ρ2 = 43/27 ≈1.5926 obtained from the analytical double shock solution (11) as well as two dotted lines at ¯ρ1 ≈1.1866 and ¯ρ2 ≈1.5866 of the shock+rarefaction solution (31). We evaluate the full holographic values of ¯ρ1,2 at the point where the z-derivative of ¯ρ is minimised, which at t = 80 happens at z = −41.29 and z = 10.26, where ¯ρ1 ≈1.1845 and ¯ρ1 ≈1.5823 respectively. In contrast to the analytical solution the contact discontinuity (see Sec. 2 and also [20]) manifests in the holographic model as a smooth crossover region that progressively broadens with time. Fig. 7 shows the local fluid velocity, as determined by diagonalising the full stress-energy tensor (solid), as well as the velocity of the charge as defined by vcharge = Jz/Jt (dashed). As 18 SciPost Phys. 11, 047 (2021) SciPost Phys. 11, 047 (2021) Figure 8: Time evolution of the energy density (left) and charge density (right) as a function of ξ = z/t. At the latest time we managed to obtain (mt = 80) the solution closely resembles the shock+rarefaction solution found in Section 2. Figure 8: Time evolution of the energy density (left) and charge density (right) as a function of ξ = z/t. At the latest time we managed to obtain (mt = 80) the solution closely resembles the shock+rarefaction solution found in Section 2. 5.1 Energy and charge density In particular this implies that in the rest frame of the steady state the charge is almost at rest throughout the contact discontinuity. Nevertheless, due to diffusion the charge does smooth out, and a small velocity profile is visible (Fig. 7 bottom, see also below. The time evolution of the charge and energy density and in particular the rarefaction wave can be better understood by showing the profiles as a function of the scaled coordinate ξ = z/t, as shown in Fig. 8. Since the width of the shock is approximately constant in time, in the scaled coordinates the shock indeed resembles more closely a true shock (i.e. a discontinuity), both for the energy and charge density. Also the rarefaction wave resembles the analytical rarefaction wave from Section 2 more closely at later times, but with the limited time span available it is not clear if it would converge to the analytical result in the late time limit. The charge density again clearly shows the two plateaus at late times, and also here it is clear that the diffusion at the contact discontinuity becomes a true discontinuity in the late time limit in these scaled coordinates. This contact discontinuity can be studied more precisely by studying a related but separate problem where we set up of two baths of charge at different chemical potential in a space at constant temperature. We simulated this situation by using the initial condition of Fig. 5, with the sole difference that we made both temperatures equal to the temperature of the cold bath. The results are shown in Fig. 9. Indeed, we find that the diffusion of charge is qualitatively different as compared to the shock and rarefaction waves. To quantify the difference we define the (time dependent) charge diffusion width ∆diff(t) as the spatial distance between the two points where the charge density is at 25% and 75% in between the two baths with lower and higher charge, respectively. On the right hand side of Fig. 9 we plot the time evolution of ∆diff which clearly follows the expected pt scaling of a diffusion process. In rescaled coordinates this indeed implies the contact discontinuity becomes a true discontinuity on a timescale of 19 SciPost Phys. 11, 047 (2021) Shock+rarefaction -30 -20 -10 0 10 20 30 0.0 0.5 1.0 1.5 2.0 2.5 m z ρ/m3, m t =40.0 SciPost Phys. 5.1 Energy and charge density 11, 047 (2021) Shock+rarefaction -30 -20 -10 0 10 20 30 0.0 0.5 1.0 1.5 2.0 2.5 m z ρ/m3, m t =40.0 Figure 10: We show a snapshot of the charge density at t = 40 for a temperature ratio of χ = 16/9 and three different ratios of the charge density, with nH/nC being 256/81, 64/27 and 1 for the blue, red and green curves respectively. In general there are two regions of constant charged, determined solely by χ and nH/nC. These two regions almost coincide for the 64/27 ratio, but are different for the blue and green evolutions. For comparison we again show the analytical shock+rarefaction solutions of Section 2 (dashed). Figure 10: We show a snapshot of the charge density at t = 40 for a temperature ratio of χ = 16/9 and three different ratios of the charge density, with nH/nC being 256/81, 64/27 and 1 for the blue, red and green curves respectively. In general there are two regions of constant charged, determined solely by χ and nH/nC. These two regions almost coincide for the 64/27 ratio, but are different for the blue and green evolutions. For comparison we again show the analytical shock+rarefaction solutions of Section 2 (dashed). pt. As explained in Sec. 2 the profile of the charge density depends on both the ratio of the χ as well as nC/nH. In Fig. 10 we show charge densities at t = 40 for nC/nH equal to 256/81 (blue, same as Fig. 5), 64/27 (red) and 1 (green). The ratio 64/27 equals χ−3/2, which implies that the third root of the charge density has the same ratio as the fourth root of the energy density, as suggested by dimensional analysis. Indeed this ratio approximately leads to a charge profile with only one constant charge region, as opposed to the other two solutions, where two separate charged regions are present. Even if the charge densities in the hot and cold bath are equal (nC = nH) there is still a non-trivial charge flow and density, as driven by the steady state of the energy density. One crucial feature of the NESS is that in particular the shock is a far-from-equilibrium effect that cannot be described by hydrodynamics. To quantify this we show in Fig. 11 (left) the transverse pressure over the energy density in the local restframe (again determined by diagonalising the stress-energy tensor). In ideal hydrodynamics of a conformal theory this ratio PT/Eloc = 1/3, however in particular near the shock region significant deviations are visible (see also solid lines in Fig. 11 (right)). For this we use the hydrodynamic constituent equations Tµν = ϵ uµuν + p[ϵ]∆µν −η[ϵ]σµν −ζ[ϵ]∆µν∇µuµ + O(∂2), where (68) σµν = ∆µα∆νβ(∇αuβ + ∇βuα) −2 3∆µν∆αβ∇αuβ , (69) ∆µν = gµν + uµuν , (70) (68) (69) (70) together with our determined local energy density ε, pressure p[ε] = ε/3, fluid velocity uµ as well as the ratio η/s = 1/4π and ζ = 0, we also compare the transverse pressure with the transverse pressure as determined from these first order viscous hydrodynamics, as shown as dashed lines in Fig. 11 (right). Indeed the evolution of the rarefaction wave can be entirely de- scribed using viscous hydrodynamics, however for the shock there are significant differences. Numerically it is more challenging to evolve profiles with χ < 9/16. However, we were able to evolve some shorter runs stably, albeit on smaller grids and with a shorter evolution time. Results for the energy density and the hydrodynamic comparison at t = 12 are shown in 20 SciPost Phys. 5.2 Shock evolution and entropy production One of the main motivations in studying the NESS in holography is a complete description of its dynamics beyond the hydrodynamic limit, which is particularly relevant for the evolu- tion of the shocks. References [15, 20] showed that at intermediate times the shock widens diffusively as governed by viscous hydrodynamics, with characteristic width wshock ∝pt. At some time, however, the entropy production within hydrodynamics is not large enough to be consistent with the total entropy production and the shock cannot continue to diffuse. The typical timescale for this transition was estimated to be equal to tdiff ∝ η sTδ2 , (71) (71) where δ = TH/TC −1 is assumed to be small. After this time it is unknown if the shock settles down to a soliton-like object of constant width, or if it continues to widen at a smaller rate. In Fig. 13 (left) we show snapshots of the time derivative of the energy density for the evolution of the shocks in Fig. 5 (which has δ = 1/3). In the right plot we show the full-width at half- maximum of the shocks shown in the left plot as a function of time. Indeed, at early times the width grows diffusively (red dashed, with a small off-set that is subleading, but can also be partly explained by the initial profile). Around t ≈20 the width starts growing more slowly, in qualitative agreement with the estimate provided in (71) (note that T = m/π). All our numerical data points indicate that this width keeps growing logarithmically in time, but we note that it is nevertheless also possible to fit a function of the form C + ae−bt, which would settle down to the soliton-like object as conjectured in [20]. As discussed in section 2, solutions to the Riemann problem in ideal hydrodynamics are not unique and physically sensible solutions need to be selected by imposing additional constraints, such as the entropy condition (13). Solutions to the holographic Riemann problem are unique and conditions such as (13) are encoded in the equations of motion of the dual gravity problem [58]. In Fig. pt. 11, 047 (2021) Fig. 12 for values of χ of 9/16 (blue, as in Fig. 5), 4/9 (red) and 16/49 (green). Interestingly, also for these larger ratios the rarefaction wave is always well described by hydrodynamics, though with larger viscous corrections as is apparent from the comparison with ideal hydro- dynamics. For the shock region deviations from viscous hydrodynamics become larger as one increases the ratio between the hot and cold baths. Fig. 12 for values of χ of 9/16 (blue, as in Fig. 5), 4/9 (red) and 16/49 (green). Interestingly, also for these larger ratios the rarefaction wave is always well described by hydrodynamics, though with larger viscous corrections as is apparent from the comparison with ideal hydro- dynamics. For the shock region deviations from viscous hydrodynamics become larger as one increases the ratio between the hot and cold baths. pt. 11, 047 (2021) Figure 11: (left) For the evolution of Fig. 6 we show the ratio of the transverse pres- sure over the energy density in the local restframe together with the shock velocities (black, dashed) computed from Eqn. (11). Most of the evolution is close to ther- mal equilibrium (PT = Eloc/3, in green in the colour coding), but around the shocks there are significant deviations. (right) For several times we present the deviations with respect to ideal hydro (solid) and first order viscous hydrodynamics (dashed), normalised to the transverse pressure itself. The entire evolution can be described by viscous hydrodynamics with better than 1% accuracy. Figure 11: (left) For the evolution of Fig. 6 we show the ratio of the transverse pres- sure over the energy density in the local restframe together with the shock velocities (black, dashed) computed from Eqn. (11). Most of the evolution is close to ther- mal equilibrium (PT = Eloc/3, in green in the colour coding), but around the shocks there are significant deviations. (right) For several times we present the deviations with respect to ideal hydro (solid) and first order viscous hydrodynamics (dashed), normalised to the transverse pressure itself. The entire evolution can be described by viscous hydrodynamics with better than 1% accuracy. Shock+rarefaction -10 -5 0 5 10 0 2 4 6 8 m z ℰ/m4, m t =12.0 -10 -5 0 5 10 -0.10 -0.05 0.00 0.05 m z T-T,hyd T (solid ideal, dashed viscous), m t =12.0 Figure 12: (top) Energy density for different heat bath temperature ratios together with the shock+rarefaction from Section 2 (dashed). (bottom) Comparison with ideal (solid) and viscous (dashed) hydrodynamics. For larger ratios ideal hydrody- namics becomes a worse description for the rarefaction wave, though viscous hy- drodynamics is applicable. The shock region has increasingly large deviations from viscous hydrodynamics as the ratio is increased. T-T,hyd T (solid ideal, dashed viscous), m t =12.0 -10 -5 0 5 10 -0.10 -0.05 0.00 0.05 m z Figure 12: (top) Energy density for different heat bath temperature ratios together with the shock+rarefaction from Section 2 (dashed). (bottom) Comparison with ideal (solid) and viscous (dashed) hydrodynamics. For larger ratios ideal hydrody- namics becomes a worse description for the rarefaction wave, though viscous hy- drodynamics is applicable. The shock region has increasingly large deviations from viscous hydrodynamics as the ratio is increased. 21 SciPost Phys. 5.2 Shock evolution and entropy production 14 we show snapshots of the divergence of the entropy current as a function of time, where sµ = 4Eloc 3T uµ, with uµ the local fluid velocity and Eloc the energy density in the -60 -40 -20 0 20 40 60 -0.10 -0.05 0.00 0.05 0.10 0.15 m z ∂tℰ/m5, m t ={10, 20, 30, 40, 50, 60, 70, 80} 1.102 log(m t) + 0.609 0.782 m t + 5.5 5.82 - 3.18 ⅇ-0.0256 m t 5 10 50 100 0 1 2 3 4 5 6 m t m wshock, FWHM Figure 13: We show the change in shape of the outgoing waves from the time deriva- tive of the energy density. Colours from yellow to red correspond to snapshots of the energy density profile from early to late times. Both, the left moving and the right moving waves disperse. On the right we show the time evolution of the full-width at half-maximum together with different numerical fits, corresponding to diffusive growth (red dashed), logarithmic growth (blue solid), or a possible exponential de- cay to a shock of constant width at late times (green dotted). -60 -40 -20 0 20 40 60 -0.10 -0.05 0.00 0.05 0.10 0.15 m z ∂tℰ/m5, m t ={10, 20, 30, 40, 50, 60, 70, 80} 1.102 log(m t) + 0.609 0.782 m t + 5.5 5.82 - 3.18 ⅇ-0.0256 m t 5 10 50 100 0 1 2 3 4 5 6 m t m wshock, FWHM m t Figure 13: We show the change in shape of the outgoing waves from the time deriva- tive of the energy density. Colours from yellow to red correspond to snapshots of the energy density profile from early to late times. Both, the left moving and the right moving waves disperse. On the right we show the time evolution of the full-width at half-maximum together with different numerical fits, corresponding to diffusive growth (red dashed), logarithmic growth (blue solid), or a possible exponential de- cay to a shock of constant width at late times (green dotted). 22 SciPost Phys. 5.2 Shock evolution and entropy production The entropy production is to a good approximation given by the sum of the entropy production of the shock and rarefaction waves as derived in Fig. 14, and also the late time value (4.07, from the red dashed fit on the right) matches well with the hydrodynamic result shown in Fig. 14 (3.77). local restframe. The entropy production is negligible in the NESS region, but a significant amount of entropy is produced by the outgoing waves. As expected from [29] the divergence of the local entropy current is however everywhere positive. Fig. 14 (right) shows the integral of the divergence of the entropy current over the waves that travel towards the cold (blue dots) and the hot side (red dots). The entropy produced by the wave moving towards the cold bath slowly decays to a constant value, similar to a shock wave, and can be compared to the analytical solution (14), which for χ = 9/16 gives Z z<0 dz ∂µsµ = π p 3m3 ‚ χ−1/4 − v tχ(3 + χ) 1 + 3χ Œ ≈0.00610. (72) (72) At the end of the simulation we find an entropy production of about 0.007, which is still higher than the value obtained from the shock+shock solution of the Riemann problem cited above, but the extrapolation shown in Fig. 14 predicts for t →∞a significantly smaller final value of about 0.0037. On the other hand, the entropy production of the wave moving towards the hot side (red dots in Fig. 14 (right)) decays to zero with a power law indicating that this wave indeed becomes at late time a rarefaction wave which has zero entropy production per definition. At the end of the simulation we find an entropy production of about 0.007, which is still higher than the value obtained from the shock+shock solution of the Riemann problem cited above, but the extrapolation shown in Fig. 14 predicts for t →∞a significantly smaller final value of about 0.0037. On the other hand, the entropy production of the wave moving towards the hot side (red dots in Fig. 14 (right)) decays to zero with a power law indicating that this wave indeed becomes at late time a rarefaction wave which has zero entropy production per definition. Lastly, we can compare the total entropy production directly with the holographic dual by evaluating the area density of the apparent horizon A as shown in Fig. 5.2 Shock evolution and entropy production 11, 047 (2021) -60 -40 -20 0 20 40 60 0 1 2 3 4 5 6 m z 103∂μsμ/m4, m t = {10, 20, 30, 40, 50, 60, 70, 80} shock rarefaction 3.77+ 28.8 m t 80.5 t0.700 10 20 50 5.0 7.5 10.0 12.5 15.0 17.5 m t 103 m3  z≶0 dz ∂μsμ Figure 14: We show the divergence of the entropy current for several times (left) as well as the integral over the left (shock, blue) and right (rarefaction, red) re- gions (right). The entropy production in the shock settles down to a constant value, whereas for the rarefaction wave the entropy production decays to zero in a power- law fashion. -60 -40 -20 0 20 40 60 0 1 2 3 4 5 6 m z 103∂μsμ/m4, m t = {10, 20, 30, 40, 50, 60, 70, 80} 103 m3  dz ∂μsμ shock rarefaction 3.77+ 28.8 m t 80.5 t0.700 10 20 50 5.0 7.5 10.0 12.5 15.0 17.5 m t 103 m3  z≶0 dz ∂μsμ Figure 14: We show the divergence of the entropy current for several times (left) as well as the integral over the left (shock, blue) and right (rarefaction, red) re- gions (right). The entropy production in the shock settles down to a constant value, whereas for the rarefaction wave the entropy production decays to zero in a power- law fashion. Apparent horizon 4.07 + 96.3 (mt)0.610 5 10 50 100 10 20 50 m t 103 m3 ∫dz ∂tsAH Figure 15: We show the entropy density as determined from the area of the apparent horizon (left) as well as time derivative of the spatial integral (right). The entropy production is to a good approximation given by the sum of the entropy production of the shock and rarefaction waves as derived in Fig. 14, and also the late time value (4.07, from the red dashed fit on the right) matches well with the hydrodynamic result shown in Fig. 14 (3.77). Apparent horizon 4.07 + 96.3 (mt)0.610 5 10 50 100 10 20 50 m t 103 m3 ∫dz ∂tsAH Figure 15: We show the entropy density as determined from the area of the apparent horizon (left) as well as time derivative of the spatial integral (right). 5.3 Extremal surfaces and entanglement entropy Let us now discuss our numerical results for the entanglement entropy in the NESS system. It is useful to first analyse some features of extremal surfaces from which we compute the entangle- ment entropy. Fig. 16 shows a typical family of such surfaces together with the radial position of the apparent horizon in a gauge where α = 0. In the top (bottom) row, we display the results for entangling regions of width ℓ= 2 (ℓ= 1.5) centered at z = −4 (z = +4) corresponding to the blue (red) region in Fig. 4. Surfaces with small ℓ(not shown here) reside mostly in the asymptotic AdS part of the geometry which explains the universal (state-independent) UV scaling of entanglement entropy. Surfaces with large ℓreach deep into the bulk and are there- fore sensitive to the geometry close to the horizon and lead to state-dependent contributions in the IR scaling of the entanglement entropy (see similar discussion in [59]). In static and boosted AdS black brane geometries, extremal surfaces that are connected to the boundary cannot enter the region beyond the horizon [60]. However, in time-dependent geometries such as the one considered here, the situation is different and there are exam- ples known, where extremal surfaces cross the apparent horizon and therefore also the event horizon in regions where the spacetime changes rapidly in time [61]. The holographic NESS 0 10 20 30 40 0.2 0.4 0.6 0.8 1.0 1.2 m t u m ℓ=2 0 2 4 6 8 10 12 14 0.75 0.80 0.85 0.90 0.95 1.00 m t u m ℓ=2 m t =2 m t =40 -5.0 -4.5 -4.0 -3.5 -3.0 0.2 0.4 0.6 0.8 1.0 1.2 m z u m ℓ=2 0 10 20 30 40 0.2 0.4 0.6 0.8 1.0 1.2 m t u m ℓ=1.5 0 5 10 15 20 0.70 0.75 0.80 0.85 m t u m ℓ=1.5 m t =2 m t =40 3.2 3.4 3.6 3.8 4.0 4.2 4.4 4.6 0.2 0.4 0.6 0.8 1.0 1.2 m z u m ℓ=1.5 Figure 16: Cross-sections of extremal surfaces for entangling regions of size ℓ= 2 centered at z = −4 (top, cold region) and of size ℓ= 1.5 centered at z = 4 (bottom, hot region) in the geometry with χ = p EC/EH = 9/16. 5.2 Shock evolution and entropy production 15 (left), whereby we use that SAH = A/4GN, and in analogy with (47) we show sAH ≡S/4πGN. In Fig. 15 (right) 23 SciPost Phys. 11, 047 (2021) we show the spatial integral of the time derivative of the apparent horizon density and it can be seen that the time evolution matches well with the sum of the entropy production of the shock and rarefaction waves from the hydrodynamic results shown in Fig. 14. 5.3 Extremal surfaces and entanglement entropy While we have not attempted to construct examples for such geodesics, we expect the situation to be similar in the holographic dual of the NESS system. system in our work is similar to a system of colliding shock waves [56], where geodesics dual to two-point functions could cross the horizon, but no such extremal surfaces were found. While we have not attempted to construct examples for such geodesics, we expect the situation to be similar in the holographic dual of the NESS system. A further effect is the warping of surfaces close to the apparent horizon in the boosted part of the geometry, i.e. in the part that corresponds to the NESS in the boundary theory. This effect is clearly visible in our example with ℓ= 2 (less pronounced for ℓ= 1.5) in the plots in the middle of Fig. 16, in which we zoom into the region close to the horizon where the geometry transitions from the static to the boosted black brane geometry. In addition, we show in the right panel of Fig. 16 cross-sections of surfaces in the u-z plane at early (t = 2) and late time (t = 40), i.e., surfaces that reside entirely in the static and in the boosted black brane geometry, respectively. At early times, when the surfaces reside entirely in the static part of the geometry, the embedding function is symmetric with respect to the center of the entangling region (located at z = ±4). At late times this symmetry is clearly broken by velocity of the steady state. In Fig. 17 we show the renormalised entanglement entropy as a function of time at these locations for several different lengths of the interval, ranging from ℓ= 0.6 till ℓ= 2.0, together with the energy density as also shown in Fig. 6. The renormalised entropy is computed as a difference to its vacuum value, for which we use a cut-off in the holographic coordinate at ucut = 0.075, in a gauge where α = 0 (see also Sec. 3 and [56]). Since the entanglement entropy of the infinite strip region has both UV and IR divergences, we choose to show a linear transformation such that its renormalised version Sren agrees with the energy density in both the black brane and the steady state regime: aSren + b = E, which in particular means the curves are insensitive to our choice of regularisation. 5.3 Extremal surfaces and entanglement entropy The plots on the left show surfaces at various different boundary times and their position relative to the appar- ent horizon whose radial position is shown in black and regions beyond the horizon are shown in gray. In the middle, we zoom into the transition region close to the hori- zon between static and boosted black brane. On the right, we show cross-sections of surfaces in the u-z plane at early (t = 2) and late time (t = 40). 0 10 20 30 40 0.2 0.4 0.6 0.8 1.0 1.2 m t u m ℓ=2 u m ℓ=1.5 m t =2 m t =40 -5.0 -4.5 -4.0 -3.5 -3.0 0.2 0.4 0.6 0.8 1.0 1.2 m z u m ℓ=2 m ℓ=1.5 0 2 4 6 8 10 12 14 0.75 0.80 0.85 0.90 0.95 1.00 m t m ℓ=2 0 10 20 30 40 0.2 0.4 0.6 0.8 1.0 1.2 m t u m ℓ=1.5 0 5 10 15 20 0.70 0.75 0.80 0.85 m t u m ℓ=1.5 u 0 10 20 30 40 0.2 0.4 0.6 0.8 1.0 1.2 m t u m ℓ1.5 0 5 10 15 20 0.70 0.75 0.80 0.85 m t u m ℓ=1.5 u m t =2 m t =40 3.2 3.4 3.6 3.8 4.0 4.2 4.4 4.6 0.2 0.4 0.6 0.8 1.0 1.2 m z u Figure 16: Cross-sections of extremal surfaces for entangling regions of size ℓ= 2 centered at z = −4 (top, cold region) and of size ℓ= 1.5 centered at z = 4 (bottom, hot region) in the geometry with χ = p EC/EH = 9/16. The plots on the left show surfaces at various different boundary times and their position relative to the appar- ent horizon whose radial position is shown in black and regions beyond the horizon are shown in gray. In the middle, we zoom into the transition region close to the hori- zon between static and boosted black brane. On the right, we show cross-sections of surfaces in the u-z plane at early (t = 2) and late time (t = 40). 24 SciPost Phys. 11, 047 (2021) system in our work is similar to a system of colliding shock waves [56], where geodesics dual to two-point functions could cross the horizon, but no such extremal surfaces were found. 5.3 Extremal surfaces and entanglement entropy 11, 047 (2021) Figure 17: We show the energy density at z = −4 (shock regime, left) and z = 4 (rarefaction regime, right) together with the time evolution of the holographic en- tanglement entropy SEE for different lengths. Since the SEE is sensitive to UV regu- larisation and length dependence we apply a linear transformation such that at early time (hot/cold) and late time (steady state) the entanglement entropy agrees with the energy density. After this rescaling the curves agree almost exactly, although shorter lengths that are more sensitive to regions closer to the boundary have a small delay (see insets). Figure 17: We show the energy density at z = −4 (shock regime, left) and z = 4 (rarefaction regime, right) together with the time evolution of the holographic en- tanglement entropy SEE for different lengths. Since the SEE is sensitive to UV regu- larisation and length dependence we apply a linear transformation such that at early time (hot/cold) and late time (steady state) the entanglement entropy agrees with the energy density. After this rescaling the curves agree almost exactly, although shorter lengths that are more sensitive to regions closer to the boundary have a small delay (see insets). Figure 18: Similarly to Figure 17, for ℓ= 1 we now show the energy density (solid) as well as the rescaled HEE (dashed, the rescaling parameters are the same as in Figure 17 for ℓ= 1) for different positions of the entangling region, varying from −4 till −14 (left, shock region) and from 4 till 14 (right, rarefaction region). Note that the rescaling is the same for all curves, which reaffirms that the evolution of the HEE is almost entirely determined by the evolution of the energy density. Figure 18: Similarly to Figure 17, for ℓ= 1 we now show the energy density (solid) as well as the rescaled HEE (dashed, the rescaling parameters are the same as in Figure 17 for ℓ= 1) for different positions of the entangling region, varying from −4 till −14 (left, shock region) and from 4 till 14 (right, rarefaction region). Note that the rescaling is the same for all curves, which reaffirms that the evolution of the HEE is almost entirely determined by the evolution of the energy density. nd it was shown that for any theory vE ≤vB [63]. and it was shown that for any theory vE ≤vB [63]. 5.3 Extremal surfaces and entanglement entropy The plots in Fig. 17 hence compare the shape of the entanglement entropy with the shape of the energy density both during the passing of the shock and rarefaction waves. From the insets it is clear that the entanglement entropy is slightly delayed as compared to the energy density, in particular for shorter intervals. This delay is expected, as the surfaces probe into the past geometry (Fig. 16), even though for larger intervals we note that the entangling geometry starts to feel the wave earlier, since the region is bounded by z ± ℓ/2. Fig. 18 shows the renormalised entanglement entropy as a function of time for intervals of ℓ= 1 located at eleven different locations ranging from z = −4 till z = −14 (left figure, shock region) and from z = 4 till z = 14 (right figure, rarefaction region). Here the same linear transformation is used as in Fig. 17 for ℓ= 1. As time progresses the shock (left) or rarefaction (right) wave passes through the interval, after which the interval settles down to the steady state regime. The values of the entanglement entropy in the cold, steady state and hot bath regions are given by 0.466, 0.835 and 1.351 respectively, as can also be analytically computed [62]. We again find a small delay of the entanglement entropy evolution, which is more pronounced for the rarefaction case. The time evolution of the entanglement entropy received some recent attention as a probe of equilibration towards a thermal state. After perturbing or quenching a quantum state, the entanglement entropy will saturate to its final value in a time tS that is at least tS ≥R/vB [63], with R the radius of the largest sphere that can be inscribed in the entangling region and vB the butterfly velocity that characterises chaotic growth of quantum operators (for our case of a neutral holographic plasma vB = p d/2(d −1) in d spacetime dimensions). The start of this equilibration process, also called entanglement tsunami [64], is characterised by the entanglement velocity, whereby SEE(t) = seqAvEt, with seq the equilibrium entropy density, A the area of the boundary of the entangling region and where this equation defines the entanglement velocity vE. For neutral holographic plasmas it was found that [64] vE = p d(d −2)1/2−1/d/(2[d −1])1−1/d vE = p d(d −2)1/2−1/d/(2[d −1])1−1/d (73) (73) 25 SciPost Phys. 5.3 Extremal surfaces and entanglement entropy For the case of the steady state formation, a simple approximation of vE is possible when the entanglement equilibration is much faster than the timescale of the perturbation of the state [16]. For the shock/rarefaction regions considered here, this would be the case when the respective shock and rarefaction velocities are much slower than vE. In that case the time evolution of the HEE can be approximated by the time evolution of the equilibrium entropy density, which in the local restframe is just proportional to T d. In this approximation the analogy of the entanglement velocity is given by [16] vav,C/H = vC/H 1 − T d C/H cosh(θ)T d ! , (74) (74) where θ = arctanh(vS) is the boost factor associated to the steady state region. As discussed for the case of two shock waves in [16], when χ →0 this velocity violates the bound on tS mentioned above for d > 2 spacetime dimensions. For χ →0 a full holographic calculation is 26 SciPost Phys. 11, 047 (2021) therefore necessary, extending the results for intermediate values of χ shown here in Figs. 17 and 18. Our small time delay of the HEE compared to the energy density can indeed be interpreted as the need to study the full HEE instead of the equilibrium entropy density. Un- fortunately in our setting it is numerically difficult to probe small enough χ and large enough entangling regions to truly investigate the butterfly bound tS ≥R/vB. We leave this to a future investigation. A promising approach for this is to use membrane theory [63,65]. therefore necessary, extending the results for intermediate values of χ shown here in Figs. 17 and 18. Our small time delay of the HEE compared to the energy density can indeed be interpreted as the need to study the full HEE instead of the equilibrium entropy density. Un- fortunately in our setting it is numerically difficult to probe small enough χ and large enough entangling regions to truly investigate the butterfly bound tS ≥R/vB. We leave this to a future investigation. A promising approach for this is to use membrane theory [63,65]. We end this section with an attempt to characterise the differences between shock and rarefaction waves in the NESS system with a new quantity that is inspired by the entanglement temperature. 5.3 Extremal surfaces and entanglement entropy In the limit where the entangling region is small compared to the length scale as given by the energy density (meaning ℓd ≪E) changes in entanglement entropy and the energy density satisfy a universal relation that is analogous to the first law of thermodynamics (dE = TdS) and is therefore called first law of entanglement entropy [66] ∆ER = Tent∆SR , (75) (75) where Tent is the entanglement temperature, ∆SR is the variation of the entanglement entropy associated to the region R and ∆ER is variation of the integral of the energy density over R. In this small size limit the entanglement temperature depends only on the theory and the shape of the chosen subregion, with where Tent is the entanglement temperature, ∆SR is the variation of the entanglement entropy associated to the region R and ∆ER is variation of the integral of the energy density over R. In this small size limit the entanglement temperature depends only on the theory and the shape of the chosen subregion, with (76) Tent = c/ℓ. (76) For stripe shaped subregions (51) and thermal states the constant c can be expressed in closed form [66] € Š2 c = 2(d2 −1)Γ 1 2 + 1 d−1  Γ € d 2(d−1) Š2 pπΓ € 1 2(d−1) Š2 Γ 1 d−1  , (77) (77) while in the limit ℓ→∞the entanglement temperature becomes equal to the thermodynamic temperature Tent = T. Inspired by (75) we define the dynamic entanglement temperature as the ratio of the total energy and the renormalised entanglement entropy inside the entangling region T dyn ent = R R dz〈T tt(t,z)〉 Sren(t) . (78) (78) The quantity (78) is well-defined for dynamic states and reduces for static states in the small ℓlimit to the entanglement temperature defined by (75). We compute T dyn ent in the NESS with χ = p EC/EH = 9/16 for entangling regions that are passed by shock and rarefaction waves. It turns out T dyn ent behaves qualitatively different when either a shock or a rarefaction wave passes the region. The results for three different sizes (ℓ= 0.6,1,1.5) of the entangling region are shown in Fig. 19. For these lengths (76) implies Tent = 0.703, 0.422, 0.281 respectively, and note that we have TC = 1/π ≈0.318, TS ≈0.367 and TH = 4/3π ≈0.424. 6 Discussion To the best of our knowledge, our work is the first successful simulation of the dynamic forma- tion of NESSs in a holographic field theory in four spacetime dimensions. We considered the evolution of energy and charge densities in particular, as well as the evolution of entanglement entropy. Let us recall our main results. Most importantly, our holographic results are consistent with a solution involving a shock wave travelling towards the cold bath and a rarefaction wave trav- elling towards the hot bath, with a steady state region forming in between. The wave moving towards the cold side approaches a steep, but smooth wave with time independent profile and finite entropy production at late times. The wave moving towards the hot side is progressively broadening and approaches a rarefaction wave with zero entropy production at late times. At sufficiently late time the properties of the NESS region (energy density, charge density, etc) are numerically very close to those of an analytical shock+rarefaction wave solution (less close to a shock+shock solution) of the Riemann problem. For the dynamics of a conserved U(1) charge density, we find that there emerge two sep- arate plateaus with different charge density inside the NESS region, as expected from the analogous Riemann problem. In contrast to the Riemann problem however, for which these plateaus are separated by a discontinuity, in our holographic simulation this transition region is realised as smooth crossover that broadens in time. We also investigated the evolution of entanglement entropy of spatial sub-regions regions crossed by our holographic shock and rarefaction waves using the Hubeny-Rangamani-Takaya- nagi prescription [18] to determine the HEE in our time dependent setting. Subject to appro- priate normalisation by which the energy density and HEE are chosen to agree in the NESS and thermal regions, the evolution of the entanglement entropy follows closely the evolution of the energy density, except for a small time delay that is more pronounced for the rarefac- tion wave than for the shock wave. Inspired by the first law of entanglement, we define the dynamical entanglement temperature as the ratio of the entanglement entropy and the spatial integral over the energy density inside the entangling region. There are many interesting future directions. A logical extension of the current work is to turn on the back-reaction of the gauge field to the metric [48]. 5.3 Extremal surfaces and entanglement entropy From the figure it is clear that for ℓ= 0.6 the dynamic entanglement temperature is closer to the small region limit (Eqn. (76)), whereas for ℓ= 1.5 the result is closer to the large region limit (the physical temperature), and we see that the dynamic entanglement temperature is always higher than either of them. One curious feature happens when a rarefaction wave passes a smaller region, in which case T dyn ent can be non-monotonic. One reason is that T dyn ent for ℓ= 0.6 is larger at late times for the rarefaction wave, even though the physical temperature has decreased from the hot temperature towards the lower steady state temperature. 27 SciPost Phys. 11, 047 (2021) shock rarefaction 10 20 30 40 0.73 0.74 0.75 0.76 0.77 mt Tent dyn m ℓ=0.6 shock rarefaction 10 20 30 40 0.49 0.50 0.51 0.52 0.53 0.54 0.55 mt Tent dyn m ℓ=1 shock rarefaction 10 20 30 40 0.40 0.42 0.44 0.46 mt Tent dyn m ℓ=1.5 Figure 19: Dynamical entanglement temperature for ℓ= 0.6 (left), ℓ= 1 (middle) and ℓ= 1.5 (right) as function of time, all for the the NESS with χ = p EC/EH = 9/16. shock rarefaction 10 20 30 40 0.40 0.42 0.44 0.46 mt Tent m ℓ=1.5 Figure 19: Dynamical entanglement temperature for ℓ= 0.6 (left), ℓ= 1 (middle) and ℓ= 1.5 (right) as function of time, all for the the NESS with χ = p EC/EH = 9/16. 6 Discussion Physically this implies that the pressure is not a function of the energy density only in the hydrodynamic regime, but also depends on the charge density. It would be interesting to see how features such as the contact discontinuity in the charge density change when the back reaction is taken into account. Including the back-reaction will also allow to study the relation of the null energy condition in the gravity dual to the dynamics of the stress tensor in the boundary theory along the lines of [67]. One could introducing a scalar field [68] with non-trivial potential to study the effect 28 SciPost Phys. 11, 047 (2021) conformal symmetry breaking on the properties of the NESS. Another possibility is to investi- gate the effect of finite coupling corrections with simulations in Gauss–Bonnet gravity [69,70]. It would also be interesting to include transverse flow, in the presence of which not only the charge density, but also the energy density can develop a contact discontinuity [71]. Further- more, it would be interesting to compare our results against solutions recently obtained from the equations of relativistic hydrodynamics of non-perfect fluids [72]. It would be very interesting to study the time evolution of HEE in membrane theory, us- ing [63,65] as a starting point to study the long time and large scale dynamics of the entan- glement entropy. In that case the extremal surface computation reduces to a minimisation problem that is much easier to study numerically with e.g. the Surface Evolver [73]. The cur- rent setting could be a perfect playground to employ membrane theory in non-homogeneous settings, as it would be possible to use the analytically available metric (43) in the shock region. Generally, such a study will provide new information on velocity bounds for the holographic shock+rarefaction wave solution. Moreover, it will also be of interest to make contact with the analysis of [74] which studies NESS using a quasinormal mode approach, in a rather different setup though that involves a forced flow across obstacles in which inhomogeneous, but time-independent states form. Finally, it is highly desirable to numerically probe the far-from-equilibrium dynamics of the system considered in this paper under more extreme conditions, for χ ≪1. Fig. 12 rep- resents our efforts in this direction, but we found it prohibitively hard to numerically achieve stable time evolution at smaller ratios of the initial energy densities. Acknowledgements It is our pleasure to thank Daniel Grumiller, Giuseppe Policastro and Luciano Rezzolla for comments on the manuscript and Koenraad Schalm for useful discussions in the early stages of this project. 6 Discussion The question whether the breakdown of our simulations at small χ is just an artefact of our numerical scheme or if it indicates a physical instability is currently not clear and deserves further investigation. A Rankine–Hugoniot jump conditions We arrive at the Rankine-Hugoniot jump condition vS(qL −qR) = fL −fR , (83) (83) where vS = x′ S(t) is the propagation speed of the shock. where vS = x′ S(t) is the propagation speed of the shock. B Sensitivity to initial conditions Numerically it is difficult to initialize the evolution of our coupled heat baths with a truly discontinuous step function. In practice we approximate the discontinuous interface by a smooth function of the form tanh(cz), which in the limit c →∞converges to the Heaviside theta function. In the following we verify that the evolution is insensitive to the choice of the constant c that determines the steepness of the initial interface. For this we compare in Fig. 20 two evolutions, where solid lines equal the evolution in Fig. 5 and the dashed lines an evolution with an 1.5 times smaller value of c. At t = 0 the smaller value of c gives a wider profile, but after a time t ≳4 the two simulations are virtually indistinguishable. [3] S. S. Gubser, I. R. Klebanov and A. M. Polyakov, Gauge theory correlators from non-critical string theory, Phys. Lett. B 428, 105 (1998), doi:10.1016/S0370-2693(98)00377-3. A Rankine–Hugoniot jump conditions In this appendix we review the derivation of the Rankine-Hugoniot jump conditions [75–79]. We start with the following Riemann problem ∂tq(t, x) + ∂x f (q(t, x)) = 0, q(0, x) = ¨ qL ∀x < 0 qR ∀x > 0 , (79) (79) where q(t, x) is a conserved charge and f (q(t, x)) the associated flux. A discontinuous solution of (79) can be obtained from the integrated conservation law ∂t ‚Z xS(t) xL dx q(t, x) + Z xR xS(t) dx q(t, x) Œ = − Z xR xL dx ∂x f (q(t, x)), (80) (80) where xS(t) parametrizes the location of the discontinuity at time t and the integration bounds are chosen such that xL < xS(t) < xR. To simplify the expression on the left hand side we use Leibniz integral rule ∂t ‚Z b(t) a(t) dx g(t, x) Œ = g(t, b(t)) d dt b(t) −g(t, a(t)) d dt a(t) + ‚Z b(t) a(t) dx ∂t g(t, x) Œ . (81) (81) 29 SciPost Phys. 11, 047 (2021) -20 -10 0 10 20 0.0 0.5 1.0 1.5 2.0 2.5 m z ℰ/m4, m t ={0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26} Figure 20: Evolution of the energy density for two different initial profiles: c = 3 2 (solid) and c = 1 (dashed). For mt ≳4 the evolution is insensitive to the initial condition. -20 -10 0 10 20 0.0 0.5 1.0 1.5 2.0 2.5 m z ℰ/m4, m t ={0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26} Figure 20: Evolution of the energy density for two different initial profiles: c = 3 2 (solid) and c = 1 (dashed). For mt ≳4 the evolution is insensitive to the initial condition. This gives This gives qL x′ S(t) + lim ε→0+ Z xS(t)−ε xL dx ∂tq(t, x) −qRx′ S(t) + lim ε→0+ Z xR xS(t)+ε dx ∂tq(t, x) = −(fR −fL), (82) where we defined fR/L = f (qL/R). The remaining two integrals vanish when taking the limits xL →xS(t) −ε and xR →xS(t) + ε. We arrive at the Rankine-Hugoniot jump condition where we defined fR/L = f (qL/R). The remaining two integrals vanish when taking the limits xL →xS(t) −ε and xR →xS(t) + ε. [1] J. Maldacena, The Large N limit of superconformal field theories and supergravity, Int. J. Theor. Phys. 38, 1113 (1999), doi:10.1023/A:1026654312961. [2] E. Witten, Anti de Sitter space and holography, Adv. Theor. Math. Phys. 2, 253 (1998), doi:10.4310/ATMP.1998.v2.n2.a2. [3] S. S. Gubser, I. R. Klebanov and A. M. Polyakov, Gauge theory correlators from non-critical [2] E. Witten, Anti de Sitter space and holography, Adv. Theor. Math. Phys. 2, 253 (1998), doi:10.4310/ATMP.1998.v2.n2.a2. [1] J. Maldacena, The Large N limit of superconformal field theories and supergravity, Int. J. Theor. Phys. 38, 1113 (1999), doi:10.1023/A:1026654312961. [2] E. Witten, Anti de Sitter space and holography, Adv. Theor. Math. Phys. 2, 253 (1998), doi:10.4310/ATMP.1998.v2.n2.a2. [3] S. S. Gubser, I. R. Klebanov and A. M. Polyakov, Gauge theory correlators from non-critical string theory, Phys. Lett. B 428, 105 (1998), doi:10.1016/S0370-2693(98)00377-3. References [1] J. Maldacena, The Large N limit of superconformal field theories and supergravity, Int. J. Theor. Phys. 38, 1113 (1999), doi:10.1023/A:1026654312961. [2] E. Witten, Anti de Sitter space and holography, Adv. Theor. Math. Phys. 2, 253 (1998), doi:10.4310/ATMP.1998.v2.n2.a2. 30 SciPost Phys. 11, 047 (2021) [4] W. Busza, K. Rajagopal and W. van der Schee, Heavy ion collisions: The Big picture and the big questions, Annu. Rev. Nucl. Part. Sci. 68, 339 (2018), doi:10.1146/annurev-nucl- 101917-020852. [5] S. A. Hartnoll, A. Lucas and S. Sachdev, Holographic quantum matter, (2016), arXiv:1612.07324. [6] H. Liu and J. Sonner, Holographic systems far from equilibrium: A review, (2018), arXiv:1810.02367. [7] A. Buchel, M. P. Heller and R. C. Myers, Equilibration rates in a strongly cou- pled nonconformal quark-gluon plasma, Phys. Rev. Lett. 114, 251601 (2015), doi:10.1103/PhysRevLett.114.251601. [8] J. Casalderrey-Solana, C. Ecker, D. Mateos and W. van der Schee, Strong-coupling dy- namics and entanglement in de Sitter space, J. High Energy Phys. 03, 181 (2021), doi:10.1007/JHEP03(2021)181. [9] D. Bernard and B. Doyon, Energy flow in non-equilibrium conformal field theory, J. Phys. A: Math. Theor. 45, 362001 (2012), doi:10.1088/1751-8113/45/36/362001. [10] D. Bernard and B. Doyon, Time-reversal symmetry and fluctuation relations in non- equilibrium quantum steady states, J. Phys. A: Math. Theor. 46, 372001 (2013), doi:10.1088/1751-8113/46/37/372001. [11] D. Bernard and B. Doyon, Non-equilibrium steady states in conformal field theory, Ann. Henri Poincaré 16, 113 (2015), doi:10.1007/s00023-014-0314-8. [12] D. Bernard and B. Doyon, A hydrodynamic approach to non-equilibrium conformal field theories, J. Stat. Mech. 033104 (2016), doi:10.1088/1742-5468/2016/03/033104. [13] D. Bernard and B. Doyon, Conformal field theory out of equilibrium: a review, J. Stat. Mech. 064005 (2016), doi:10.1088/1742-5468/2016/06/064005. [14] M. Medenjak, G. Policastro and T. Yoshimura, T ¯T-deformed conformal field theories out of equilibrium, Phys. Rev. Lett. 126, 121601 (2021), doi:10.1103/PhysRevLett.126.121601. [15] A. Taroni, Protection mechanism, Nat. Phys. 11, 5 (2014), doi:10.1038/nphys3220. [16] J. Erdmenger, D. Fernández, M. Flory, E. Megías, A.-K. Straub and P. Witkowski, Time evolution of entanglement for holographic steady state formation, J. High Energy Phys. 10, 034 (2017), doi:10.1007/JHEP10(2017)034. [17] S. Ryu and T. Takayanagi, Holographic derivation of entanglement entropy from the anti- de Sitter space/conformal field theory correspondence, Phys. Rev. Lett. 96, 181602 (2006), doi:10.1103/PhysRevLett.96.181602. [18] V. E. Hubeny, M. Rangamani and T. Takayanagi, A covariant holographic entangle- ment entropy proposal, J. High Energy Phys. 07, 062 (2007), doi:10.1088/1126- 6708/2007/07/062. [19] H.-C. Chang, A. Karch and A. References Yarom, An ansatz for one dimensional steady state configu- rations, J. Stat. Mech. P06018 (2014), doi:10.1088/1742-5468/2014/06/P06018. 31 SciPost Phys. 11, 047 (2021) [20] A. Lucas, K. Schalm, B. Doyon and M. J. Bhaseen, Shock waves, rarefaction waves, and nonequilibrium steady states in quantum critical systems, Phys. Rev. D 94, 025004 (2016), doi:10.1103/PhysRevD.94.025004. [21] M. Spillane and C. P. Herzog, Relativistic hydrodynamics and non-equilibrium steady states, J. Stat. Mech. 103208 (2016), doi:10.1088/1742-5468/2016/10/103208. [22] R. Pourhasan, Non-equilibrium steady state in the hydro regime, J. High Energy Phys. 02, 005 (2016), doi:10.1007/JHEP02(2016)005. [23] I. Amado and A. Yarom, Black brane steady states, J. High Energy Phys. 10, 015 (2015), doi:10.1007/JHEP10(2015)015. [24] C. P. Herzog, M. Spillane and A. Yarom, The holographic dual of a Riemann prob- lem in a large number of dimensions, J. High Energy Phys. 08, 120 (2016), doi:10.1007/JHEP08(2016)120. [25] D. Fernández, A. Rajagopal and L. Thorlacius, Non-equilibrium steady states in quan- tum critical systems with Lifshitz scaling, J. High Energy Phys. 12, 115 (2019), doi:10.1007/JHEP12(2019)115. [26] C. Ecker, D. Grumiller, W. van der Schee, S. Sheikh-Jabbari and P. Stanzer, Quantum null energy condition and its (non)saturation in 2d CFTs, SciPost Phys. 6, 036 (2019), doi:10.21468/SciPostPhys.6.3.036. [27] C. Ecker, Entanglement entropy from numerical holography, (2018), arXiv:1809.05529. [28] A. Bressan, Hyperbolic conservation laws: An illustrated tutorial, in Lecture Notes in Math- ematics, Springer Berlin Heidelberg, ISBN 9783642321603 (2012), doi:10.1007/978-3- 642-32160-3_2. [29] P. Glorioso and H. Liu, The second law of thermodynamics from symmetry and unitarity, (2016), arXiv:1612.07705. [30] S. Grozdanov and J. Polonyi, Viscosity and dissipative hydrodynamics from effective field theory, Phys. Rev. D 91, 105031 (2015), doi:10.1103/PhysRevD.91.105031. [31] P. Kovtun, G. D. Moore and P. Romatschke, Towards an effective action for relativistic dissipative hydrodynamics, J. High Energy Phys. 07, 123 (2014), doi:10.1007/JHEP07(2014)123. [32] M. Crossley, P. Glorioso and H. Liu, Effective field theory of dissipative fluids, J. High Energy Phys. 09, 095 (2017), doi:10.1007/JHEP09(2017)095. [33] F. M. Haehl, R. Loganayagam and M. Rangamani, Topological sigma models & dissipative hydrodynamics, J. High Energy Phys. 04, 001 (2016), doi:10.1007/JHEP04(2016)039. [34] K. Jensen, N. Pinzani-Fokeeva and A. Yarom, Dissipative hydrodynamics in superspace, J. High Energy Phys. 09, 127 (2018), doi:10.1007/JHEP09(2018)127. [35] B. Tóth and B. Valkó, Onsager relations and eulerian hydrodynamic limit for systems with several conservation laws, J. Stat. Phys. 112, 497 (2003), doi:10.1023/A:1023867723546. [36] R. M. Grisi and G. M. Schütz, Current symmetries for particle systems with several conser- vation laws, J. References Stat. Phys. 145, 1499 (2011), doi:10.1007/s10955-011-0341-5 32 SciPost Phys. 11, 047 (2021) [37] B. Doyon, Lecture notes on generalised hydrodynamics, SciPost Phys. Lect. Notes 18, (2020), doi:10.21468/SciPostPhysLectNotes.18. [38] A. H. Taub, Relativistic Rankine-Hugoniot equations, Phys. Rev. 74, 328 (1948), doi:10.1103/PhysRev.74.328. [39] D. Cassani and D. Martelli, Supersymmetry on curved spaces and superconformal anoma- lies, J. High Energy Phys. 10, 025 (2013), doi:10.1007/JHEP10(2013)025. [40] I. Papadimitriou, Supercurrent anomalies in 4d SCFTs, J. High Energy Phys. 07, 038 (2017), doi:10.1007/JHEP07(2017)038. [41] J. P. Gauntlett and J. B. Gutowski, All supersymmetric solutions of mini- mal gauged supergravity in five-dimensions, Phys. Rev. D 68, 105009 (2003), doi:10.1103/PhysRevD.68.105009, [Erratum: Phys. Rev. D 70, 089901, doi:10.1103/PhysRevD.70.089901]. [42] E. Kiritsis, String theory in a nutshell, Princeton University Press, Princeton, USA, ISBN 9780691155791, (2019). [43] J. D. Bekenstein, Black holes and the second law, Lett. Nuovo Cimento 4, 737 (1972), doi:10.1007/BF02757029. [44] S. W. Hawking, Particle creation by black holes, Commun. Math. Phys. 43, 199 (1975), doi:10.1007/BF02345020. [45] P. M. Chesler and L. G. Yaffe, Holography and colliding gravitational shock waves in asymptotically AdS5 spacetime, Phys. Rev. Lett. 106, 021601 (2011), doi:10.1103/PhysRevLett.106.021601. [46] J. Casalderrey-Solana, M. P. Heller, D. Mateos and W. van der Schee, From full stopping to transparency in a holographic model of heavy ion collisions, Phys. Rev. Lett. 111, 181601 (2013), doi:10.1103/PhysRevLett.111.181601. [47] P. M. Chesler and L. G. Yaffe, Numerical solution of gravitational dynamics in asymptotically anti-de Sitter spacetimes, J. High Energy Phys. 07, 086 (2014), doi:10.1007/JHEP07(2014)086. [48] J. Casalderrey-Solana, D. Mateos, W. van der Schee and M. Triana, Holographic heavy ion collisions with baryon charge, J. High Energy Phys. 09, 108 (2016), doi:10.1007/JHEP09(2016)108. [49] W. van der Schee, Gravitational collisions and the quark-gluon plasma, (2014), arXiv:1407.1849. [50] K. Skenderis, Lecture notes on holographic renormalization, Class. Quantum Grav. 19, 5849 (2002), doi:10.1088/0264-9381/19/22/306. [51] M. P. Heller, R. A. Janik and P. Witaszczyk, Characteristics of thermalization of boost-invariant plasma from holography, Phys. Rev. Lett. 108, 201602 (2012), doi:10.1103/PhysRevLett.108.201602. [52] C. Holzhey, F. Larsen and F. Wilczek, Geometric and renormalized entropy in conformal field theory, Nucl. Phys. B 424, 443 (1994), doi:10.1016/0550-3213(94)90402-2. [53] M. Srednicki, Entropy and area, Phys. Rev. Lett. 71, 666 (1993), doi:10.1103/PhysRevLett.71.666. 33 SciPost Phys. 11, 047 (2021) [54] P. Calabrese and J. Cardy, Entanglement entropy and quantum field theory, J. Stat. Mech.: Theor. Exp. P06002 (2004), doi:10.1088/1742-5468/2004/06/P06002. [55] P. Calabrese and J. Cardy, Evolution of entanglement entropy in one-dimensional systems, J. Stat. References Mech. P04010 (2005), doi:10.1088/1742-5468/2005/04/P04010. [56] C. Ecker, D. Grumiller, P. Stanzer, S. A. Stricker and W. van der Schee, Exploring nonlocal observables in shock wave collisions, J. High Energy Phys. 11, 054 (2016), doi:10.1007/JHEP11(2016)054. [57] C. Ecker, D. Grumiller and S. A. Stricker, Evolution of holographic entangle- ment entropy in an anisotropic system, J. High Energy Phys. 07, 146 (2015), doi:10.1007/JHEP07(2015)146. [58] C. Eling and Y. Oz, Holographic screens and transport coefficients in the fluid-gravity corre- spondence, Phys. Rev. Lett. 107, 201602 (2011), doi:10.1103/PhysRevLett.107.201602. [59] C. Ecker, D. Grumiller, H. Soltanpanahi and P. Stanzer, QNEC2 in deformed holographic CFTs, J. High Energy Phys. 03, 213 (2021), doi:10.1007/JHEP03(2021)213. [60] V. E. Hubeny, Extremal surfaces as bulk probes in AdS/CFT, J. High Energy Phys. 07, 093 (2012), doi:10.1007/JHEP07(2012)093. [61] J. Abajo-Arrastia, J. Aparício and E. López, Holographic evolution of entanglement entropy, J. High Energy Phys. 11, 149 (2010), doi:10.1007/JHEP11(2010)149. [62] J. Erdmenger and N. Miekley, Non-local observables at finite temperature in AdS/CFT, J. High Energy Phys. 03, 034 (2018), doi:10.1007/JHEP03(2018)034. [63] M. Mezei and D. Stanford, On entanglement spreading in chaotic systems, J. High Energy Phys. 05, 065 (2017), doi:10.1007/JHEP05(2017)065. [64] H. Liu and S. J. Suh, Entanglement tsunami: Universal scaling in holographic thermaliza- tion, Phys. Rev. Lett. 112, 011601 (2014), doi:10.1103/PhysRevLett.112.011601. [65] A. Nahum, J. Ruhman, S. Vijay and J. Haah, Quantum entanglement growth under random unitary dynamics, Phys. Rev. X 7, 031016 (2017), doi:10.1103/PhysRevX.7.031016. [66] J. Bhattacharya, M. Nozaki, T. Takayanagi and T. Ugajin, Thermodynamical prop- erty of entanglement entropy for excited states, Phys. Rev. Lett. 110, 091602 (2013), doi:10.1103/PhysRevLett.110.091602. [67] A. Almheiri, A. Milekhin and B. Swingle, Universal constraints on energy flow and SYK thermalization, (2019), arXiv:1912.04912. [68] M. Attems, J. Casalderrey-Solana, D. Mateos, D. Santos-Oliván, C. F. Sopuerta, M. Triana and M. Zilhão, Paths to equilibrium in non-conformal collisions, J. High Energy Phys. 06, 154 (2017), doi:10.1007/JHEP06(2017)154. [69] S. Grozdanov and W. van der Schee, Coupling constant corrections in a holo- graphic model of heavy ion collisions, Phys. Rev. Lett. 119, 011601 (2017), doi:10.1103/PhysRevLett.119.011601. [70] A. Folkestad, S. Grozdanov, K. Rajagopal and W. van der Schee, Coupling constant correc- tions in a holographic model of heavy ion collisions with nonzero baryon number density, J. High Energy Phys. 12, 093 (2019), doi:10.1007/JHEP12(2019)093. 34 SciPost Phys. 11, 047 (2021) [71] P. Mach, Instabilities of the Riemann problem in relativistic hydrodynamics, AIP Conf. Proc. 1458, 459 (2012), doi:10.1063/1.4734459. [72] M. References Chabanov, L. Rezzolla and D. H. Rischke, General-relativistic hydrodynamics of non- perfect fluids: 3+1 conservative formulation and application to viscous black hole accretion, Mon. Not. Roy. Astron. Soc. 505, 5910 (2021), doi:10.1093/mnras/stab1384. [73] M. Mezei and W. van der Schee, Black holes often saturate entanglement entropy the fastest, Phys. Rev. Lett. 124, 201601 (2020), doi:10.1103/PhysRevLett.124.201601. [74] J. Sonner and B. Withers, Universal spatial structure of nonequilibrium steady states, Phys. Rev. Lett. 119, 161603 (2017), doi:10.1103/PhysRevLett.119.161603. [75] P. D. Lax, Hyperbolic systems of conservation laws II, Comm. Pure Appl. Math. 10, 537 (1957), doi:10.1002/cpa.3160100406. [76] P. D. Lax, The formation and decay of shock waves, Amer. Math. Monthly 79, 227 (1972), doi:10.1080/00029890.1972.11993023. [77] R. Menikoff and B. J. Plohr, The Riemann problem for fluid flow of real materials, Rev. Mod. Phys. 61, 75 (1989), doi:10.1103/RevModPhys.61.75. [78] J. Smoller and B. Temple, Global solutions of the relativistic Euler equations, Commun. Math. Phys. 156, 67 (1993), doi:10.1007/BF02096733. [79] J. M. Martí and E. Müller, The analytical solution of the Riemann problem in relativistic hydrodynamics, J. Fluid Mech. 258, 317 (1994), doi:10.1017/S0022112094003344. 35
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The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra
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The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer Artículos atravesados por (o cuestionando) la idea del sujeto -y su género- como una construcción psicobiológica de la cultura. Articles driven by (or questioning) the idea of the subject -and their gender- as a cultural psychobiological construction Vol. 5 (2020), enero-diciembre ISSN 2469-0783 https://datahub.io/dataset/2020-5-e132 THE BEATIFIC EXPERIENCE OF BEING: A PHENOMENOLOGY OF THE CHAKRASAMVARA TANTRA LA EXPERIENCIA BEATIFICA DEL SER: UNA FENOMENOLOGIA DEL CHAKRASAMVARA TANTRA Rudolph Bauer rbauer@rsbauer.net Center for Consciousness Studies and Washington Center for Phenomenological and Existential Psychotherapy Studies. United States of America Cómo citar este artículo / Citation: Bauer R. (2020). «The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra». Revista Científica Arbitrada de la Fundación MenteClara, Vol. 5 (132). DOI: https://doi.org/10.32351/rca.v5.132 Copyright: © 2020 RCAFMC. Este artículo de acceso abierto es distribuido bajo los términos de la licencia Creative Commons Attribution 4.0 International License (CC BY 4.0). Recibido: 18/12/2019. Aceptado: 11/01/2020 Publicación online: 18/01/2020 Conflicto de intereses: None to declare. Abstract This article is a phenomenological elaboration of the Chakrasamvara Tantra. The Tibetan Chakrasamvara Tantra brings forth a naturalistic understanding of the process of the Embodiment of Being and the process of the invocation of the Bliss of Embodied Being. The Chakrasamvara Tantra, beautifully describes the experience of the Beatific Vision of Being, as well the invocation of the Beatific experience of Being, the Beatific experience of primordial luminous awareness. Resumen Este artículo es una elaboración fenomenológica del Chakrasamvara Tantra. El tibetano Chakrasamvara Tantra presenta una comprensión naturalista del proceso de la encarnación del Ser y el proceso de invocación de la bienaventuranza del Ser Encarnado. El Chakrasamvara Tantra, describe bellamente la experiencia de la visión Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 1 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer beatífica del ser, así como la invocación de la experiencia beatífica del Ser, la experiencia beatífica de la conciencia luminosa primordial. Keywords: tantra; Chakrasamvara; beatific vision; luminous awareness Palabras Claves: tantra; Chakrasamvara; visión beatífica; conciencia luminosa Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 2 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer Introduction The Chakrasamvara experience of our Beatific Vision and our lived Beatific experience takes place within our life just as it is, and just as we are. The Chakrasamvara Tantra describes the foundational experience of Being and the Univocity of Being through which all hierarchal-ness is deconstructed. Within this deconstruction of hierarchy, a subtle unstructured luminous equality consciousness becomes present. The Univocity of Being means the complete sameness and complete oneness of Being. Human beings can bring forth the experience of the non-duality of equality consciousness within the phenomenological duality of human beings. This Univocal-ness means there is a difference within form, but not within essence, not within Being (Gray, 2007). The qualities of Being are Spaciousness, Luminosity, Energy, and Knowingness. There are other qualities such a Purity, Compassion, and Self Manifestation. Our focus is on the Quality of Bliss, Beatific Bliss. Bliss is an ontological quality of Being. This ontological quality of Being infuses our personal and collective experience of existence. The Chakrasamvara Tantra illuminates the Univocity of Being within phenomenological difference. Univocal-ness is a language description of the complete oneness and sameness of Being. Within Being and the selfmanifestation of Being, there is a oneness of non-hierarchal existence. The Univocal-ness is equality consciousness and the equal vision of the Beatific-ness of the Purity of Being as beings. In theological language God or Deus is neither above nor below and God is within everything and everyone as the Divinity of Being. God is a Univocal collective experience of Being. In philosophical language Being is. Being is not a being. But Being selfmanifests as all beings and as the Being of all beings. In the language of Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 3 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer Dzogchen all phenomena are the Dharmakaya. All phenomena are the Purity of the Dharmakaya. All beings are the self-manifestations of the ground of Being. The ground of Being is the Dharmakaya of Pure Potentiality. There is no ontological difference within the Oneness of the field of Being. There is a difference in form, but not within Being. This is pantheistic experience! Immanence of Bliss The Chakrasamvara is a Tantra elaborating within the field of immanence the inherent Bliss of Being and the Bliss within the phenomenological manifestation of Being. The Chakrasamvara Tantra sets forth the immanent path of self- liberation through the experience of the Bliss of Being. Chakrasamvara is a Tantra focused on the intrinsic experience of self-liberation in our life, just as it is and just as we are. The experience of the Bliss of Being is the source of self-liberation. The Chakrasamvara Tantra is a discourse on and within the field of immanence. In this field of immanence, there is this foundational experience of equality consciousness and equal vision. The field of immanence is the field of Being as Oneness. Within the Chakrasamvara Tantra there is neither above nor below or better or best in this luminous field of the plane of immanence. The plane of immanence is the plane of the field of awareness infinite in its horizons, vast and multidimensional Oneness. The field of primordial awareness is within the immanence of the field of Being. Immanence means the essence of Being is within all phenomena and is within all experience and is completely within the self -manifestation of world. Immanence means within phenomena within us, within life is the luminous spacious field of Being. The field of Being is Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 4 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer embodied within us and within the phenomena of the world. There is no beyond within the field of immanence. The Chakrasamvara Tantra elaborates the Univocity of Being and the naturalistic equality of consciousness of the plane of immanence, the plane of the luminous field of Being. Being is not a being, but Being selfmanifests as the Being of all beings. Transcendental Forms of Liberation and Immanent Forms of Liberation The foundational transcendental experience of the non-dualistic experience of self- liberation is simply “I Alone Exist”. The foundational immanent experience of the non-dualistic experience of self-liberation within the field of immanence is simply that ‘you and I’ are indivisible within and as the non-dualistic field of Being. Within the field of immanence duality exists within non-duality and within non-duality duality exists. Equality consciousness is the experience of the univocalness of Being within the difference of all the forms of Being. Within the duality of beings, there is the non-duality of Being. And within the nonduality of Being, there is the duality of beings. Through our own being, we can experience Being itself. And through the being of another we can experience Being itself. We live in the sea of Being and we are within the sea of Being. We are the sea of Being. The Bliss of Existence is The Bliss of Being The Chakrasamvara is the tantra of innate Bliss of existing-ness. This existing-ness goes beyond the formulation of life and death of our singular incarnations. The Chakrasamvara is the tantra of the innate Bliss of Existing-ness. This existing-ness goes beyond the formulation of Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 5 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer life and death of our singular incarnations. The Chakrasamvara is the Tantra of the embodiment of Bliss that is the very essence of the sphere of Being. Bliss is the essence of Being. Being is not a being, and Being manifests within us as infinite manifestations of beings, and these beings are the Being-ness of Being itself. Within Being there is only oneness, and the oneness is totally undisturbed by the difference of forms within beings and between beings. We are Being becoming beings who are alive in time and beings who become Being in deathlessness. We appear from Being as beings and we disappear as beings into Being. We re-appear from Being as beings, and again in time and through time we dis-appear back into Being. Being becoming beings is life and beings becoming Being is deathlessness. Embodiment of Being: Bliss Overcomes Suffering This Chakrasamvara Tantra is the tantra of the pervasiveness of the Bliss within our human experience of Being-ness, and this bliss overcomes suffering. This bliss is both within the realm of good and evil, and yet beyond the realm of good and evil. This bliss of the Beatific-ness of ontological Being is the Beatific embodiment of our own Being. We embody the Bliss of Being. We embody Being and we are embodied by Being within Being. The Bliss of embodied human experience is the focus of the Chakrasamvara Tantra. This beatific experience is the bliss of our experience of the unfolding of our ongoing embodied continuity of Being. Our embodiment of Being becomes the medium of the field of Being unfolding within self-liberation. The body is the medium of the field of awareness which is the field of Being. The knowing of Being is awareness. Awareness knows Being and awareness is the knowingness of Being. Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 6 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer This embodiment is the unfolding bringing forth of the luminous subtle sphere of luminous channels and luminous chakras of our Being in our embodiment. The subtle luminous energy field is of central importance within the Chakrasamvara Tantra. Our embodiment of Being is the embodiment of light becoming flesh and flesh becoming enlightened. As we embody the luminous Being of our being, we are simultaneously embodying the light of Being itself. The light of Being is the light of our awareness. Beatific Vision and Beatific Experience This beatific experience of Being can be experienced by us in every situation and in every context and in every unfolding event of Being. This beatific experience of Being unfolds both within pleasure as well as within pain. This beatific experience of Being unfolds both within beauty and within terror, within peace and within war, within love and within hate, within perversity and within purity. A mantra which expresses this tantric dimension of experiencing Being is: Om Ah Hum Bodichitta Maha Suka Jnana Dhatu Ah. Bodhicitta is the Great Compassion. Maha Suka is the Great Bliss which is Compassion, Jnana is Direct Knowing of Being, Dhatu Ah means Direct Knowing of Being in every situation. The Beatific-ness of our luminous embodied experience of pure primordial awareness is the experience of the flesh of the world to use Merleau Ponty’s language describing ontological embodiment (Morris, 2018). Human experience is the intertwining of mind, awareness, embodiment and Being. Human experience is both ontic and ontological to use Heideggerian language. In experience, we experience the phenomena of Being, and the Being of the phenomena (Capobianco, 2014). Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 7 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer The Beatific Field of Being Beatific experience means Beatific Knowing-ness, Beatific Being-ness and Beatific Radiance. The radiance of Being brings forth the unfolding of the beatific experience of our life just as it is. This beatific vision and experience of beatific -ness is continuously given and open to us within every experience and within all experience. This beatific experience is within the realm of our ongoing continuity of our experience of innate awareness of the field of Being. This beatific realm of human experience is not earned or merited. This beatific realm of experience is given to us. This beatific realm of experience comes with the territory of our manifested nature of Being. Beatific experience is the very nature of human awareness, human gnosis and human jnana. Beatific experience is the Bliss of Being. The inherent divinity of our human experience, reflects the immanence of Being within us both as our personal experience and our collective experience. This Beatific experience of Vision and Bliss is not a transcendental experience beyond human phenomena and beyond our mind and beyond our embodiment. This Beatific experience and Beatific vision is manifested in all the different dimensions of our humanness. The Beatific experience is experienced and manifested in all the dimensions or kayas. This is the dimension of ordinary life world of Being, as well as the dimension of the archetypal manifestations of Being as well as the dimension of pure potentiality of Being! Beatific experience happens in each of the dimensions of this multidimensional world of our existing-ness. The ongoing continuous experience of the radiance of the Being of self -illumination is fully experienced within the realm of immanence of Being. Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 8 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer The ongoing experience of transcendence is hierarchical and dissociative. The transcendental quest dissociates us, separates us from the immanence of divinity of appearance and experience. The dissociative and detachment of the transcendental quest can foreclose for us the experience of the Being of phenomena. Transcendental method separates and dissociates our beatific experience of the Being of phenomena from the realm of pure awareness. Transcendental methodologies are dissociative and remove us from the immediacy of Beatific Life in our ordinary life world and the immediacy of archetypal realm within our ordinary life world. Transcendental methodology dissociates us from our beatific experience of external phenomena as well as our inner most phenomena of awareness. Awareness is the Gnosis/Jnana of Direct Knowing When ‘you and I’ become aware of our own awareness, we enter into direct knowing of gnosis or jnana. We enter into tantra. Tantra is the unfolding experience of awareness of awareness. In this awareness of awareness and through this field of awareness, we directly experience and directly know Being within Being itself. This gnosis, this jnana, this direct perception knows non-duality, knows oneness, knows indivisibleness. Gnosis is the knowing of oneness. Gnosis is the knowing of nonduality and gnosis is the direct knowing of our direct perception of Luminous Being. Just as our awareness as gnosis knows the non-duality of Being within beings, our mind knows duality, our mind knows the duality of phenomena, and the duality within phenomena. Our awareness knows Being, and our awareness knows the Being of Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 9 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer phenomena. Our mind knows form, our mind knows the form of beings and things. Our mind knows phenomena both subtle and gross phenomena. Our mind knows difference. So when we integrate our mind into our awareness field, into our gnosis, into our field of direct knowing of Being, we can know the duality of phenomena within the non-duality of Being; and we can know nonduality of Being within the duality of beings. This direct knowing of Being within and through phenomena is the immediate unfolding of selfliberation in our life. The experiencing the Being of phenomena is self liberation. To experience the Being of phenomena is to experience Bliss. To experience the Being of our own Being is to experience the Bliss of Being. Mind as a Knower of Forms, Awareness as a Knower of Being We have two ways of knowing. Our mind knows forms, things, both subtle and gross. Our mind knows dualities, our mind knows me and you, us and them, this and that. Our mind knows entities and beings, our mind knows time. Our mind knows difference. Our mind knows thoughts, our mind knows affects, emotions and feelings. Our mind knows sensation, our mind knows memory. Our mind knows images of memory. Our mind knows phenomena. Our mind knows the phenomena of otherness, our mind knows the dualities of phenomena and the dualities within phenomena (Bauer, 2019 a). Our awareness knows Being directly and our awareness knows the Being-ness of Beings directly. Our awareness knows the Bliss of Being, the Bliss of Being-ness, the Bliss of Existing. Our awareness knows timelessness. Our awareness does not know forms. Our awareness does not know emotions and does not know affective states. Our awareness Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 10 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer knows spaciousness, our awareness knows luminosity, our awareness knows energy, our awareness knows awareness within ourselves and within others. Our awareness knows timelessness, and our awareness knows timelessness within time. Awareness knows the bliss of Being within beings. Bliss is not an affect and Bliss is not an emotion. Bliss is not a affect of our mind and bliss is not an emotion of our mind. The experience of bliss is not a function of our mind. Bliss is the experience of the manifestation of Being as beings, including our own Being. This manifestation of Being is experienced within the field of our awareness. Bliss is the experience of our awareness knowing and experiencing Being. Awareness is the direct knowingness of Being. Bliss is the nature of Being and Bliss is the experience of Being including our own Being and the Being of our own innermost awareness. The experience of Bliss is intrinsic to the experience of Being. Bliss is the innate sense of Being. Bliss is our sense of the Being of phenomena. Bliss can be the sense of our experience of the Being of a person. Bliss is the sense of Being. Bliss is the sense of the Beingness within beings (Bauer, 2019 b). The forms of a being may have affective, emotional and cognitive implications for the knowingness of minds. The experience of the forms of a being have affective, relational, emotional and experiential implication. The forms of a being have affective and emotional resonance. Form is a psychological experience. Form is an aesthetic experience. Form has emotional, relational and emotional implications for our experience of embodied mind. The Being of beings has the resonance of the field of Being. The field of the Being of beings has and is a field of ontological resonance and attunement. We can experience within our awareness the resonance of the Being of beings. We can experience within our own awareness the Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 11 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer resonance of Being itself. We are in resonance with the sphere of Being. The sphere of Being is the resonance of pure Being. Resonance of Mind and Resonance of Awareness There are two ways of resonance. There is resonance of Being and there is the resonance of our mind’s affective and emotional States. Our mind of thinking, feeling, sensation, memory and imagination has emotional and affective states of resonance. Our mind is a series of emotional or affective states of relational resonance. Our mind has resonance to the minds of others. The minds of others have resonance to our mind. Awareness is a relational field of the resonance of Being. There is also awareness of mind and the experiences of mind. Awareness experiences the resonance of Being and the dimensions of Being within beings and within the Being of phenomena. Awareness experiences the Being of phenomena and the phenomena of Being. Awareness also experiences the lack of Being and the absence of Being. One Knower Although there are two ways of knowing, naturally there is only one knower and there is the natural intertwining of mind and awareness. The natural union of mind and awareness brings forth the experience of the form of phenomena and the Being of the phenomena. Form of phenomena and the Being of the phenomena are known through the union of mind and awareness within the one knower. The form of phenomena is known through the mind and the Being of phenomena is known through awareness. As we unfold from childhood into adulthood for some the mind as the knower of form splits from awareness the knower of Being. Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 12 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer A person who lives in mind only knows the form of phenomena and such a person may suffer the lack of the sense of presence of Being. For many, there is the loss of the Bliss of Being. Living in mind alone with a foreclosure on our awareness of Being, results in the loss of the presence of Being within our own self and within our experience of the world. As such a person, we may live without the sense of the Bliss of our Being and the Bliss of the Being of the world. Without the knowing of awareness the Bliss of Being is absent. When we live within the intertwining of mind and awareness, we can experience affective responses within the context of the Bliss of Being. We can even feel pain within the context of the bliss of Being. We can feel hatred within the context of the bliss of Being. We can feel love and beloved-ness within the context of Being. We can experience shame within the Bliss of Being. We can experience afflictive emotions within the Bliss of Being. This is most important to know! Bliss is inclusive of the vast range of affective and afflictive feelings. The Bliss of Being does not exclude affective or afflictive experience as some would have you think. This limiting kind of religious thinking is distorted and dissociative. We can integrate the mind and the functions of mind into and within the field of awareness which is the field of Being and the field of Bliss. The ongoing continuity of experience of Being is the experience of Bliss. If awareness disappears Bliss disappears. The mind can experience pleasure and pain but not Bliss. Bliss can infuse the mind and infuse the experience of the mind. The absence of Being as experience by awareness will feel like vast emptiness and have its own emotional terror for the mind. Sometimes for a person, such emptiness of Being, feels like a vast depression beneath depression. Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 13 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer Religion Mythologizes and Mystifies Religion mythologizes and mystifies the naturalistic direct knowing of awareness. Religion mythologizes and mystifies the direct knowing of Being. Religion moralizes the natural liberation of living naturally and immediately within the field of Being. The relentlessly patriarchal and theocentric context of religion institutionalizes the naturalistic experience of the Beatific-ness of our life experience of the field of Being. Religion likes to think it owns Bliss and is itself the source of the Purity of Bliss. The transcendentalism of religion dissociates the beatific experience from the immediacy of ordinary life experience. Transcendentalism dissociates us from both the external phenomena of our being in the world, and from our experience of our innermost experience of our innermost sense of Being. This unhappy sequence of detachment can bring forth the experience that our living experience is unreal and the world itself is unreal and illusionary. All phenomena are considered by these transcendental religions as a distraction from the experience of the Purity of Being. Of course, this way of seeing is a tragic distortion of the natural experience of the field of Being as the source and as the selfmanifestation of phenomena. Most of these religious transcendental traditions have dissociated mind from awareness, so that phenomena that are only known by mind are dissociated from the sense of Being. When the embodiment of awareness is foreclosed, the Bliss of Being is absent. In this dissociative context the Bliss of Being is often foreclosed (Bauer, 2020). Self-Liberation Through Bliss Religion mystifies the living within Being as Being by creating theologies of realization. These theologies of realization of God often Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 14 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer described as requiring eons and eons of praxis in order for the great event to happen and take place. Life is waiting and waiting and more waiting. Waiting for Godot! Religion and its relentless patriarchal institutionalization and Patriarchal domination as the One Who knows even implies the mystification of the power of granting this realization of Being or in their language the realization of God. This realization of Being is naturally given in everyone. The nature of Being itself gives the Bliss of Being to all beings, just as they are. This ontological gift of Being and the Beingness of Being is not the gift of some aging patriarchal male figure. It is equally true that human beings have the power of the selfmanifestation of the light of their own awareness. All human beings have the power of timeless awareness in time. All human beings have the power of the compassionate transmission of the field of Being into another person. Chakrasamvara as A Tantra of the Realm of Immanence The Chakrasamvara Tantra invokes the archetypal power of experiencing the beatific experience within and as the realm of the immanence of Being. This means we can experience the beatific-ness of Being within our experience of beings, including our own being. We can experience all phenomena within the realm of the immanence as Pure Being. Our own Being is within the realm of immanence, the immanence of Pure Being. As a Shaivite person of long ago declared “the Bliss of Samadhi is the Bliss of the World”. We can experience through all and within all appearances the indivisibleness between appearance and Being, between being and Being itself. There is no difference of Being within and between beings. This Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 15 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer luminous oneness of Being is the unfolding experience of beatific bliss. There is no ontological difference of Being within the phenomenological difference of beings. Being is univocal. Being is sameness, complete sameness within Being and within beings. The luminous oneness of Being is the unfolding experience of Beatific Bliss. There is no ontological difference of Being within the phenomenological difference of beings. Being is univocal. Being is sameness, complete sameness within all beings. There is a difference within Forms, but not within Being. The Givenness of Being and The Givenness of Self Liberation The experience of the non-duality of our own Being as Being itself is self- liberating. This is the natural givenness of self- liberation within the unfolding of our life experience. Our life experience is the selfmanifestation of Being within us as us. Being is the self-manifestation of our life experience. The experience of the Beingness of my own Being liberates me from the containment of the various forms of experience. All my experience is the self-manifestation of Being as my own being. Being liberates me through the bliss of Being. My Being is Being itself becoming a being as me. The completeness of Being infuses my experience with bliss. The potentiality of Being is the potentiality of my own being which is my own innermost awareness. The bliss of my awareness is the bliss of Pure Being as a being. The experience of the Being of my own being can be the experience of beatific-ness and the experience of my own Being can be my vision of beatific-ness that is completely within my field of Being. The experience of Being in and of itself is beatific-ness. The experience of the selfmanifestation of Being becoming my own being is the beatific experience. Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 16 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer The experience of a being as Being itself is the beatific experience of selfliberation. To experience the Being of your own being and to experience the Being of another being is the beatific experience of Being. To experience the purity of Being in and of itself is the pure Beatific vision of the beatific experience. This does not mean human beings are not distorted in character and action. The purity of Being is beyond character and beyond action. To experience the purity of Being is always selfliberating from the containment of the forms of phenomena, the circumstances of phenomena and the containment of the character of phenomena. To experience the Being of phenomena is to experience the purity of phenomena. To experience Beatific-ness is to experience the bliss of the Being of phenomena. Bliss is the experience of the Beatific-ness of the Being of phenomena. Beatific experience is in essence the Bliss of Being. Bliss and Beatific are completely correlational. The bliss of Being goes beyond right and wrong, goes beyond good and evil, goes beyond better and best and even goes beyond truth and falsity. Bliss is within us as our very Being which is Being itself. Bliss is innate. Bliss is the manifestation of the ground of Being. The ongoing continuity of experience of the manifestation of Being is Bliss. Self- liberation happens through the Bliss of our Being. Just as we are! The Gaze of Being and the Being of Our Gaze We can experience the field of Being of phenomena through our gaze. The gaze of our awareness is the gaze of and through the field of Being. The light of our gaze experiences the light of phenomena. The light of phenomena is the light of Being. The light of our gaze experiences the luminous Being of phenomena. The Being of phenomena and the Being Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 17 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer of personhood is illuminated through our embodied gaze of our luminous embodied awareness. Our gaze is the gaze of our Being manifesting the illumination of the Being of phenomena as well as the character of phenomena. The gaze is not an objectified seeing of mind alone, but rather our gaze is the inter-subjective inside to inside self-illumination of Being of self and the Being of phenomena. The gaze of our Being illuminates the Being of phenomena. The gaze of our Being is the selfillumination of the light of our Being which is Being itself. The Gaze of Being is the Bliss of Being. We gaze not with our eyes alone but we gaze from within the field of our fully embodied awareness. We gaze through our eyes, we gaze through our heart- mind continuum and we gaze through our fully embodied field of Being. The gaze of embodied awareness takes place within the field of immanence. The gaze of immanence is the gaze of gnosis, the direct knowing of Being within beings and the knowing of Being within phenomena. This is pantheistic experience! This is naturalistic pantheistic experience of non-dual Being within the duality of beings. This is the naturalistic pantheistic experience of duality of beings within the nonduality of Being. This is the Bliss of Being as beings. This experience of the gaze goes beyond the sense of sight as we have already described. The sense of this bliss filled knowingness permeates the sense of smell. A person who is embodying the field of Being may experience exquisite sense of fragrance arising within and around their body and the bodies of others. This bliss filled direct knowingness of embodied being permeates the sense of touch. A person who is embodying the field of Being may experience the field through touch. This experience of bliss filled tactile- Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 18 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer ness may both arise from touching and from being touched. Through tactile experience we touch the field of Being and are touched by and through the field of embodied Being. To use Merleau Ponty’s metaphor we touch the flesh of Being. We touch the Being of flesh (Merleau-Ponty, 2013). This bliss filled sense of direct knowingness fills our sense of sound. A person who has embodied Being and experiences the Bliss of Being may feel the permeability of their sense of hearing by sublime sounds and vibrational states of bliss filled experience. This bliss full sense of knowing fills our sense of time within timelessness and our sense of timelessness within time. The sense of time itself becomes a most bliss full and permeating state. Taste can be infused with Bliss full experience and energy of Bliss and so within the embodied field of Being a person can experience Amrita. As the sense of Amrita arises within us there is the inner sensuous experience of a sense of the rasa of liquid like taste permeating our embodiment. The inner chakras are filled with the sense of a taste of viscous sense of liquid light. This bliss filled sense of field of Being can metabolize pain. The field of the bliss of Being can open contracted states of pain, dissolving the sensations of pain. The bliss filled opening of the field of perception results in pain no longer so completely dominating and organizing our sense of Being as self. This bliss filled sense of Being can metabolize psychological suffering. The Bliss of Being infuses the sphere of suffering and this infusion profoundly unbinds us. The sense of Being converges with our sense of self. Our sense of Being and our sense of self are one. Our sense of self becomes the Bliss of Being. The sense of self is an onto cosmological Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 19 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer sense of Being. Our sense of Being is the sense of Bliss. There are many doorways of this Bliss, and many events of Bliss. The sense of Bliss is the innate intrinsic sense of our innermost Being becoming. The Bliss of Being is always becoming and becoming and becoming. In truth liberation is not a simplistic event. Liberation is not an All done event! Liberation is not a fixed state! Liberation is infinite in its becoming, life after life, death after death. Liberation of Being is forever and ever unfolding and forever and ever becoming and becoming. The universe is forever and ever unfolding and becoming. Being is becoming! Infinity is not a fixed state. Infinity is not bound in time or place. The religious understanding that realization and liberation is a time bound and time limited event is the form of reification and concretization of that which can never be reified and never concretized (Muktananda, 1978). Pure Land of Bliss Tradition The Chakrasamvara Tantra is deeply reflective of the ancient Pure Land tradition’s description of the Pure Land of Bliss (Halkias, 2012). Of course, the Pure Land of Bliss is Sukhavati. As Ju Mipham in his commentary on his wonderful text “The Sun Like Instructions of a Sage” describes how our aspiration to dwell in the Pure Land of Bliss is of the essence. And secondly, to experience within our awareness the sense of the Light of Being is also of essence (Cook, 2016). Many people think that Sukhavati is a pure land realm that only exists after death. This is not the truth of the realm of Sukhavati. From the esoteric Dzogchen view, Sukhavati exists both in our ordinary life realm, and as well as within the Sambogakaya realm while we are living in the Nirmanakaya realm. After death or after the time bound event of our dissolving from living within the Nirmanakaya realm, we dissolve into Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 20 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer Sambogakaya realm which is the Realm of Rapture. This archetypal dimension is the Bliss of Rapture! The Bliss of Rapture is for everyone. Absolutely everyone. There is no exclusion of anyone who passes through the realm of death. We all dissolve into the realm of Rapture. This is the Pure Land of Bliss that is the nature of Rapture. The great compassion of Being is infinite in its horizon, vast and inconceivable. The great compassion of Pure Being is not the concrete cruel judgmental-ness of the distorted Mind of Patriarchal Power and Patriarchal Priesthoods. Most religions are encapsulated in patriarchal institutionalization. The Great compassion is beyond good and evil, beyond right and wrong, beyond better and best and even, yes even beyond truth and falsity. The Dakini’s delight within this luminous understanding. This esoteric Dzogchen understanding is that the Pure Land of Bliss is the Buddha field. The Buddha field is not a person. The Buddha field in actuality is the experience of our non-dual nature of awareness. This non-dual field of primordial awareness is the source of the different dimensions of Being as well as actually being the different dimensions of Being. In becoming aware of awareness, we experience the Pure Land of Bliss. The Pure Land of Bliss is the Pure Field of the Bliss of the Being of our ordinary life realm, as well as the Pure Field of the Bliss of the Archetypal Sambogakaya realm and as well as the Pure Field of the Bliss of the realm of pure potentiality of the Dharmakaya. By sense of the Light, Ju Mipham languages the Light of Being’s selfmanifestation as the Buddha Amitabha. Of course, the Buddha Amitabha is not a person but the archetypal light of Being manifesting itself in “us as us”. Ju Mipham says explicitly that entering and dwelling in this Pure land is not for a later time. He is implying the land of Pure Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 21 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer Bliss is Now. The Presence of the Pure Land of Bliss is Now, always and forever Now. You will always exist in nowness. Ju Mipham further describes how dwelling in this land of Pure Bliss does not depend on merit and does not depend on our accomplishments such as being a Bodhisattva. There are no required conditions to enter the pure land of Bliss. And most of all Being in the Pure Land of Bliss does not require death. The Pure Land of Bliss is not simply an afterdeath moment or after death realm. The Pure Land of Bliss is here and now. The Pure Land of Bliss is here and now life after life and death after death. The Pure Land of Bliss is timeless awareness becoming time. Timelessness awareness is always manifesting and becoming time forever and ever. This pure land of Bliss is the presence of the Pure Field of Being in “you as you”. You are always in this field of Being, life after life and death after death. Being is the Pure Land of Bliss. This Pure land of Pure Bliss is present now as this life. This Pure Land of Pure Bliss is present, as you dissolve through the doorway of death. From being located in the ordinary life world of the Nirmanakaya dimension of Pure Being, through the doorway of dying you move into the Pure Bliss of Sambogakaya dimension of the Pure Being of great rapture. This Pure Land Realm of Bliss is described as the Pure Land of Bliss in early Sacred Text of Mahayana. You may then dissolve further into the Bliss of Pure Being of Dharmakaya dimension, the realm of Pure Potentiality of Pure Being. This is the Pure Realm of Pure Being of Pure Bliss of Potential Space. In time you may again manifest in the ordinary life world realm, as well as remaining in the archetypal realm of the Sambogakaya dimension of Pure Land of Bliss. Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 22 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer You may wonder as you experience Ju Mipham’s understanding that the nature of Pure Lands of Bliss is existentially so available and existentially so present. Why then is the experience of the Bliss of Being so hidden and so obscured for so many? Ju Mipham does focus on the power of self-effort as well as the power of the field of Being to bring forth the Pure Land experience. Self-effort seems to be in the Dharma of aspiration and attunement to the field of Being/awareness in the different dimensions of the Kaya’s. Conclusion The compassionate power of the field of Being/awareness is the luminous power of the field within its different dimensions and manifestations of and as the Kaya’s. The power of the field of Being which is the power of the Pure Land of Bliss, liberates us naturally. The Pure Land of Bliss is beyond right and wrong, good and evil, better and best and even truth and falsity. The Pure Land of Bliss is beyond the truth as Judgement. The Pure Land of Bliss is the truth of self-revelation and selfillumination. The field of Being reveals itself to us as us. The Pure Land of Bliss is the field of Being in the self-revelation of its essence. The Pure Land of Bliss is totally free of patriarchal distortion and the theocentric confusion of royalty and spirituality. The pure land of Bliss is totally free of the distorted confusion of the aberrational theocentric judgement of heaven and hells, of torture and liberation, of rewards and everlasting punishment by unending torture. The Pure Land of Bliss is free of the patriarchal relentless love of torture and relentless unending cruelty for the sake of their “would be” God, who is simply the mirror of their own mind. Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 23 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer The Pure Land of Bliss is the nature of Being. The pure land of Bliss is one voice. The Pure Land of Bliss is equality consciousness. The Pure land of Bliss is the pure Being of awareness being unborn and undying. The Pure Land of Bliss is manifest in all circumstance, all context, all situations and all events of Being. Within every event is the Bliss of the radiance of Being. Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 24 The Beatific Experience of Being: A Phenomenology of The Chakrasamvara Tantra Rudolph Bauer References Bauer, R. (2019). Mind As Knower of Forms, And Awareness as The Knower of Being: A Phenomenological View. MenteClara Foundation’s Peer-reviewed Journal, Vol.4 (2), 4753. doi: https://doi.org/10.32351/rca.v4.2.86 See at: https://fundacionmenteclara.org.ar/revista/index.php/RCA/article/view/86 Bauer, R. (2019). Ontology of Bliss: A Phenomenology. MenteClara Foundation’s Peerreviewed Journal, Vol.4 (2), 55-70. doi: https://doi.org/10.32351/rca.v4.2.87 See at: https://fundacionmenteclara.org.ar/revista/index.php/RCA/article/view/87 Bauer, R. (2020). Human Egalitarianism and the Patriarchal Illusion: A Phenomenological View. MenteClara Foundation’s Peer-reviewed Journal, Vol.5 (122). doi: https://doi.org/10.32351/rca.v5.122 See at: https://fundacionmenteclara.org.ar/revista/index.php/RCA/article/view/122 Capobianco, R. (2014). Heidegger's Way of Being, University of Toronto Press. Cook, L. (2016). JU MI PHAM ON PURE LAND DOCTRINE AND PRACTICE, Master of Arts Thesis Advisor: James Gentry Centre for Buddhist Studies, Kathmandu University. Gray, D. B. (2007). The Cakrasamvara Tantra (The discourse of Śrī Heruka). American Institute of Buddhist Studies. Halkias, G. T. (2012). Luminous Bliss: a religious history of Pure Land literature in Tibet. University of Hawai'i Press. Merleau-Ponty, M. (2013). Phenomenology of perception. Routledge. Morris, David (2018) Merleau- Ponty's Developmental Ontology, North Western University Studies In Phenomenology and Existential Philosophy, Northwestern University Press, Evanston, Illnois. Muktananda, S. (1978). Play of consciousness. Harper & Row. Revista Científica Arbitrada de la Fundación MenteClara Vol. 5 (2020), ISSN 2469-0783 25
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Effects of Nursing Education on Awareness of Risk Factors for Colorectal Cancer
Asian Pacific journal of cancer prevention
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DOI:http://dx.doi.org/10.7314/APJCP.2015.16.14.5763 Effects of Nursing Education on Awareness of Risk Factors for Colorectal Cancer DOI:http://dx.doi.org/10.7314/APJCP.2015.16.14.5763 Effects of Nursing Education on Awareness of Risk Factors for Colorectal Cancer RESEARCH ARTICLE Abstract Background: The objective of this study is to determine the effect of nursing education on awareness of risk factors for colorectal cancer. Materials and Methods: In this descriptive study, the sample is consisted of 132 volunteer students studying in the 1st and 4th grades of School of Health Nursing Department during the fall semester of 2014-2015. Data were collected via a questionnaire including information on the socio-demographic features of the participants and the correlating risk factors of colorectal cancer, prepared by researchers in view of the literature. The questionnaire was distributed to students and completed during class time. Before presenting the questionnaires to the respondents, informed consent was obtained from each. The data obtained were analyzed with a statistical package (SPSS). At first, a Kolmogorov-Smirnow test was performed on the research data. However, since it was seen that variables did not have a normal distribution, the Wilcoxon Signed Ranks Test was applied. P values of <0.05 were considered statistically significant. Percentages, means and standard deviations were also utilized for evaluation. Results: Of the total of 132 students participating in this study, 85.6% (n=113) were female, and 14.4% (n=19) were male. The average age was 20.5±2.04. 54.5 % of the students (n=72) were 4th graders and 45.5 % (n=60) were first graders. Total score averages of first graders on risk awareness was X=12 ± 7.24, and fourth graders was X=16.93 ± 7.71. The difference between these two scores were found to be statistically significant (Z= -9,333; p=0.000). Conclusions: Nursing education was found out to have a positive influence on the students’ awareness of risk factors for colorectal cancer. Keywords: Colorectal cancer - awareness of risk factors - nursing education Asian Pac J Cancer Prev, 16 (14), 5763-5766 It was stated that colorectal cancer was the third most commonly diagnosed cancer with a percentage of 9.7 % in the world. More than a half of both cancer cases (56.8%) and deaths from cancer (64.9%) was found to be in the least developed countries (GLOBOCAN 2012; Tastan et al., 2013; WHO, 2014; WHO, 2015). New cases are estimated to double the number as nearly as 70 % in the next two years. Leading behavioral and dietary risks in about 30% of cancer deaths are higher body mass index, inadequate fruit and vegetable intake, physical inactivity, tobacco and alcohol use. Tobacco use is the most important risk factor for 20% of global cancer deaths. Abstract More than 60% of total annual new cases in the world are seen in Africa, Asia and Central and South America. These regions comprise the 70% of cancer deaths worldwide. It is expected that annual cancer cases will rise from 14 million in 2012 to 22 within the next 2 decades (WHO, 2014; WHO, 2015). One of the most reliable surveillance systems in terms of cancer statistics is in the United States (US). American Cancer Society estimates that a total of 141,210 people were diagnosed with colorectal cancer and 49,380 people died due to colorectal cancer in 2011 in the USA. It is the third most common cancer in both men and women Effects of Nursing Education on Awareness of Risk Factors for Colorectal Cancer Funda Akduran, Nursan Cinar* School of Health Sciences, Esentepe Campus, Sakarya University, Sakarya, Turkey *For correspondence: ndede@sakarya.edu.tr Asian Pacific Journal of Cancer Prevention, Vol 16, 2015 5 Asian Pacific Journal of Cancer Prevention, Vol 16, 2015 5763 School of Health Sciences, Esentepe Campus, Sakarya University, Sakarya, Turkey *For correspondence: ndede@sakarya.edu.tr Introduction Opinions of 1st and 4th Grade Student Nurses on the Risk Factors of Colorectal Cancer Risk Factors 1st Grade (N:60) 4th Grade (N:72) (n, %) (n, %) Familial history of cancer: Increases cancer risk 38 (63.3) 65 (90.3) Involves no risk 7 (11.7) 3 (4.32) I don’t know 15 (25.0) 4 (5.6) Familial colorectal cancer Increases cancer risk 28 (46.7) 64 (88.9) Involves no risk 12 (20.0) 5 (6.9) I don’t know 20 (33.3) 3 (4.2) Race and ethnicity Increases cancer risk 28 (46.7) 53 (73.6) Involves no risk 11 (18.3) 6 (8.3) I don’t know 21 (35.0) 13 (18.1) Smoking Increases cancer risk 55 (91.7) 65 (90.3) Involves no risk 1 (1.7) 1 (1.4) I don’t know 4 (6.7) 6 (8.3) Hoookah use Increases cancer risk 49 (81.7) 63 (87.59 Involves no risk 2 (3.3) 2 (2.8) I don’t know 9 (15.0) 7 (9.7) Excess alcohol consumption Increases cancer risk 51 (85.0) 63 (87.5) Involves no risk 3 (5.0) 3 (4.2) I don’t know 6 (10.0) 6 (8.3) Physical inactivity Increases cancer risk 37 (61.7) 52 (72.2) Involves no risk 8 (13.3) 8 (11.1) I don’t know 15 (25.0) 12 (16.7) Stress Increases cancer risk 53 (88.3) 67 (93.1) Involves no risk 4 (6.7) 2 (2.8) I don’t know 3 (5.0) 3 (4.2) Exposure to pelvic radiation Increases cancer risk 46 (76.7) 65 (90.3) Involves no risk 1 (1.7) 3 (4.2) I don’t know 13 (21.7) 4 (5.6) Obesity Increases cancer risk 31 (51.7) 57 (79.2) Involves no risk 8 (13.3) 4 (5.6) I don’t know 21 (35.0) 11 (15.3) Unhealthy diet Increases cancer risk 55 (91.7) 65 (90.3) Involves no risk 1 (1.7) 3 (4.32) I don’t know 4 (6.7) 4 (5.6) Long-term red / processed meat consumption Increases cancer risk 55 (91.7) 65 (90.3) Involves no risk 1 (1.7) 3 (4.2) I don’t know 4 (6.7) 4 (5.6) Fatty food consumption Increases cancer risk 43 (71.7) 63 (87.5) Involves no risk 3 (5.0) 2 (2.8) I don’t know 14 (23.3) 7 (9.7) Table 1. Opinions of 1st and 4th Grade Student Nurses on the Risk Factors of Colorectal Cancer As health professionals, nurses have the duty to protect the health of society as well as performing curative services. There are few studies on the effects of nursing education on colorectal cancer risk awareness. Introduction Cancer is major burden worldwide and a leading cause of mortality (Stubbings et al., 2009; Al-Azri et al., 2014). The incidence of different types of cancer has increased in the past 20 years and is expected to rise further with an estimated 13.1 million deaths per annum by 2030 (WHO, 2014). The incidence of cancer in Turkiye is similar to the world’s in general. Age standardized rate of cancer in men was 269.7, and 173.3 in women in Turkey, 2009 (per 100000 people). It was announced that colorectal cancer incidence for men was 21 in 100.000 in Turkiye (T.R. Ministry of Health, Annual Health Statistics, 2013). According to the 2009 cancer statistics, nearly 98 thousand men and 63 thousand women get cancer every year in Turkiye. Among the most common 5 cancer types, colorectal cancer ranks the 4th for men and the 3rd for women. According to data from the year 2012, among the top five most commonly diagnosed cancers, colorectal cancers were ranked the third in men and the second in women. According to data GLOBOCAN 2012, a total of 14.1 million new cancer cases in the world were seen in 2012 and 8.2 million deaths occurred as a result of cancer. 5763 Funda Akduran and Cinar Nursan assessed; it was seen that for the 1st graders the most well-known risk factors “smoking”, “unhealthy diets” and “long-term red meat / processed meat consumption” rated first with a percentage of 17 %; “stress” rated second with a percentage of 88.3 % and “excess alcohol consumption” rated third with a percentage of 85 %. When the least known risk factors for the same group were examined “subclinical hypothyroidism” ranked first with 25%,”the and also ranks third as the cause of cancer-related deaths (Colorectal Cancer Facts &Figures 2013). Since early stage cancers are less deadly and can be treated better than late-stage cancers, if cancer awareness is created, early diagnosis increases the chance of a cure and improves the quality of life in cancer patients. Therefore, health professionals’, particularly nurses’ (colorectal) cancer- related risk awareness should be increased during their professional training and they should be informed about early diagnosis and screening programs of cancer (Andsoy et al., 2014; WHO, 2015 http://www.worldcancerday.org). “subclinical hypothyroidism” ranked first with 25%,”the Table 1. Introduction Future research on increasing the awareness of nursing students on the risk factors of cancer will help to shape training programs and make effective use of nursing practices combined with evidence based practices. Based on these requirements, this study was carried out to determine the effect of nursing education on colorectal cancer risk awareness. Materials and Methods Being a descriptive study, its sample was consisted of 132 volunteering students studying in the 1st and 4th grades of School of Health Nursing Department during the fall semester of 2014-2015. Data were collected via a questionnaire including information on the socio- demographic features of the participants and a 24-item questionnaire on the risk factors of colorectal cancers. The assessment of items on colorectal cancer was performed by scoring the right answers “1 point”, wrong answers “-1 point” and “0” for the answer “I don’t know”. The questionnaire was distributed to students and completed during class time. Before presenting the questionnaires to the respondents, informed consent was obtained from each student. Only once a respondent confirmed that they understood the purpose of survey were they handed the questionnaire form. The respondents when required to answer all the questions and hand the questionnaire back to the researcher. The data obtained was analyzed by Statistical Package (SPSS). At first, Kolmogorov- Smirnow test was performed on the research data. However, since it was seen that variables didn’t have a normal distribution, Wilcoxon Signed Ranks Test was applied. P values of <0.05 were considered statistically significant. Percentage, mean and standard deviation were also utilized for evaluation. Asian Pacific Journal of Cancer Prevention, Vol 16, 2015 5764 Results A total of 132 students participated in this study. 85.6 % of the participants (n=113) were female, and 14.4 % (n=19) were male. The average age of the participants was 20.46±2.04, with a minimum age of 17 years and a maximum age of 31 years. 54.5 % of the students (n=72) were 4th graders and 45.5 % (n=60) were first graders. When the risk factors that are least and most well- known among 1st and 4th grade nursing students were Asian Pacific Journal of Cancer Prevention, Vol 16, 2015 5764 DOI:http://dx.doi.org/10.7314/APJCP.2015.16.14.5763 DOI:http://dx.doi.org/10.7314/APJCP.2015.16.14.5763 Effects of Nursing Education on Awareness of Risk Factors for Colorectal Cancer nd with 38.3%, d with 41.7%. enior students “the presence elvic radiation processed meat nce of another the third row included “familial colon cancer in the family” as the most well-known risk factor with a percentage of 88,9%. The least known risk factors for the same group were found out to be “HIV positive patients” in the first row with 37.5 % rate, “subclinical hypothyroidism” rated second with 40.3 % and “taking chemotherapy for prostate cancer” rated third with 62.5 %. DOI:http://dx.doi.org/10.7314/APJCP.2015.16.14.5763 Effects of Nursing Education on Awareness of Risk Factors for Colorectal Cancer nd with 38.3%, d with 41.7%. enior students “the presence elvic radiation processed meat nce of another the third row included “familial colon cancer in the family” as the most well-known risk factor with a percentage of 88,9%. The least known risk factors for the same group were found out to be “HIV positive patients” in the first row with 37.5 % rate, “subclinical hypothyroidism” rated second with 40.3 % and “taking chemotherapy for prostate cancer” rated third with 62.5 %. presence of chronic diseases” ranked second with 38.3%, and “HIV-positive patients” ranked third with 41.7%. The most well-known risk factors for Senior students were; “Stress” ranked first with 93.1% ; “the presence of cancer in the family”, “smoking”, “pelvic radiation exposure”, “unhealthy diets”, “red meat / processed meat consumption in the long term”, “ presence of another cancer beforehand” ranked second with 90,3% rate, and First grade students’ risk awareness total score average was found to be X = 12 X = 16.93 ± 7.24 while it was X=16,93 ± 7.71 for the last year students. The difference was found to be statistically significant (Z = -9.333; P = .000). Table 1.1. Results Opinions of 1st and 4th Grade Student Nurses on the Risk Factors of Colorectal Cancer Table 1.1. Opinions of 1st and 4th Grade Student Nurses on the Risk Factors of Colorectal Cancer Risk Factors 1st Grade (N:60) 4th Grade (N:72) (n. %) (n. %) Inadequate fruit/vegetable consumption Increases cancer risk 35 (58.3) 55 (76.4) Involves no risk 12 (20.0) 9 (12.5) I don’t know 13 (21.7) 8 (11.1) Inadequate cereal consumpt. Increases cancer risk 27 (45.0) 47 (65.3) Involves no risk 11 (18.3) 10 (13.9) I don’t know 22 (36.7) 15 (20.8) Part. After 50 years Increases cancer risk 33 (55.0) 52 (72.2) Involves no risk 10 (16.7) 8 (11.1) I don’t know 17 (28.3) 12 (16.7) Another type of cancer prev. Increases cancer risk 44 (73.3) 65 (90.3) Involves no risk 6 (10.0) 3(4.2) I don’t know 10 (16.7) 4(5.6) Large intestine polyps Increases cancer risk 29 (48.3) 55 (76.4) Involves no risk 7 (11.7) 6 (8.3) I don’t know 24 (40.0) 11 (15.3) Inflammatory intestine dis. Increases cancer risk 36 (60.0) 62 (86.1) Involves no risk 4 (6.7) 4 (5.6) I don’t know 20 (33.3) 6 (8.3) Presence of a chronical dis. Increases cancer risk 23 (38.3) 49 (68.1) Involves no risk 9 (15.0) 8 (11.1) I don’t know 28 (46.7) 15 (20.8) Some types of occupations Increases cancer risk 31 (51.7) 58 (80.6) Involves no risk 8 (13.3) 2 (2.8) I don’t know 21 (35.0) 12 (16.7) Taking radiotherapy for prostate cancer Increases cancer risk 28 (46.7) 45 (62.5) Involves no risk 5 (8.3) 8 (11.1) I don’t know 27 (45.0) 19 (26.4) HIV positive patients Increases cancer risk 25 (41.7) 27 (37.5) Involves no risk 10 (16.7) 15 (20.8) I don’t know 25 (41.7) 30 (41.7) Subclinical hypothyroidism Increases cancer risk 15 (25.0) 29 (40.3) Involves no risk 9 (15.0) 10 (13.9) I don’t know 36 (60.0) 33 (45.8) Table 2. A Comparison of Colorectal Cancer Risk Factor Awareness Scores of 1st and 4th Grade Nursing Students Discussion In this study, conducted to determine the effect of nursing education on awareness of the risk of colorectal cancer, it was assessed that nursing education positively affected the students’ awareness of the risk for colorectal cancer. While first year students emphasized factors such as smoking, unhealthy diet and alcohol use among the most common risk factors, senior students reported factors such as stress, the presence of cancer in the family and exposure to pelvic radiation as the most important risk factors. It can be stated that education influences the awareness of students on risk factors. Tobacco use, alcohol use, unhealthy diet and physical inactivity, obesity, age older than 50 years, genetic predisposition, including hereditary polyposis and nonpolyposis syndromes, are the main cancer risk factors worldwide (MOH, 2009; NCR, 2009; WHO, 2014). The common other risk factors for CRC include dietary practices such as high consumption of fat, red meat, and low consumption of fiber and vegetables (Umar et al., 2009; Huxley et al., 2009). Meat intake is associated with the risk of colorectal cancer (Kim et al., 2011; Woo et al., 2014; Anderson et al., 2015). It is seen that students in the study group are aware of the fact that long term red meat consumption increases cancer risk, because a total of 75 % of them (n=99) have stated this issue. However, it is observed that there are risk factors less known also by senior students. The least known risk factor among the students were found out to be subclinical hypothyroidism. In a case-control study (Guifang et al., 2014) performed by Guifang and colleagues on 273 colorectal cancer patients, subclinical hypothyroidism was found to be an independent risk factor for colorectal cancer. In conclusion, nursing education positively affects the students’ awareness of the risk for colorectal cancer, but it was shown that some risk factors were not known enough by the students. Nursing students should be informed on the most common risk factors for colorectal cancer in accordance with evidence-based studies and they should be directed to further reading and research on this topic. This study will contribute to new studies on the subject. Limitation: this study was carried out in a particular university, so it can not be generalized for the whole university students and geographical regions. Similar studies among university students in different cultural groups and different geographical regions can be performed in the future. Asian Pacific Journal of Cancer Prevention, Vol 16, 2015 Discussion 5765 Asian Pacific Journal of Cancer Prevention, Vol 16, 2015 Funda Akduran and Cinar Nursan Acknowledgements Thanks for the students who participated in this study Thanks for the students who participated in this study References Al-Azri M, AL-Rasbi K, Al-Hinai M,Davidson R ,Al-Maniri A. Awareness of Risk Factors for Cancer among Omani adults- A Community Based Study (2014). Asian Pac J Cancer Prev, 15, 5401-6. Andersen V, Ulla Vogel (2015). Interactions between meat intake and genetic variation in relation to colorectal cancer. Genes Nutr, 10, 448. Andsoy II, Gul A (2014). Breast, cervix and colorectal cancer knowledge among nurses in Turkey. Asian Pac J Cancer Prev, 15, 2267-72. Colorectal Cancer Facts &Figures 2011-2013 (2013). http:// www.cancer.org/acs/groups/content/@epidemiology. surveilance/documents/document/acspc-028323.pdf GLOBOCAN 2012: Estimated Cancer Incidence, Mortality and Prevalence Worldwide in 2012. http://globocan.iarc.fr/Pages/ fact_sheets_cancer.aspx Huxley RR, Ansary-Moghaddam AA, Clifton P, et al (2009) The impact of dietary and life style risks of colorectal cancer: a quantitative overview of the epidemiology evidence. Int J Cancer, 125, 171-80. Kim J, Park S, Nam BH (2011). The risk of colorectal cancer is associated with the frequency of meat consumption in a population-based cohort in Korea. Asian Pac J Cancer Prev, 12, 2371-6 Ministry of Health of Jordan (MOH)-(2009) Cancer incidence in Jordan, report of 2008. Non-Communicable Diseases Control Section, Amman, Jordan. Mua G, Mub X, Xingc H, et al (2014). Subclinical hypothyroidism as anindependent risk factor for colorectalneoplasm. Clin Res Hepatol Gastroenterol, 14. National Cancer Registry (NCR) (2009) Cancer incidence in Jordan report of 2008. Non-communicable diseases control section, Amman, Jordan Stubbings S, Robb K, Waller J, et al (2009). Development of a measurement tool to assess public awareness of cancer. Br J Cancer, 101, 13-17. Tastan S, Andsoy II, Iyigun E (2013). Evaluation of the knowledge, behavior and health beliefs of individuals over 50 regarding colorectal cancer screening. Asian Pac J Cancer Prev, 14, 5157-63 Turkiye Cumhuriyeti, Saglik Bakanligi Saglik Istatistikleri Yilligi (2013). http://sbu.saglik.gov.tr/Ekutuphane/ kitaplar/sa%C4%9Fl%C4%B1k%20istatistik%20 y%C4%B1ll%C4%B1%C4%9F%C4%B1%202013.pdf. Umar A, Greenwald P (2009) Alarming colorectal cancer incidence trends: a case for early detection. Cancer Epidemiol Biomarkers Prev, 18, 1672-3. Woo HD, Park S, Oh K, Kim HJ, Shin HR, Moon HK, Kim J (2014). Diet and cancer risk in the Korean population: a meta- analysis. Asian Pac J Cancer Prev, 15, 8509-19. WHO World Health Organization (2014). http://www.who.int/ mediacentre/factsheets/fs297/en/. WHO World Health Organization (2015). http://www.who.int/ cancer/en/ WHO World Health Organization (2015). http://www. worldcancerday.org/ Asian Pacific Journal of Cancer Prevention, Vol 16, 2015 5766
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https://figshare.com/articles/journal_contribution/Supplementary_Figure_3_from_Analyzing_the_Pivotal_Trial_That_Compared_Sunitinib_and_IFN-_in_Renal_Cell_Carcinoma_Using_a_Method_That_Assesses_Tumor_Regression_and_Growth/22445048/1/files/39896096.pdf
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Supplementary Figure 1 from Analyzing the Pivotal Trial That Compared Sunitinib and IFN-α in Renal Cell Carcinoma, Using a Method That Assesses Tumor Regression and Growth
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nitinib) nitinib) SigDiff p<=.05 p>.05 .0018 g 0006 .0012 .0000 .0006 1300 Evaluation # 6 11.5 1 nib) nib) SigDiff p<=. p>.05 .0018 g 0006 .0012 .0006 .0000 1300 Evaluation # 6 11.5 nitinib) nitinib) SigDiff p<=.0 p>.05 .0090 .0120 g .0060 .0090 .0000 .0030 ) 0 600 Evaluation # 3 6 inib) inib) SigD p< p> .0090 .0120 g .0060 .0090 .0030 .0000 600 Evaluation # 3 6 nitinib) nitinib) SigDiff p<=.0 p>.05 .0045 g 0015 .0030 .0000 .0015 700 Evaluation # 3 7 inib) inib) SigD p< p> .0045 g 0015 .0030 .0015 .0000 700 Evaluation # 3 7 nitinib) nitinib) SigDiff p<=.0 .0030 .0040 g .0020 .0030 .0000 .0010 ) 500 Evaluation # 3 5.5 nib) nib) SigDif p<= .0030 .0040 g .0020 .0030 .0010 .0000 500 Evaluation # 3 5.5 nitinib) nitinib) SigDiff p<=.05 p>.05 .0066 .0088 g .0044 .0066 .0000 .0022 1400 Evaluation # 3 11 1 .0000 1400 Evaluation # 3 11 nib) nib) .0066 .0088 g .0044 .0066 .0022 nitinib) nitinib) SigDiff p<=.05 p>.05 .0060 .0080 g .0040 .0060 .0000 .0020 1400 Evaluation # 3 10.5 18 tinib) tinib) SigDiff p<=. p>.0 .0060 .0080 g .0040 .0060 .0020 .0000 1400 Evaluation # 3 10.5 nitinib) nitinib) SigDiff p<=.0 p>.05 .0120 .0150 g .0060 .0090 .0000 .0030 ) 0 900 Evaluation # 3 8 1 inib) inib) SigDi p< p> .0120 .0150 g .0060 .0090 .0030 .0000 900 Evaluation # 3 8 nitinib) nitinib) SigDiff p<=.0 p>.05 .0024 .0032 g .0016 .0024 .0000 .0008 ) 0 1200 Evaluation # 3 9.5 tinib) tinib) SigDif p<= p>. .0024 .0032 g .0016 .0024 .0008 .0000 1200 Evaluation # 3 9.5 erferon) erferon) SigDiff p<=.05 .0012 .0016 g .0008 .0012 .0000 .0004 ) 1400 Evaluation # 3 10.5 18 eron) eron) SigD p< .0012 .0016 g .0008 .0012 .0004 .0000 1400 Evaluation # 3 10.5 rferon) rferon) SigDiff p<=.0 p>.05 .0030 .0040 g .0020 .0030 .0000 .0010 ) 500 Evaluation # 3 6 ron) ron) Sig p p .0030 .0040 g .0020 .0030 .0010 .0000 0 Evaluation # 3 6 erferon) erferon) SigDiff p<=. .0036 g 0012 .0024 .0000 .0012 ) 3 500 Evaluation # 3 6 eron) eron) SigD p< .0036 g 0012 .0024 .0012 SigD p .0000 0 Evaluation # 3 6 erferon) erferon) SigDiff p<=.0 .0012 .0016 g .0008 .0012 .0000 .0004 700 Evaluation # 3 7 eron) eron) SigDi p< .0012 .0016 g .0008 .0012 .0004 SigD p .0000 0 Evaluation # 3 7 erferon) erferon) SigDiff p<=.05 .0090 .0120 g .0060 .0090 .0000 .0030 s) 3 500 Evaluation # 3 5.5 8 feron) feron) SigDif p<= .0090 .0120 g .0060 .0090 .0030 SigDi p< SigDi p< .0000 500 Evaluation # 3 5.5 erferon) erferon) SigDiff p<=.05 p>.05 .0045 .0060 g .0030 .0045 .0000 .0015 600 Evaluation # 3 6.5 1 eron) eron) SigDif p<= p>. .0045 .0060 g .0030 .0045 .0015 .0000 600 Evaluation # 3 6.5 erferon) erferon) SigDiff p<=.05 p>.05 .0075 .0100 g .0050 .0075 .0000 .0025 600 Evaluation # 3 6.5 1 feron) feron) SigDif p<= p>.0 .0075 .0100 g .0050 .0075 .0025 .0000 600 Evaluation # 3 6.5 rferon) rferon) SigDiff p<=.05 p>.05 .0060 .0080 g .0040 .0060 .0000 .0020 500 Evaluation # 3 5.5 8 eron) eron) SigDif p<= p>. .0060 .0080 g .0040 .0060 .0020 SigD p< p> .0000 500 Evaluation # 3 5.5
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https://europepmc.org/articles/pmc6349209?pdf=render
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The signal pathway for the repressive effect of dipyridamole on myofibroblast transdifferentiation
Journal of Cellular and Molecular Medicine
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1 | INTRODUCTION junction formation, and exocytosis. In the present study, the effects of dipyridamole against renal fibrosis, the late stage CKD, were investigated in a system without platelet aggregation. In addition, the mechanism by which dipyridamole exerted its effects was exam- ined. Renal fibrosis is the common final pathway of various chronic kidney diseases (CKDs), irrespective of the initial causes of nephropathy. Decline of renal function, glomerular filtration rate, has been exhib- ited to be highly associated with the progression of tubulointerstitial fibrosis.1 Fibrosis is considered to occur via a variety of events, which increase the level of transforming growth factor‐β1 (TGF‐β1), a profibrotic cytokine, in renal tissue. TGF‐β1 induces the emergence of myofibroblasts, myofibroblast transdifferentiation, followed by the accumulation of extracellular matrices such as type I collagen, ie, fibrosis.2 The myofibroblast is characterized by the expression of α‐smooth muscle actin (α‐SMA) in the cytoplasm. Thus, α‐SMA is generally accepted as a marker of fibrosis.3-5 Dipyridamole is in clini- cal use as an anti‐platelet agent. The reno‐protective effects exerted by dipyridamole have been demonstrated in animal models6 and humans with the early stage CKD.7 In almost all of these experi- ments and studies, the amelioration effects of dipyridamole on pro- teinuria were indicated to be mediated by the repression of platelet aggregation which was generally recognized in CKD. S H O R T C O M M U N I C A T I O N S H O R T C O M M U N I C A T I O N 2.1 | Reagents and cells H89, a selective PKA inhibitor, was purchased from Sigma‐Aldrich (St Louis, MO, USA). 4‐methylphenyl‐2,4,6‐trimethylphenylsulfone (ESI‐05), a selective Epac inhibitor, N6‐phenyladenosine‐3′,5′‐cyclic monophosphate (Phe‐cAMP), a PKA activator, and 8‐bromo‐2′‐O‐ methyladenosine‐3′,5′‐cyclic monophosphate‐acetoxymethyl ester (O‐Me‐cAMP), an Epac activator, were obtained from Biolog Life Science (Bremen, Germany). NRK49F cells (normal rat kidney fibrob- lasts) were provided by the RIKEN BRC through the National Bio‐ Resource Project of MEXT, Japan. Dipyridamole increases cAMP levels by inhibiting phosphodi- esterase in a variety of cells including platelets. The cAMP acts through three pathways of its downstream: protein kinase A (PKA), exchange factor directly activated by cAMP (Epac),8 and cyclic nucleotide‐gated (CNG) ion channels.9 In the Epac pathway, the increased intracellular cAMP binds to Epac, a guanine nucleotide exchange factor, followed by activation of the low molecular weight G‐protein Rap. Epac contributes to numerous pathophysiological pro- cesses, including proliferation, differentiation, cell adhesion, cell p p y al of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2018 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine. 1608 | wileyonlinelibrary.com/journal/jcmm J Cell Mol Med. 2019;23:1608–1612. Received: 26 December 2017 | Revised: 10 October 2018 | Accepted: 11 October 2018 DOI: 10.1111/jcmm.14006 Received: 26 December 2017 | Revised: 10 October 2018 | Accepted: 11 October 2018 DOI: 10.1111/jcmm.14006 Received: 26 December 2017 | Revised: 10 October 2018 | Accepted: 11 October 2018 DOI: 10.1111/jcmm.14006 1608 | wileyonlinelibrary.com/journal/jcmm S H O R T C O M M U N I C A T I O N © 2018 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Ce - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - e under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any mediu properly cited. g p p y e Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Mo Qiong Yan | Keisuke Ina | Seiichi Chiba | Huixing Wei | Shuji Tatsukawa | Yoshihisa Fujikura Qiong Yan | Keisuke Ina | Seiichi Chiba | Huixing Wei | Shuji Tatsukawa | Yoshihisa Fujikura Department of Molecular Anatomy, Faculty of Medicine, Oita University, Yufu, Oita, Japan Correspondence Keisuke Ina, Department of Molecular Anatomy, Faculty of Medicine, Oita University, Yufu, Oita, Japan. Email: kina@oita-u.ac.jp p Keisuke Ina, Department of Molecular Anatomy, Faculty of Medicine, Oita University, Yufu, Oita, Japan. Email: kina@oita-u.ac.jp Funding information This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. addition of 2 ng/ml TGF‐β1. They were exposed to 3 μmol/L dipyri- damole for 30 minutes before a treatment of TGF‐β1. They were cultured for 48 hours after TGF‐β1 was added. Then cell lysates were prepared by adding ice cold protein extraction reagent (modi- fied RIPA) with proteinase inhibitors. They (10 μg protein) were applied by 10% SDS‐PAGE electrophoresis and blotted to a polyvinylidene difluoride filter membrane. The membranes were incubated with anti‐α‐SMA, or anti‐GAPDH antibody. The mem- branes were then incubated with appropriate horseradish peroxi- dase‐conjugated secondary antibodies. Immunoreactive bands were visualized by using the ECL system, and the intensity of the bands was measured by Image Quant TL (GE Healthcare, Buckinghamshire, UK). were exposed to stimulants and/or inhibitors in the medium with 0.5% FBS. addition of 2 ng/ml TGF‐β1. They were exposed to 3 μmol/L dipyri- damole for 30 minutes before a treatment of TGF‐β1. They were cultured for 48 hours after TGF‐β1 was added. Then cell lysates were prepared by adding ice cold protein extraction reagent (modi- fied RIPA) with proteinase inhibitors. They (10 μg protein) were applied by 10% SDS‐PAGE electrophoresis and blotted to a polyvinylidene difluoride filter membrane. The membranes were incubated with anti‐α‐SMA, or anti‐GAPDH antibody. The mem- branes were then incubated with appropriate horseradish peroxi- dase‐conjugated secondary antibodies. Immunoreactive bands were visualized by using the ECL system, and the intensity of the bands was measured by Image Quant TL (GE Healthcare, Buckinghamshire, UK). 2.3 | Immunofluorescence microscopy In order to identify the cell type, a monolayer culture of the cells was grown on a two‐well Labtek chamber slide (AS ONE, Osaka, Japan). Cell cultures were divided into three groups: the control, the 2 ng/mL TGF‐β1, and the 2 ng/mL TGF‐β1 + 3 μmol/L dipyridamole group. After treatments, the cells of each group were fixed in 4% paraformaldehyde and subjected to indirect immunofluorescence labelling for α‐SMA. In brief, the cells were permeabilized with 0.5% Triton X‐100 in PBS for 20 minutes, washed with PBS, and incu- bated with the primary antibody against α‐SMA (Sigma‐Aldrich, St Louis, MO, USA; 1:800 dilution) for 2 hours at room temperature (RT). After washing, they were incubated with FITC‐conjugated goat anti‐mouse IgG secondary antibody (Caltag Laboratories, Burlingame, CA, USA; 1:200 dilution) for 1 hour at RT, followed by DAPI nuclear staining. After staining, the cells were rinsed, observed, and pho- tographed using an Olympus BX 60 microscope equipped with epi‐ fluorescence optics. As a negative control, the primary antibody was replaced with mouse nonimmune serum. 2.5 The cell lysates were subjected to RT‐PCR for α‐SMA at 24 hour after the addition of TGF‐β1. Total RNA was isolated from the cells using the RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. cDNA was prepared using the Tran- scriptor First Strand cDNA Synthesis kit (Roche Diagnostics, Basel, Switzerland). Quantitative RT‐PCR was performed using the UPL Probe PCR Master Mix and analysed with a Light Cycler 96 System (Roche Diagnostics). All gene expression values were normalized using GAPDH as a housekeeping gene. The primers of α-SMA used in PCR amplification were from Roche Diagnostics and are as follows: Forward Primer TGCCATGTATGTGGCTATTCA, Reverse Primer ACCAGTTGTACGTCCAGAAGC. 2.2 | Cell culture NRK49F cells were cultured in D‐MEM supplemented with 10% FBS (JRH Biosciences, Lenexa, KS, USA), 100 IU/mL penicillin and 100 μg/mL streptomycin in a humidified 5% CO2‐95% atmospheric air incubator at 37°C. Throughout this study, cells from passages 3 to 8 were used. Five × 104 cells were seeded in 1.5 mL medium with 10% FBS and cultured for 24 hours. After washing, they were preincubated in a serum‐free medium for 30 minutes. Then they J Cell Mol Med. 2019;23:1608–1612. 1609 YAN ET AL. YAN ET AL. 2.7 | Statistics The amount of intracellular cAMP at 1 hour after addition of dipyridamole was measured by using a cAMP enzyme immunoas- say kit from Cayman Chemical according to the manufacturer's instructions. Quantitative data were compared using Wilcoxon's test or Student's t test of the software package JMP (SAS Institute, Cary, NC, USA). P‐values less than 0.05 were considered statistically significant. FIGURE 2 Contribution of cAMP pathways to suppressive effects of dipyridamole on α‐SMA expression. A, Alteration of cAMP levels in the cytoplasm yielded by dipyridamole. After incubation the lysates of the cells were subjected to EIA of cAMP. Bar graph shows relative intracellular cAMP levels. *P < 0.01 vs control. B, Effect of the inhibitor of PKA or Epac pathway on α‐SMA expression. After incubation with the reagents for 48 hours, the cell lysates were subjected to Western blots for α‐SMA. Representative Western blots and relative quantification are provided. *P < 0.005 vs control;**P < 0.005 vs TGF‐β1 group; NS not significant vs TGF‐ β1 + dipyridamole group; ***P < 0.01 vs TGF‐β1 + dipyridamole group. C, Effect of the activator of PKA or Epac pathway on α‐SMA expression. After incubation with the reagents the cell lysates were subjected to Western blots for α‐SMA. Representative Western blots and relative quantification of α‐SMA are shown. *P < 0.001 vs control; **P < 0.05; ***P < 0.001 vs TGF‐β1 group. D, Effect of the inhibitor or the activator of Epac pathway on α‐SMA mRNA expression. The cell lysates were subjected to RT‐PCR. Bar graph shows relative values of α‐SMA mRNA levels normalized to GAPDH signal. *P < 0.01 vs control; **P < 0.05 vs TGF‐ β1 group; ***P < 0.05 vs TGF‐β1 + dipyridamole group FIGURE 2 Contribution of cAMP pathways to suppressive effects of dipyridamole on α‐SMA expression. A, Alteration of cAMP levels in the cytoplasm yielded by dipyridamole. After incubation the lysates of the cells were subjected to EIA of cAMP. Bar graph shows relative intracellular cAMP levels. *P < 0.01 vs control. B, Effect of the inhibitor of PKA or Epac pathway on α‐SMA expression. After incubation with the reagents for 48 hours, the cell lysates were subjected to Western blots for α‐SMA. Representative Western blots and relative quantification are provided. *P < 0.005 vs control;**P < 0.005 vs TGF‐β1 group; NS not significant vs TGF‐ β1 + dipyridamole group; ***P < 0.01 vs TGF‐β1 + dipyridamole group. 1610 | 1610 | 1610 YAN ET AL. 2.4 | Western blots The cells were exposed to inhibitors of cAMP pathways, 5 μmol/L H89 or 3 μmol/L ESI‐05, and activators of cAMP pathways, 30 μmol/ L Phe‐cAMP or 10 μmol/L O‐Me‐cAMP for 1 hour before the 1 Effect of dipyridamole on of α‐SMA. After incubation with nts, the cells were subjected to orescence or Western blots for Immunofluorecence for α‐SMA s treated with or without TGF‐β1 sence or absence of ole. Bar = 30 μm. B, The ell lysates from three groups ected to immunoblot analysis odies against α‐SMA and The experiments were repeated s, and one representative blot is APDH reprobe is shown to te lane load. The molecular kD are on the left. Bar graph tive α‐ SMA band densities d to GAPDH signal.*P < 0.01 vs P < 0.05 vs TGF‐β1 group FIGURE 1 Effect of dipyridamole on expression of α‐SMA. After incubation with the reagents, the cells were subjected to immunofluorescence or Western blots for α‐SMA. A, Immunofluorecence for α‐SMA in the cells treated with or without TGF‐β1 in the presence or absence of dipyridamole. Bar = 30 μm. B, The NRK49F cell lysates from three groups were subjected to immunoblot analysis with antibodies against α‐SMA and GAPDH. The experiments were repeated three times, and one representative blot is shown. GAPDH reprobe is shown to demonstrate lane load. The molecular weights in kD are on the left. Bar graph shows relative α‐ SMA band densities normalized to GAPDH signal.*P < 0.01 vs control;**P < 0.05 vs TGF‐β1 group FIGURE 1 Effect of dipyridamole on expression of α‐SMA. After incubation with the reagents, the cells were subjected to immunofluorescence or Western blots for α‐SMA. A, Immunofluorecence for α‐SMA in the cells treated with or without TGF‐β1 in the presence or absence of dipyridamole. Bar = 30 μm. B, The NRK49F cell lysates from three groups were subjected to immunoblot analysis with antibodies against α‐SMA and GAPDH. The experiments were repeated three times, and one representative blot is shown. GAPDH reprobe is shown to demonstrate lane load. The molecular weights in kD are on the left. Bar graph shows relative α‐ SMA band densities normalized to GAPDH signal.*P < 0.01 vs control;**P < 0.05 vs TGF‐β1 group 2.8 Immunofluorescence for α‐SMA revealed that TGF‐β1 induced, to a large extent, expression of α‐SMA forming stress fibre (Figure 1A). Dipyridamole repressed TGF‐β1‐induced α‐SMA expression by the normal range (almost none) as shown by immunofluorescence (Fig- ure 1A) and Western blots for α‐SMA (Figure 1B). Dipyridamole suppressed TGF‐β1‐induced myofibroblast transdifferentiation in the in vitro system without platelets (Figure 1). To our knowledge, this is the first report that dipyridamole exerted protective effects against fibrosis corresponding to tubulointerstitial lesions in CKD. Dipyridamole caused the elevation of intracellular cAMP levels (Fig- ure 2A). To determine which pathway of cAMP was involved in the repressive effects of dipyridamole against fibrosis, the cells were exposed to inhibitors or activators of each pathway. H89, a selective PKA inhibitor, did not influence the suppressive action of dipyridamole against TGF‐β1‐induced α‐SMA expression (Figure 2B). Also, N6‐Phenyl‐cAMP, a PKA activator, exacerbated TGF‐β1‐stimu- lated α‐SMA expression (Figure 2C). These results may indicate that even if PKA had been activated through cAMP levels elevated by dipyridamole, it would not have suppressed TGF‐β1‐induced α‐SMA expression. On the other hand, ESI‐05, a selective Epac inhibitor, reduced the suppressive effect of dipyridamole on α‐SMA expres- sion induced by TGF‐β1 (Figure 2B,D). Besides, 8‐Br‐2′‐O‐Me‐ cAMP‐AM, an Epac activator, inhibited TGF‐β1‐induced myofibrob- last transformation (Figure 2C,D). These data indicated that Epac activation caused by dipyridamole blocked α‐SMA expression stimu- lated by TGF‐β1. Taken together, the suppressive effects of dipyri- damole against increased α‐SMA expression were considered to be exerted via activation of the Epac pathway following elevation of cAMP levels, while the adverse effect of PKA activation was, if present, limited. There are some reports concerning the effects of both pathways in the downstream of cAMP on fibrosis. Generally, both the PKA and Epac pathways suppressed fibrosis.10 However, the PKA activator was shown to attenuate fibrosis yielded by exposure of pulmonary fibroblasts to TGF‐β1, while the Epac In conclusion, dipyridamole suppressed TGF‐β1‐induced α‐SMA expression via Epac pathway activation. This protective effect of dipyridamole against fibrosis was not mediated by platelet aggrega- tion and was directly exerted on fibroblasts. The Epac pathway pro- vides a new pharmacological approach of dipyridamole for treatment of fibrosis in CKD. The authors confirm that there are no conflicts of interest. The authors confirm that there are no conflicts of interest. Keisuke Ina http://orcid.org/0000-0001-8366-917X Keisuke Ina http://orcid.org/0000-0001-8366-917X 2.7 | Statistics C, Effect of the activator of PKA or Epac pathway on α‐SMA expression. After incubation with the reagents the cell lysates were subjected to Western blots for α‐SMA. Representative Western blots and relative quantification of α‐SMA are shown. *P < 0.001 vs control; **P < 0.05; ***P < 0.001 vs TGF‐β1 group. D, Effect of the inhibitor or the activator of Epac pathway on α‐SMA mRNA expression. The cell lysates were subjected to RT‐PCR. Bar graph shows relative values of α‐SMA mRNA levels normalized to GAPDH signal. *P < 0.01 vs control; **P < 0.05 vs TGF‐ β1 group; ***P < 0.05 vs TGF‐β1 + dipyridamole group YAN ET AL. 1611 FIGURE 3 The diagram of the action mechanism of dipyridamole. Dipyridamole inhibits phosphodiesterase, followed by the elevating level of intracellular cAMP. cAMP stimulates Epac pathway, leading to repression of TGF‐β1 signal pathway, Smads pathway, which induces α‐SMA expression. Thus, dipyridamole represses myofibroblast transdifferentiation. PDE, phosphodiesterase; TF, transcription factor FIGURE 3 The diagram of the action mechanism of dipyridamole. Dipyridamole inhibits phosphodiesterase, followed by the elevating level of intracellular cAMP. cAMP stimulates Epac pathway, leading to repression of TGF‐β1 signal pathway, Smads pathway, which induces α‐SMA expression. Thus, dipyridamole represses myofibroblast transdifferentiation. PDE, phosphodiesterase; TF, transcription factor activator did not affect it.11 In contrast, it was demonstrated that the PKA activator induced fibrosis by mesangial cells.12 The differ- ent effects between the results of the present study and the find- ings of these reports might be because of the difference in the cells used. The question of which process of the TGF‐β1 signalling pathways did dipyridamole block via Epac pathway activation will be resolved in the next paper. AUTHORS CONTRIBUTIONS QY, KI, and YF conceived and supervised the study; QY, KI, and SC designed experiments; QY, HW, and ST performed experiments; QY, KI, and SC analysed data; QY, KI, and SC wrote the manuscript; QY, KI, and YF made the manuscript revisions. ORCID Keisuke Ina http://orcid.org/0000-0001-8366-917X 1612 | 1612 YAN ET AL. YAN ET AL. REFERENCES 1. Hodgkins KS, Schnaper HW. Tubulointerstitial injury and the pro- gression of chronic kidney disease. Pediatr Nephrol. 2012;27:901‐ 909. 2. Meng XM, Nikolic-Paterson DJ, Lan HY. TGF‐β: the master regulator of fibrosis Nat Rev Nephrol. 2016;12:325‐338. 2. Meng XM, Nikolic-Paterson DJ, Lan HY. TGF‐β: the master regulator of fibrosis Nat Rev Nephrol. 2016;12:325‐338. 3. Wipff PJ, Rifkin DB, Meister JJ, Hinz B. Myofibroblast contraction activates latent TGF‐beta1 from the extracellular matrix. J Cell Biol. 2007;179:1311‐1323. 10. Insel PA, Murray F, Yokoyama U, et al. cAMP and Epac in the regu- lation of tissue fibrosis. Br J Pharmacol. 2012;166:447‐456. 11. Ayabe S, Kido T, Hori M, et al. Prostaglandin D2 inhibits collagen secretion from lung fibroblasts by activating the DP receptor. J Phar- macol Sci. 2013;121:312‐317. 4. Hinz B. Myofibroblast. Exp Eye Res. 2016;142:56‐70. 5. Gillespie SR, Tedesco LJ, Wang L, Bemstein AM. The deubiquitylase USP10 regulates integrin β1 and β5 and fibrotic wound healing. J Cell Sci. 2017;130:3481‐3495. 12. Singh LP, Green K, Alexander M, et al. Hexosamines and TGF‐β1 use similar signaling pathways to mediate matrix protein synthesis in mesangial cells. Am J Physiol Renal Physiol. 2004;286:F409‐ F416. 6. Balakumar P, Varatharajan R, Nyo YH, et al. Fenofibrate and dipyri- damole treatments in low‐doses either alone or in combination blunted the development of nephropathy in diabetic rats. Pharmacol Res. 2014;90:36‐47. 7. Liu XJ, Geng YQ, Xin SN, et al. Antithrombotic drug therapy for IgA nephropathy: a meta analysis of randomized controlled trials. Intern Med. 2011;50:2503‐2510. How to cite this article: Yan Q, Ina K, Chiba S, Wei H, Tatsukawa S, Fujikura Y. The signal pathway for the repressive effect of dipyridamole on myofibroblast transdifferentiation. J Cell Mol Med. 2019;23:1608–1612. https://doi.org/10.1111/jcmm.14006 8. Rooij JD, Zwartkruis FT, Verheijen MHG, et al. Epac is a Rap 1 gua- nine‐nucleotide‐exchange factor directly activated by cyclic AMP. Nature. 1998;396:474‐477. 9. Biel M, Michalakis S. Cyclic nucleotide‐gated channels. Handb Exp Pharmacol. 2009;191:111‐136. 9. Biel M, Michalakis S. Cyclic nucleotide‐gated channels. Handb Exp Pharmacol. 2009;191:111‐136.
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https://europepmc.org/articles/pmc4484888?pdf=render
English
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GLIPR1-ΔTM synergizes with docetaxel in cell death and suppresses resistance to docetaxel in prostate cancer cells
Molecular cancer
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* Correspondence: timthomp@mdanderson.org †Equal contributors 1Department of Genitourinary Medical Oncology – Research, Unit 18-3, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, USA Full list of author information is available at the end of the article Abstract Background: Docetaxel is the first chemotherapy agent approved for treatment of metastatic castration-resistant prostate cancer (mCRPC). The limited survival benefit associated with the quick emergence of resistance and systemic toxicity diminished its efficacy. JNK-mediated apoptosis is one of the mechanisms of docetaxel activity whereas ERK1/2-c-Myc-CXCR4 signaling is implicated in the development of resistance and induction of migration. The aim of this study was to evaluate the hypothesis that the combination treatment with docetaxel and GLIPR1-ΔTM will synergistically induce greater cell death and inhibit the emergence of resistance and development of metastatic potential in prostate cancer (PCa) cells. Methods: The synergistic effects of the docetaxel and GLIPR1-ΔTM were evaluated with DNA fragmentation, DAPI staining and MTS using paired t-test and isobologram study. The effects of the drugs on JNK and ERK1/2-c-Myc-CXCR4 signaling were evaluated with Western blot, DNA fragmentation, and MTS assays using the JNK inhibitor SP600125, and CXCR4 siRNA. The results of docetaxel and GLIPR1-ΔTM combination on migration were examined with scratch assay using the CXCR4 inhibitor AMD3100 while our hypothesis was examined in vivo using VCaP orthotopic xenograft model. Results: We found that GLIPR1-ΔΤΜ synergized with docetaxel to induce apoptosis in VCaP and PC-3 PCa cells through induction of JNK signaling and concomitant inhibition of ERK1/2-c-Myc-CXCR4 signaling. We showed that JNK activation mediates the apoptotic effects of the drug combination and that CXCR4 knockdown increases its efficacy. We also found that the addition of GLIPR1-ΔΤΜ to docetaxel decreases the migration of VCaP and PC-3 cells. The combination treatment with docetaxel and GLIPR1-ΔTM inhibited tumor growth and decreased metastatic potential in VCaP xenografts more than single agents did. Conclusions: Our data suggested that addition of GLIPR1-ΔTM treatment in PCa cells increases the efficacy of docetaxel and may inhibit the emergence of drug resistance; potentially permitting a decrease of docetaxel dose for patients with mCRPC eliminating its systemic toxicities. Keywords: Prostate cancer, GLIPR1-ΔTM, Docetaxel, JNK, ERK1/2, c-Myc, CXCR4, Combination treatmen * Correspondence: timthomp@mdanderson.org †Equal contributors 1Department of Genitourinary Medical Oncology – Research, Unit 18-3, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, USA Full list of author information is available at the end of the article © 2015 Karanika et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. GLIPR1-ΔTM synergizes with docetaxel in cell death and suppresses resistance to docetaxel in prostate cancer cells Styliani Karanika1†, Theodoros Karantanos1†, Shinji Kurosaka2†, Jianxiang Wang1, Takahiro Hirayama2, Guang Yang1, Sanghee Park1, Alexei A. Golstov3, Ryuta Tanimoto4, Likun Li1 and Timothy C. Thompson1* RESEARCH Open Access GLIPR1-ΔTM synergizes with docetaxel in cell death and suppresses resistance to docetaxel in prostate cancer cells Styliani Karanika1†, Theodoros Karantanos1†, Shinji Kurosaka2†, Jianxiang Wang1, Takahiro Hirayama2, Guang Yang1, Sanghee Park1, Alexei A. Golstov3, Ryuta Tanimoto4, Likun Li1 and Timothy C. Thompson1* Abstract Karanika et al. Molecular Cancer (2015) 14:122 DOI 10.1186/s12943-015-0395-0 RESEARCH Open Access GLIPR1-ΔTM synergizes with docetaxel in cell death and suppresses resistance to docetaxel in prostate cancer cells Styliani Karanika1†, Theodoros Karantanos1†, Shinji Kurosaka2†, Jianxiang Wang1, Takahiro Hirayama2, Guang Yang1, Sanghee Park1, Alexei A. Golstov3, Ryuta Tanimoto4, Likun Li1 and Timothy C. Thompson1* Abstract Karanika et al. Molecular Cancer (2015) 14:122 DOI 10.1186/s12943-015-0395-0 Karanika et al. Molecular Cancer (2015) 14:122 DOI 10.1186/s12943-015-0395-0 Background signaling [17]. The same report showed that CXCR4 can, in turn, activate ERK1/2; these signaling activities establish a positive feedback resistance loop in response to doce- taxel [17]. Overall, these findings support the concept that activation of ERK1/2-c-Myc-CXCR4 pathway can promote the development of resistance to docetaxel and potentially inhibit the JNK apoptotic signaling. The survival of patients with metastatic castration- resistant prostate cancer (mCRPC) remains poor despite the introduction of novel antiandrogens such as enzaluta- mide and abiraterone [1, 2]. Taxanes, in particular docetaxel and cabazitaxel, are the only chemotherapy agents that have been shown to increase survival in mCRPC patients [3, 4] and recent evidence suggests that these agents are particularly effective in patients with high Gleason score primary disease [5]. Recently, cabazitaxel was shown to be effective in patients who progressed under abiraterone and enzalutamide after failure of docetaxel suggesting that taxanes may still be a reasonable therapeutic approach for these patients [18]. The combination of docetaxel with a novel agent may be the most reasonable approach to increase the apoptotic effects of docetaxel and delay or inhibit the development of resistance. Such combination therapy also has the potential to reduce effective doses of docetaxel, thereby decreasing the incidence of docetaxel side effects such as myelo- suppression [19]. Numerous studies failed to show improvement of docetaxel efficacy when it was com- bined with other targeted agents such as dasatinib and zibotentan [20, 21]. Despite the long period of docetaxel use, the exact mechanism(s) of its function is not well-understood. Docetaxel is believed to stabilize microtubules by arresting their de-polymerization, leading to disruption of normal mitosis, G2/M arrest, and inhibition of cell proliferation [6]. This agent inhibits Bcl-2 and Bcl-xL activity through decreased gene expression and posttranslational phos- phorylation, promoting apoptosis in PCa cells [6–8]. In melanoma cells, docetaxel induces apoptosis through activation of the c-Jun NH2-terminal kinase (JNK) pathway, but it also activates the ERK1/2 (Extracellular signal-regulated kinase 1/2) signaling which seems to inhibit its apoptotic effects [9]. In addition, docetaxel increases reactive oxygen species (ROS) production, which promotes JNK activation in androgen receptor (AR)- negative PCa cells [10]. Collectively, these data suggest that docetaxel promotes cancer cell death through apoptosis mediated by JNK activation. The gene encoding the human glioma pathogenesis- related protein 1 (GLIPR1), a p53 target, is downregulated in PCa due to methylation of its promoter [22, 23]. Li et al. Abstract The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated Page 2 of 13 Karanika et al. Molecular Cancer (2015) 14:122 Background demonstrated that GLIPR1 upregulation leads to accumula- tion of ROS and subsequent activation of the JNK pathway and downregulation of Bcl-2 [24]. GLIPR1 was also found to be associated with destablizing phosphorylation of β- catenin and c-Myc, leading to their degradation [25]. Our group recently showed that GLIPR1-ΔTM is selectively taken up by PCa cells; activates apoptosis through ROS accumulation; and downregulates c-Myc [26]. Collectively, these results indicate that GLIPR1-ΔTM may be a good candidate for combination therapy with docetaxel, since it promotes PCa specific cell death through JNK activation, whereas it downregulates c-Myc signaling which has been extensively associated with the emergence of resistance to docetaxel through ERK1/2-c-Myc-CXCR4 signaling. Even when mCRPC initially responds to treatment with docetaxel, the disease eventually becomes resistant, which can be attributed to numerous molecular mechanisms according to recent studies in different types of cancer. Mhaidat et al. demonstrated that in melanoma cells treated with docetaxel, activation of PKCδ is associated with proapoptotic responses through JNK activation, as mentioned above, while activation of PKCε enhances pro- survival signaling through ERK1/2 activation [11]. These results indicate that under docetaxel treatment, one pathway downstream of PKC may lead to apoptosis and another associated with ERK signaling may lead to cell survival and resistance to docetaxel. Of note, multiple recent reports demonstrated opposed effects and negative crosstalk between JNK and ERK1/2 signaling [12–15], suggesting that ERK1/2 activation by doce- taxel may inhibit its JNK-mediated apoptotic effects. Leonetti et al. found that treatment combining docetaxel with antisense oligodeoxynucleotides against Bcl-2 and c-Myc led to lower PC-3 cell survival in vitro, and had higher antitumor efficacy in PC-3 xenografts, than did docetaxel alone, suggesting that Bcl-2 and c-Myc upregu- lation may promote resistance to docetaxel as well [16]. Finally, a recent report showed that docetaxel induces the activation of ERK, which stabilizes c-Myc protein, and stimulates CXCR4 (C-X-C chemokine receptor type 4) In the current study, we report that GLIPR1-ΔΤΜ increases the sensitivity of PCa cells to docetaxel in a syn- ergistic way through additive induction of JNK-mediated apoptosis in VCaP and PC-3 cells and concurrent inhib- ition of ERK1/2-c-Myc-CXCR4-mediated development of resistance. The addition of GLIPR1-ΔTM to docetaxel was found to decrease the migration of PCa cells while this combination additively decreased tumor growth and metastatic potential in VCaP xenografts. GLIPR1-ΔΤΜ and docetaxel synergistically decreased survival of VCaP and PC-3 cells in vitro To test the hypothesis that GLIPR1-ΔTM sensitizes PCa cells to docetaxel, we used VCaP cells and PC-3 cells. Both cell lines were derived from bone metastases of Page 3 of 13 Karanika et al. Molecular Cancer (2015) 14:122 Karanika et al. Molecular Cancer (2015) 14:122 Docetaxel significantly decreased survival of normal prostate cells (RWPE-1) even at the lowest (0.5nM) concen- tration (p < 0.0001) (Fig. 1a). At 2.5 μg/ml GLIPR1-ΔΤΜ resulted in significantly decreased survival of VCaP cells (p = 0.002), and at 10 μg/ml resulted in significantly decreased survival of PC-3 cells (p = 0.0005) compared to control treatment (Fig. 1b). The IC50 was 34.8 μg/ml for VCaP cells and 154 μg/ml for PC-3 cells. Interestingly, only 160 μg/ml GLIPR1-ΔTM decreased survival of normal prostate cells (RWPE-1) (p = 0.002) (Fig. 1b), which is consistent with our previous results [25] showing that GLIPR1-ΔTM is selectively taken up by cancerous cells, promoting their apoptosis, while normal prostate cells are not sensitive to this agent. PCa. VCaP cells were derived from a patient with mCRPC, while PC-3 cells are androgen receptor-negative metastatic PCa cells. We also included RWPE-1 cells, which are epithelial cells derived from the peripheral zone of an histologically normal adult human prostate and transfected with a single copy of human papillomavirus 18 [26]. The three cell lines were treated for 48 h with various concen- trations of docetaxel (0.5, 1, 2, 5, 10, 20, 50, 75, and 100nM) and GLIPR1-ΔΤΜ (1, 2, 5, 10, 20, 40, 80,and 160 μg/ml) in different serum concentrations (0.1 % for PC-3 cells and 0.5 % for VCaP and RWPE-1 cells), and MTS assay was performed to evaluate the dose response and the IC50 for each single-agent treatment. At a concentration of 0.5nM, docetaxel resulted in significantly lower survival of both PCa cell lines (p = 0.004 for VCaP cells, p = 0.03 for PC-3 cells) than did the control treatment (Fig. 1a). The IC50 was 69.8nM for VCaP cells and 70.5nM for PC-3 cells. To investigate the potential synergy of docetaxel and GLIPR1-ΔTM in inducing anti-cancer effects, we treated VCaP and PC-3 cells with various combinations of the Fig. 1 GLIPR1-ΔTM reduced VCaP and PC-3 cells’ survival synergistically with docetaxel. a. Docetaxel dose–response curves of VCaP, PC-3, and RWPE-1 cells treated for 48 h, determined using MTS assay. At 0.5nM, docetaxel significantly decreased cell survival in the three cell lines. GLIPR1-ΔΤΜ and docetaxel synergistically decreased survival of VCaP and PC-3 cells in vitro The IC50 was 69.8nM for VCaP cells and 70.5nM for PC-3 cells. b. GLIPR1-ΔTM dose–response curves of VCaP, PC-3, and RWPE-1 cells treated for 48 h, determined using MTS assay. At 2.5 μg/ml and 10 μg/ml, GLIPR1-ΔTM significantly decreased survival of VCaP and PC-3 cells, respectively. Only 160 μg/ml decreased survival of RWPE-1 cells. The IC50 was 34.8 μg/ml for VCaP cells and 154 μg/ml for PC-3 cells. c. The addition of 10 μg/ml GLIPR1-ΔTM increased the efficacies of all doses of docetaxel in inhibiting VCaP cells’ survival, based on MTS assay. d. The addition of 10 μg/ml GLIPR1-ΔTM increased the efficacies of 0.5, 1, and 2nM docetaxel in inhibiting PC-3 cells’ survival as determined by MTS assay, and the addition of 80 μg/ml GLIPR1-ΔTM increased the efficacies of 10, 20, and 50nM docetaxel. e. Isobologram analysis showed that GLIPR1-ΔTM and docetaxel synergistically induced cell death in VCaP cells. f. Isobologram analysis showed that GLIPR1-ΔTM and docetaxel induced cell death synergistically in PC-3 cells. The results are presented as the mean ± standard error from at least three independent experiments Fig. 1 GLIPR1-ΔTM reduced VCaP and PC-3 cells’ survival synergistically with docetaxel. a. Docetaxel dose–response curves of VCaP, PC-3, and RWPE-1 cells treated for 48 h, determined using MTS assay. At 0.5nM, docetaxel significantly decreased cell survival in the three cell lines. The IC50 was 69.8nM for VCaP cells and 70.5nM for PC-3 cells. b. GLIPR1-ΔTM dose–response curves of VCaP, PC-3, and RWPE-1 cells treated for 48 h, determined using MTS assay. At 2.5 μg/ml and 10 μg/ml, GLIPR1-ΔTM significantly decreased survival of VCaP and PC-3 cells, respectively. Only 160 μg/ml decreased survival of RWPE-1 cells. The IC50 was 34.8 μg/ml for VCaP cells and 154 μg/ml for PC-3 cells. c. The addition of 10 μg/ml GLIPR1-ΔTM increased the efficacies of all doses of docetaxel in inhibiting VCaP cells’ survival, based on MTS assay. d. The addition of 10 μg/ml GLIPR1-ΔTM increased the efficacies of 0.5, 1, and 2nM docetaxel in inhibiting PC-3 cells’ survival as determined by MTS assay, and the addition of 80 μg/ml GLIPR1-ΔTM increased the efficacies of 10, 20, and 50nM docetaxel. e. Isobologram analysis showed that GLIPR1-ΔTM and docetaxel synergistically induced cell death in VCaP cells. f. Isobologram analysis showed that GLIPR1-ΔTM and docetaxel induced cell death synergistically in PC-3 cells. GLIPR1-ΔTM increased the apoptotic effect of docetaxel in VCaP and PC-3 cells Given the known apoptotic effects of GLIPR1-ΔTM and docetaxel in PCa cells, we hypothesized that the decreased survival of PCa cells treated with combina- tions of these two agents is mainly due to increased apoptosis. To test this hypothesis, we used DAPI staining and DNA fragmentation assay to examine apoptosis in VCaP and PC-3 cells. We included RWPE-1 cells as a control. VCaP and RWPE-1 cells were treated with 0.5 % serum-containing medium for 24 h, and PC-3 cells were treated with 0.1 % serum- containing medium for 24 h. Then, cells were treated with various concentrations of GLIPR1-ΔTM (0, 10, 20, and 40 μg/ml) for 1 h followed by addition of various concentrations of docetaxel (0, 0.5, 1, 2, 5, and 10nM). Forty-eight hours later, DAPI staining was evaluated. At 10 μg/ml, GLIPR1-ΔTM in combination with all docetaxel concentrations significantly increased the percentage of apoptotic VCaP cells (p < 0.001) (Fig. 2a). In PC-3 cells, 10 μg/ml GLIPR1-ΔTM significantly increased the apoptotic effects of 0.5nM (p = 0.014) and 10nM (p = 0.033) docetaxel, while 20 μg/ml GLIPR1-ΔTM significantly increased the apoptosis induced by 1nM docetaxel (p = 0.016) and 40 μg/ml GLIPR1-ΔΤΜ increased the apoptotic effect of 2nM docetaxel (p = 0.0095) (Fig. 2b). In RWPE-1 cells, GLIPR1-ΔTM did not increase the apoptosis induced by any dose of docetaxel, which is consistent with the results of the cell survival assay and our previous data showing that GLIPR1-ΔTM selectively induces apoptosis in PCa cells but not in normal prostate cells. In RWPE-1 cells, 1nM docetaxel induced apoptosis (p = 0.0025) (Fig. 2c). We next investigated the effect of the combination of 1nM docetaxel and 10 μg/ml GLIPR1-ΔTM on JNK and ERK1/2-c-Myc-CXCR4 signaling at 24 h for VCaP cells and 48 h for PC-3 cells. In order to evaluate the role of JNK signaling in apoptosis and ERK1/2-c-Myc-CXCR4 loop, we included the JNK inhibitor SP600125 in these experiments, a known agent which acts through inhibiting JNK phosphorylation [27]. VCaP and PC-3 cells were treated with 0.5 % or 0.1 % serum-containing medium, re- spectively, for 24 h. Then, cells were treated with 10 μg/ml GLIPR1-ΔTM for 1 h followed by addition of 1nM doce- taxel with or without 1 μM SP600125 for 24 or 48 h. Western blot experiments were conducted at least three times and our results reflect at least three independ- ent experiments. Combination treatment with docetaxel and GLIPR1-ΔTM induced JNK signaling and inhibited the docetaxel-induced ERK1/2-c-Myc-CXCR4 signaling resistance loop, increasing apoptosis through maximal JNK activation We have previously demonstrated that endogenous GLIPR1 activates JNK signaling [22] and docetaxel was also found to induce JNK signaling and subsequent apoptosis in melanoma cells [9]. Initially, we hypothesized that the greater apoptotic effect of the combination of these two agents is mediated by JNK activation and inhibition of ERK1/2-c-Myc-CXCR4 signaling by GLIPR1-ΔTM. To test this hypothesis, we initially examined the effect of com- bination treatment on JNK and ERK1/2-c-Myc-CXCR4 signaling. To select the right time-point for this evaluation during treatment using the lowest effective doses, we examined survival of VCaP and PC-3 cells treated with 1, 2, or 5nM docetaxel or 10, 20, or 40 μg/ml GLIPR1-ΔTM. The time-response curves were different in VCaP and PC-3 cells. In particular, 1nM docetaxel and 10 μg/ml GLIPR1-ΔTM significantly decreased the survival of VCaP cells at 24 h (p = 0.03 for docetaxel and p = 0.001 for GLIPR1-ΔTM) (Fig. 3a) and the sur- vival of PC-3 cells at 48 h (p < 0.001 for docetaxel and p = 0.007 for GLIPR1-ΔTM) (Fig. 3b). GLIPR1-ΔΤΜ and docetaxel synergistically decreased survival of VCaP and PC-3 cells in vitro The results are presented as the mean ± standard error from at least three independent experiments Page 4 of 13 Karanika et al. Molecular Cancer (2015) 14:122 two agents: 0.5, 1, 2, 5, 10, 20, 50, and 75nM docetaxel in both cell lines; 0, 10, 20, and 40 μg/ml GLIPR1-ΔTM in VCaP cells; and 0, 10, 20, 40, and 80 μg/ml GLIPR1-ΔTM in PC-3 cells. At 10 μg/ml, GLIPR1-ΔTM significantly increased the efficacy of docetaxel in VCaP cells at all docetaxel doses (Fig. 1c) and significantly increased the efficacy of docetaxel at 0.5, 1, and 2nM docetaxel in PC-3 cells (Fig. 1d). At 80 μg/ml, GLIPR1-ΔTM signifi- cantly increased the efficacy of higher doses of docetaxel (10, 20, and 50nM) (Fig. 1d). for 10nM docetaxel) (Fig. 2d). In PC-3 cells, 10 μg/ml GLIPR1-ΔTM enhanced the apoptotic effects of all doses of docetaxel (p = 0.001 for 0.5nM docetaxel; p < 0.001 for 1, 2, 5, and 10nM docetaxel) (Fig. 2e). GLIPR1-ΔTM did not increase the apoptotic effects of any docetaxel doses in RWPE-1 cells, in which 0.5nM docetaxel induced apoptosis (p = 0.0094) (Fig. 2f). Collectively, these results demon- strated that GLIPR1-ΔTM enhanced the apoptotic activity of docetaxel in VCaP and PC-3 PCa cells without substan- tially affecting normal prostate cells. for 10nM docetaxel) (Fig. 2d). In PC-3 cells, 10 μg/ml GLIPR1-ΔTM enhanced the apoptotic effects of all doses of docetaxel (p = 0.001 for 0.5nM docetaxel; p < 0.001 for 1, 2, 5, and 10nM docetaxel) (Fig. 2e). GLIPR1-ΔTM did not increase the apoptotic effects of any docetaxel doses in RWPE-1 cells, in which 0.5nM docetaxel induced apoptosis (p = 0.0094) (Fig. 2f). Collectively, these results demon- strated that GLIPR1-ΔTM enhanced the apoptotic activity of docetaxel in VCaP and PC-3 PCa cells without substan- tially affecting normal prostate cells. To evaluate whether the effects of combination treat- ments on survival were super-additive (synergistic), 50 % of maximum efficacy was used to determine the fixed ratio, and multiple combination doses with the same efficacy were included. Isobologram analysis showed that the effects were synergistic (Fig. 1e, f). Combination treatment with docetaxel and GLIPR1-ΔTM induced JNK signaling and inhibited the docetaxel-induced ERK1/2-c-Myc-CXCR4 signaling resistance loop, increasing apoptosis through maximal JNK activation GLIPR1-ΔTM increased the apoptotic effect of docetaxel in VCaP and PC-3 cells GLIPR1-ΔΤΜ did not increase the apoptotic effect of any docetaxel dose in RWPE-1 cells, while 0.5nM docetaxel significantly increased the percentage of apoptotic cells, based on DNA fragmentation. The results are presented as the mean ± standard error from at least three independent experiments Fig. 2 GLIPR1-ΔTM increased the apoptotic effect of docetaxel in VCaP and PC-3 cells. a. The addition of 10 μg/ml GLIPR1-ΔΤΜ increased the apoptotic effects of all docetaxel’s doses in VCaP cells, measured by DAPI staining. b. The addition of 10 μg/ml GLIPR1-ΔΤΜ increased the apoptotic effects of all docetaxel doses in PC-3 cells, measured by DAPI staining. c. GLIPR1-ΔΤΜ did not increase the apoptotic effect of any docetaxel dose in RWPE-1 cells, while 1nM docetaxel significantly increased the percentage of apoptotic cells, based on DAPI staining. d. The addition of 10 μg/ml GLIPR1-ΔΤΜ increased the apoptotic effects of all docetaxel doses in VCaP cells, measured by DNA fragmentation. e. The addition of 10 μg/ml GLIPR1-ΔΤΜ increased the apoptotic effects of all docetaxel doses in PC-3 cells, measured by DNA fragmentation. f. GLIPR1-ΔΤΜ did not increase the apoptotic effect of any docetaxel dose in RWPE-1 cells, while 0.5nM docetaxel significantly increased the percentage of apoptotic cells, based on DNA fragmentation. The results are presented as the mean ± standard error from at least three independent experiments the combination of docetaxel and GLIPR1-ΔTM was sig- nificantly increased when SP600125 was added (p < 0.001 for both cell lines) according to MTS assay. Additionally, in PC-3 cells, we also found that the addition of SP600125 increased the survival when added to docetaxel (p = 0.048) which is consistent with the JNK-mediated apoptotic effect of docetaxel. Through DNA fragmentation assay, we found that the addition of SP600125 decreased the apoptotic effect of docetaxel (p < 0.001 for VCaP and PC-3 cells), GLIPR1-ΔTM (p < 0.001 for VCaP cells and p = 0.002 for PC-3 cells) and combination therapy (p < 0.001 for VCaP and PC-3 cells). Collectively, these data suggested that docetaxel and GLIPR1-ΔΤΜ com- bination treatment synergistically increased apoptosis by maximal activation of JNK, together with suppres- sion of ERK1/2 signaling, which further increased JNK signaling through a derepression mechanism. Finally, the when used as single agents (Fig. 4a, b). GLIPR1-ΔTM increased the apoptotic effect of docetaxel in VCaP and PC-3 cells The quantitative data are presented as supplementary data (Additional file 1: Figure S1). Representative blots are presented in the Fig. 4. Combin- ation treatment increased JNK phosphorylation in VCaP and PC-3 cells more than docetaxel or GLIPR1-ΔTM did According to DNA fragmentation assay, 10 μg/ml GLIPR1-ΔTM in combination with all docetaxel doses increased apoptosis in VCaP cells (p = 0.0014 for 0.5, 1, and 2nM docetaxel; p = 0.0028 for 5nM docetaxel; p = 0.0012 Page 5 of 13 Page 5 of 13 Karanika et al. Molecular Cancer (2015) 14:122 Fig. 2 GLIPR1-ΔTM increased the apoptotic effect of docetaxel in VCaP and PC-3 cells. a. The addition of 10 μg/ml GLIPR1-ΔΤΜ increased the apoptotic effects of all docetaxel’s doses in VCaP cells, measured by DAPI staining. b. The addition of 10 μg/ml GLIPR1-ΔΤΜ increased the apoptotic effects of all docetaxel doses in PC-3 cells, measured by DAPI staining. c. GLIPR1-ΔΤΜ did not increase the apoptotic effect of any docetaxel dose in RWPE-1 cells, while 1nM docetaxel significantly increased the percentage of apoptotic cells, based on DAPI staining. d. The addition of 10 μg/ml GLIPR1-ΔΤΜ increased the apoptotic effects of all docetaxel doses in VCaP cells, measured by DNA fragmentation. e. The addition of 10 μg/ml GLIPR1-ΔΤΜ increased the apoptotic effects of all docetaxel doses in PC-3 cells, measured by DNA fragmentation. f. GLIPR1-ΔΤΜ did not increase the apoptotic effect of any docetaxel dose in RWPE-1 cells, while 0.5nM docetaxel significantly increased the percentage of apoptotic cells, based on DNA fragmentation. The results are presented as the mean ± standard error from at least three independent experiments Fig. 2 GLIPR1-ΔTM increased the apoptotic effect of docetaxel in VCaP and PC-3 cells. a. The addition of 10 μg/ml GLIPR1-ΔΤΜ increased the apoptotic effects of all docetaxel’s doses in VCaP cells, measured by DAPI staining. b. The addition of 10 μg/ml GLIPR1-ΔΤΜ increased the apoptotic effects of all docetaxel doses in PC-3 cells, measured by DAPI staining. c. GLIPR1-ΔΤΜ did not increase the apoptotic effect of any docetaxel dose in RWPE-1 cells, while 1nM docetaxel significantly increased the percentage of apoptotic cells, based on DAPI staining. d. The addition of 10 μg/ml GLIPR1-ΔΤΜ increased the apoptotic effects of all docetaxel doses in VCaP cells, measured by DNA fragmentation. e. The addition of 10 μg/ml GLIPR1-ΔΤΜ increased the apoptotic effects of all docetaxel doses in PC-3 cells, measured by DNA fragmentation. f. GLIPR1-ΔTM increased the apoptotic effect of docetaxel in VCaP and PC-3 cells Based on our Western blot data, docetaxel alone increased the ERK1/2 phosphorylation (modestly in VCaP cells), and c-Myc and CXCR4 protein levels whereas the combination treatment reduced ERK1/2 phosphorylation and c-Myc and CXCR4 protein levels in both cell lines. In contrast, the addition of SP600125 to the combination treatment increased ERK1/2 phosphorylation and protein levels of c-Myc and CXCR4 (Fig. 4a, b). To further test our hypothesis that JNK mediates the apoptotic effects of docetaxel and GLIPR1-ΔΤΜ com- bination treatment, we treated VCaP and PC-3 cells with DMSO, docetaxel, GLIPR1-ΔΤΜ or combination treat- ment with or without JNK inhibitor, SP600125, and per- formed MTS and DNA fragmentation assays to evaluate survival and apoptosis, respectively. We found that the percentage of survived VCaP and PC-3 cells treated with Karanika et al. Molecular Cancer (2015) 14:122 Page 6 of 13 Fig. 3 Time-dependent curves of docetaxel and GLIPR1-ΔTM efficacies in VCaP and PC-3 cells treated with 1, 2, or 5nM docetaxel or 10, 20, or 40 μg/ml GLIPR1-ΔTM. a,b. 1nM docetaxel and 10 μg/ml GLIPR1-ΔΤΜ significantly decreased survival of VCaP cells at 24 h (p = 0.03 for docetaxel and p = 0.001 for GLIPR1-ΔTM). c,d. Time-dependent curves of docetaxel and GLIPR1-ΔTM efficacies in PC-3 cells treated with 1, 2, or 5nM docetaxel or 10, 20, or 40 μg/ml GLIPR1-ΔTM showed that 1nM docetaxel and 10 μg/ml GLIPR1-ΔΤΜ significantly decreased survival of these cells at 48 h (p < 0.001 for docetaxel and p = 0.007 for GLIPR1-ΔTM). The results are presented as the mean ± standard error from at least three independent experiments Fig. 3 Time-dependent curves of docetaxel and GLIPR1-ΔTM efficacies in VCaP and PC-3 cells treated with 1, 2, or 5nM docetaxel or 10, 20, or 40 μg/ml GLIPR1-ΔTM. a,b. 1nM docetaxel and 10 μg/ml GLIPR1-ΔΤΜ significantly decreased survival of VCaP cells at 24 h (p = 0.03 for docetaxel and p = 0.001 for GLIPR1-ΔTM). c,d. Time-dependent curves of docetaxel and GLIPR1-ΔTM efficacies in PC-3 cells treated with 1, 2, or 5nM docetaxel or 10, 20, or 40 μg/ml GLIPR1-ΔTM showed that 1nM docetaxel and 10 μg/ml GLIPR1-ΔΤΜ significantly decreased survival of these cells at 48 h (p < 0.001 for docetaxel and p = 0.007 for GLIPR1-ΔTM). GLIPR1-ΔTM increased the apoptotic effect of docetaxel in VCaP and PC-3 cells The results are presented as the mean ± standard error from at least three independent experiments docetaxel (p < 0.001), GLIPR1-ΔΤΜ (p < 0.001) and com- bination (p = 0.041) (Fig. 5b) in VCaP cells. According to DNA fragmentation assay, we found that knockdown of CXCR4 increased the apoptotic effect of docetaxel (p < 0.001), GLIPR1-ΔΤΜ (p < 0.001) and combination (p = 0.01) in VCaP cells (Fig. 5c). In PC-3 cells, we found that CXCR4 downregulation reduced the survival of cells treated with docetaxel (p < 0.001), GLIPR1-ΔΤΜ (p < 0.001) and combination (p < 0.001) (Fig. 5d). According to DNA fragmentation assay, we found that CXCR4 knockdown increased the apoptotic effect of docetaxel (p < 0.001), GLIPR1-ΔΤΜ (p < 0.001) and combination (p < 0.001) in PC-3 cells (Fig. 5e). These data suggested that CXCR4 downregulation further potentiated the apop- totic effect of each single agent and their combination as well, when was combined with them, confirming that the inhibition of the ERK1/2-c-Myc-CXCR4 resistance pathway led to increased apoptosis. In our proposed combination treatment, GLIPR1-ΔΤΜ worked as the key molecule which reduced CXCR4 levels through suppression of ERK1/2-c-Myc, and consequently maximally increased JNK-induced apoptotic signaling stimulated by docetaxel through ERK1/2 downregulation and JNK dere- pression. Given the known role of CXCR4 as an inducer of migration and metastasis in PCa [28], and based on our re- sults that GLIPR1-ΔTM inhibited the docetaxel-induced ERK1/2-c-Myc-CXCR4 signaling, we evaluated the hypoth- esis that the combination of GLIPR1-ΔΤΜ and docetaxel ERK1/2-c-Myc-CXCR4 docetaxel-induced resistance loop [17], was downregulated by the drug combination which led to reduced migration activity. CXCR4 knockdown potentiated the apoptotic effects of docetaxel and the combination treatment with docetaxel and GLIPR1-ΔTM decreased the migration of VCaP and PC-3 cells We showed that the addition of GLIPR1-ΔTM decreased the docetaxel-mediated ERK1/2-c-Myc-CXCR4 induc- tion in VCaP and PC-3 cells. GLIPR1-ΔΤΜ was ex- pected to further activate the apoptosis and inhibited the development of resistance through this pathway. We evaluated the effects of the CXCR4 downregulation on docetaxel and GLIPR1-ΔTM treatment in terms of apoptosis and survival of VCaP and PC-3 cells. Thus, we treated VCaP and PC-3 cells with CXCR4si7 and CXCR4si8 siRNAs for 48 h and found that the most effective siRNA in terms of downregulation of CXCR4 is the CXCR4si7. Consequently, we treated VCaP and PC- 3 cells with CXCR4si7 for 24 h and then treated them with GLIPR1-ΔΤΜ and docetaxel for 24 and 48 h as described above. Western blot experiments were con- ducted three times and the quantitative data are presented as supplementary data (Additional file 1: Figure S1). We evaluated the survival with MTS assay and apoptosis with DNA fragmentation assay. We found that the treatment with CXCR4si reduced the survival of cells treated with Page 7 of 13 Karanika et al. Molecular Cancer (2015) 14:122 Fig. 4 GLIPR1-ΔΤΜ synergized with docetaxel in activating JNK/c-Jun through JNK phosphorylation, whereas addition of GLIPR1-ΔΤΜ to docetaxel reduced ERK1/2 signaling. a,b. VCaP and PC-3 cells were treated with 1nM docetaxel, 10 μg/ml GLIPR1-ΔTM, or both and then, we added JNK inhibitor (SP600125) 1 μΜ to single agents or to their combination. Total treatment administration lasted for 24 h (VCaP cells) or 48 h (PC-3 cells), and the effects on JNK and ERK1/2 signaling were evaluated via western blot. JNK phosphorylation was increased synergistically with the combination of docetaxel and GLIPR1-ΔΤΜ, a pathway that leads to apoptosis; whereas ERK1/2 phosphorylation, which results in drug resistance and migration through c-Myc-CXCR4, was reduced by administration of this combination. These activities were reversed by the JNK inhibitor, SP600125. Western blot experiments were conducted three times and the quantitative data are presented as supplementary data. c,d. Under the same conditions and treatments in both cell lines, we performed MTS and DNA fragmentation assay to evaluate the percentage of survived cells and cell apoptosis, respectively. CXCR4 knockdown potentiated the apoptotic effects of docetaxel and the combination treatment with docetaxel and GLIPR1-ΔTM decreased the migration of VCaP and PC-3 cells We found that, in both cell lines, the combination treatment of docetaxel and GLIPR1-ΔΤΜ resulted in statistically significant decrease in the percentage of survived cells and increase of apoptotic cells (VCaP: p < 0.001 compared to both single agents in MTS assay, p = 0.02 compared to GLIPR1-ΔΤΜ and p < 0.001 compared to docetaxel according to DNA fragmentation assay, PC-3: p = 0.001 compared to both single agents in MTS assay, p < 0.001 compared to both single agents according to DNA fragmentation assay) but this observation was reversed significantly when we added the JNK inhibitor (SP600125) to the combination docetaxel and GLIPR1-ΔΤΜ (p < 0.001 for both cells lines according to both techniques). The results are presented as the mean ± standard error from at least three independent experiments. e. Signaling effects of the combination treatment of docetaxel and GLIPR1-ΔΤΜ. Docetaxel induces JNK phosphorylation (apoptosis pathway); whereas it concomitantly induces ERK1/2 phoshorylation (drug resistance and migration pathway). JNK and ERK1/2 pathways can demonstrate reciprocal inhibition. GLIPR-ΔΤΜ induces JNK signaling but inhibits the ERK1/2-c-Myc-CXCR4 resistance loop. Thus, docetaxel and GLIPR1-ΔΤΜ combination treatment leads to JNK pathway dominance over the ERK1/2 pathway, and apoptosis dominates over drug resistance and invasion/migration Fig. 4 GLIPR1-ΔΤΜ synergized with docetaxel in activating JNK/c-Jun through JNK phosphorylation, whereas addition of GLIPR1-ΔΤΜ to Fig. 4 GLIPR1-ΔΤΜ synergized with docetaxel in activating JNK/c-Jun through JNK phosphorylation, whereas addition of GLIPR1-ΔΤΜ to docetaxel reduced ERK1/2 signaling. a,b. VCaP and PC-3 cells were treated with 1nM docetaxel, 10 μg/ml GLIPR1-ΔTM, or both and then, we added JNK inhibitor (SP600125) 1 μΜ to single agents or to their combination. Total treatment administration lasted for 24 h (VCaP cells) or 48 h (PC-3 cells), and the effects on JNK and ERK1/2 signaling were evaluated via western blot. JNK phosphorylation was increased synergistically with the combination of docetaxel and GLIPR1-ΔΤΜ, a pathway that leads to apoptosis; whereas ERK1/2 phosphorylation, which results in drug resistance and migration through c-Myc-CXCR4, was reduced by administration of this combination. These activities were reversed by the JNK inhibitor, SP600125. Western blot experiments were conducted three times and the quantitative data are presented as supplementary data. c,d. Under the same conditions and treatments in both cell lines, we performed MTS and DNA fragmentation assay to evaluate the percentage of survived cells and cell apoptosis, respectively. CXCR4 knockdown potentiated the apoptotic effects of docetaxel and the combination treatment with docetaxel and GLIPR1-ΔTM decreased the migration of VCaP and PC-3 cells We found that, in both cell lines, the combination treatment of docetaxel and GLIPR1-ΔΤΜ resulted in statistically significant decrease in the percentage of survived cells and increase of apoptotic cells (VCaP: p < 0.001 compared to both single agents in MTS assay, p = 0.02 compared to GLIPR1-ΔΤΜ and p < 0.001 compared to docetaxel according to DNA fragmentation assay, PC-3: p = 0.001 compared to both single agents in MTS assay, p < 0.001 compared to both single agents according to DNA fragmentation assay) but this observation was reversed significantly when we added the JNK inhibitor (SP600125) to the combination docetaxel and GLIPR1-ΔΤΜ (p < 0.001 for both cells lines according to both techniques). The results are presented as the mean ± standard error from at least three independent experiments. e. Signaling effects of the combination treatment of docetaxel and GLIPR1-ΔΤΜ. Docetaxel induces JNK phosphorylation (apoptosis pathway); whereas it concomitantly induces ERK1/2 phoshorylation (drug resistance and migration pathway). JNK and ERK1/2 pathways can demonstrate reciprocal inhibition. GLIPR-ΔΤΜ induces JNK signaling but inhibits the ERK1/2-c-Myc-CXCR4 resistance loop. Thus, docetaxel and GLIPR1-ΔΤΜ combination treatment leads to JNK pathway dominance over the ERK1/2 pathway, and apoptosis dominates over drug resistance and invasion/migration can inhibit migration of VCaP and PC-3 cells more than docetaxel alone. We treated VCaP and PC-3 cells with 0.5 % or 0.1 % serum-containing medium, respectively, followed by 1nM docetaxel, with or without the addition of 10 μg/ml GLIPR1-ΔΤΜ hour before the initiation of doce- taxel treatment. After 24 h cell migration was assessed by scratch assay. As a positive control, we used 25 μg/ml AMD3100, a CXCR4 inhibitor, as previously described [29]. The addition of GLIPR1-ΔΤΜ to docetaxel signifi- cantly decreased the number of migrated VCaP cells (p < 0.001) (Fig. 5f) and PC-3 cells (p < 0.001) than docetaxel alone did (Fig. 5g). Karanika et al. Molecular Cancer (2015) 14:122 Page 8 of 13 Fig. 5 CXCR4si increased the sensitivity of VCaP and PC-3 cells to docetaxel and reduced cell migration trend when combined with docetaxel. a. Western blot in VCaP and PC-3 cells to evaluate the efficacy of CXCR4si7 and CXCR4si8 siRNAs. The results are presented as the mean ± standard error from three independent experiments. Quantitative data of western blots on 2 different CXCR4siRNAs for validation and determination of their effect size are provided in Supplementary Data. b. CXCR4 knockdown potentiated the apoptotic effects of docetaxel and the combination treatment with docetaxel and GLIPR1-ΔTM decreased the migration of VCaP and PC-3 cells CXCR4 knockdown decreased the survival of VCaP cells when was combined with GLIPR1-ΔTM (p < 0.001), docetaxel (p < 0.001) and combination (p = 0.004) than the CXCR4 knockdown alone did according to MTS assay. c. CXCR4 knockdown increased the apoptosis of VCaP when was combined with GLIPR1-ΔTM (p < 0.001), docetaxel (p < 0.001) and combination (p = 0.041) than the CXCR4 knockdown did according to DNA fragmentation assay. The results are presented as the mean ± standard error from at least three independent experiments. d. CXCR4 knockdown decreased the survival of PC-3 cells when was combined with GLIPR1-ΔTM (p < 0.001), docetaxel (p < 0.001) and combination (p = 0.01) than the CXCR4 knockdown alone did according to MTS assay. e. CXCR4 knockdown increased the apoptosis of PC-3 cells when combined with GLIPR1-ΔTM (p < 0.001), docetaxel (p < 0.001) and combination (p < 0.001) than the CXCR4 knockdone alone did. The results are presented as the mean ± standard error from at least three independent experiments. f. Migration of VCaP cells was evaluated by scratch assay after 24 h of treatment with 1nM docetaxel with or without the addition of 10 μg/ml GLIPR1-ΔΤΜ or 25 μg/ml AMD3100, a known CXCR4 inhibitor. The addition of GLIPR1-ΔTM significantly decreased the number of migrated cells (p < 0.001). g. Migration of PC-3 cells was evaluated by scratch assay after 24 h of treatment with 1nM docetaxel with or without the addition of 10 μg/ml GLIPR1-ΔΤΜ or 25 μg/ml AMD3100. The addition of GLIPR1-ΔTM significantly decreased the number of migrated cells (p < 0.001). The migration assay experiments were conducted twice and the presented results are the averages of these two independent experiments CXCR4 knockdown potentiated the apoptotic effects of docetaxel and the combination treatment with docetaxel and GLIPR1-ΔTM decreased the migration of VCaP and PC-3 cells CXCR4 knockdown decreased the survival of VCaP cells when was combined with GLIPR1-ΔTM (p < 0.001), docetaxel (p < 0.001) and combination (p = 0.004) than the CXCR4 knockdown alone did according to MTS assay. c. CXCR4 knockdown increased the apoptosis of VCaP when was combined with GLIPR1-ΔTM (p < 0.001), docetaxel (p < 0.001) and combination (p = 0.041) than the CXCR4 knockdown did according to DNA fragmentation assay. The results are presented as the mean ± standard error from at least three independent experiments. d. CXCR4 knockdown decreased the survival of PC-3 cells when was combined with GLIPR1-ΔTM (p < 0.001), docetaxel (p < 0.001) and combination (p = 0.01) than the CXCR4 knockdown alone did according to MTS assay. e. CXCR4 knockdown increased the apoptosis of PC-3 cells when combined with GLIPR1-ΔTM (p < 0.001), docetaxel (p < 0.001) and combination (p < 0.001) than the CXCR4 knockdone alone did. The results are presented as the mean ± standard error from at least three independent experiments. f. Migration of VCaP cells was evaluated by scratch assay after 24 h of treatment with 1nM docetaxel with or without the addition of 10 μg/ml GLIPR1-ΔΤΜ or 25 μg/ml AMD3100, a known CXCR4 inhibitor. The addition of GLIPR1-ΔTM significantly decreased the number of migrated cells (p < 0.001). g. Migration of PC-3 cells was evaluated by scratch assay after 24 h of treatment with 1nM docetaxel with or without the addition of 10 μg/ml GLIPR1-ΔΤΜ or 25 μg/ml AMD3100. The addition of GLIPR1-ΔTM significantly decreased the number of migrated cells (p < 0.001). The migration assay experiments were conducted twice and the presented results are the averages of these two independent experiments Fig. 5 CXCR4si increased the sensitivity of VCaP and PC-3 cells to docetaxel and reduced cell migration trend when combined with docetaxel. Fig. 5 CXCR4si increased the sensitivity of VCaP and PC-3 cells to docetaxel and reduced cell migration trend when combined with docetaxel. a. Western blot in VCaP and PC-3 cells to evaluate the efficacy of CXCR4si7 and CXCR4si8 siRNAs. The results are presented as the mean ± standard error from three independent experiments. Quantitative data of western blots on 2 different CXCR4siRNAs for validation and determination of their effect size are provided in Supplementary Data. b. Combination treatment with docetaxel and GLIPR-ΔΤΜ inhibited growth and metastasis of VCaP othotopic xenografts IVIS signal (photons/second) than GLIPR1-ΔTM alone did (p = 0.012) but docetaxel alone did not (p = 0.16) (Fig. 6a). However, the tumors that were treated with com- bination therapy had significantly lower wet weight than the tumors in the mice treated with docetaxel alone (p = 0.028) or GLIPR1-ΔTM alone (p = 0.0025) did (Fig. 6b). We collected lymph node samples from all mice and evaluated them for the presence of metastatic PCa cells as evidenced by cytokeratin 18 staining. Neither of the two To validate the efficacy of the combination of GLIPR1- ΔTM and docetaxel in vivo, we treated nude mice bearing VCaP orthotopic tumors with PBS (control), docetaxel alone, GLIPR1-ΔTM alone, or the combination of these two agents. Three weeks after the initiation of treat- ment, combination treatment significantly decreased the Page 9 of 13 Karanika et al. Molecular Cancer (2015) 14:122 Fig. 6 Docetaxel GLIPR1-ΔΤΜ combination treatment inhibited growth and metastasis in VCaP orthotopic xenografts. a. Nude mice bearing VCaP xenografts were treated with docetaxel, GLIPR1-ΔΤΜ, or both. Combination treatment significantly decreased the IVIS signal (photons/s) than GLIPR1-ΔΤΜ alone did (p = 0.012) but docetaxel alone did not (p = 0.16). b. Combination treatment decreased significantly the wet weight of VCaP xenografts rather thad GLIPR1-ΔΤΜ alone (p = 0.0025) and docetaxel alone (p = 0.028) did. c. Mouse lymph node tissues were stained for cytokeratin 18 to evaluate the presence of metastatic VCaP cells. The combination of docetaxel and GLIPR1-ΔΤΜ resulted in a lower incidence of LN metastasis than control treatment did (p = 0.04), whereas single-agent treatments did not result in a significant reduction Fig. 6 Docetaxel GLIPR1-ΔΤΜ combination treatment inhibited growth and metastasis in VCaP orthotopic xenografts. a. Nude mice bearing VCaP xenografts were treated with docetaxel, GLIPR1-ΔΤΜ, or both. Combination treatment significantly decreased the IVIS signal (photons/s) than GLIPR1-ΔΤΜ alone did (p = 0.012) but docetaxel alone did not (p = 0.16). b. Combination treatment decreased significantly the wet weight of VCaP xenografts rather thad GLIPR1-ΔΤΜ alone (p = 0.0025) and docetaxel alone (p = 0.028) did. c. Mouse lymph node tissues were stained for cytokeratin 18 to evaluate the presence of metastatic VCaP cells. Combination treatment with docetaxel and GLIPR-ΔΤΜ inhibited growth and metastasis of VCaP othotopic xenografts The combination of docetaxel and GLIPR1-ΔΤΜ resulted in a lower incidence of LN metastasis than control treatment did (p = 0.04), whereas single-agent treatments did not result in a significant reduction agents significantly altered the emergence of metastasis, but combination therapy decreased the incidence of me- tastasis than control treatment did (p = 0.04) (Fig. 6c). ERK1/2-c-Myc-CXCR4 resistance loop and consequently to suppress the inhibitory effects of ERK1/2 on JNK signaling, driving JNK signaling. Thus, the efficacy of the combination of these two agents is suggested to be mediated through synergistic apoptotic activity driven by dominant JNK signaling and downregulation of ERK1/ 2-c-Myc-CXCR4-mediated drug resistance and migration. Cell viability assay Cell viability was analyzed using an MTS CellTiter 96 Aqueous One Solution Cell Proliferation Assay (Promega, Madison, WI) according to the manufacturer’s instructions as previously described [30]. After appropriate cell treat- ment (96-well assay plate) 20 μl of CellTiter 96® Aqueous One Solution Reagent were added into each well. The plate was intubated for 2 h at 37 °C in a humidified 5 % CO2 chamber. The absorbance at 490 nm was recorded using the 96-well plate reader. Discussion In the present study we tested our hypothesis that GLIPR1-ΔΤΜ can synergize with docetaxel (one of the two chemotherapy agents approved for the treatment of mCRPC) and whether the combination treatment can lead to greater cell death than treatment with docetaxel alone does. We showed that the combination of these two agents had synergistic effects on decreasing cell survival of VCaP and PC-3 cells. Apoptosis was the main mechanism for cell death, as demonstrated with DAPI staining and DNA fragmentation assay. Of note, the combination treatment appeared to lead to additive induction of JNK signaling since GLIPR1-ΔΤΜ was found to inhibit the We further tested our hypothesis regarding the JNK hyperactivation via JNK inhibitor administration using two biological assays to assess the effect on survival and apoptosis and western blot to monitor the signaling changes. We found that the addition of the inhibitor to the combination treatment resulted in increased survival and reduced apoptosis compared to combination treat- ment alone in both PCa cell lines; whereas on Western blots we observed a marked reduction in JNK phosphor- ylation together with a concomitant increase in ERK1/2 Karanika et al. Molecular Cancer (2015) 14:122 Page 10 of 13 Page 10 of 13 phosphorylation, and c-Myc and CXCR4 protein levels compared to combination treatment without inhibitor. We further tested the effect of CXCR4 downregulation on combination treatment to determine its role as a central component of the ERK1/2-c-Myc-stimulated resistance loop. In support of our hypothesis, we found that CXCR4 knockdown combined with the combination treatment further enhanced apoptosis and reduced the survival of the cells. This finding demonstrates the opposing biological effects of GLIPR1-ΔΤΜ on c-Myc- CXCR4-mediated drug resistance and migration [17, 28]. In consideration of this mechanism we tested our hypoth- esis via migration assay and found that docetaxel and GLIPR1-ΔΤΜ combination treatment resulted in signifi- cantly reduced numbers of migrated cells than docetaxel alone did, mimicking the result of docetaxel combined with CXCR4 inhibitor and supporting our hypothesis for a role for GLIPR1-ΔΤΜ suppression of PCa cell migration. Conclusions The results of our study demonstrated that docetaxel and GLIPR1-ΔΤΜ combination treatment leads to increased JNK-mediated apoptosis compared to single agent treat- ment. These activities are accompanied by inhibition of ERK1/2-c-Myc-CXCR4 signaling, which results in de- repression of JNK signaling, leading to maximal JNK-mediated apoptotic effects. In addition docetaxel and GLIPR1-ΔΤΜ combination treatment may suppress migration through downregulation of the ERK1/2-c-Myc- CXCR4 drug resistance pathway and reduces metastatic potential in vivo. Based on our results, its conceivable that GLIPR1-ΔΤΜ (which is currently progressing toward clinical trials) or therapy agents that act through similar mechanisms may be used together with reduced dosage of docetaxel with potentially greater therapeutic efficacy than docetaxel alone, and with probably fewer adverse effects. It is also conceivable that docetaxel and GLIPR1-ΔΤΜ combination treatment could possibly result in delay in developing docetaxel resistance. Further preclinical and clinical studies will be needed to develop GLIPR1-ΔΤΜ therapy through clinical trials and to evaluate the safety and efficacy of this combination in patients with mCRPC. Purification of recombinant GLIPR1-ΔΤΜ Purification of recombinant GLIPR1-ΔΤΜ GLIPR1-ΔTM coding sequence was obtained from normal prostate tissue by RT-PCR using specific primers (forward: 5′CCCAAGCTTGCAAATATTTTG CCAGAT3′, reverse: 5ATAGT TTAGCGGCCGCTCT GTTACGTGGATATAT3′). The PCR product was digested with restriction enzymes Hinlll and NotI and inserted into pSectag/ Hygro2 Hinlll and NotI sites to generate pSec-GLIPR1-ΔTM as previously described [24, 26]. Conditioned medium from 293 Freestyle cells transfected with pSec-GLIPR1-ΔTM was collected and centrifuged, and GLIPR1-ΔTM was purified using Ni-NTA agarose. To test our treatment combination effectiveness in vivo, we treated nude mice bearing VCaP orthotopic xenografts with docetaxel, GLIPR1-ΔΤΜ, or both for 3 weeks. Combination treatment decreased IVIS signal than GLIPR1-ΔΤΜ did and decreased significantly tumor weight than both single-agent treatments did. The finding that the incidence of lymph node metastasis was significantly lower in animals treated with the combination treatment than in control-treated animals is consistent with our in vitro data and may be re- lated to the inhibition of the docetaxel-induced ERK1/2-CXCR4-c-Myc axis by GLIPR1-ΔTM. Cell lines and reagents The non-tumorigenic RWPE-1 cells (from the American Type Culture Collection) were grown in complete keratinocyte serum-free medium. PC-3 and VCaP prostate cancer cells were grown as described previously [26]. All cell lines were validated by short tandem repeat DNA fingerprinting with the AmpFlSTR Identifier Kit (Applied Biosystems, Inc., Foster City, CA) at the Characterized Cell Line Core Facility of The University of Texas MD Anderson Cancer Center. Docetaxel and AMD3100, a CXCR4 inhibitor, were purchased from Sigma-Aldrich (St. Louis, MO). SP600125, a JNK inhibitor, was purchased from Santa Cruz. Isobologram analysis h ff f d The effects of drug combinations were categorized as additive, synergistic, or antagonistic by isobologram analysis as previously described [31], and IC50 was used to determine the fixed ratio. A graph of equally effective dose pairs (isoboles) for a single effect level is presented. Specifically, a particular effect level of 50 % of the maximum is selected, and doses of docetaxel and GLIPR1-ΔTM (each alone) that give this effect are plotted as axial points in a Cartesian plot. The straight line connecting axial and vertical axes is the locus of points (dose pairs) that will produce this effect in a simply additive combination. This line of additivity allows a comparison with the actual dose pair that produces this effect level experimentally. An actual dose pair below the straight line attains this effect with lesser quantities and is super-additive (synergistic), while the dose pair denoted above the straight line means greater quantities are required and is therefore sub-additive. Western blot analysis temperature to rehydrate for 15 min. The DAPI stock solution was diluted to 3 μM in staining buffer (100 mM Tris, pH 7.4, 150 mM NaCl, 1 mM CaCl2, 0.5 mM MgCl2, 0.1 % Nonidet P-40). After adding the solution the cell suspension was centrifuged and the supernatant was discarded. 1 mL of DAPI diluted in staining buffer was added and the cells were intubated for 15 min at room temperature. The cells’ staining was analyzed by flow cytometry. For evaluation of JNK and ERK1/2-c-Myc-CXCR4 sig- naling, PC-3 cells were treated for 24 h with RPMI-1640 medium containing 0.1 % serum and VCaP cells were treated for 24 h with Dulbecco modified Eagle medium (DMEM) containing 0.5 % serum. Then, cells were treated with 10 μg/ml GLIPR1-ΔΤΜ for 1 h followed by the addition of 1nM docetaxel with or without 1μΜ SP600125 and lysates were collected 24 h later (VCaP cells) and 48 h later (PC-3 cells). Antibodies against GLIPR1-ΔΤΜ (Myc-tag), phospho-JNK, JNK, phospho- ERK1/2, ERK1/2, c-Myc, and CXCR4 were all purchased from Cell Signaling Technology (Danvers, MA), and anti- body against GAPDH was purchased from Santa Cruz. When indicated, densitometric analysis was performed and quantification of integrated density was assessed using the NIS-Elements-AR software program (version 3.0; Nikon) followed by GAPDH normalization. Tumor induction in mice, treatment protocols, and immunohistochemical analysis VCaP cells were transduced with lentivirus stably ex- pressing luciferase. Aliquots of 2 × 106 VCaP-luciferase cells in 25 μl of PBS were injected directly into the right lobe of the dorsolateral prostate in athymic nude male mice (Taconic Farms, Hudson, NY) to induce orthotopic tumors. The tumors were allowed to grow for 14 days before treatment. Mice were treated with 10 mg/kg docetaxel intraperitonealy weekly, 20 μg of GLIPR1-ΔTM intraperitonealy three times per week, or both. The control group was treated with PBS. Tumor size was monitored by measuring the luminescence signal using the IVIS 200 imaging system (PerkinElmer, Wellesley, MA). After 3 weeks of treatment, tumor-bearing mice were sacri- ficed, and the tumors were collected and weighed. Lymph nodes were also collected, and antibody to cytokeratin 18 (DAKO, Carpinteria, CA; catalog no. M701029-2) was used for immunostaining on formalin-fixed paraffin-embedded lymph node tissues. All tissue sections were processed by using an avidin–biotin peroxidase complex kit (Vector Laboratories, Burlingame, CA) as previously described [32]. DNA fragmentation assay DNA f i DNA fragmentation assay was performed using a Cell Death Detection ELISA Kit (Roche, Mannheim, Germany) according to manufacturer’s protocol as previously described [26]. The assay is a photometric enzyme- immunoassay for the qualitative and quantitative in vitro determination of cytoplasmic histone-associated DNA fragments (mono- and oligonucleosomes) after induced cell death. Apoptosis analysis Apoptotic nuclear morphology was evaluated with fluor- escence microscopy after 4′,6-diamidino-2-phenylindole (DAPI) staining (2 μg/ml). DNA fragmentation analysis was performed using Cell Death Detection ELISA (Roche Applied Science, Indianapolis, IN) according to the manufacturer’s instructions. After the appropriate treatment, a cell suspension of 2 × 105 cells was collected, the cells were pelleted by centrifugation and the super- natant was discarded. 1 mL of PBS was added and the full volume of re-suspended cells was transferred to 4 mL of absolute ethanol at −20 °C by pipetting the cell suspension slowly into the ethanol while vortexing at top speed. The cells were intubated in ethanol at −20 °C for 5–15°min. The ethanol was discarded and 5 mL of PBS at room Page 11 of 13 Karanika et al. Molecular Cancer (2015) 14:122 Scratch assay PC 3 ll (1 PC-3 cells (1 × 105) and VCaP cells (2 × 105) were seeded in six-well plates and incubated overnight to achieve confluency. Next day, PC-3 cells were treated for 24 h with RPMI-1640 medium containing 0.1 % serum, and VCaP cells were treated for 24 h with DMEM containing 0.5 % serum. Then, the cell layer in each well was scratched using a plastic pipette tip, and cells were treated with 10 μg/ml GLIPR1-ΔΤΜ for 1 h followed by the addition of 1nM docetaxel for 24 h. Cells were visu- alized under a microscope and photographed for the evaluation of migration. RNA interference Knockdown of CXCR4 was achieved by transient trans- fection of VCaP cells with a pool of CXCR4-specific siRNA (Invitrogen), and a pool of non-targeting siRNA (NCsi) (Invitrogen), as control, by using Lipofectamine RNAiMax transfection reagent (Invitrogen). VCaP cells were seeded at a density of 1.0 × 106 in six-well plates. Cells were transfected with 20nM CXCR4si or NCsi the following day. 24 h later cells were treated with DMSO or 1 and 2nM of docetaxel in Dulbecco modified Eagle medium (DMEM) containing 0.5 % serum. Page 12 of 13 Page 12 of 13 Karanika et al. Molecular Cancer (2015) 14:122 Statistical analysis 2. Scher HI, Fizazi K, Saad F, Taplin ME, Sternberg CN, Miller K, et al. Increased survival with enzalutamide in prostate cancer after chemotherapy. N Engl J Med. 2012;367:1187–97. The results are presented as the mean ± standard error from at least three independent experiments. Comparisons of groups were appropriately analyzed using the Student-t test and the Mann–Whitney U test. P values less than 0.05 were considered statistically significant and all tests were two-tailed. Fisher analysis was used to compare the incidences of lymph node metastasis in animal tissues. The isobologram study was used for the determination of synergy as described above. 3. Tannock IF, de Wit R, Berry WR, Horti J, Pluzanska A, Chi KN, et al. Docetaxel plus prednisone or mitoxantrone plus prednisone for advanced prostate cancer. N Engl J Med. 2004;351(15):1502–12. 4. de Bono JS, Oudard S, Ozguroglu M, Hansen S, Machiels JP. Prednisone plus cabazitaxel or mitoxantrone for metastatic castration-resistant prostate cancer progressing after docetaxel treatment: a randomised open-label trial. Lancet. 2010;376(9747):1147–54. 5. van Soest RJ, de Morrée ES, Shen L, Tannock IF, Eisenberger MA, de Wit R. Initial Biopsy Gleason Score as a Predictive Marker for Survival Benefit in Patients with Castration-resistant Prostate Cancer Treated with Docetaxel: Data from the TAX327 Study. Eur Urol. 2014;66(2):330–6. 6. Pienta KJ. Preclinical mechanisms of action of docetaxel and docetaxel combinations in prostate cancer. Semin Oncol. 2001;28(4 Suppl 15):3–7. 6. Pienta KJ. Preclinical mechanisms of action of docetaxel and docetaxel combinations in prostate cancer. Semin Oncol. 2001;28(4 Suppl 15):3–7. 7. Haldar S, Basu A, Croce CM. Bcl2 is the guardian of microtubule integrity. Cancer Res. 1997;57(2):229–33. Abbreviations 11. Mhaidat NM, Thorne RF, Zhang XD, Hersey P. Regulation of docetaxel-induced apoptosis of human melanoma cells by different isoforms of protein kinase C. Mol Cancer Res. 2007;5(10):1073–81. JNK: c- Jun NH2-terminal kinase; ROS: Reactive oxygen species; AR: Androgen receptor; mCRPC: Metastatic castrate resistant prostate cancer; GLIPR1: Gene encoding the human glioma pathogenesis-related protein 1; ERK1/2: Extracellular signal-regulated kinase1/2; CXCR4: C-X-C chemokine receptor type 4. 12. Xia Z, Dickens M, Raingeaud J, Davis RJ, Greenberg ME. Opposing effects of ERK and JNK-p38 MAP kinases on apoptosis. Science. 1995;270(5240):1326–31. 13. Shen YH, Godlewski J, Zhu J, Sathyanarayana P, Leaner V, Birrer MJ. Cross- talk between JNK/SAPK and ERK/MAPK pathways: sustained activation of JNK blocks ERK activation by mitogenic factors. J Biol Chem. 2003;278(29):26715–21. Epub 2003 May 8. 1. Ryan CJ, Smith MR, de Bono JS, Molina A, Logothetis CJ, de Souza P, et al. Abiraterone in metastatic prostate cancer without previous chemotherapy. N Engl J Med. 2013;368:138–48. Funding This work was supported in part by National Cancer Institute grant R0150588 (to T.C.T.); National Cancer Institute grant P50140388, the Prostate Cancer Specialized Program of Research Excellence at The University of Texas MD Anderson Cancer Center; the NIH through MD Anderson’s Cancer Center Support Grant, CA16672; DOD grant PC093932; and Tony’s Prostate Cancer Research Foundation. 18. Pezaro CJ, Omlin AG, Altavilla A, Lorente D, Ferraldeschi R, Bianchini D, et al. Activity of Cabazitaxel in Castration-resistant Prostate Cancer Progressing After Docetaxel and Next-generation Endocrine Agents. Eur Urol. 2014;66(3):459–65. Additional file combinations in prostate cancer. Semin Oncol. 2001;28(4 Suppl 15):3–7. 7. Haldar S, Basu A, Croce CM. Bcl2 is the guardian of microtubule integrity. Cancer Res. 1997;57(2):229–33. Additional file 1: Figure S1. Quantitative Data of Westerns Blots (relevant to Fig. 4a, b). A. VCaP cells densitomentry data B. PC-3 cells densitometry data. Figure S2 Quantitative data of Western Blots on 2 different CXCR4siRNAs for validation and determination of their effect size (relevant to Fig. 5a). A. CXCR4si7 is statistically significant in inhibiting CXCR4 protein expression than NCsi is (p < 0.001) and CXCR4si8 is (p = 0.002) in VCaP cells. B. CXCR4si7 is statistically significant in inhibiting CXCR4 protein expression than NCsi is (p < 0.001) and CXCR4si8 is (p = 0.01) in PC-3 cells. 8. Haldar S, Chintapalli J, Croce CM. Taxol induces bcl-2 phosphorylation and death of prostate cancer cells. Cancer Res. 1996;56(6):1253–5. 8. Haldar S, Chintapalli J, Croce CM. Taxol induces bcl-2 phosphorylation and death of prostate cancer cells. Cancer Res. 1996;56(6):1253–5. 9. Mhaidat NM, Zhang XD, Jiang CC, Hersey P. Docetaxel-induced apoptosis of human melanoma is mediated by activation of c-Jun NH2-terminal kinase and inhibited by the mitogen-activated protein kinase extracellular signal-regulated kinase 1/2 pathway. Clin Cancer Res. 2007;13(4):1308–14. 10. Rabi T, Bishayee A. d -Limonene sensitizes docetaxel-induced cytotoxicity in human prostate cancer cells: Generation of reactive oxygen species and induction of apoptosis. J Carcinog. 2009;8:9. Competing interests The data included in this manuscript are relevant to intellectual property that has been licensed by Baylor College of Medicine to Progression Therapeutics, Inc., a private biotechnology start-up company. T.C. Thompson is an inventor of record on patents that are included in this licensing agreement. 14. Monick MM, Powers LS, Gross TJ, Flaherty DM, Barrett CW, Hunninghake GW. Active ERK contributes to protein translation by preventing JNK-dependent inhibition of protein phosphatase 1. J Immunol. 2006;177(3):1636–45. Author details 1 19. Sinibaldi VJ. Docetaxel treatment in the elderly patient with hormone refractory prostate cancer. Clin Interv Aging. 2007;2(4):555–60. 1Department of Genitourinary Medical Oncology – Research, Unit 18-3, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, USA. 2Department of Urology, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan. 3Department of Thoracic & Cardio Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. 4Department of Urology, Thomas Jefferson University Hospital, Philadelphia, PA, USA. 20. Araujo JC, Trudel GC, Saad F, Armstrong AJ, Yu EY, Bellmunt J, et al. Docetaxel and dasatinib or placebo in men with metastatic castration-resistant prostate cancer (READY): a randomised, double-blind phase 3 trial. Lancet Oncol. 2013;14(13):1307–16. Epub 2013 Nov 8. 21. Fizazi KS, Higano CS, Nelson JB, Gleave M, Miller K, Morris T, et al. Phase III, randomized, placebo-controlled study of docetaxel in combination with zibotentan in patients with metastatic castration-resistant prostate cancer. J Clin Oncol. 2013;31(14):1740–7. Received: 27 February 2015 Accepted: 29 May 2015 Received: 27 February 2015 Accepted: 29 May 2015 22. Ren C, Li L, Yang G, Timme TL, Goltsov A, Ren C, et al. RTVP-1, a tumor suppressor inactivated by methylation in prostate cancer. Cancer Res. 2004;64(3):969–76. Authors’ contributions 15. Nordström E, Fisone G, Kristensson K. Opposing effects of ERK and p38-JNK MAP kinase pathways on formation of prions in GT1-1 cells. FASEB J. 2009;23(2):613–22. TCT, SKA, TK and SKU conceived and designed the study. TCT, SKA and TK wrote the paper. SKA, TK, SKU, and JW performed MTS, DNA fragmentation and isobologram studies. TK and SKA performed Western blot analysis. TK, SKA and LL performed scratch assay. GY performed cytokeratin staining. TH, SP, AG and RT designed and conducted the xenograft model experiment. All authors contributed, read and approved the final manuscript. TCT, SKA, TK and SKU conceived and designed the study. TCT, SKA and TK wrote the paper. SKA, TK, SKU, and JW performed MTS, DNA fragmentation and isobologram studies. TK and SKA performed Western blot analysis. TK, TCT, SKA, TK and SKU conceived and designed the study. TCT, SKA and TK wrote the paper. SKA, TK, SKU, and JW performed MTS, DNA fragmentation and isobologram studies. TK and SKA performed Western blot analysis. TK, SKA and LL performed scratch assay. GY performed cytokeratin staining. TH, SP, AG and RT designed and conducted the xenograft model experiment. All authors contributed, read and approved the final manuscript. 16. Leonetti C, Biroccio A, D’Angelo C, Semple SC, Scarsella M, Zupi G. Therapeutic integration of c-myc and bcl-2 antisense molecules with docetaxel in a preclinical model of hormone-refractory prostate cancer. Prostate. 2007;67(13):1475–85. SKA and LL performed scratch assay. GY performed cytokeratin staining. TH, SP, AG and RT designed and conducted the xenograft model experiment. All authors contributed, read and approved the final manuscript. 17. Hatano K, Yamaguchi S, Nimura K, Murakami K, Nagahara A, Fujita K, et al. Residual prostate cancer cells after docetaxel therapy increase the tumorigenic potential via constitutive signaling of CXCR4, ERK1/2 and c-Myc. Mol Cancer Res. 2013;11(9):1088–100. Karanika et al. Molecular Cancer (2015) 14:122 References 1. Ryan CJ, Smith MR, de Bono JS, Molina A, Logothetis CJ, de Souza P, et al. Abiraterone in metastatic prostate cancer without previous chemotherapy N Engl J Med. 2013;368:138–48. 23. Ren C, Li L, Goltsov AA, Timme TL, Tahir SA, Wang J, et al. mRTVP-1, a novel p53 target gene with proapoptotic activities. Mol Cell Biol. 2002;22(10):3345–57. Page 13 of 13 Page 13 of 13 Karanika et al. Molecular Cancer (2015) 14:122 Karanika et al. Molecular Cancer (2015) 14:122 24. Li L, Abdel Fattah E, Cao G, Ren C, Yang G, Goltsov AA, et al. Glioma pathogenesis-related protein 1 exerts tumor suppressor activities through proapoptotic reactive oxygen species-c-Jun-NH2 kinase signaling. Cancer Res. 2008;68(2):434–43. 25. Li L, Ren C, Yang G, Fattah EA, Goltsov AA, Kim SM, et al. GLIPR1 suppresses prostate cancer development through targeted oncoprotein destruction. Cancer Res. 2011;71(24):7694–704. 26. Karantanos T, Tanimoto R, Edamura K, Hirayama T, Yang G, Golstov AA, et al. Systemic GLIPR1-ΔTM protein as a novel therapeutic approach for prostate cancer. Int J Cancer. 2014;134(8):2003–13. 27. Bennett BL, Sasaki DT, Murray BW, O’Leary EC, Sakata ST, Xu W, et al. SP600125, an anthrapyrazolone inhibitor of Jun N-terminal kinase. Proc Natl Acad Sci U S A. 2001;98(24):13681–6. 28. Singh S, Singh UP, Grizzle WE, Lillard Jr JW. CXCL12-CXCR4 interactions modulate prostate cancer cell migration, metalloproteinase expression and invasion. Lab Invest. 2004;84(12):1666–76. 29. Domanska UM, Timmer-Bosscha H, Nagengast WB, Oude Munnink TH, Kruizinga RC, Ananias HJ, et al. CXCR4 inhibition with AMD3100 sensitizes prostate cancer to docetaxel chemotherapy. Neoplasia. 2012;14(8):709–18. 30. Tabata K, Kurosaka S, Watanabe M, Edamura K, Satoh T, Yang G, et al. Tumor growth and metastasis suppression by Glipr1 gene-modified macrophages in a metastatic prostate cancer model. Gene Ther. 2011;10:969–78. 31. Fivelman QL, Adagu IS, Warhurst DC. Modified fixed-ratio isobologram method for studying in vitro interactions between atovaquone and proguanil or dihydroartemisinin against drug-resistant strains of Plasmodium falciparum. Antimicrob Agents Chemother. 2004;48:4097–102. g 32. Yang G, Goltsov AA, Ren C, Kurosaka S, Edamura K, Logothetis R, et al. Caveolin-1 upregulation contributes to c-Myc-induced high-grade prostatic intraepithelial neoplasia and prostate cancer. Mol Cancer Res. 2012;10(2):218–29. 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An AAV9 coding for frataxin clearly improved the symptoms and prolonged the life of Friedreich ataxia mouse models
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Received 30 July 2014; accepted 30 July 2014 1Centre de Recherche du Centre Hospitalier Universitaire de Québec and Department of Molecular Medecine, Faculty of Medecine, Laval University, Québec, Canada; 2Fred N. Eshelman Distinguished Professor of Gene Therapy Vice Chair, Division of Molecular Pharmaceutics, UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA; 3Centre de recherche, Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada. Correspondence: JP Tremblay (JacquesP.Tremblay@crchul.ulaval.ca) An AAV9 coding for frataxin clearly improved the symptoms and prolonged the life of Friedreich ataxia mouse models Catherine Gérard1, Xiao Xiao2, Mohammed Filali1, Zoé Coulombe1, Marie Arsenault3, Jacques Couet3, Juan Li2, Marie-Claude Drolet3, Pierre Chapdelaine1, Amina Chikh1 and Jacques P Tremblay1 Friedreich ataxia (FRDA) is a genetic disease due to increased repeats of the GAA trinucleotide in intron 1 of the frataxin gene. This mutation leads to a reduced expression of frataxin. We have produced an adeno-associated virus (AAV)9 coding for human frataxin (AAV9-hFXN). This AAV was delivered by intraperitoneal (IP) injection to young conditionally knockout mice in which the frataxin gene had been knocked-out in some tissues during embryogenesis by breeding them with mice expressing the Cre recombinase gene under the muscle creatine kinase (MCK) or the neuron-specific enolase (NSE) promoter. In the first part of the study, different doses of virus were tested from 6 × 1011 v.p. to 6 × 109 v.p. in NSE-cre mice and all leading to an increase in life spent of the mice. The higher and the lower dose were also tested in MCK-cre mice. A single administration of the AAV9-hFXN at 6 × 1011 v.p. more than doubled the life of these mice. In fact the MCK-cre mice treated with the AAV9-hFXN were sacrificed for further molecular investi- gations at the age of 29 weeks without apparent symptoms. Echography analysis of the heart function clearly indicated that the cardiac systolic function was better preserved in the mice that received 6 × 1011 v.p. of AAV9-hFXN. The human frataxin protein was detected by ELISA in the heart, brain, muscles, kidney, and liver with the higher dose of virus in both mouse models. Thus, gene therapy with an AAV9-hFXN is a potential treatment of FRDA. hods & Clinical Development (2014) 1, 14044; doi:10.1038/mtm.2014.44; published online 8 October 2014 Molecular Therapy — Methods & Clinical Development (2014) 1, 14044; doi:10.1038/mtm.2014.44; published INTRODUCTION designated as NSE-cre. These mice reproduced important progres- sive pathophysiological and biochemical features of the human dis- ease: cardiac hypertrophy without skeletal muscle involvement. The NSE mice also express large sensory neuron dysfunctions without alteration of the small sensory and motor neurons. Friedreich ataxia (FRDA) is an autosomal recessive neurodegen- erative and cardiac disease, caused by a trinucleotide (GAA) repeat expansion in the first intron of the frataxin gene located in chromo- some 9.1 The mutation in the intron 1 of the frataxin gene leads to a reduced expression of the frataxin gene without changing the protein. The mechanism of this pathology has been reviewed by Pandolfo et al.2,3 Neurons and cardiomyocytes are particularly sensi- tive to the reduction of frataxin.4–6 Thus, neurological and cardiac symptoms appear in or before the second decade of life.7–11 There are also some systemic involvements, such as diabetes mellitus and scoliosis. Cardiomyopathy and associated arrhythmias lead to early death.9,12 In the present article, we tested different quantity of virus from 6 × 109 virus particles (v.p.) to 6 × 1011 v.p. The injection of the virus clearly prolonged the life of the treated mice for all the quantity tested. Also, the administration of 6 × 1011 v.p. of an adeno-associated virus (AAV)9 coding for the human frataxin to the MCK-cre and to the NSE-cre not only increased the expres- sion of the frataxin protein in these mouse models of FRDA but clearly reduced their heart hypertrophy and improved their heart function. We are thus proposing that an AAV coding for frataxin could be a treatment for FRDA. Mice homozygous for a conditional frataxin allele (Frda exon 4 located between 2 LoxP, named FrdaL3/L3) have been crossed by Puccio et al.13 with mice heterozygous for the deletion of Frda exon 4 (Frda L-/L3) that also carried a tissue-specific Cre transgene under the control of the muscle creatine kinase (MCK) or the neuron-­ specific enolase (NSE) promoter. The MCK promoter induced a knockout of the exon 4 in the heart and the striated muscle and the resulting mice were called MCK-cre. The NSE promoter lead to a knockout of the Frda exon 4 not only in the brain but also in the heart, muscles, kidney, and liver and the resulting mice were Citation: Molecular Therapy — Methods & Clinical Development (2014) 1, 14044; doi:10.1038/mtm.2014.44 © 2014 The American Society of Gene & Cell Therapy  All rights reserved 2329-0501/14 Citation: Molecular Therapy — Methods & Clinical Development (2014) 1, 14044; doi:10.1038/mtm.2014.44 © 2014 The American Society of Gene & Cell Therapy  All rights reserved 2329-0501/14 www.nature.com/mtm An AAV9 coding for frataxin C Gérard et al. In the other organs of these NSE-cre mice, most of the time two bands were observed indicating that the frataxin gene was not floxed in all cells. The floxed frataxin allele was more abundant in the brain than in the muscle, liver, and kidneys. These results indicated that NSE-cre mice Effects of AAV9-FXN treatment on body weight. The growth curve of the NSE-cre was followed for the treated and not treated mice. The NSE-cre curve was significantly lower than that of the L3/L3 mice (Figure 1). When these mice received the AAV9-hFXN at 5–9 days, their growth curves were improved compared to the NSE-cre mice that did not receive the treatment. This was observed for all the viral doses tested. However, they did not reach the body weight of the L3/L3 mice for male (Figure 1a) and female mice (Figure 1b). Only the males receiving 6 × 1011 v.p. (d1/10) seem to follow the curve of the L3/L3 but there were only three mice in this group. Table 1  Animal score Score Characteristics Action 0 Lively and active animal None. Smooth coat No lack of comfort Observe once per week. 1 Mouse moves normally but often on the tip of their toes. Wet food into the cage. May have the back lightly curved. Observe daily. 2 Mouse moves normally but on the tip of their toes. Wet food into the cage. Mouse mostly lively. Observe twice a day. Hair slightly spiky. Back curved. Could have a abnormal breathing but not difficult. 3 Mouse has difficulties to walk and moves less. Wet food into the cage. Back curved and hair very spiky. Observe twice a day. Difficulties to eat. Could have an abnormal and difficult breathing. Should be sacrificed within 4 hours. 4 Mouse does not move or moves with pain. Should be sacrificed immediately. Very spiky hair. Could have lifeless, sunk or closed eyes. Difficulties to eat. Could have a breathing insufficiency. Figure 1  Evolution of neuron-specific enolase (NSE)-cre mouse weight. The body weight of the different groups of mice was followed until their sacrifice. In a, the male mice: L3/L3 (n = 26), NSE-cre mice treated with the AAV9-hFXN at 6 × 1011 v.p. (named AAV9-hFXN; n = 12), at 3 × 1011 v.p. (named d1/2; n = 0), at 6 × 1010 v.p. (named d1/10; n = 3), at 3 × 1010 v.p. An AAV9 coding for frataxin C Gérard et al. (named d1/20; n = 2), at 1.2 × 1010 v.p. (named d1/50; n = 5), at 6 × 109 v.p. (named d1/100; n = 3) and the untreated mice (named no treatment; n = 33). In b, the female mice: L3/L3 (n = 20), NSE-cre mice treated with the AAV9-hFXN at 6 × 1011 v.p. (n = 17), at 3 × 1011 v.p. (n = 3), at 6 × 1010 v.p. (n = 2), at 3 × 1010 v.p. (n = 3), at 1.2 × 1010 v.p. (n = 3), at 6 × 109 v.p. (n = 4) and the untreated mice (n = 33). The untreated NSE-cre had the lowest body weight. The growth curve of the NSE-cre mice was clearly improved by the AAV9-hFXN treatment for both sex groups. 0 5 10 15 20 25 30 35 40 0 50 100 150 200 250 0 50 100 150 Age in days Age in days 200 250 Male body weight (g) L3/L3 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 No treatment L3/L3 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 No treatment 0 5 10 15 20 25 Female body weight (g) a b 0 5 10 15 20 25 30 35 40 0 50 100 150 200 250 Age in days Male body weight (g) L3/L3 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 No treatment a b a 0 50 100 150 Age in days Age in days 200 250 L3/L3 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 No treatment 0 5 10 15 20 25 Female body weight (g) b b Figure 1  Evolution of neuron-specific enolase (NSE)-cre mouse weight. The body weight of the different groups of mice was followed until their sacrifice. In a, the male mice: L3/L3 (n = 26), NSE-cre mice treated with the AAV9-hFXN at 6 × 1011 v.p. (named AAV9-hFXN; n = 12), at 3 × 1011 v.p. (named d1/2; n = 0), at 6 × 1010 v.p. (named d1/10; n = 3), at 3 × 1010 v.p. (named d1/20; n = 2), at 1.2 × 1010 v.p. (named d1/50; n = 5), at 6 × 109 v.p. (named d1/100; n = 3) and the untreated mice (named no treatment; n = 33). In b, the female mice: L3/L3 (n = 20), NSE-cre mice treated with the AAV9-hFXN at 6 × 1011 v.p. (n = 17), at 3 × 1011 v.p. An AAV9 coding for frataxin C Gérard et al. 2 have a complete KO of the frataxin gene in the heart and a partial KO in the other organs investigated. have a complete KO of the frataxin gene in the heart and a partial KO in the other organs investigated. the liver, the heart, the kidneys, and the brain. For the MCK-cre mice, a delta allele band was observed only in the muscle and in the heart corresponding with the specificity of the MCK promoter (Supplementary Figure S1b on the left). Sometimes, a very light delta band (L-) appeared in the brain of some animals. For the NSE- cre mice, a delta band was observed in all the investigated tissues (the brain, the liver, the heart, the skeletal muscles, and the kidney) (Supplementary Figure S1b on the right). PART 1: study on the NSE-cre mice PART 1: study on the NSE-cre mice PART 1: study on the NSE-cre mice Behavior of the experimental mice without the AAV9-hFXN treatment. The NSE-cre were initially normally active but had signs of kyphosis and they walked on the tip of their toes (score 1, Table 1). After weaning, they showed a rapid degeneration of their physical condition. They progressively became more curved, their fur appeared ruffled (bent back, bristly hairs) and finally their general activity decreased. At the end of their life, they lost progressively some body weight and had difficulties to move, to walk, to breathe and to feed themselves (score 3 and 4, Table 1). They had to be sacrificed due to ethical concerns around 35 ± 18 days (mean ± SEM) (Figure 1). The expression of the frataxin gene was also investigated by RT-PCR in several tissues. The upper 332 bp band corresponded to the unfloxed frataxin mouse mRNA (Supplementary Figure S1c, left side). A second band was observed under 332 bp. As indicated by sequenc- ing this lower band (designated as floxed band) corresponded to the mouse frataxin mRNA deleted of exon 4. For the MCK-cre mice, the unfloxed frataxin band was observed in liver, kidney, and brain and the floxed band was observed only in muscles and heart.l In the NSE-cre mice, the floxing of the conditional frataxin gene was different (Supplementary Figure S1c right side). For all these mice, we observed only the floxed mRNA in the heart. RESULTSi Confirmation of the frataxin gene knockout in the experimental mice PCR amplifications of the genomic DNA of various tissues were made to verify the KO of the frataxin gene (Supplementary Figure S1). The delta allele (L-) resulted in a 263 bp band due to exon 4 exci- sion. Different organs were analyzed: the muscle (Tibialis anterior), An AAV9 coding for frataxin C Gérard et al. An AAV9 coding for frataxin C Gérard et al. (n = 3), at 6 × 1010 v.p. (n = 2), at 3 × 1010 v.p. (n = 3), at 1.2 × 1010 v.p. (n = 3), at 6 × 109 v.p. (n = 4) and the untreated mice (n = 33). The untreated NSE-cre had the lowest body weight. The growth curve of the NSE-cre mice was clearly improved by the AAV9-hFXN treatment for both sex groups. Molecular Therapy — Methods & Clinical Development (2014) 14044 © 2014 The American Society of Gene & Cell Therapy An AAV9 coding for frataxin C Gérard et al. 3 intensity remained strong with the different quantities of virus. The human frataxin was not observed in the brain for the three lower doses of virus, probably because the limit of detection was reached. intensity remained strong with the different quantities of virus. The human frataxin was not observed in the brain for the three lower doses of virus, probably because the limit of detection was reached. Detection of human frataxin after the AAV9-hFXN treatment. An AAV9 coding for the human frataxin (AAV9-hFXN) was injected IP in NSE-cre mice between 5 and 9 days of age. Their organs were collected at the time of the sacrifice. A PCR for the human frataxin was made on genomic DNA to detect the presence of the human frataxin transgene. This transgene was detected in all the investigated tissues (i.e., brain, heart, muscle, kidney, and liver) for 6 × 1011 v.p. injected (Figure 2a on the left). Dilutions 1/10 and 1/20 were also tested in the same conditions. The human frataxin band was observed in muscle, liver, and heart for these dilutions. The intensity of the band decreased with the dilutions, but the strongest band was always detected in the heart. RT-PCR also produced similar results (Figure 2a on the right). For an injection of 6 × 1011 v.p., human frataxin expression was observed in all tissues tested, with the strongest band in the heart and the intensity of the bands were decreasing with the dilutions of the virus. Effects of AAV9-hFXN treatment on mouse survival. A score from 0 to 4 was created to estimate the NSE-cre health (0 corresponding to no symptoms and 4 a state of health requiring immediate sacrifice; cf Supplementary Information). An AAV9 coding for frataxin C Gérard et al. (b) Finally, an ELISA test (Dipstick) was made to detect the human FXN protein in skeletal muscle (M), liver (L), heart (H), kidney (K), and brain (B). The human frataxin protein was estimated in these tissues in NSE-cre mice treated with AAV9-hFXN at 6 × 1011 v.p. (n = 9), at 3 × 1011 v.p. (n = 4), at 6 × 1010 v.p. (n = 3), at 3 × 1010 v.p. (n = 3), at 1.2 × 1010 v.p. (n = 3), at 6 × 109 v.p. (n = 3). The presence of human frataxin was strong with the highest dose of virus and decreased in the tissues with the dilutions except for the heart where the frataxin was still strong at the lowest viral dose. 0 1 2 3 4 5 6 7 8 9 10 M L H K B Dipstick semi quantification AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 hFXN Ctrl hFXN (407 pb) cDNA AAV-hFXN d/10 d1/20 hFXN (407 pb) gDNA M L H K B M L H K B a b hFXN (407 pb) cDNA AAV-hFXN d/10 d1/20 hFXN (407 pb) gDNA M L H K B M L H K B a a b 0 1 2 3 4 5 6 7 8 9 10 M L H K B Dipstick semi quantification AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 hFXN Ctrl b Figure 2  Detection of the hFXN transgene in various tissues of neuron-specific enolase (NSE)-cre. (a) on the left: The human frataxin (hFXN) transgene was detected by polymerase chain reaction (PCR) in the DNA of muscles (M), L (liver), heart (H), kidney (K), and brain (B) of mice injected with AAV-hFXN at 6 × 1011 v.p. (named AAV-hFXN) and in 6 × 1010 v.p. (named d1/10) and in 3 × 1010 v.p. (named d1/20). a, on the right: The expression of the human frataxin transgene (hFXN) was then detected by RT-PCR in all these tissues. (b) Finally, an ELISA test (Dipstick) was made to detect the human FXN protein in skeletal muscle (M), liver (L), heart (H), kidney (K), and brain (B). The human frataxin protein was estimated in these tissues in NSE-cre mice treated with AAV9-hFXN at 6 × 1011 v.p. (n = 9), at 3 × 1011 v.p. (n = 4), at 6 × 1010 v.p. (n = 3), at 3 × 1010 v.p. An AAV9 coding for frataxin C Gérard et al. The NSE-cre mice were evaluated every day after the weaning (21 days) because of the great variability of the progression of the disease and mortality. When the mice were treated with the AAV9-hFXN, the score was around 1.5 at 21 days, while the average score was 2.0 for the untreated NSE-cre. However, the score of the treated NSE-cre mice decreased (i.e., they were less sick) over the following 3 days while the score of the untreated mice increased. The scores were significantly different between the two groups between 21 and 40 days. The time between the injection and the first score of 0 (i.e., no symptom) was also estimated. In average, 20 ± 5.8 days after the viral injection for 6 × 1011 v.p. and 15.7 ± 2.6 days for 6 × 109 v.p., all the symptoms of the disease had disappeared (Figure 3a). Some mice reached a 0 score but were later scored at 0.5 or 1. For the estimation of the time where no symptoms were detected, we considered the first time the mouse score reached 0. However, these NSE mice have later developed Finally, the presence of human frataxin protein was investigated using a specific dipstick test. No human frataxin was detected in L3/L3 mice and in model mice that were injected with saline rather than with the AAV9-hFXN (data not shown). However, the hFXN was detected in all tissues from both mouse models injected with 6 × 1011 v.p of AAV9-hFXN (Figure 2b). With the dilution, the intensity of the band diminished in all organs except for the heart where the Molecular Therapy — Methods & Clinical Development (2014) 14044 © 2014 The American Society of Gene & Cell Therapy Figure 2  Detection of the hFXN transgene in various tissues of neuron-specific enolase (NSE)-cre. (a) on the left: The human frataxin (hFXN) transgene was detected by polymerase chain reaction (PCR) in the DNA of muscles (M), L (liver), heart (H), kidney (K), and brain (B) of mice injected with AAV-hFXN at 6 × 1011 v.p. (named AAV-hFXN) and in 6 × 1010 v.p. (named d1/10) and in 3 × 1010 v.p. (named d1/20). a, on the right: The expression of the human frataxin transgene (hFXN) was then detected by RT-PCR in all these tissues. An AAV9 coding for frataxin C Gérard et al. 0.0 0.5 1.0 1.5 2.0 2.5 3.0 L3/L3 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 No treatment % Heart to body weight a b 0.00 0.05 0.10 0.15 0.20 L3/L3 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 No treatment Heart weightening † † † † † † † * * * a b Survival depending on AAV doses 0 5 10 15 20 25 30 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 Days after injection to be asymptomatic 0.0 0.5 1.0 1.5 2.0 2.5 3.0 L3/L3 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 No treatment % Heart to body weight a b 0.00 0.05 0.10 0.15 0.20 L3/L3 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 No treatment Heart weightening † † † † † † † * * * 3 0 a b 0.00 0.05 0.10 0.15 0.20 L3/L3 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 No treatment Heart weightening * * * a 0.0 0.5 1.0 1.5 2.0 2.5 3.0 L3/L3 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 No treatment % Heart to body weight † † † † † † † b b 0 40 80 120 160 200 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 No treatment Age in days † † † † † † Figure 4  AAV-hFXN treatment reduced heart hypertrophy in neuron- specific enolase (NSE)-cre mice. The weight of the mouse heart treated or not with the AAV9-hFXN was measured (a) and expressed at sacrifice as a percentage of the whole body weight (b). The groups were composed of L3/L3 (n = 20), NSE-cre treated with AAV9-hFXN at 6 × 1011 v.p. (named AAV9-hFXN; n = 11), at 3 × 1011 v.p. (named d1/2; n = 5), at 6 × 1010 v.p. (named d1/10; n = 4), at 3 × 1010 v.p. (named d1/20; n = 5), at 1.2 × 1010 v.p. (named d1/50; n = 8), at 6 × 109 v.p. (named d1/100; n = 6) and untreated mice (n = 27). The weight of the heart was significantly different from the control L3/L3 and from the untreated mice for the three lowest quantity of virus (*P < 0.05; d1/20, d1/50, and d1/100) (a). The normalized weight was similar to that of L3/L3 for all the treated mice and significantly different (†P ≤ 0.0001) from that of the nontreated NSE-cre mice (b). Figure 3  Improved life survival of the neuron-specific enolase (NSE)-cre mice treated with AAV9-frataxin. An AAV9 coding for frataxin C Gérard et al. (a) A score was created to evaluate daily the health of the NSE-cre mice. The score goes from 0, which corresponds to a normal phenotype, to 4, where the signs of discomfort (loss of weight, difficulties to walk or to feed) led to the sacrifice of the mice. The score started after weaning, at 21 days. The delay between the injection and a score of zero (no symptoms) was determined for all doses of AAV9- hFXN at 6 × 1011 v.p. (named AAV9-hFXN; n = 14), at 3 × 1011 v.p. (named d1/2; n = 7), at 6 × 1010 v.p. (named d1/10; n = 5), at 3 × 1010 v.p. (named d1/20; n = 5), at 1.2 × 1010 v.p. (named d1/50; n = 8), at 6 × 109 v.p. (named d1/100; n = 6). (b) The survival was also estimated for all these groups. The injection of AAV9-hFXN clearly improved the general health of the NSE-cre mice for all viral doses (†P ≤ 0.0001): AAV9-hFXN at 6 × 1011 v.p. (n = 18), at 3 × 1011 v.p. (n = 5), at 6 × 1010 v.p. (n = 4), at 3 × 1010 v.p. (n = 5), at 1.2 × 1010 v.p. (n = 8), at 6 × 109 v.p. (n = 6) when compared to the untreated mice (n = 58). body weight (Figure 4b). This percentage was 0.57 ± 0.11 for L3/ L3 mice. The effect of the treatment was strong for all the NSE-cre treated mice, the percentage passing from 1.91 ± 0.61 (not treated) to 0.81 ± 0.23 with the AAV9-hFXN treatment 6 × 1011 v.p. All the treated mice were significantly different from the nontreated mice and not significantly different from the L3/L3 mice. nervous system symptoms, their score rapidly increased and they had to be sacrificed for ethical concerns. The survival of the mice was also evaluated after the AAV9-hFXN injection. It is important to note that some mice were sacrificed voluntary to investigate cardiac parameters while other had to be sacrificed for ethical concerns. For treated NSE-cre mice injected with 6 × 1011 v.p., 6 mice from the 18 mice in that group were vol- untary sacrificed at 96 and 122 days. An AAV9 coding for frataxin C Gérard et al. (named d1/2; n = 7), at 6 × 1010 v.p. (named d1/10; n = 5), at 3 × 1010 v.p. (named d1/20; n = 5), at 1.2 × 1010 v.p. (named d1/50; n = 8), at 6 × 109 v.p. (named d1/100; n = 6). (b) The survival was also estimated for all these groups. The injection of AAV9-hFXN clearly improved the general health of the NSE-cre mice for all viral doses (†P ≤ 0.0001): AAV9-hFXN at 6 × 1011 v.p. (n = 18), at 3 × 1011 v.p. (n = 5), at 6 × 1010 v.p. (n = 4), at 3 × 1010 v.p. (n = 5), at 1.2 × 1010 v.p. (n = 8), at 6 × 109 v.p. (n = 6) when compared to the untreated mice (n = 58). a b Survival depending on AAV doses 0 40 80 120 160 200 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 No treatment Age in days † † † † † † 0 5 10 15 20 25 30 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 Days after injection to be asymptomatic 4 Figure 4  AAV-hFXN treatment reduced heart hypertrophy in neuron- specific enolase (NSE)-cre mice. The weight of the mouse heart treated or not with the AAV9-hFXN was measured (a) and expressed at sacrifice as a percentage of the whole body weight (b). The groups were composed of L3/L3 (n = 20), NSE-cre treated with AAV9-hFXN at 6 × 1011 v.p. (named AAV9-hFXN; n = 11), at 3 × 1011 v.p. (named d1/2; n = 5), at 6 × 1010 v.p. (named d1/10; n = 4), at 3 × 1010 v.p. (named d1/20; n = 5), at 1.2 × 1010 v.p. (named d1/50; n = 8), at 6 × 109 v.p. (named d1/100; n = 6) and untreated mice (n = 27). The weight of the heart was significantly different from the control L3/L3 and from the untreated mice for the three lowest quantity of virus (*P < 0.05; d1/20, d1/50, and d1/100) (a). The normalized weight was similar to that of L3/L3 for all the treated mice and significantly different (†P ≤ 0.0001) from that of the nontreated NSE-cre mice (b). An AAV9 coding for frataxin C Gérard et al. (n = 6) when compared to the untreated mice (n 58) a b Survival depending on AAV doses 0 40 80 120 160 200 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 No treatment Age in days † † † † † † 0 5 10 15 20 25 30 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 Days after injection to be asymptomatic Figure 4  AAV-hFXN treatment reduced heart hypertrophy in neuron- specific enolase (NSE)-cre mice. The weight of the mouse heart treated or not with the AAV9-hFXN was measured (a) and expressed at sacrifice as a percentage of the whole body weight (b). The groups were composed of L3/L3 (n = 20), NSE-cre treated with AAV9-hFXN at 6 × 1011 v.p. (named AAV9-hFXN; n = 11), at 3 × 1011 v.p. (named d1/2; n = 5), at 6 × 1010 v.p. (named d1/10; n = 4), at 3 × 1010 v.p. (named d1/20; n = 5), at 1.2 × 1010 v.p. (named d1/50; n = 8), at 6 × 109 v.p. (named d1/100; n = 6) and untreated mice (n = 27). The weight of the heart was significantly different from the control L3/L3 and from the untreated mice for the three lowest quantity of virus (*P < 0.05; d1/20, d1/50, and d1/100) (a). The normalized weight was similar to that of L3/L3 for all the treated mice and significantly different (†P ≤ 0.0001) from that of the nontreated NSE-cre mice (b). 0.0 0.5 1.0 1.5 2.0 2.5 3.0 L3/L3 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 No treatment % Heart to body weight a b 0.00 0.05 0.10 0.15 0.20 L3/L3 AAV9-hFXN d1/2 d1/10 d1/20 d1/50 d1/100 No treatment Heart weightening † † † † † † † * * * C Gérard et al. Figure 3  Improved life survival of the neuron-specific enolase (NSE)-cre mice treated with AAV9-frataxin. (a) A score was created to evaluate daily the health of the NSE-cre mice. The score goes from 0, which corresponds to a normal phenotype, to 4, where the signs of discomfort (loss of weight, difficulties to walk or to feed) led to the sacrifice of the mice. The score started after weaning, at 21 days. The delay between the injection and a score of zero (no symptoms) was determined for all doses of AAV9- hFXN at 6 × 1011 v.p. (named AAV9-hFXN; n = 14), at 3 × 1011 v.p. Molecular Therapy — Methods & Clinical Development (2014) 14044 An AAV9 coding for frataxin C Gérard et al. (n = 3), at 1.2 × 1010 v.p. (n = 3), at 6 × 109 v.p. (n = 3). The presence of human frataxin was strong with the highest dose of virus and decreased in the tissues with the dilutions except for the heart where the frataxin was still strong at the lowest viral dose. Molecular Therapy — Methods & Clinical Development (2014) 14044 © 2014 The American Society of Gene & Cell Therapy An AAV9 coding for frataxin C Gérard et al. An AAV9 coding for frataxin C Gérard et al. body weight (Figure 4b). This percentage was 0.57 ± 0.11 for L3/ L3 mice. The effect of the treatment was strong for all the NSE-cre treated mice the percentage passing from 1 91±0 61 (not treated) Figure 3  Improved life survival of the neuron-specific enolase (NSE)-cre mice treated with AAV9-frataxin. (a) A score was created to evaluate daily the health of the NSE-cre mice. The score goes from 0, which corresponds to a normal phenotype, to 4, where the signs of discomfort (loss of weight, difficulties to walk or to feed) led to the sacrifice of the mice. The score started after weaning, at 21 days. The delay between the injection and a score of zero (no symptoms) was determined for all doses of AAV9- hFXN at 6 × 1011 v.p. (named AAV9-hFXN; n = 14), at 3 × 1011 v.p. (named d1/2; n = 7), at 6 × 1010 v.p. (named d1/10; n = 5), at 3 × 1010 v.p. (named d1/20; n = 5), at 1.2 × 1010 v.p. (named d1/50; n = 8), at 6 × 109 v.p. (named d1/100; n = 6). (b) The survival was also estimated for all these groups. The injection of AAV9-hFXN clearly improved the general health of the NSE-cre mice for all viral doses (†P ≤ 0.0001): AAV9-hFXN at 6 × 1011 v.p. (n = 18), at 3 × 1011 v.p. (n = 5), at 6 × 1010 v.p. (n = 4), at 3 × 1010 v.p. (n = 5), at 1.2 × 1010 v.p. (n = 8), at 6 × 109 v.p. An AAV9 coding for frataxin C Gérard et al. of AAV9-hFXN PART 3: behavior study and echocardiography on NSE-cre and MCK-cre injected with 6 × 1011 v.p. of AAV9-hFXN PART 3: behavior study and echocardiography on NSE-cre and MCK-cre injected with 6 × 1011 v.p. of AAV9-hFXN Behavior and echocardiography tests were also made on untreated mice and mice treated with the highest dose of 6 × 1011 v.p. of AAV9- hFXN because human frataxin was detected in the mouse brain only at that dose. 0 5 10 15 20 25 30 35 Female body weight (g) 0 50 100 150 200 250 Age in days Age in days L3/L3 AAV9-hFXN d1/100 No treatment b b Effects of AAV9-hFXN treatment on behavior. The following behavior parameters were analyzed: distance traveled, immobile time, rear duration, and episode immobile (Figure 8a–d). The behavior of the MCK-cre mice was not different from that of L3/L3 mice (Figure 8). On the contrary, the NSE-cre mice were clearly different from the L3/ L3 for all these parameters. These mice were less active (Figure 8a,c). However, after the injection with the AAV9-hFXN, the NSE-cre mice (NSE-cre-AAV) got back to normal activities (Figure 8a–d). The NSE- cre treated mice appeared quite normal and were clearly different from the NSE mutants that did not receive the AAV9-FXN treatment. Other more specific tests were also made on these mice but no significant effects were observed between the treated and untreated mice (data not shown). Figure 5  Evolution of muscle creatine kinase (MCK)-cre mouse weight. In a, the growth curves of the male mice: L3/L3 mice (n = 26), MCK-cre untreated (no treatment; n = 67) and MCK-cre mice treated with the AAV9-hFXN at 6 × 1011 v.p. (AAV9-hFXN; n = 8) as well as at 6 × 109 v.p. (d1/100; n = 2). In b, the growth curves of the female mice: L3/L3 mice (n = 20), MCK-cre untreated (n = 47) and MCK-cre mice treated with the AAV9-hFXN at 6 × 1011 v.p. (n = 7) as well as at 6 × 109 v.p. (n = 3). There was no difference between the L3/L3 and the different MCK-cre mice groups. Effects of AAV9-hFXN treatment on cardiac function. Echocardiography examination was also made on these mice (Figure  9). An AAV9 coding for frataxin C Gérard et al. Despite the voluntary sacrifice of some mice for the two highest quantities of virus injected, the average survival of the NSE-cre mice was significantly increased from 35 ± 18 days (untreated) to 103 ± 32 and 135 ± 40 with the injection of 6 × 1011 v.p. and 3 × 1011 v.p. of AAV9-hFXN respectively (Figure 3b). All the quantities of virus led to a significant increase of the survival compared to the untreated mice. The survival was doubled with v.p. dilutions from 1/100 to 1/20. The 6 × 1011 v.p dose of virus increased the survival by roughly threefolds. PART 2: study on the MCK-cre micei PART 2: study on the MCK-cre micei The results obtained in the first part with the NSE-cre mice showed a strong presence of human frataxin protein in the heart of the treated mice with a single injection of 6 × 109 v.p. For the study of the MCK-cre mice, we thus decided to focus only on the highest and lowest doses of virus because the major health problem of the MCK- cre is due to the deletion of frataxin in heart. Effects of AAV9-FXN treatment on body weight. The MCK-cre mice followed the same body weight growth curve as the L3/L3 mice. The growth curve of these MCK-cre mice was not modified by the administration of AAV9-hFXN at 6 × 1011 v.p. and 6 × 109 v.p. (d1/100) (Figure 5a,b). Effects of AAV9-hFXN treatment on cardiac function. At the time of sacrifice, the weight of the heart of the mice treated or not with the different doses of AAV9-hFXN was measured (Figure 4a). There was no significant heart weight difference between the L3/L3, the NSE-cre, and the treated NSE-cre mice with 6 × 1011 v.p. to 6 × 1010 v.p. (d1/10). However, because of the difference in body weight, we also expressed the heart weight as a percentage of the total Detection of human frataxin after the AAV9-hFXN treatment. The presence of the virus was detected by PCR in genomic DNA (Figure  6a on the left) and by RT-PCR (Figure 6a on the right) following a treatment with 6 × 1011 v.p. As for NSE-cre mice, the strongest band was observed for the heart tissue. An AAV9 coding for frataxin C Gérard et al. The injection of AAV9-hFXN ameliorated significantly the stroke volume (a), the cardiac output (b) and the systolic (c) and diastolic (d) diameters of the MCK-cre mice (Figure 9, on the left). The relative wall thickness, the fractional shortening and the fractional ejection were also ameliorated in the MCK-cre treated mice (Supplementary Figures S2 and S3). The injection of AAV9-hFXN had no effect on the stroke volume and the cardiac output of NSE- cre mice. However, the treatment restored the diastolic and systolic diameters of the heart of NSE-cre mice (Figure 9c,d, on the right). human frataxin protein was also detected with the dipstick method (Figure 6b). Following the injection of 6 × 1011 v.p. of AAV9-hFXN, the presence of frataxin was observed in all tissues tested, the stronger bands being in muscle, liver, and heart. Following the administration of 6 × 109 v.p., the human frataxin protein was still observed in all the organs except in the brain where no protein was detected. However, the frataxin concentrations were lower than following the administration of the higher quantity of virus. An AAV9 coding for frataxin C Gérard et al. The presence of Molecular Therapy — Methods & Clinical Development (2014) 14044 © 2014 The American Society of Gene & Cell Therapy An AAV9 coding for frataxin C Gérard et al. 5 Figure 5  Evolution of muscle creatine kinase (MCK)-cre mouse weight. In a, the growth curves of the male mice: L3/L3 mice (n = 26), MCK-cre untreated (no treatment; n = 67) and MCK-cre mice treated with the AAV9-hFXN at 6 × 1011 v.p. (AAV9-hFXN; n = 8) as well as at 6 × 109 v.p. (d1/100; n = 2). In b, the growth curves of the female mice: L3/L3 mice (n = 20), MCK-cre untreated (n = 47) and MCK-cre mice treated with the AAV9-hFXN at 6 × 1011 v.p. (n = 7) as well as at 6 × 109 v.p. (n = 3). There was no difference between the L3/L3 and the different MCK-cre mice groups. 0 5 10 15 20 25 30 35 Male body weight (g) L3/L3 AAV9-hFXN d1/100 No treatment 0 5 10 15 20 25 30 35 Female body weight (g) 0 50 100 150 200 250 Age in days 0 50 100 150 200 250 Age in days L3/L3 AAV9-hFXN d1/100 No treatment a b doses of AAV9-hFXN reduced heart weight. The heart weight was expressed as a percentage of the total body weight. This percentage was higher for the untreated mice than for the control L3/L3 mice (Figure 7c). It was however significantly decreased with both doses of virus. doses of AAV9-hFXN reduced heart weight. The heart weight was expressed as a percentage of the total body weight. This percentage was higher for the untreated mice than for the control L3/L3 mice (Figure 7c). It was however significantly decreased with both doses of virus. 0 5 10 15 20 25 30 35 Male body weight (g) L3/L3 AAV9-hFXN d1/100 No treatment 0 5 10 15 20 25 30 35 Female body weight (g) 0 50 100 150 200 250 Age in days 0 50 100 150 200 250 Age in days L3/L3 AAV9-hFXN d1/100 No treatment a b 0 5 10 15 20 25 30 35 Male body weight (g) L3/L3 AAV9-hFXN d1/100 No treatment 0 50 100 150 200 250 Age in days a b a PART 3: behavior study and echocardiography on NSE-cre and MCK-cre injected with 6 × 1011 v.p. Molecular Therapy — Methods & Clinical Development (2014) 14044 © 2014 The American Society of Gene & Cell Therapy DISCUSSION FRDA i d For the MCK-cre mice, among the 14 mice treated with 6 × 1011 v.p. AAV9-hFXN, only 4 died between 80 and 116 days, 10 were sacrificed for cardiac analysis (4 mice at 203 days, 4 mice at 251 days, and 2 mice at 253 days). Perdomini et al.14 also increased sig- nificantly the survival of the MCK-cre mice through an intravenous injection of 5.4 × 1013 vg/kg of AAVrh10 (this corresponds to about 5 × 1011 v.p. per young mouse) coding for for the human frataxin. The viral dose injected per mouse or rat was around 1011 g.c. ou v.p. per animal in many publications.14,16,17 Bish et al.17 also tested various dilutions of the AAV vector (2.5 × 1011, 2.5 × 1010, and 2.5 × 109 viral particules. They found that the expression in heart was diminished with the dilution contrarily to our results with the NSE-cre where the frataxin protein stayed at high quantity for all the dilution of virus tested in heart (Figure 2b). Our study clearly showed that with a quantity of 6 × 1011 v.p., the frataxin protein was detected in the brain of mice but with only 6 × 109 v.p., the heart function was still improved as well as the survival of the mice. This suggests that the quantity of virus injected could be adjusted to the targeting organ, with a lower quantity for the heart and a higher quantity to reach the brain. The MCK-cre mice were used for this study because they have more specific cardiac symptoms of FRDA compared to the NSE-cre mice, which lack of frataxin in almost every organ. The NSE-cre mice were however useful because of its severe early onset symptoms, which permitted to detect rapidly clear differences following an effective treatment with the AAV9-hFXN. This absence of frataxin expression starts during the embryo- logical development of the conditional KO mice bred with a mouse expressing the Cre gene. Our results confirmed the previous report that the NSE-cre mice have a lower than normal weight and develop progressive neurological symptoms and hunched stance.13 The age of death of the untreated MCK-cre mice was similar in all research groups (76 ± 10 days)13 and 65 ± 10 days14 versus 71 ± 20 days for us. DISCUSSION FRDA i d Effects of AAV9-hFXN treatment on survival and cardiac function. The MCK-cre mice had no behavioral difference with the L3/L3 mice when they were young. Indeed, their behavior and body weight gain were similar to those of L3/L3 mice. However, the mouse health regressed suddenly after 50 days. They had periods of difficulty to breathe, to walk and within 24–48 hours they had to be sacrificed due to ethical concerns. The age of sacrifice varied between 71 ± 20 days (mean ± SEM) (Figure 7a). 10 MCK-Cre mice treated with 6 × 1011 v.p. of AAV9-hFXN were voluntary sacrificed at 203 or 251 days. For MCK-cre mice, the survival went from 71 ± 20 days without treatment to 194 ± 67 days following a 6 × 1011 v.p. AAV treatment (Figure 7a). Both doses of AAV9-hFXN (i.e., 6 × 1011 v.p. and 6 × 109 v.p.) significantly improved the survival of these mice. The weight of the heart was also measured as well as the body weight. The heart weight of MCK-cre was significantly higher than that of control L3/ L3 mouse heart, due to a clear cardiac hypertrophy (Figure 7b). Both FRDA is due to a reduced expression of frataxin following an expan- sion of a trinucleotide (GAA) repeat in intron 1.1 Frataxin is a mito- chondrial protein and its reduction leads in turn to a mitochondrial miss-function (for a review of the pathological mechanism, see Pandolfo et al.3). There is increased oxidative stress and accumula- tion of iron in the mitochondria. These changes, particularly the increased oxidative stress, lead to cell death, including neurons and cardiomyocytes. This progressive cell death results in several neuro- logical and cardiac symptoms. The transgenic NSE-cre and MCK-cre mouse models were devel- oped by Dr Puccio.13 The MCK-cre model of FRDA has floxed frataxin gene in the heart and the muscles in which the Cre recombinase is expressed. We have detected no expression of mouse frataxin in these tissues. However, for the NSE-cre mice, there was a complete knockout of the mouse frataxin gene only in the heart and a partial KO in the muscle, liver, kidney, and brain. Our results in the MCK- cre and the NSE-cre confirmed the previously published results.13 © 2014 The American Society of Gene & Cell Therapy An AAV9 coding for frataxin C Gérard et al. C Gérard et al. DISCUSSION FRDA i d Figure 6  Detection of the hFXN transgene in various tissues of muscle creatine kinase (MCK)-cre. (a) The human frataxin (hFXN) transgene was detected by polymerase chain reaction (PCR) not only in the DNA of muscles (M), L (liver), heart (H), kidney (K), and brain (B) of the mice injected with AAV9-hFXN at 6 × 1011 v.p. (on the left) but also the expression of human frataxin (on the right). (b) Finally, an ELISA test (Dipstick) was made to detect the human FXN protein in the tissues of MCK-cre mice treated with AAV9-hFXN at 6 × 1011 v.p. (named AAV9-hFXN; n = 8) and at 6 × 109 v.p. (named d1/100; n = 4). The presence of human frataxin was strongest with the highest viral doses and decreased in all tissues with the dilution. a b hFXN Ctrl 0 1 2 3 4 5 6 7 8 9 10 M L H K B Dipstick semi-semi quantification AAV9-hFXN d1/100 AAV-hFXN hFXN (407 pb) gDNA hFXN (407 pb) cDNA M L H K B M L H K B 6 a b hFXN Ctrl 0 1 2 3 4 5 6 7 8 9 10 M L H K B Dipstick semi-semi quantification AAV9-hFXN d1/100 AAV-hFXN hFXN (407 pb) gDNA hFXN (407 pb) cDNA M L H K B M L H K B b M Figure 6  Detection of the hFXN transgene in various tissues of muscle creatine kinase (MCK)-cre. (a) The human frataxin (hFXN) transgene was detected by polymerase chain reaction (PCR) not only in the DNA of muscles (M), L (liver), heart (H), kidney (K), and brain (B) of the mice injected with AAV9-hFXN at 6 × 1011 v.p. (on the left) but also the expression of human frataxin (on the right). (b) Finally, an ELISA test (Dipstick) was made to detect the human FXN protein in the tissues of MCK-cre mice treated with AAV9-hFXN at 6 × 1011 v.p. (named AAV9-hFXN; n = 8) and at 6 × 109 v.p. (named d1/100; n = 4). The presence of human frataxin was strongest with the highest viral doses and decreased in all tissues with the dilution. The lower AAV dose (6 × 109 v.p.) increased significantly the survival of NSE-cre mice. The longer survival was obtained for the three highest viral doses even if some mice were voluntarily sacrificed for experiments. Molecular Therapy — Methods & Clinical Development (2014) 14044 © 2014 The American Society of Gene & Cell Therapy DISCUSSION FRDA i d The weight of the mouse heart treated or not with the AAV9-hFXN was measured at the time of sacrifice (b) and expressed as a percentage of the whole body weight (c). The heart weight of the MCK-cre was higher than that of the L3/L3; this hypertrophy was prevented by the AAV9-hFXN treatment. The normalized heart weights of the untreated MCK-cre mice were higher than that of the wt mice. The treatment with AAV9-hFXN ameliorated the percentage compared to the control and the lowest quantity led to the same value than the control L3/L3. The *** indicate significant difference at P less than 0.0001. P ≤ 0.05*; P ≤ 0.001**; P ≤ 0.0001***. chamber dimension and a reduction in left ventricular fractional shortening,19 which were also observed in our study. In our stud- ies, the average age of the untreated MCK-cre mice tested for echo- cardiography was 70 days (59–71 days for the 11 mice). However, one mouse was evaluated at 131 days corresponding to a late stage since the untreated mice lived an average of 71 days. volume ejected by the left ventricle during the systole while the car- diac output corresponds to this volume multiplied by the heart fre- quency to obtain the ejected volume per minute. The stroke volume of the MCK-cre mice is about only haft of that of normal mice. Thus the MCK-cre mice have cardiac insufficiency. The fractional shorten- ing, the stroke volume and the cardiac output were all significantly improved in the MCK-cre mice treated with AAV9-hFXN.f The percentage of fractional ejection was significantly reduced from 51% for the wt mice to 32% for the MCK-cre mice, a symp- tom similar to that of the FRDA patients. The AAV9-hFXN treatment permitted to increase the fractional ejection to 43% without com- pletely restoring the function (Supplementary Figure S3). The same observation was made for the stroke volume, which was reduced in FRDA patient. The stroke volume of wt mice was 0.042 ml, this decreased to 0.02 ml in MCK-cre mice. The treatment of these mice when they were only 5–9 days old with AAV9-hFXN prevented the reduction of the stroke volume. Thus, these treated MCK-cre mice had an average stroke volume of 0.034 ml. The fractional heart shortening is reduced in the MCK-cre mice. This means that the left ventricle in diastole and in systole varies less during the cardiac cycle. DISCUSSION FRDA i d Thus, the average age of sacrifice of the treated mice was significantly igher than that of the untreated mice for both MCK-cre groups treated at the higher (n = 14) and the lower (n = 5) viral doses. The weight of the mouse eart treated or not with the AAV9-hFXN was measured at the time of sacrifice (b) and expressed as a percentage of the whole body weight (c). The eart weight of the MCK-cre was higher than that of the L3/L3; this hypertrophy was prevented by the AAV9-hFXN treatment. The normalized heart weights of the untreated MCK-cre mice were higher than that of the wt mice. The treatment with AAV9-hFXN ameliorated the percentage compared o the control and the lowest quantity led to the same value than the control L3/L3. The *** indicate significant difference at P less than 0.0001. P ≤ .05*; P ≤ 0.001**; P ≤ 0.0001***. 0 50 100 150 200 250 No treatment AAV9-hFXN d1/100 Age in days Survival depending on AAV doses a b c 0.00 0.05 0.10 0.15 0.20 0.25 L3/L3 AAV9-hFXN d1/100 No treatment Heart weightening L3/L3 AAV9-hFXN d1/100 No treatment 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 % Heart to body weight * *** ** *** ** * ** *** *** 0 50 100 150 200 250 No treatment AAV9-hFXN d1/100 Age in days Survival depending on AAV doses a *** *** Survival depending on AAV doses a b 0.00 0.05 0.10 0.15 0.20 0.25 L3/L3 AAV9-hFXN d1/100 No treatment Heart weightening ** * ** b c L3/L3 AAV9-hFXN d1/100 No treatment 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 % Heart to body weight * *** ** *** c Figure 7  Improved life survival of the muscle creatine kinase (MCK)-cre mice treated with AAV9-frataxin. (a) Without treatment, the MCK-cre had to be sacrificed at an average age of 71 ± 20 days (no treatment; n = 37). However, the MCK-cre injected intraperitoneally (i.p.) with 6 × 1011 v.p. or 6 × 109 v.p. of AAV9-hFXN were voluntary sacrificed after 180 days for further investigation. Thus, the average age of sacrifice of the treated mice was significantly higher than that of the untreated mice for both MCK-cre groups treated at the higher (n = 14) and the lower (n = 5) viral doses. DISCUSSION FRDA i d In the case of the NSE-cre mice, the age of death was a little higher in our results 35 ± 18 days than in those of Dr Puccio (24 ± 9 days)13 and Dr Payne groups (28 ± 2 days).15 The difference in mouse survival could be due to the difference in the mouse hous- ing (the accessibility to the food and after the weaning, a wild type female remained in the cage with the sick mice to help them to make a nest and to take care of themselves). Both mutants are thus very severe models of the disease and have a short life expectancy without treatment. Our results clearly demonstrated that the IP administration of an AAV9 vector cod- ing for human frataxin significantly increased up to two times the life expectancy of both NSE-cre and MCK-cre mice with high and low quantity of virus. Vyas et al.15 also increased by around 50% the survival of the NSE-cre mice by intrainjection of Tat-frataxin protein twice a week with a maximum of 88 days of survival. In our study, among the 18 NSE-cre mice treated with 6 × 1011 v.p. AAV9-hFXN, only one died at 46 days, the other ones lived more than 74 days and five were sacrificed for the cardiac analysis at 96 and 121 days. In Friedreich’s patient, a hypertrophic cardiomyopathy was observed due to a thickening of the ventricular walls.18 In general, the global systolic function is preserved but at the end of their life, the ejection fraction is reduced. The MCK-cre and NSE-cre model reproduce the cardiomyopathy as well as the biochemical features observed in FRDA patients.13–15 In the MCK model, after 6 weeks, this cardiomyopathy is characterized by an increased in left ventricular end-distolic chamber dimensions and left ventricular end-systolic An AAV9 coding for frataxin C Gérard et al. 7 gure 7  Improved life survival of the muscle creatine kinase (MCK)-cre mice treated with AAV9-frataxin. (a) Without treatment, the MCK-cre had to be acrificed at an average age of 71 ± 20 days (no treatment; n = 37). However, the MCK-cre injected intraperitoneally (i.p.) with 6 × 1011 v.p. or 6 × 109 v.p. f AAV9-hFXN were voluntary sacrificed after 180 days for further investigation. © 2014 The American Society of Gene & Cell Therapy Molecular Therapy — Methods & Clinical Development (2014) 14044 DISCUSSION FRDA i d The reason for this reduced variation is that the ventricle is contracting less during the systole. The stroke volume is the blood For the NSE-cre mice, less difference were observed compared to the wt mice. In our study, the stroke volume as well as the cardiac output was significantly lower for the NSE-cre mice while the ejec- tion fraction and the fractional shortening was similar between the wt and the NSE mice (Figure 8 and Supplementary Figures S2 and S3). The same conclusion was made by Vyas et al.15 study by com- paring wt and NSE-cre mice. They used Tat-frataxin protein to treat the disease, and even though the survival of the treated mice was increased, these cardiac parameters were not significantly amelio- rated, and this was also the case in our study for the stroke volume and the cardiac output. However, it should be noted that although the AAV9-hFXN was detected as well as the protein in the brain of our mice injected with 6 × 1011 v.p., the mice did develop nervous symptoms (abnormal leg An AAV9 coding for frataxin C Gérard et al. C Gérard et al. Figure 8  Cage activity. The activity was estimated for the different groups of mice (L3/L3, n = 11; muscle creatine kinase (MCK)-cre, n = 15; MCK-cre treated with 6 × 1011 v.p. of AAV9-hFXN, n = 7; neuron-specific enolase (NSE)-cre, n = 4 and NSE-cre treated with 6 × 1011 v.p. of AAV9-hFXN, n = 5) as the distance traveled in meters (a), the mean rear duration in seconds (b), the duration of immobility in seconds (c), and the number of immobile episodes (d). The injection of AAV9-hFXN significantly improved the distance traveled (a) and the mean rear duration (b) of the NSE-cre treated mice. The *** indicate significant difference at P less than 0.0001. P ≤ 0.05*; P ≤ 0.001**; P ≤ 0.0001***. DISCUSSION FRDA i d 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 Distance traveled (m) 0 0 20 40 60 80 100 120 Time immobile (s) 2 4 6 8 10 12 14 Episode immobile (s) 0 1 2 3 4 5 6 7 8 9 Mean rear duration (s) * * * * * * a b c d L3/L3 MCK-cre MCK-cre-AAV NSE-cre-AAV NSE-cre L3/L3 MCK-cre MCK-cre-AAV NSE-cre-AAV NSE-cre L3/L3 MCK-cre MCK-cre-AAV NSE-cre-AAV NSE-cre L3/L3 MCK-cre MCK-cre-AAV NSE-cre-AAV NSE-cre 8 0 20 40 60 80 100 120 Time immobile (s) * c L3/L3 MCK-cre MCK-cre-AAV NSE-cre-AAV NSE-cre 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 Distance traveled (m) * * a L3/L3 MCK-cre MCK-cre-AAV NSE-cre-AAV NSE-cre c a 0 1 2 3 4 5 6 7 8 9 Mean rear duration (s) * * b L3/L3 MCK-cre MCK-cre-AAV NSE-cre-AAV NSE-cre 0 2 4 6 8 10 12 14 Episode immobile (s) * d L3/L3 MCK-cre MCK-cre-AAV NSE-cre-AAV NSE-cre b d Figure 8  Cage activity. The activity was estimated for the different groups of mice (L3/L3, n = 11; muscle creatine kinase (MCK)-cre, n = 15; MCK-cre treated with 6 × 1011 v.p. of AAV9-hFXN, n = 7; neuron-specific enolase (NSE)-cre, n = 4 and NSE-cre treated with 6 × 1011 v.p. of AAV9-hFXN, n = 5) as the distance traveled in meters (a), the mean rear duration in seconds (b), the duration of immobility in seconds (c), and the number of immobile episodes (d). The injection of AAV9-hFXN significantly improved the distance traveled (a) and the mean rear duration (b) of the NSE-cre treated mice. The *** indicate significant difference at P less than 0.0001. P ≤ 0.05*; P ≤ 0.001**; P ≤ 0.0001***. movement when they were hold up by the tail (see Supplementary Video S1). These symptoms are potentially the consequence of insufficient expression of frataxin in the brain of these mice start- ing during early embryogenesis. It is reported that the NSE mice have spongiform degeneration as in brain cortex and the deletion of frataxin in other organs like the liver should explain the short lifetime.13,20 The mode of administration as well as the serotype of the AAV used are both very important for the diffusion and the expression in the organism. To treat specifically the heart, some experiments where made with a direct injection of AAV in the thoracic cham- ber or directly into the pericardia tissue. DISCUSSION FRDA i d Piras et al.16 showed that the AAV9 were detected in heart and in lung but the expression was only observed in the heart. Another article from Bish et al.17 compared different AAV serotypes 1–9 injected intrapericardially. They found that AAV9 led to the higher expression in heart. They also shown that even through following intrapericardiac injection, the presence of the virus was detected in all other tissues it was a strongly expressed only in the heart.f The recent article from Dr. Puccio’s group showed that the intra- venous injection of an AAVrh10-hFXN in 3 weeks old MCK mice also increased the survival and preserved of the heart’s activity. The virus was particularly present in the heart, the liver, and the dorsal root ganglia but the expression was lower in skeletal muscles.14 Piras et al.16 indicated that AAV9 can deliver a shRNA with good efficacy to the heart while Aschauer et al.21 indicated that it can infect neurons very effectively. Our genomic analysis indicated that the AAV9-hFXN injection resulted in strong presence of the human frataxin transgene in muscle, heart, and brain. The expression of human frataxin in the different organs parallels the intensity of bands in the genomic result. Nevertheless, the presence of human frataxin protein was also strong in liver in our mice. This strong expression of frataxin in the liver was also observed in a recent article from Puccio’s group14 by using a AAVrh10 to deliver the human frataxin to mice. Compared to this study, we demonstrated that an IP injection of an AAV9 led not only to a high detection of frataxin in heart, in liver (which was observed in Puccio’s group) but also in skeletal muscle. In view to all the results obtained and with the different modes of injection described previously, we conclude that a simple IP injec- tion is as effective as a venous or a direct cardiac injection to obtain a significant effect in the heart and in the brain, at least with the AAV9 serotype. Therefore, our results suggest that the administration of an AAV9 coding for human frataxin may be able to increase the expression of frataxin in the brain and the heart of FRDA patients. The increased expression of the frataxin may reduce or prevent the development of nervous system and cardiac symptoms. Molecular Therapy — Methods & Clinical Development (2014) 14044 © 2014 The American Society of Gene & Cell Therapy DISCUSSION FRDA i d The exposition to an AAV has been shown to induce an immune response.22–24 Thus, many humans have preformed antibodies to AAV and this has led to the failure of the early clinical trials conducted with AAV2.25 However, a recent clinical trial for hemophilia B using an An AAV9 coding for frataxin C Gérard et al. C Gérard et al. Figure 9  AAV9-frataxin treatment improved heart function of muscle creatine kinase (MCK)-cre mice. Stroke volume (a), cardiac output (b), systolic (c), and diastolic (d) diameters were evaluated by echocardiography under isoflurane anesthesia. All these parameters were improved in the MCK-cre that received 6 × 1011 v.p. of AAV9-hFXN compared to untreated MCK-cre mice. In neuron-specific enolase (NSE)-cre mice, only the systolic and diastolic diameters were enhanced. The *** indicate significant difference at P less than 0.0001. P ≤ 0.05*; P ≤ 0.001**; P ≤ 0.0001***. L3/L3 NSE-cre NSE-cre-AAV 0 5 10 15 20 Cardiac output (ml/min) L3/L3 MCK-cre MCK-cre-AAV 0 5 10 15 20 Cardiac output (ml/min) L3/L3 NSE-cre 0.00 0.01 0.02 0.03 0.04 0.05 Stroke volume (ml) L3/L3 MCK-cre MCK-cre-AAV 0.00 0.01 0.02 0.03 0. 04 0.05 Stroke volume (ml) L3/L3 NSE-cre NSE-cre-AAV 0.00 0.20 0.40 Systolic diameter (mm) L3/L3 MCK-cre MCK-cre-AAV 0.00 0.10 0.20 0.30 0.40 0.50 Systolic diameter (mm) L3/L3 NSE-cre NSE-cre-AAV 0.00 0.20 0.40 0.60 Diastolic diameter (mm) L3/L3 MCK-cre MCK-cre-AAV 0.00 0.20 0.40 0.60 Diastolic diameter (mm) *** * * ** *** * ** ** * *** * ** NSE-cre-AAV * ** ** ** a b c d 9 L3/L3 NSE-cre 0.00 0.01 0.02 0.03 0.04 0.05 Stroke volume (ml) ** NSE-cre-AAV * L3/L3 MCK-cre MCK-cre-AAV 0.00 0.01 0.02 0.03 0. 04 0.05 Stroke volume (ml) *** * ** a a L3/L3 MCK-cre MCK-cre-AAV 0 5 10 15 20 Cardiac output (ml/min) *** * ** b b L3/L3 NSE-cre NSE-cre-AAV 0 5 10 15 20 Cardiac output (ml/min) ** ** L3/L3 MCK-cre MCK-cre-AAV 0.00 0.10 0.20 0.30 0.40 0.50 Systolic diameter (mm) *** * * c c L3/L3 NSE-cre NSE-cre-AAV 0.00 0.20 0.40 Systolic diameter (mm) * L3/L3 MCK-cre MCK-cre-AAV 0.00 0.20 0.40 0.60 Diastolic diameter (mm) ** d d L3/L3 NSE-cre NSE-cre-AAV 0.00 0.20 0.40 0.60 Diastolic diameter (mm) ** Figure 9  AAV9-frataxin treatment improved heart function of muscle creatine kinase (MCK)-cre mice. Stroke volume (a), cardiac output (b), systolic (c), and diastolic (d) diameters were evaluated by echocardiography under isoflurane anesthesia. DISCUSSION FRDA i d All these parameters were improved in the MCK-cre that received 6 × 1011 v.p. of AAV9-hFXN compared to untreated MCK-cre mice. In neuron-specific enolase (NSE)-cre mice, only the systolic and diastolic diameters were enhanced. The *** indicate significant difference at P less than 0.0001. P ≤ 0.05*; P ≤ 0.001**; P ≤ 0.0001***. ACTGAAGCTTATCAAGCATCTTTTCCGGAATAG 3′. The forward primer also contained the Kozak sequence GCCACC before the start codon ATG and the reverse primer had two stop codons at the end of the coding sequence. The vectors were then packaged in AAV9 capsid using the adenovirus-free, triple plasmid DNA transfection method and purified twice with CsCl gradient (1). AAV vector genome (v.g.) copies/ml were titrated by a standard dot-blot assay. AAV8 has been very successful because most humans do not have pre-formed antibodies to this serotype of the virus.26 Puccio et al.14 detected no immune reaction in mice after one intra-venous injec- tion of AAVrh10-hFXN. Although an immune response will probably develop in the FRDA patients following the systemic delivery of an AAV8, AAV9, or AAVrh10 coding for frataxin, this will not be a prob- lem since no readministration of the virus will be required. The main problem facing this potential therapy is that the large-scale produc- tion of AAV vector under GMP conditions remains difficult. ACTGAAGCTTATCAAGCATCTTTTCCGGAATAG 3′. The forward primer also contained the Kozak sequence GCCACC before the start codon ATG and the reverse primer had two stop codons at the end of the coding sequence. The vectors were then packaged in AAV9 capsid using the adenovirus-free, triple plasmid DNA transfection method and purified twice with CsCl gradient (1). AAV vector genome (v.g.) copies/ml were titrated by a standard dot-blot assay. AAV8 has been very successful because most humans do not have pre-formed antibodies to this serotype of the virus.26 Puccio et al.14 detected no immune reaction in mice after one intra-venous injec- tion of AAVrh10-hFXN. Although an immune response will probably develop in the FRDA patients following the systemic delivery of an AAV8, AAV9, or AAVrh10 coding for frataxin, this will not be a prob- lem since no readministration of the virus will be required. The main problem facing this potential therapy is that the large-scale produc- tion of AAV vector under GMP conditions remains difficult. Reproduction of the mutant mice Supplementary Figure S1a summarizes the different mouse geno- types (Puccio 2001). DISCUSSION FRDA i d Mice homozygous for a conditional allele of Frda (FrdaL3/L3) and heterozygous FrdaL3/L:NSE-cre (NSE-cre), which carried a tissue-specific Cre transgene under the control of the neu- ron-specific enolase (NSE), were gifts from Dr M Payne laboratory (Indiana University School of Medicine) following the permission of Dr Puccio (Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France) who generated these mice.13 These mice were bred in our animal facility to produce FrdaL-/L-:NSE-Cre (NSE- cre). In these mice, both conditional knockout frataxin genes are © 2014 The American Society of Gene & Cell Therapy Molecular Therapy — Methods & Clinical Development (2014) 14044 MATERIALS AND METHODS AAV vector construction and viral vector production The AAV vector plasmids were made and packaged in AAV9 capsids as previously described.27–29 Specifically, the AAV vec- tor plasmid dsAAV-CB-hFrataxin (AAV9-hFXN) was derived from plasmid dsAAV-CB-GFP30 by replacing the GFP gene with the human frataxin coding sequence, which was polymerase chain reaction (PCR) amplified with the following primers: Forward: 5′ TAGTGCTAGCCACCATGTGGACTCTCGGGCGCCG 3′ and reverse: 5′ Molecular Therapy — Methods & Clinical Development (2014) 14044 © 2014 The American Society of Gene & Cell Therapy An AAV9 coding for frataxin C Gérard et al. Table 2  Polymerase chain reaction parameters Gene name Primer sequences Tm Nb of cycles Enzyme Delta FXN allele (Fw) (Rev) 5′-CTG TTT ACC ATG GCT GAG ATC TC-3′ 62,5 35 Terra 5′-GTA GCT GGC TGG GAA ATG AA-3′ mFXN (Fw) (Rev) 5′-CTG CGT GGT GCA TTT GAG GAA C-3′ 62 35 Taq 360 5′-CAT GCA GAG ACA CGC CGT CAT GA-3′ hFXN (Fw) (Rev) 5′-AAC GTG GCC TCA ACC AGA TTT G-3′ 62 30 Taq 360 5′-TAA GGC TTT AGT GAG CTC TGC G-3′ m β-actin (Fw) (Rev) 5′-ATA CGC TGC GCT GGT CGT C-3′ 58 30 Taq 360 5′-AGG ATG GCG TGA GGG AGA GC-3′ An AAV9 coding for frataxin C Gérard et al. 10 knocked out in the neurons and in other tissues expressing the Cre gene. Two hemizygous males B6.FVB(129S4)-Tg(Ckmm-cre)5Khn/J were also purchased from the Jackson laboratory (stock # 006475) and used to generate FrdaL-/L-:MCK-cre (MCK-cre). In these mice, both conditional KO frataxin genes are knocked in skeletal muscle fibers and in cardiac cells. For the experiments, FrdaL3/L3 mice were used as control mice in many experiments. All the experiences were approved by the animal care committee of the Centre Hospitalier de l’Université Laval. knocked out in the neurons and in other tissues expressing the Cre gene. Two hemizygous males B6.FVB(129S4)-Tg(Ckmm-cre)5Khn/J were also purchased from the Jackson laboratory (stock # 006475) and used to generate FrdaL-/L-:MCK-cre (MCK-cre). In these mice, both conditional KO frataxin genes are knocked in skeletal muscle fibers and in cardiac cells. For the experiments, FrdaL3/L3 mice were used as control mice in many experiments. All the experiences were approved by the animal care committee of the Centre Hospitalier de l’Université Laval. The weight of the mice was evaluated after weaning and until their death. RT-PCR The total RNA was extracted using the Trizol reagent from a part of the different tissues. First-strand cDNAs were synthesized using 1 µg total RNA with the oligo (dt) primer and Superscript III reverse tran- scriptase. PCR was performed with 2 µl of the cDNA solution using the primers specific for β-actin (reference gene), human frataxin (hFXN), and mouse frataxin (mFXN). The PCR parameters are presented in Table 2. PCR products were then separated by electrophoresis in 1% agarose gels and were stained with RedSafe (Chembio, St Albans, Herts AL2 3UG). A picture of the gel was obtained with the GelDoc program (BioRad, Mississauga, Ontario, Canada) under UV light. DNA extraction DNA was extracted from different tissues (muscle, liver, heart, kid- ney, and brain). Briefly, a part of the recovered tissue was incubated with 50 µl of proteinase K (10 mg/ml) in a lysis buffer at 56 °C until the solution became clear. Digested tissues were then mixed with 500 µl of a solution of phenol/chloroform/isoamyl alcohol (25:24:1) and centrifuged 3 minutes at 13,000 rpm. The upper solution was recovered and mixed with the same volume of chloroform and cen- trifuged again. The upper solution was recovered and 50 µl of 5 mol/l sodium chloride was added before the addition of 1 ml of 100% etha- nol. After a 8-minute centrifugation at 13,000 rpm, the pellets were washed in 70% alcohol before another centrifugation. The pellets were then dried before the suspension of the DNA in sterile water. PCR was performed with 50 ng of the genomic DNA solution using primers specific for delta and human frataxin (hFXN). The annealing temperatures and the PCR parameters are presented in the Table 2. Two mouse models were used in this study: the MCK-cre and NSE- cre mice. Homozygous conditional knockout mice FrdaL3/L3 were bred with heterozygote mice FrdaL3/+ also expressing the Cre gene under the MCK promoter. Some of the offsprings were homozygous for the conditional KO frataxin gene and also had the MCK-cre gene. Therefore these mice had both frataxin genes KO in their skeletal muscles and heart starting during embryogenesis. These mice are designated as “MCK-cre” mutants. MCK-cre mice (injected or not with saline) were used as untreated controls. Similarly, homozygous conditional knockout mice FrdaL3/L3 were bred with heterozygote mice FrdaL3/+ also expressing the Cre gene under the NSE promoter. Some of the offsprings were homozygous for the conditional KO frataxin gene and also had the NSE-cre gene. The mice were named “NSE-cre”. MATERIALS AND METHODS An estimation of the mouse behavior was done each week for the MCK-cre and twice a day for the NSE-cre mice because of the sever- ity of their disease. Their health was scored from 0 (normal behavior) to 4 (severe cardiac or respiratory insufficiency (Table 1) requiring immediate sacrifice due to ethical concern. At the time of euthanasia, the body and heart weight was measured. Different tissues (Tibialis anterior muscle, the liver, the kidneys, the heart, and the brain) were recovered and directly frozen in liquid nitrogen for analyzes. The FrdaL3/L3 mice have the completed mouse frataxin gene but there is LoxP site on each side of the exon 4. When these mice were bred with mice expressing the Cre gene, mice without exon 4 were obtained because the Cre enzyme had cut both LoxP sites and deleted exon 4. This frataxin allele deleted of exon 4 is called the delta allele (L-). The deletion of exon 4 led to a nonfunctional frataxin gene. Molecular Therapy — Methods & Clinical Development (2014) 14044 © 2014 The American Society of Gene & Cell Therapy Administration of AAV9-hFXN A genotype analysis was made in 4 days old mice using the tail tip. The MCK-cre or NSE-cre mice were then injected with a single intra- peritoneal (IP) injection of viral particles in 60 µl of saline between 5 and 9 days. Control mice were injected with saline. A point of surgi- cal glue was applied to the skin just after removing the needle to keep the liquid inside the mice. In the first part of the study, different quantities of viral particles were injected in NSE-cre mice: 6 × 1011, 3 × 1011 (d1/2), 6 × 1010 (d1/10), 3 × 1010 (d1/20), 1.2 × 1010 (d1/50), and 6 × 109 (d1/100) v.p. For the second part of the study, only the highest and lowest doses were tested (6 × 1011 and 6 × 109 viral par- ticles) on MCK-cre mice. In the third part, only the higher quantity of virus was used in NSE-cre and MCK-cre mice for more specific evalu- ations, such as echocardiography. ACKNOWLEDGMENTS This work has been supported by grants from the Canadian Association for Familial Ataxia, by the Association Française contre les Ataxies Familiales and from the Canadian Institute of Health Research. 29. Xiao, X, Li, J and Samulski, RJ (1998). Production of high-titer recombinant adeno- associated virus vectors in the absence of helper adenovirus. J Virol 72: 2224–2232. 30. Wang, Z, Zhu, T, Rehman, KK, Bertera, S, Zhang, J, Chen, C et al. (2006). Widespread and stable pancreatic gene transfer by adeno-associated virus vectors via different routes. Diabetes 55: 875–884. The authors declare no conflict of interest. The authors declare no conflict of interest. 28. Wang, Z, Ma, HI, Li, J, Sun, L, Zhang, J and Xiao, X (2003). Rapid and highly efficient transduction by double-stranded adeno-associated virus vectors in vitro and in vivo. Gene Ther 10: 2105–2111. Quantification of the frataxin protein by ELISA The human frataxin protein in various mouse tissues was quanti- fied using the Dipstick Array of Abcam (cat # ab109881, Cambridge, MA). This is an immunologic sandwich assay using two monoclonal antibodies specific for two antigens present in the mature form of frataxin. One antibody is immobilized on the nitrocellulose mem- brane of the dipstick in a thin line perpendicular to the length of the dipstick while the other is gold-conjugated with gives the red signal proportional to the level of frataxin. To compare and to pool the different organs and mice, a range from 1 to 10 was established to “semi-quantify” the density of the frataxin band. 14. Perdomini, M, Belbellaa, B, Monassier, L, Reutenauer, L, Messaddeq, N, Cartier, N et al. (2014). Prevention and reversal of severe mitochondrial cardiomyopathy by gene therapy in a mouse model of Friedreich’s ataxia. Nat Med 20: 542–547. 15. Vyas, PM, Tomamichel, WJ, Pride, PM, Babbey, CM, Wang, Q, Mercier, J et al. (2012). A TAT-frataxin fusion protein increases lifespan and cardiac function in a conditional Friedreich’s ataxia mouse model. Hum Mol Genet 21: 1230–1247. Friedreich’s ataxia mouse model. Hum Mol Genet 21: 1230–1247. 16. Piras, BA, O’Connor, DM and French, BA (2013). Systemic delivery of shRNA by AAV9 provides highly efficient knockdown of ubiquitously expressed GFP in mouse heart, but not liver. PLoS ONE 8: e75894. 17. Bish, LT, Morine, K, Sleeper, MM, Sanmiguel, J, Wu, D, Gao, G et al. (2008). Adeno- associated virus (AAV) serotype 9 provides global cardiac gene transfer superior to AAV1, AAV6, AAV7, and AAV8 in the mouse and rat. Hum Gene Ther 19: 1359–1368. AAV6, AAV7, and AAV8 in the mouse and rat. Hum Gene Ther 19: 1359–1 18. Weidemann, F, Eyskens, B, Mertens, L, Di Salvo, G, Strotmann, J, Buyse, G et al. (2003). Quantification of regional right and left ventricular function by ultrasonic strain rate and strain indexes in Friedreich’s ataxia. Am J Cardiol 91: 622–626. Evaluation of heart function by echocardiography strain indexes in Friedreich’s ataxia. Am J Cardiol 91: 622–626. A complete M-Mode, 2D, and Doppler echocardiogram was per- formed on the mice under 1.5% inhaled isoflurane anesthesia using L17-7 and S12 probes with a HD11XE echograph (Philips Medical Imaging, Andover, MA). Statistical analyses The experimental values were presented as means ± SD. Statistical analysis was performed using the StatView statistical package (StatView 5; SAS Institute, Cary, NC). Comparisons of different vari- ables between groups were performed using analysis of variance techniques. Differences were considered statistically significant at P ≤ 0.05*; P ≤ 0.001**; P ≤ 0.0001***. 24. Herzog, RW (2007). Immune responses to AAV capsid: are mice not humans after all? Mol Ther 15: 649–650. 25. Manno, CS, Pierce, GF, Arruda, VR, Glader, B, Ragni, M, Rasko, JJ et al. (2006). Successful transduction of liver in hemophilia by AAV-Factor IX and limitations imposed by the host immune response. Nat Med 12: 342–347. transduction of liver in hemophilia by AAV-Factor IX and limitations imposed by the host immune response. Nat Med 12: 342–347. 26. Nathwani, AC, Tuddenham, EG, Rangarajan, S, Rosales, C, McIntosh, J, Linch, DC et al. (2011). Adenovirus-associated virus vector-mediated gene transfer in hemophilia B. N Engl J Med 365: 2357–2365. References 1. Campuzano, V, Montermini, L, Moltò, MD, Pianese, L, Cossée, M, Cavalcanti, F et al. (1996). Friedreich’s ataxia: autosomal recessive disease caused by an intronic GAA triplet repeat expansion. Science 271: 1423–1427. 1. Campuzano, V, Montermini, L, Moltò, MD, Pianese, L, Cossée, M, Cavalcanti, F et al. (1996). Friedreich’s ataxia: autosomal recessive disease caused by an intronic GAA triplet repeat 1. Campuzano, V, Montermini, L, Moltò, MD, Pianese, L, Cossée, M, Cavalcanti, F et al. (1996) Friedreich’s ataxia: autosomal recessive disease caused by an intronic GAA triplet repeat 1. Campuzano, V, Montermini, L, Moltò, MD, Pianese, L, Cossée, M, Cavalcanti, F et al. (1996). Friedreich’s ataxia: autosomal recessive disease caused by an intronic GAA triplet repeat expansion. Science 271: 1423–1427. 31. Drolet, MC, Roussel, E, Deshaies, Y, Couet, J and Arsenault, M (2006). A high fat/ high carbohydrate diet induces aortic valve disease in C57BL/6J mice. J Am Coll Cardiol 47: 850–855. 2. Pandolfo, M (2006). Iron and Friedreich ataxia. J Neural Transm Suppl 70: 143–14 2. Pandolfo, M (2006). Iron and Friedreich ataxia. J Neural Transm Suppl 70: 143–146. 3. Pandolfo, M (2012). Friedreich ataxia. Handb Clin Neurol 103: 275–294. 32. Plante, E, Lachance, D, Beaudoin, J, Champetier, S, Roussel, E, Arsenault, M et al. (2009). Comparative study of vasodilators in an animal model of chronic volume overload caused by severe aortic regurgitation. Circ Heart Fail 2: 25–32. 3. Pandolfo, M (2012). Friedreich ataxia. Handb Clin Neurol 103: 275–294. 4. Becker, E and Richardson, DR (2001). Frataxin: its role in iron metabolism and the pathogenesis of Friedreich’s ataxia IntJBiochemCellBiol 33: 1 10 4. Becker, E and Richardson, DR (2001). Frataxin: its role in iron metabolism and the pathogenesis of Friedreich’s ataxia. Int J Biochem Cell Biol 33: 1–10. pathogenesis of Friedreich’s ataxia. Int J Biochem Cell Biol 33: 1–10. 5. Wallis, J, Shaw, J, Wilkes, D, Farrall, M, Williamson, R, Chamberlain, S et al. (1989). Prenatal diagnosis of Friedreich ataxia. Am J Med Genet 34: 458–461. 5. Wallis, J, Shaw, J, Wilkes, D, Farrall, M, Williamson, R, Chamberlain, S et al. (1989). Prenatal diagnosis of Friedreich ataxia. Am J Med Genet 34: 458–461. This work is licensed. under a Creative Commons Attribution- NonCommercial-ShareAlike 3.0 Unported License. Quantification of the frataxin protein by ELISA Different parameters (left ventricular dimen- sions, fractional shortening, stroke volume, and cardiac output and frequency) were evaluated as previously described.31,32 At the end of the protocol and under anesthesia, the heart was quickly removed, freed from connective tissue, and weighed. 19. Huang, ML, Sivagurunathan, S, Ting, S, Jansson, PJ, Austin, CJ, Kelly, M et al. (2013). Molecular and functional alterations in a mouse cardiac model of Friedreich ataxia: activation of the integrated stress response, eIF2a phosphorylation, and the induction of downstream targets. Am J Pathol 183: 745–757. 20. Perdomini, M, Hick, A, Puccio, H and Pook, MA (2013). Animal and cellular models of Friedreich ataxia. J Neurochem 126 (suppl 1) 65–79. 21. Aschauer, DF, Kreuz, S and Rumpel, S (2013). Analysis of transduction efficiency, tropism and axonal transport of AAV serotypes 1, 2, 5, 6, 8 and 9 in the mouse brain. PLoS ONE 8: e76310. 22. Ohshima, S, Shin, JH, Yuasa, K, Nishiyama, A, Kira, J, Okada, T et al. (2009). Transduction efficiency and immune response associated with the administration of AAV8 vector into dog skeletal muscle. Mol Ther 17: 73–80. 23. Hauck, B, Murphy, SL, Smith, PH, Qu, G, Liu, X, Zelenaia, O et al. (2009). Undetectable transcription of cap in a clinical AAV vector: implications for preformed capsid in immune responses. Mol Ther 17: 144–152. Open-field activity Mice were placed in a rectangular cage made of clear Plexiglas identical in size to their home-cage (width: 18 cm, length: 28 cm, height: 12 cm) and equipped with a video-tracking system (Side Molecular Therapy — Methods & Clinical Development (2014) 14044 An AAV9 coding for frataxin C Gérard et al. 11 9. Harding, AE (1981). Friedreich’s ataxia: a clinical and genetic study of 90 families with an analysis of early diagnostic criteria and intrafamilial clustering of clinical features. Brain 104: 589–620. 9. Harding, AE (1981). Friedreich’s ataxia: a clinical and genetic study of 90 families with an analysis of early diagnostic criteria and intrafamilial clustering of clinical features. Brain 104: 589–620. 9. Harding, AE (1981). Friedreich’s ataxia: a clinical and genetic study of 90 families with an analysis of early diagnostic criteria and intrafamilial clustering of clinical features. Brain 104: 589–620. view, Any maze, Stoelting, Wood Dale, IL). Each mouse was placed in this cage without its usual bedding for a single 2-minute session with the experimenter out of its view. Distance traveled, time spent immobile and rearing frequency and duration were recorded. After each trial, fecal boli were removed and the floor was wiped clean with a damp cloth and dried. 10. Lynch, DR, Farmer, JM, Balcer, LJ and Wilson, RB (2002). Friedreich ataxia: effects of genetic understanding on clinical evaluation and therapy. Arch Neurol 59: 743–747. 11. Pandolfo, M (1999). Molecular pathogenesis of Friedreich ataxia. Arch Neurol 56: 1201–1208. 12. Singh, G, Binstadt, BA, Black, DF, Corr, AP and Rummans, TA (2001). Electroconvulsive therapy and Friedreich’s ataxia. J ECT 17: 53–54. 13. Puccio, H, Simon, D, Cossée, M, Criqui-Filipe, P, Tiziano, F, Melki, J et al. (2001). Mouse models for Friedreich ataxia exhibit cardiomyopathy, sensory nerve defect and Fe-S enzyme deficiency followed by intramitochondrial iron deposits. Nat Genet 27: 181–186. Quantification of the frataxin protein by ELISA References The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/ licenses/by-nc-sa/3.0/ 6. Rötig, A, de Lonlay, P, Chretien, D, Foury, F, Koenig, M, Sidi, D et al. (1997). Aconitase and mitochondrial iron-sulphur protein deficiency in Friedreich ataxia. Nat Genet 17: 215–217. This work is licensed. under a Creative Commons Attribution- NonCommercial-ShareAlike 3.0 Unported License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/ licenses/by-nc-sa/3.0/ 6. Rötig, A, de Lonlay, P, Chretien, D, Foury, F, Koenig, M, Sidi, D et al. (1997). Aconitase and mitochondrial iron-sulphur protein deficiency in Friedreich ataxia. Nat Genet 17: 215–217. 7. Babady, NE, Carelle, N, Wells, RD, Rouault, TA, Hirano, M, Lynch, DR et al. (2007). Advancements in the pathophysiology of Friedreich’s Ataxia and new prospects for treatments. Mol Genet Metab 92: 23–35. 7. Babady, NE, Carelle, N, Wells, RD, Rouault, TA, Hirano, M, Lynch, DR et al. (2007). Advancements in the pathophysiology of Friedreich’s Ataxia and new prospects for treatments. Mol Genet Metab 92: 23–35. 8. Cooper, JM and Schapira, AH (2003). Friedreich’s Ataxia: disease mechanisms, antioxidant and Coenzyme Q10 therapy. Biofactors 18: 163–171. 8. Cooper, JM and Schapira, AH (2003). Friedreich’s Ataxia: disease mechanisms, antioxidant and Coenzyme Q10 therapy. Biofactors 18: 163–171. Molecular Therapy — Methods & Clinical Development (2014) 14044 CONFLICT OF INTEREST 27. Rabinowitz, JE, Rolling, F, Li, C, Conrath, H, Xiao, W, Xiao, X et al. (2002). Cross-packaging of a single adeno-associated virus (AAV) type 2 vector genome into multiple AAV serotypes enables transduction with broad specificity. J Virol 76: 791–801. The authors declare no conflict of interest. © 2014 The American Society of Gene & Cell Therapy © 2014 The American Society of Gene & Cell Therapy
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International Relations and/as Thread-work: A Dialogue on Threads, War, and Conflict
Contemporary voices
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Thread 1. Reflections on curating, exhibiting and making Thread 1. Reflections on curating, exhibiting and making Abstract This intervention reflects on the opportunities for textile art, and its exhibition and making, to inform our study of conflict, violence, and resistance in International Relations. In a dialogue drawing on the Threads, War and Conflict exhibition at the Byre Theatre, St Andrews, this piece grounds our understanding of violence and its resistance through engagement with materials displayed at and promoting the exhibition. Our discussion of the exhibition and its associated events draws on metaphors of thread-work to explore the contributions of textile to international relations and the possibilities that textiles’ material, affective and transgressive politics hold. Keywords: textiles; textile exhibition; visual IR; curation; IR methodology; arpilleras Keywords: textiles; textile exhibition; visual IR; curation; IR methodology; arpilleras From 3-29 April 2019, the exhibition Threads, war and conflict brought a selection of conflict textiles from around the world to St Andrews, Scotland.1 Hosted by the University of St Andrews’ School of International Relations in collaboration with the Byre Theatre, the exhibition and its associated events programme aimed to explore war, conflict and its many layers of hope and suffering. Featuring a selection of textiles from the Conflict Textiles collection,2 including arpilleras3 and protest banners, the exhibition was curated around key topics addressed in the School of International Relations including resistance, the ethics of warfare, and migration and displacement. The process of curating the exhibition and its associated events unfolded organically, drawing together students, academics, Scottish cultural institutions and interested members of the public. Not only did this process create space for conversations around the diverse topics of war and conflict addressed with(in) the textiles, but it also provided rich opportunities for collaborative teaching, research and engagement. These opportunities resulted in several collaborative outcomes from the exhibition, including an international academic-practitioner workshop at the Byre Theatre, and a collective textile made by students and lecturers from Scottish Higher Education Institutions across a series of workshops, which will now join the Conflict Textiles collection. The conversations and collaborations inaugurated in St  Andrews continue within this dialogue and, indeed, in the Special Issue as a whole. This creative opening more specifically takes the form of a dialogue between Selena Jamalullail, a School of International Relations student who served as exhibition tour guide and participated in the collective textile workshops associated with the exhibition, and Roberta Bacic, curator of the Conflict Textiles collection. International Relations and/as thread-work: a dialogue on Threads, war and conflict Authors: Selena Jamalullail , Independent Researcher, UK, Roberta Bacic , Conflict Textiles, UK, Lydia C. Cole , University of York, UK, Laura Mills , University of St Andrews, UK Selena Jamalullail is an independent researcher interested in the intersection between art exhibitions and global discourse on politics. She attended the University of St  Andrews during 2016-2020 and achieved a Joint Honours degree in Art History and International Relations. While a student, she participated in the Threads, War and Conflict exhibition at the Byre Theatre (St Andrews) as an exhibition tour guide. Curator Roberta Bacic is a Chilean Human Rights advocate and researcher living in Northern Ireland. Since 2007 she has curated more than 150 international exhibitions of arpilleras in museums, universities, art galleries, embassies and community spaces worldwide. Over time, these exhibitions have expanded from Chilean arpilleras focused on the Pinochet dictatorship, to include quilts and other textile narratives of loss, resistance, testimony, protest and healing from around the world. The use of textile language in contested spaces has been at the centre of her curatorial work. In 2019 she curated, with assistance of Breege Doherty, Threads, War and Conflict, commissioned by Lydia Cole at University of St Andrews. Lydia Cole is an Associate Lecturer at the University of York. Her most recent research has engaged with arts and global politics, with a focus on grassroots arts for change in Bosnia and Herzegovina. In 2019, she was Associate Lecturer at the University of St Andrews, where she commissioned and co-curated Threads, war and conflict, as well as coordinated and led its associated events programme. The exhibition featured arpilleras and textile banners from the Conflict Textiles collection. Laura Mills is a Lecturer in International Relations at the University of St Andrews. She was a member of the Threads, war and conflict curatorial team, including staff co-lead of the Master’s student workshops resulting in a collective textile for the Conflict Textiles collection. Her research explores how everyday life and culture are co-constitutive of global politics through examinations of cultural diplomacy, war, militarism, security, aesthetics and creative methods. Her first monograph, Post-9/11 US cultural diplomacy: the impossibility of cosmopolitanism, is forthcoming with Routledge New International Relations Series. Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 Abstract Lydia Cole and Laura Mills, two members of the Threads, war and conflict team, tied together the threads of their conversation. This approach enables insights from a cross- section of those engaged in the exhibition to be woven together in order to reveal and unpick how curating the (hi)stories of conflict textiles can produce alternative ways of knowing and doing International Relations (IR). Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 2 Over a year since the exhibition, this dialogue reflects back, beginning with a discussion of the textile workshops, then moving to explore the exhibition, its curation and its pieces. In this way, this reflective dialogue unravels the threads of war and conflict examined in the exhibition and its associated events. Throughout, the dialogue draws upon the language associated with thread-work to explore the tactile, emotional, interactive, non-linear, symbolic, transgressive and politically powerful qualities of the exhibition, its featured textiles, and the textile-making it enables. It does so by engaging with material artefacts of the exhibition – the collective textile workshops poster, the events programme bookmark, and the textiles themselves – to demonstrate how they produce these material effects for arpilleristas and makers, for exhibition curators and visitors, and for students and researchers of IR. Unravelling and (re)connecting in Threads, war and conflictl Selena: Focusing on Threads, war and conflict, I’d like to initiate a dialogue with you about the opportunities that textile art exhibitions offer to inform our study of conflict and violence; particularly how they offer alternative narratives in IR through stitching stories of resistance. Specifically, I’d like to focus on how textiles and weaving offer a discursive method, a different language. Looking now at the poster for the Master’s Textiles Workshops (see Figures 1 and 2), I am interested in approaching our discussion from the exhibition’s outcomes and tracing back to the beginning of Threads, war and conflict. Figures 1 and 2: Poster for Responding to Threads, war and conflict: letters to arpilleristas, Master’s Textiles Workshops, University of St Andrews, 2019. Images: Conflict Textiles and Laura Mills. Figures 1 and 2: Poster for Responding to Threads, war and conflict: letters to arpilleristas, Master’s Textiles Workshops, University of St Andrews, 2019. Images: Conflict Textiles and Laura Mills. Figures 1 and 2: Poster for Responding to Threads, war and conflict: letters to arpilleristas, Master’s Textiles Workshops, University of St Andrews, 2019. Images: Conflict Textiles and Laura Mills. Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 3 Roberta: I find it very original the way you are going to deconstruct from the outcome, and to see how much was predictable or not predictable because the plan will not always turn out as we expect it. S: Yes, I am interested in seeing how there are changes and unexpected events, which always arise when events are realised. This poster documents the workshops that accompanied the exhibition, in which a group of students came together for three workshops to create a collective textile inspired by the exhibition. Local textile artist Sheila Mortlock provided materials and some techniques, but we could use our own creativity, ideas and exhibition inspiration to influence our works. R: You had to relate to the exhibition. You had the space from where to connect and from where to be creative, but you were given a framework. S: It was inspiring to see the diversity of pieces in the exhibition and how they related to one another. We all participated in creating the collective textile but through the making of our own individual pieces, through our interpretation of the workshops’ prompt, as well as our own understandings and meanings of resistance, violence and political conflict. Unravelling and (re)connecting in Threads, war and conflictl The content of the arpilleras that resulted from these workshops was just as diverse as the pieces in the exhibition. How do you go about drawing these various threads, or pieces, together within the exhibition itself? R: What is important is the relationship of the curatorial line. The title of the exhibition determines the way you choose which pieces to display. It relates to the way you relate to the topic. Each piece is not chosen at random but in fluent connection to the issues that you want to portray. S: Do you feel that textiles and exhibitions become a form of expression? Does approaching the study of IR through these lenses – through looking at those creating these works – offer students, exhibition visitors and other viewers a new perspective? R: I don’t know how much of a new perspective it is. Sewing has always been there, and the reflection you do while sewing is there, but it hasn’t been incorporated as a discourse or a language that could give you information on content, feeling and experience. In the last few years, there has been a resurgence of this kind of discourse, and a recognition that we have multiple capacities to express – because what happens to us touches us in so many ways. The textile gives you this incredible capacity to work through your emotions. So, it is not this line from beginning to middle to end; you go around instead. Some textiles get special attention because they deal with memory, resistance and narratives. They can do many things when you learn to talk through them but also when you learn to read through them. So, it is not only to be able to express it, but also to decipher it. You will not always be able to respond Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 with sewing but very often you will need to be able to read other forms of communication in the sewing. S: Definitely. As someone who was involved with sharing the exhibition with others, you realise how you can perceive a story from its visual depiction. It requires participation to understand the piece: coming up close to it, inspecting, discussing with others. In these workshops, it took a long time to put together something not only visual but also deliver something tangible. Unravelling and (re)connecting in Threads, war and conflictl The engagement with the pieces was really key. R: I think what is also important is that the narrative is intertwined with the technique with which you are going to tell this story. You are using a needle. You are taking action. I think for many of the arpilleristas, the idea that they could take action in front of a state that would not listen to them, would not do things for them, would deny the events, the sole exercise of being part of the dynamic process of acting gives a power to the discourse. S: And that contributes to the understanding of its subjects and themes as active Threads of resistance: the textile language of Chilean arpilleras S: This segues into our first textile piece (see Figure 3). Figure 3: Anonymous (c1980) ¡Adiós Pinochet! / Goodbye Pinochet!. Arpillera, Chile. Photo Colin Peck, © Conflict Textiles Threads of resistance: the textile language of Chilean arpilleras S: This segues into our first textile piece (see Figure 3). Threads of resistance: the textile language of Chilean arpilleras S: This segues into our first textile piece (see Figure 3). Figure 3: Anonymous (c1980) ¡Adiós Pinochet! / Goodbye Pinochet!. Arpillera, Chile. Photo Colin Peck, © Conflict Textiles Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 5 R: ‘Goodbye Pinochet!’ R: ‘Goodbye Pinochet!’ S: I remember this piece dearly. It has such a specific place in history that you can trace within it. Can you explain a little bit more about this piece? R: This is an example of a Chilean arpillera: three-dimensional textiles from Latin America, of Chilean origin, which became a medium primarily for women to denounce the human rights abuses and repression of the Pinochet dictatorship in Chile, 1973-1990. In this particular piece, there are many readings and layers. There is a cultural landscape. You can see we have the mountains which guide us to understand we are in Chile because it is the Andes – that determines where you are physically. The other element important here is the sun. In spite of all these difficulties, the sun is there for the people. As a symbol, it has a political connotation: the sun rises for everybody, it makes no distinction. These kinds of textile – the arpilleras – also incorporated specific elements that we can read and decode. We have the electricity cables and you can see people tapping into the electricity, highlighting the disparity of access to these resources. So that locates us immediately in the shanty town where people are taking action, living daily life in conditions of poverty. – also incorporated specific elements that we can read and decode. We have the electricity cables and you can see people tapping into the electricity, highlighting the disparity of access to these resources. So that locates us immediately in the shanty town where people are taking action, living daily life in conditions of poverty. Another important element is the simplicity of the stitch and the materials. It requires that you understand and are able to read those twists in the language, that those scraps of material hold meaning. The grey material you see on the ground is from school uniforms. The blanket stitch on the border marks this as a picture, a picture that you want people to look at. But the message is very clear. What makes this so interesting is that this is very tactile but on the other hand the discourse is very direct. It is not sophisticated. Threads of resistance: the textile language of Chilean arpilleras S: This segues into our first textile piece (see Figure 3). It is an example of direct language and demands: out the tyrant! They are not making aggressive accusations, they are saying: “Just go, goodbye Pinochet”. They are not speaking about revenge because they don’t believe that they have the time or the energy for that, but they find that their actions could aid the removal of Pinochet. I find it very powerful that this piece has been able to be in the most incredible spaces. It was in the Victoria and Albert Museum in the Disobedient objects exhibition for a few months.4 Thinking about the textile through the lens of a disobedient object, against the idea that women should be silent and at home, we also see a message of transgression: to go beyond what is expected of you or demanded from you, you can live it and relive it in your own context. S: When I remember these pieces, I recall how some of them were done in secret, hidden away or smuggled elsewhere. R: They were smuggled, as well as bought, by volunteers and people of good faith who wanted to support the women and the movement and wanted to contribute to denouncing what was going on in the country, which was being hidden by the economic success in the beginning through statistics. This didn’t mean that life was good for these women. Because Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 6 they didn’t count. If you keep them hidden and silent, then if one person earns one thousand and the other nothing, you still have a good average of five hundred and that makes it okay. S: I see these pieces as forms of resistance. In this piece, they are not proposing violence, but it is still a form and subject of expression that was suppressed. To be able to do these pieces is a reflection of them trying to assert their own voice and identity. I remember this piece, La cueca sola (see Figure 4). The creator, Violeta Morales, was well known, a prominent activist. The dance that the textile piece depicts was also a form of resistance. How can we interpret this resistance in the form of textiles and stitching? Figure 4: Morales, V. (1989) La cueca sola / Dancing cueca alone. Arpillera, Chile. Photo: Martin Melaugh, © Conflict Textiles Figure 4: Morales, V. Threads of resistance: the textile language of Chilean arpilleras S: This segues into our first textile piece (see Figure 3). (1989) La cueca sola / Dancing cueca alone. Arpillera, Chile. Photo: Martin Melaugh, © Conflict Textiles R: In the case of Violeta Morales, she was a very active woman. She used all the mediums she had at hand to denounce torture in Chile. That was her fundamental denunciation because her brother had been disappeared and the people she had interviewed, who came out of the prison where her brother had been, were talking about torture. She used the arpillera, she used marches, she used singing, she used dancing. She was extremely purposed, acted very strongly, and became part of a performance group that undertook these actions in public space outdoors, not only indoors like this textile that she made. They would have danced in the streets of Santiago, knowing and wanting to be arrested, to denounce what was going Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 7 on to the people in the streets as they were oblivious. What they wanted was to occupy the streets and to bring into public knowledge what was going on in parts of Santiago most affected by the dictatorship. S: Did the production of these arpilleras see a spike at the time? Their creators had lost their husbands, brothers and other family members who were disappeared. Left behind, they chose to create these arpilleras. Is it because of these circumstances that we see so many of these textile pieces from Chile? R: They were not popular in Chile. You couldn’t have them; you couldn’t show them because they were considered subversive. What happened is the dissemination of arpilleras with the production of many more occurring thanks to the international solidarity movement that decided to support the women because they also needed to earn a living. Women had no jobs; their husbands had disappeared or their sons couldn’t do it. Through these networks, they also got a bit of income. So, it becomes a denunciation, but also a way of earning their life. Many groups, like Amnesty or Caritas, and international organisations in the UK would have acquired arpilleras and sold them amongst solidarity movements in England with three intentions. First, to help the women financially. Second, to spread the news of what was going on, using them almost like a newspaper. Third, to create networks of support internally in the country and externally acting together. Threads of resistance: the textile language of Chilean arpilleras S: This segues into our first textile piece (see Figure 3). It was those networks, especially in the UK, that helped to gain asylum for Chileans who were in prison. The only way to be released was if they were able to go somewhere as refugees. The arpilleras were just one of the voices among other expressions. The power of this was in the possibility of commercialising, discussing, exhibiting them, and creating these networks of solidarity. S: Do you think that because of the conditions – that they had to create the arpilleras with scrap material, needle and thread – the arpillera was a particularly accessible medium for these women to create and engage with these networks, and then earn a living? R: Well, one of the prides of the arpillerista is not to buy material. The use of these scrap materials is symbolic. They are scraps of your own or a loved one’s clothes. Violeta Morales once gave an interview where she said they were so poor that they would cut pieces of their blouses. It is the opposite of the concept of a quilt-maker, who would have so much material and would always pick the one that fits best. They did with what they could, and they were proud of themselves to be able to produce these with very little. Threads of anti-militarism: from the local to the global S: These two arpilleras come from the particular context of the Pinochet regime. This next one, Digital death, is much more contemporary (see Figure 5) and was made in Ireland. Do you see crossovers with how the arpillera is used? Is this creator also trying to do the same thing or is it completely different when it comes to materials and style? Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 Figure 5: Stockdale, D. (2014) Digital death. Arpillera, Republic of Ireland. Photo: Martin Melaugh, © Conflict Textiles R: It is not. I am very happy that you chose this one for our discussion. Deborah Stockdale is a textile artist who has made quilts and has expressed herself for forty years with textile art. She had done pieces that were about different issues, even social issues, but she hadn’t positioned herself like how an arpillerista does. When she found the arpilleras, she found another way to stitch about what was going on in the world. To use a language very comfortable for her to tell uncomfortable stories. It was as if she thought: “If the Chilean women can do it, I can also do it. I can create what I need to create.” an women can do it, I can also do it. I can create what I Figure 5: Stockdale, D. (2014) Digital death. Arpillera, Republic of Ireland. Photo: Martin Melaugh, © Conflict Textiles was as if she thought: “If the Chilean women can do it, I can also do it. I can create what I need to create.” This piece is very symbolic in the sense that its genesis was in my home, in a discussion with two friends involved in a movement for the abolition of war, about the use of this violence, that can be done so comfortably from home, from computers. We now have the possibility for one person in one country to decide who the target is going to be and where. That you can destroy whole villages because you want to destroy one person. This piece is in response to that. Stitching is like your own handwriting. Though you and I might have the same pen, it will come out differently. Here, Deborah is reflecting, responding and engaging with the arpillera language with her own kind of perspective and through her own research. S: Yes, her own mark. Threads of anti-militarism: from the local to the global For me, this piece is more explicit than those previously discussed, but is also as emotionally impactful on the viewer. How do you think this piece represents conflict and violence differently? R: For me it is a reflection, it comes from a deep conversation, trying to embrace the consequences of war through technology and being “so sophisticated”. For those who suffer the bombing on the ground, it is not going to be so sophisticated. You are going to be destroyed and you won’t even know where this comes from, you won’t even be able to respond. The other textiles we have discussed were explicit in different ways – wanting Pinochet to go. Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 Here, we have an image of this man comfortable in his office, listening to whatever he is listening to, the drone targeting the village and people afraid because they can hear the drone. I can relate this very much to the carpets made in Afghanistan that depicted the plane bombings in a time when there were no mobile phones or cameras to take photographs of these bombs. They were woven as a kind of picture and could even be used in court as a kind of testimony to demonstrate who had come to bomb them. Yet, Digital death is quite a composed piece. It reflects the people and action from a distance. Unfortunately, from the textile we don’t see the colours of the image of the girl. It is very blue in real life. This is important because this represents a 2014 art installation called #NotABugSplat.5 The installation is of a massive photograph of a girl who lost both her parents and two young siblings in a drone attack. The artist collective who created the installation placed it on the land in the heavily bombed Khyber Pakhtunkhwa region of Pakistan so that when a drone flew overhead, they could see this girl as a remembrance of the survivors and innocent victims. It is full of different materials, and to make this piece, Deborah researched a lot, even down to the proportions and sizes of the characters and objects. S: The next textile also speaks to the role of technology in today’s conflict. It’s no ****** computer game!! (see Figure 6) is striking for its colours. Threads of anti-militarism: from the local to the global It has a silk fabric that immediately gave me the impression it was more contemporary, but its subject also reflects our distance from conflict in the world. Figure 6: Campbell, T. and Campbell, I. (2012) It’s no ******* computer game!! Banner, Wales. Photo: Lydia Cole, © Conflict Textiles Figure 6: Campbell, T. and Campbell, I. (2012) It’s no ******* computer game!! Banner, Wales. Photo: Lydia Cole, © Conflict Textiles Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 Contemporary Voices, Unravelling the Threads of War and Conflict, December 20 10 R: The difference lies in the purpose of the textile. This one is a banner, so it can be used to march and denounce, while the other is a picture. I find this a very powerful piece and Thalia and Ian Campbell have been very active members of so many movements in the UK which have denounced militarism. S: To me this is interesting because today we are so used to seeing posters, images, photographs and videos. This was made in 2012, so it is fairly recent compared to the Chilean arpilleras. What do you think is the difference in understanding of the message when it is displayed on something that has taken a lot of time to make, like this banner, as opposed to a poster for a protest? R: I think some people learn better by reading, others by hearing. I think you have to use all the systems that you can, and you have to try to engage people from all their senses and their abilities. I don’t think one alone is better than the other. It is the different uses of expression. I think it is the effectiveness and the right moment to use it in the right place. It is not very easy to go with a big banner to a small meeting. You need space and time, and you need to locate the pieces in the context in which they can be appreciated. S: What do you think it offers the creators of such pieces, since it takes much more time for them to create a textile such as this versus making something on the computer in a matter of minutes to print? R: I think it is your own way of contributing to a cause or to express yourself. Threads of anti-militarism: from the local to the global Sometimes you can take many photos and you don’t like any, you don’t feel any represents what you wanted to say. This is the long-standing purpose from beginning to completion. In textiles, you only see the pieces that are completed. You have to have the momentum for that. Making is a process, you must have a trigger, you must have internal space, physical space, an environment of support, in a way that at least lets you do it. Threads’ emotional, tactile and intimate politics S: This next piece, My daughter’s wedding, was created in a workshop (see Figure 7). It is made by a mother who depicts her daughter’s wedding that she could not attend because her documents were revoked. The piece can be connected to the increased hostility surrounding immigration in Europe. 11 Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 Figure 7: Mansouri, F. (2017) LA BODA DE MI HIJA / My daughter’s wedding. Arpillera, Catalonia, Spain. Photo: Ricard Díez, © Conflict Textiles R: Yes, it was made in a workshop in Catalonia. It also demonstrates how sometimes you can be deceived by the image, the colours and everything, depicting something so beautiful, but you have to be careful what you read because behind the scenes there might be something different happening. S: What role do you see emotion playing in this particular piece and in the wider significance of textile-making? R: I think the emotional is always present in the tactile element of the textile. Don’t forget that there are two things you have to do every day of your life: dress yourself and eat. Textile is thus something quotidian that will appear in everything. Interestingly enough, I was talking to an artist yesterday about the times that we are living in. Issues related to the environment and Covid-19 are showing us the importance of reusing and repurposing materials. That we can’t continue polluting, using disposable throwaway items, paper napkins and all of that. I think we will also see a recurrence of textile work. I have begun organising exhibitions online in response. We have been encouraging people in lockdown and/or staying at home to engage and use what they have at hand. So, it is also an opportunity to reflect on how we can express our emotions and our actions by using what we have on hand. I usually say: ‘No list, just bring scraps of materials and you will find you have more than you need’. S: If you completely rely on what you have and don’t search for any fancy materials, you realise that it is hard to distinguish which periods these textiles are from. Materials are materials. R: This piece as well has so much volume and texture. Connections, collaborations and curating in Threads, war and conflicti Connections, collaborations and curating in Threads, war and conflict S: This brings me to our final piece: the bookmark outlining the exhibition programme (see Figure 8). Why did the organisers choose to do a bookmark to represent the programme? S: This brings me to our final piece: the bookmark outlining the exhibition programme (see Figure 8). Why did the organisers choose to do a bookmark to represent the programme? Figure 8: Bookmark with the Threads, war and conflict programme. University of St Andrews, 2019. R: Conflict Textiles have been featured on bookmarks for a while. A bookmark is usable. It is not just for the opening of the event. The beautiful thing is you can keep it over the years, a reminder. On the other hand, it’s a nice exercise to write the programme with brief enough information to make you want to know more. If you look at the bookmark, you can see a stitch that details each activity. S: Yes, the visuality of the logo and stitches marking each event becomes a powerful thread itself. Can you speak a little bit to the time of curating and creating this programme? What was that process like? La Cueca Sola / Dancing Cueca Alone, 1989 © Conflict Textiles http://cain.ulster.ac.uk/conflicttextiles The University of St Andrews is a charity registered in Scotland, No: SC013532. 3rd-29th April: ‘Threads, War and Conflict’ at The Byre Theatre 29th March-29th April: ‘Threads, War and Conflict: Satellite Exhibition’ at University of St Andrews Library 12th, 19th, 26th April: Masters Workshops, ‘Responding to Threads, War and Conflict: Letters to Arpilleristas’ (by invitation only) 9th March: ‘Threads, War and Conflict: An Exhibition of Women’s Conflict Textiles from Around the World’ at the Red Box, Verdant Works, 2-3.30pm 3rd April: Exhibition Launch at the Studio, The Byre Theatre, 4.15-5.45pm 8th April: ‘Visualising War and the Expressive Arts’ with School of Classics, 1.30-6.30pm 22nd April: ‘Knowing Through Needlework? Conflict Textiles and the Study of War and Violence in International Politics’ with Dr Berit Bliesemann de Guevara (Aberystwyth University), Arts Lecture Theatre, 5-7pm 24th April: Threads, War and Conflict Conference (by invitation only) 26th April: Creative Evening at Studio, The Byre Theatre, 6-9pm Figure 8: Bookmark with the Threads, war and conflict programme. University of St Andrews, 2019. Figure 8: Bookmark with the Threads, war and conflict programme. University of St Andrews, 2019. Threads’ emotional, tactile and intimate politics When choosing pieces with Lydia for Threads, war and conflict, we had to find pieces that appealed to our curatorial line, with its common thread of everyday experiences of war and conflict, and its layers of hope and suffering. This included textiles about bombs, lack of free movement and hunger. It is important that we can weave these textiles together to show what is happening. Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 12 S: I agree. I love this textile for how three-dimensional it is. It goes to show that you can really think out of the box and get creative when it comes to sewing and needlework. It also speaks to it as a form of language. This is also so interesting, as some of the makers did not have prior experience in textile-making or thread-work. In that sense, textile language is not two-dimensional; it has many variations. R: I always say that the little mistakes you have in sewing are like spelling mistakes. The more practice you have, the less spelling mistakes you have. It is another skill, another language, another technique. Sometimes we are told that we have to be proficient in everything. But if we give it patience, time, a little dedication and value, you discover things within yourself. The value of the textile lies in more than just its looks. Not everything in life is beautiful either. Some pieces appeal to you because of their modesty! S: I definitely find that the mistakes we identify in the textile are probably the most interesting because they remind you that someone hand-made them. This also tells a story. S: I definitely find that the mistakes we identify in the textile are probably the most interesting because they remind you that someone hand-made them. This also tells a story. Connections, collaborations and curating in Threads, war and conflicti R: Conflict Textiles have been featured on bookmarks for a while. A bookmark is usable. It is not just for the opening of the event. The beautiful thing is you can keep it over the years, a reminder. On the other hand, it’s a nice exercise to write the programme with brief enough information to make you want to know more. If you look at the bookmark, you can see a stitch that details each activity. S: Yes, the visuality of the logo and stitches marking each event becomes a powerful thread itself. Can you speak a little bit to the time of curating and creating this programme? What was that process like? R: Well, it was quite organic. So, it wasn’t an exhibition that came ready made from Northern Ireland. We went physically, myself and Breege, Assistant Curator of Conflict Textiles, to St Andrews and spent two full days with the organisers, giving them space and time to talk about what they expected, and what they wanted to do with the exhibition. That is what started it, involving everyone with the role of curation, helping each other, collaborating and Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 13 building. Then adding ideas about what would be significant for the kind of topics they were developing in their lectures, connected to the students that were there at the time, because it is very versatile material – at once so ordinary yet so sophisticated – that can speak to people across different backgrounds, experiences and perspectives. S: Yes, we had some researchers and academics, but we also had Master’s students and the general public. R: This connection of different voices was extremely good, and we agreed from the beginning to have a satellite exhibition in the University library, so that people could know that even though it was an arpillera exhibition with materials that were very simple, it had given space for lots of research, scholarship and interpretation. Everybody has to live their lives, there is no more or less important life. It is how you can engage with what you do in daily life. Connections, collaborations and curating in Threads, war and conflicti So that was the idea, and also to space them in a way that the exhibitions in some way, for me, are an excuse for all the activities that take place during the time – to have the conversations, the workshops, the visits, the challenges, and keep the momentum from beginning to end, and that the end is never a conclusion but only the last step of this part of the process. Conclusion: tying threads This dialogue has traced the Threads, war and conflict exhibition in reverse – from outcome to opening – to unravel the possibilities of International Relations and/as thread-work. Framing itself around material artefacts of the exhibition – the collective textile workshops poster, selected textiles featured in the exhibition and the events programme bookmark – the dialogue weaves together the various threads of their material effects. The discussion of the collective textile workshops and exhibition events has placed emphasis on the collaborative participation within the exhibition. This was particularly borne out in the textile workshops in which students and academics across Scottish Higher Education Institutions produced textile responses to the exhibition. Participants engaged as arpilleristas, responding to themes of home, loss and resistance to violence within the resulting textiles. From the beginning, participants knew that the textile would form part of a broader collaborative textile to be archived within the Conflict Textiles collection. This mode of collective making not only generated renewed understandings of the arpilleras themselves, but also generated further insights into loss and resistance to violence in global contexts. In this way, through this interactivity, an affective and tactile politics emerges as a powerful creative site for “knowing” and “doing” IR. Focusing on five textiles that were featured in the exhibition has both highlighted the diversity of the textiles and elucidated the exhibition’s central themes of resistance, the ethics of warfare, and migration and displacement. The textiles selected for discussion here stand out because they all work to transgress conventional assumptions of embroidered works, prompting us to consider instead the political potency of arpilleras in terms of their narratives, symbols, usage and intended audiences. Indeed, visitors to the exhibition remarked on the way that these seemingly everyday objects, nevertheless, seemed to speak loudly of resistance to violence. The reflection on the exhibition’s bookmark further highlights the intertwining connections of voices, people and events within the exhibition and its curation. As Roberta remarks, the organising team at St Andrews cultivated this connection throughout by creating opportunities for the sharing of stories through conversation and making (see Cole, 2019). In each of these forms of interactivity – collaborative making, engaged looking and connective curating – the affective and tactile politics of engaging with conflict textiles were placed at the fore. S: Do you have a final take-away from the St Andrews exhibition at the Byre Theatre? S: Do you have a final take-away from the St Andrews exhibition at the Byre Theatre? R: I would say it was a very well-lived exhibition. All the times we spent together were extremely enjoyable and, I would say, smooth, even in the most difficult moments. There was always a warm atmosphere of being involved; we were all in the same boat. That is something that sewing gives you; there is not this competitive element that is so often pervasive in academia. Here, everybody helps the other, it comes naturally. We were all there to accomplish this, and I valued very much when, for the opening, we also had a textile artist who had worked with me in Liverpool. She had come from a very remote part of the end of Scotland, to be here after ten years of not being involved with arpilleras. So, we brought together new and old voices. We renewed commitments. And after St Andrews, she came to the launch of my exhibition here in March and contributed a doll that she had made twenty- five years ago. There is a sense here that textile triggers emotions. It triggers an exploration of memory, both of what has happened and been happening. Although in this moment you may not be sewing, it brings to mind memories of when you have before. For example, you may have told the stories of losing relatives you love through the language of textile, using a piece of cloth from the T-shirt of your father. Experiencing the textiles through an exhibition can bring all this to mind. That triggering of emotions and experiences was extremely well achieved by this exhibition. I also think Lydia had a very good team, knowing exactly what she was after, but also flexible, not just working toward the final goal. Each exhibition is owned by the collective that organises, prepares and lives it, and then has it there as a testimony for the future, because in our archive it is there forever. Our exhibitions are always an invitation to participate, not just to be a spectator. Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 14 Conclusion: tying threads Originally made in Chile to document violence and resistance during the Pinochet dictatorship, the form has since been taken up in other contexts including Peru, Colombia, Zimbabwe and Northern Ireland. 4 For further information on Disobedient objects at the Victoria and Albert Museum, London, see: https://cain.ulster.ac.uk/conflicttextiles/search-quilts2/fullevent1/?id=129 (Accessed: 23 February 2021). 5 For further information on the #NotABugSplat project and installation, see https:// notabugsplat.com/ (Accessed: 2 August 2021). 5 For further information on the #NotABugSplat project and installation, see https:// notabugsplat.com/ (Accessed: 2 August 2021). Bibliography #NotABugSplat collective (2014) ‘A giant art installation targets predator drone operators’, #NotABugSplat [Online]. Available at: https://notabugsplat.com/ (Accessed: 18 June 2021). Andrä, C., Bliesemann de Guevara, B., Cole, L. and House, D. (2020) ‘Knowing through needlework: curating the difficult knowledge of conflict textiles’, Critical Military Studies, 6 (3-4), pp. 341-359. Cole, L. (2019) Threads, war and conflict and its associated programme [Online]. Available at: https://cain.ulster.ac.uk/conflicttextiles/mediafiles/1321_Threads-War-and-Conflict- Photo-Essay-compressed-240619.pdf (Accessed: 18 June 2021). Conclusion: tying threads In crafting space for connection and creation where this politics makes itself felt, conflict textiles emerge as a powerful creative site for “knowing” and “doing” IR differently. Throughout the dialogue, we have revealed the wider communities of care which emerge through the textiles, as well as in their curating. Collaboration between the Threads team (as temporary custodians) and the Conflict Textiles permanent curatorial team helped to curate an exhibition whose legacies of collectivity, creativity and care of/for makers, curators, spectators and IR scholars continue to make themselves felt. In this way, curating the (hi) stories of conflict textiles contributes to alternative forms of IR knowledge production. Engaging with conflict textiles demands the unravelling and weaving together of their Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 15 multiple narrative threads. Acting with these stories of loss, violence and its resistance, we argue that curating can form part of a process of embodied connection to stories of war and conflict that reach far beyond the academy. In this dialogue, we follow others (Andrä, Bliesemann de Guevara, Cole and House, 2020) in urging for future research into textile art as a language and methodology for the study of conflict, violence and resistance in IR. The exhibition and this dialogue present an alternative language for our study of IR, one that invites a more organic, emotional and tactile participation in politics based on the humble scraps of material we can all find at home. 1 For further information on Threads, war and conflict, see https://cain.ulster.ac.uk/ conflicttextiles/search-quilts2/fullevent1/?id=196 (Accessed: 2 August 2021). 1 For further information on Threads, war and conflict, see https://cain.ulster.ac.uk/ conflicttextiles/search-quilts2/fullevent1/?id=196 (Accessed: 2 August 2021). 2 For further information on the Conflict Textiles collection, see https://cain.ulster.ac.uk/ conflicttextiles/ (Accessed: 2 August 2021). 2 For further information on the Conflict Textiles collection, see https://cain.ulster.ac.uk/ conflicttextiles/ (Accessed: 2 August 2021). 2 For further information on the Conflict Textiles collection, see https://cain.ulster.ac.uk/ conflicttextiles/ (Accessed: 2 August 2021). 3 The term arpillera refers to stitched “textile pictures” (Andrä, Bliesemann de Guevara, Cole and House, 2020, p. 342). Originally made in Chile to document violence and resistance during the Pinochet dictatorship, the form has since been taken up in other contexts including Peru, Colombia, Zimbabwe and Northern Ireland. 3 The term arpillera refers to stitched “textile pictures” (Andrä, Bliesemann de Guevara, Cole and House, 2020, p. 342). Bibliography g p y #NotABugSplat collective (2014) ‘A giant art installation targets predator drone operators’, #NotABugSplat [Online]. Available at: https://notabugsplat.com/ (Accessed: 18 June 2021). g p y #NotABugSplat collective (2014) ‘A giant art installation targets predator drone operators’, #NotABugSplat [Online]. Available at: https://notabugsplat.com/ (Accessed: 18 June 2021). #NotABugSplat collective (2014) ‘A giant art installation targets predator drone operators’, #NotABugSplat [Online]. Available at: https://notabugsplat.com/ (Accessed: 18 June 2021). Andrä, C., Bliesemann de Guevara, B., Cole, L. and House, D. (2020) ‘Knowing through needlework: curating the difficult knowledge of conflict textiles’, Critical Military Studies, 6 (3-4), pp. 341-359. Andrä, C., Bliesemann de Guevara, B., Cole, L. and House, D. (2020) ‘Knowing through needlework: curating the difficult knowledge of conflict textiles’, Critical Military Studies, 6 (3-4), pp. 341-359. Andrä, C., Bliesemann de Guevara, B., Cole, L. and House, D. (2020) ‘Knowing through needlework: curating the difficult knowledge of conflict textiles’, Critical Military Studies, 6 (3-4), pp. 341-359. Cole, L. (2019) Threads, war and conflict and its associated programme [Online]. Available at: https://cain.ulster.ac.uk/conflicttextiles/mediafiles/1321_Threads-War-and-Conflict- Photo-Essay-compressed-240619.pdf (Accessed: 18 June 2021). Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 16 Images Figures 1 and 2: University of St Andrews (2019) Master’s workshops: responding to Threads, war and conflict: letters to arpilleristas [Poster]. Available at: https://cain.ulster.ac.uk/ conflicttextiles/mediafiles/1269_Masters-Workshops-Poster-final-240219.pdf (Accessed: 2 August 2021). Figure 3: Anonymous (c1980) ¡Adiós Pinochet! / Goodbye Pinochet. [Arpillera, Chile], Conflict Textiles [Online]. Available at: https://cain.ulster.ac.uk/conflicttextiles/search- quilts2/fulltextiles1/?id=32 (Accessed: 2 August 2021). Figure 4: Morales, V. (1989) La cueca sola / Dancing cueca alone [Arpillera, Chile], Conflict Textiles [Online]. Available at: https://cain.ulster.ac.uk/conflicttextiles/search-quilts2/ fulltextiles1/?id=414 (Accessed: 2 August 2021). Figure 5: Stockdale, D. (2014) Digital death [Arpillera, Republic of Ireland], Conflict Textiles [Online]. Available at: https://cain.ulster.ac.uk/conflicttextiles/search-quilts2/ fulltextiles1/?id=279 (Accessed: 2 August 2021). Figure 6: Campbell, T. and Campbell, I. (2012) It’s no ******* computer game!! [Banner, Wales], Conflict Textiles [Online]. Available at: https://cain.ulster.ac.uk/conflicttextiles/ search-quilts2/fulltextiles1/?id=373 (Accessed: 2 August 2021). Figure 7: Mansouri, F. (2017) LA BODA DE MI HIJA / My daughter’s wedding [Arpillera, Catalonia/Spain], Conflict Textiles [Online]. Available at: https://cain.ulster.ac.uk/ conflicttextiles/search-quilts2/fulltextiles1/?id=410 (Accessed: 2 August 2021). Figure 8: University of St Andrews (2019) Threads, war and conflict programme [Bookmark]. Available at: https://cain.ulster.ac.uk/conflicttextiles/mediafiles/1280_Threads-War-Conflict- bookmarks-0319-DU37413.pdf (Accessed: 2 August 2021) Figure 8: University of St Andrews (2019) Threads, war and conflict programme [Bookmark]. Available at: https://cain.ulster.ac.uk/conflicttextiles/mediafiles/1280_Threads-War-Conflict- bookmarks-0319-DU37413.pdf (Accessed: 2 August 2021) Contemporary Voices, Unravelling the Threads of War and Conflict, December 2021 17
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Sorbose resistant mutants in Neurospora crassa
Fungal genetics reports
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Sorbose resistant mutants in Neurospora crassa Sorbose resistant mutants in Neurospora crassa W. Klingmüller F. Kaudewitz Follow this and additional works at: https://newprairiepress.org/fgr This work is licensed under a Creative Commons Attribution-Share Alike 4.0 License. Fungal Genetics Reports Fungal Genetics Reports Fungal Genetics Reports Fungal Genetics Reports Volume 4 Volume 4 Article 7 Recommended Citation Recommended Citation Klingmüller, W., and F. Kaudewitz (1963) "Sorbose resistant mutants in Neurospora crassa," Fungal Genetics Reports: Vol. 4, Article 7. https://doi.org/10.4148/1941-4765.2151 This Research Note is brought to you for free and open access by New Prairie Press. It has been accepted for inclusion in Fungal Genetics Reports by an authorized administrator of New Prairie Press. For more information, please contact cads@k-state.edu. his research note is available in Fungal Genetics Reports: https://newprairiepress.org/fgr/vol4/iss1/7 Klingmiiller, W. and F. Kaudewitz. Sorbose resistant mutants in Neurospora crossa. and Pxockman, Nature 193, 556, 1962). By treating conidia with nitrous acid, mutants have been produced that are not blocked~iingm~ller, Erwin-E!aur- Gedochtnisvorlesungen III, 1963, Ak CI d emie-Verlog-Berlin, in press). Such sorbose resistant mutants (S-) hove been induced in strain F68, which is adenine-deficient (4 S- mutants isolated so far), as well as in strain 74-OR 23- IA de Serres, from which F 68 originated (IO S- mutants isolated so far). By crossing the S- mutants to tester strains, they could be shown to be of chromosomol origin. The 4 mutants induced in strain F 68 map in the left arm of linkage group VI, close to the yellow marker. One of the mutants induced in the wild type maps in linkage group 1. The latter is intermediate in sorbose resistance between the wild type and the 4 former S- mutants. There are also mutants induced in an S- strain by further treatment with nitrous acid, which are more resistant than the four S- mutants. By germinating wild type conidia in liquid medium free of sorbose for up to 9 hours, and then pouring in sorbose-containing agar medium it could be shown that sorbose blocks germination 0s well cx early stages of growth. Thus there is no preferential phase of development at which the sorbose block seems to act. General growth characteristics of the mutants as compared to wild type ore: The mutants germinate and grow (colonial) on solid fructose, sucrose, and glucose media in spite of added sorbose. The wild type does not germinate and grow on fructore/sorbose media, grows only very weakly on sucrose/sorbose media, but grows well on glucose/sorbose media (all sugars filter-sterilized). Germination of the wild type and of two S- mutants on media containing different sugars as carbon source is given in table I. Table I: Germination percentage of wild type and 2 sorbose-resistant mutants of Neurospora on agar media with different Carbohydrates. All media con- taining 0. I% sorbose, Fries’ minimal plus 1.5% ogar. Cultures were checked after 5 days; glucose cultures after 3 days. Table I: Germination percentage of wild type and 2 sorbose-resistant mutants of Neurospora on agar media with different Carbohydrates. All media con- taining 0. I% sorbose, Fries’ minimal plus 1.5% ogar. Cultures were checked after 5 days; glucose cultures after 3 days. Abstract Abstract Sorbose resistant mutants in Neurospora crassa Klingmiiller, W. and F. Kaudewitz. Sorbose Growth of Neurospora on filter-sterilized sucrose resistant mutants in Neurospora crossa. media is blocked by sorbose (De Serres, Kblmork and Pxockman, Nature 193, 556, 1962). By treating conidia with nitrous acid, mutants have been produced that are not blocked~iingm~ller, Erwin-E!aur- Gedochtnisvorlesungen III, 1963, Ak CI d emie-Verlog-Berlin, in press). Klingmiiller, W. and F. Kaudewitz. Sorbose resistant mutants in Neurospora crossa. Carbohydrate Strains added 74 A Sl/25 Y 0 34.0 41.4 sucrose, 0.01% 15.0 49.7 67.5 maltose, 0.01% 22.9 69.0 86.6 glucose, 0.01% 86.5 99.0 64.7 iructose, 0.01% 0.7 89.5 68.4 ‘mannose, 0.01% 87.4 100.0 85.0 galactose, 0.01% 16. I 80.0 84.5 xylose, 0.01% 95.0 96.5 74.5 glycerol, 0.5% 2.8 100.0 64.5 arch for the step(s) in sugar metabolism at which sorbose acts in the wild type is under way.-- nstitut fur Erbbiologie, Berlin-Dahlem, Ehrenbergstr. 26. Carbohydrate Strains added 74 A Sl/25 Y 0 34.0 41.4 sucrose, 0.01% 15.0 49.7 67.5 maltose, 0.01% 22.9 69.0 86.6 glucose, 0.01% 86.5 99.0 64.7 iructose, 0.01% 0.7 89.5 68.4 ‘mannose, 0.01% 87.4 100.0 85.0 galactose, 0.01% 16. I 80.0 84.5 xylose, 0.01% 95.0 96.5 74.5 glycerol, 0.5% 2.8 100.0 64.5 A search for the step(s) in sugar metabolism at which sorbose acts in the wild type is under way.-- Max-Planck-Institut fur Erbbiologie, Berlin-Dahlem, Ehrenbergstr. 26. A search for the step(s) in sugar metabolism at which sorbose acts in the wild type is under way.-- Max-Planck-Institut fur Erbbiologie, Berlin-Dahlem, Ehrenbergstr. 26. A search for the step(s) in sugar metabolism at which sorbose acts in the wild type is under way.-- Max-Planck-Institut fur Erbbiologie, Berlin-Dahlem, Ehrenbergstr. 26.
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Resistance to <i>Orobanche crenata</i> Forsk. in lentil (<i>Lens culinaris</i> Medik.): exploring some potential altered physiological and biochemical defense mechanisms
Journal of plant interactions
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Journal of Plant Interactions Journal of Plant Interactions ISSN: (Print) (Online) Journal homepage: https://www.tandfonline.com/loi/tjpi20 Youness En-nahli, Hicham El Arroussi, Shiv Kumar, Outmane Bouhlal, Rachid Mentag, Kamal Hejjaoui, Ahmed Douaik, Zouhaier Abbes, Nour Eddine Es- Safi & Moez Amri Youness En-nahli, Hicham El Arroussi, Shiv Kumar, Outmane Bouhlal, Rachid Mentag, Kamal Hejjaoui, Ahmed Douaik, Zouhaier Abbes, Nour Eddine Es- Safi & Moez Amri To cite this article: Youness En-nahli, Hicham El Arroussi, Shiv Kumar, Outmane Bouhlal, Rachid Mentag, Kamal Hejjaoui, Ahmed Douaik, Zouhaier Abbes, Nour Eddine Es-Safi & Moez Amri (2021) Resistance to Orobanche￿crenata Forsk. in lentil (Lens￿culinaris Medik.): exploring some potential altered physiological and biochemical defense mechanisms, Journal of Plant Interactions, 16:1, 321-331, DOI: 10.1080/17429145.2021.1949498 To link to this article: https://doi.org/10.1080/17429145.2021.1949498 To link to this article: https://doi.org/10.1080/17429145.2021.1949498 © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group Published online: 19 Jul 2021. Submit your article to this journal Article views: 548 View related articles View Crossmark data 1. Introduction (Singh and Singh 2014). It is an important staple food crop particularly among the poor populations and smallholder farmers (Çarman 1996). As other legumes crops, lentil is considered as a pivotal component for sustainable agricul- ture due to its ability to fix nitrogen in the soil, which makes practical to use it in rotation with cereals (Shah et al. 2003). Morocco is the second major producer of lentil in Africa with more than 40,000 ha cultivated area (Taha et al. 2018), and total annual production of 30,670 tons (Idrissi et al. 2020). It account about 14% of the total legume cultivated area in the country. In Morocco, Lentil is mainly cultivated under rainfed conditions in the dry areas where drought is the major abiotic constraints limiting the crop production and productivity due to low and irregular rainfall (Idrissi et al. 2020). Attack by the parasitic weed O. crenata seems to be the most important biotic stress limiting the (Singh and Singh 2014). It is an important staple food crop particularly among the poor populations and smallholder farmers (Çarman 1996). As other legumes crops, lentil is considered as a pivotal component for sustainable agricul- ture due to its ability to fix nitrogen in the soil, which makes practical to use it in rotation with cereals (Shah et al. 2003). Morocco is the second major producer of lentil in Africa with more than 40,000 ha cultivated area (Taha et al. 2018), and total annual production of 30,670 tons (Idrissi et al. 2020). It account about 14% of the total legume cultivated area in the country. In Morocco, Lentil is mainly cultivated under rainfed conditions in the dry areas where drought is the major abiotic constraints limiting the crop production and productivity due to low and irregular rainfall (Idrissi et al. 2020). Attack by the parasitic weed O. crenata seems to be the most important biotic stress limiting the Lentil (Lens culinaris Medik.) is the third-most important cool-season grain legume in the world after chickpea and pea. It is widely grown as a rainfed crop on 3.85 million hec- tares area and accounted for 6% of the total global pulses production with 3.59 million tonnes and average yield of 0.93 tn ha−1 (Sehgal et al. 2021). Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=tjpi20 Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=tjpi20 JOURNAL OF PLANT INTERACTIONS 2021, VOL. 16, NO. 1, 321–331 https://doi.org/10.1080/17429145.2021.1949498 JOURNAL OF PLANT INTERACTIONS 2021, VOL. 16, NO. 1, 321–331 https://doi.org/10.1080/17429145.2021.1949498 ABSTRACT Management of broomrape (Orobanche crenata Fosk.) that causes important damages on lentil production becomes a veritable concern in the Mediterranean region. Eighty lentil accessions were evaluated for resistance to O. crenata under field and controlled conditions. Both genotypes ILL6415 and ILL7723 expressed the highest resistance level under field and pot experiment with low Orobanche infestation and relatively high seed yield (50.1 g m−2). Such resistance was associated with physiological and biochemical changes in metabolites profiling. In total, 109 and 115 metabolites were identified in the lipophilic phase of both ILL6415 and ILL7723, respectively, against only 92 metabolites recorded for susceptible check Zaaria. Significant differences were observed in metabolite concentrations (fatty acids, sterols alkanes) between roots and shoots of susceptible and resistant infested plants. Accumulation of α-linolenic acid and arachidic acid was more pronounced in the resistant genotypes ILL6415, ILL7723 which could be associated with resistance pathways involved in the resistance to O. crenata. KEYWORDS Orobanche crenata; Lens culinaris Medik; resistance; metabolomics © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. CONTACT Moez Amri moez.amri@um6p.ma PLANT-PLANT INTERACTIONS Resistance to Orobanche crenata Forsk. in lentil (Lens culinaris Medik.): exploring some potential altered physiological and biochemical defense mechanisms Resistance to Orobanche crenata Forsk. in lentil (Lens culinaris Medik.): exploring some potential altered physiological and biochemical defense mechanisms Youness En-nahlia,b,c, Hicham El Arroussid, Shiv Kumar c, Outmane Bouhlalc, Rachid Mentage, Kamal Hejjaouic, Ahmed Douaik e, Zouhaier Abbes f, Nour Eddine Es-Safib and Moez Amri a Youness En-nahlia,b,c, Hicham El Arroussid, Shiv Kumar c, Outmane Bouhlalc, Rachid Mentage, Kamal Hejjaouic, Ahmed Douaik e, Zouhaier Abbes f, Nour Eddine Es-Safib and Moez Amri a aAfrican Integrated Plant and Soil Research Group (AiPlaS), University Mohammed VI Polytechnic (UM6P), Ben Guerir, Morocco; bMaterials Science Center (MSC), Mohammed V University in Rabat, LPCMIO, Ecole Normale Supérieure, Rabat, Morocco; cInternational Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco; dMoroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat, Morocco; eNational Institute of Agricultural Research (INRA), Rabat, Morocco; fField Crop Laboratory, National Institute for Agricultural Research of Tunisia (INRAT), Carthage University, Tunis, Tunisia © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. p ARTICLE HISTORY Received 17 May 2021 Accepted 25 June 2021 KEYWORDS Orobanche crenata; Lens culinaris Medik; resistance; metabolomics PI = OIN∗OSV/100 Several control methods have been tested but none of them resulted in complete and successful control of the para- site (Abbes et al. 2019). Breeding for resistance is considered as the most economically feasible and environment friendly control method (Amri et al. 2019). This strategy has shown promising success and many resistance sources were ident- ified in faba bean, Chickpea, sunflower and tomato (Kharrat et al. 2010; Nefzi et al. 2016; Amri et al. 2019; Bai et al. 2020; Cvejić et al. 2020). However, breeding for resistance to broomrape remains complicated because of the limited source of the resistance and the low heritability of the genes and QTLs associated with that resistance (Pérez-De- Luque et al. 2005; Amri et al. 2021). Indeed, a better under- standing and development of solid knowledge about the resistance mechanisms involved and the interaction between the host and the parasite will help to improve the resistance level and develop new breeding material (Pérez-De-Luque et al. 2007; Trabelsi et al. 2017; Abbes et al. 2020). Lentil is poorly competitive with O. crenata, which can cause com- plete yield loss under high infested conditions. Unfortu- nately, studies on lentil resistance to O. crenata and the interaction between host and parasite are still insufficient. A recent scientific report showed that the metabolomics profile of the parasite is different from that of the host, which means that the parasite may have a self-regulating in metabolism (Amir 2016; Clermont et al. 2019). Some other studies reported that environmental stresses cause changes in primary and secondary plant metabolisms which depend on plant resistance strategies (Hasanuzzaman et al. 2013). OIN: Percentage of lentil plants showing at least one emerged shoots of orobanche per row. OSV: level of damage (1–9 scale) caused by the parasite on lentil growth and seed production (Abbes et al. 2007). 2.2. Pot experiment Lentil genotypes used to identify the resistance levels under field conditions during cropping seasons 2017–2018 and 2018/2019. 1. Introduction The major production regions are South Asia and China (44.3%), North America (41%), Central and West Asia and North Africa – CWANA (6.7%), Sub-Saharan Africa (3.5%) and Australia (2.5%) (Kumar et al. 2013). Lentil has been cultivated for more than 10,000 years for its important agronomic and socioeconomic roles worldwide (Erskine et al. 2011). With high protein level and an important amount of carbo- hydrates, fibers, minerals and antioxidant compounds, lentil is considered as one of the most nutritious legume crop Y. EN-NAHLI ET AL. 322 production and the development of the crop especialy in Zaair region which is the most important production area in the country. In fact, O. crenata is an holoparasitic plants completely dependent on the host for its nutritional require- ments. Its is considered as a serious threat that causes impor- tant damages and yield losses on many legume crops in the Mediterranean region and Sub-Sahan Africa (Amri et al. 2021). During the last decades, attack by this parasite has burden lentil production and productivity in Morocco (Kumar et al. 2015; Abu-Irmaileh and Labrada 2017; Idrissi et al. 2020). The continuous spread of this threat and important damages that causes on lentil and other host crops often force farmers to give up growing these crops (Amri et al. 2019). Recent assessment conducted in Morocco reported 51% estimated infested legumes cultivated areas with an average yield loss of 30–40% (Abu-Irmaileh and Labrada 2017). were planted end of November according to an alpha lattice design with two replications. For each genotype, 30 seeds were planted in 1 m row with 30 cm inter-row spacing. The local cv. Bakria which is reported to be moderately sus- ceptible to O. crenata was used as check. Hand weeding was done when necessary and neither herbicide nor fertilizer were applied. The following parameters were recorded before and at crop maturity, Number of days to flowering (D2F), days to Orobanche emergence (D2OE), Orobanche incidence (OIN), Orobanche severity (OSV), Emerged Oro- banche number per plant (EON), Emerged Orobanche dry weight per plant (EODW), biological yield g m−2 (BY) and seed yield g m−2 (SY), the harvest index (HI) and parasitism index (PI). The PI was calculated according to the following formula: Table 1. Lentil genotypes used to identify the resistance levels under field conditions during cropping seasons 2017–2018 and 2018/2019. Region Country of origin/Entry IG number Americas MEX (5645-ILL351, 502), ARG (4605, 268), CAN (4738), CHL (468, 361), URY (4778), ICA (10952, 10912), Europe ESP (4926, 5628-ILL915, 5653), FRA (6528), ITA (5418) DEU (4881), POL (705), UKR (82), UNK (4345, 6415), RUS (4830, 597, 4819), CZE (4409), YUG (2230- ILL624), GRC (304), HRV (4915), North and Sub- Saharan Africa ETH (5639-ILL207), DZA (4781), MAR (7726, Chakkouf, Bakria, Zaaria), SDN (1861), Asia IND (4164), IRN (223, 257), AFG (213), JOR (5384, 5562, 5244), LBN (5626-ILL840, 840, 191), PSE (4606), NPL (3485, 3487), PAK (6350), SYR (6870, 6848, 490), TUR (590, 71), ARM (619), Others LIRL-22-107, LIRL-21-187, 6002, 6021, 8009, 9951, 88527, 6025, LIRL-22-109, 9850, 8090, 7213, LC960254, 8195, 7982, 7984, 7685, 7701, 6783, 7668, 8622, 7934, 6015, 8068, 7723, 7532 2.2. Pot experiment Out of the 80 tested genotypes, five lines selected for their resistance to O. crenata were subjected to a confirmation pot experiment under controlled conditions with two Oro- banche treatments (infested and non-infested). The five selected lines all with two released varieties (Bakria and Zaaria) were planted in 2 l pots. Infested pots were inocu- lated with O. crenata seeds (collected during previous sea- sons on faba bean plants) at a density of 20 mg.kg−1 soil. Four replications were considered for each genotype/treat- ment and planting was performed mid-November with 3–4 seeds per pot. Pots were watered when necessary to keep plants at good soil moisture. After emergence, the number of lentil plants was reduced to only one plant per pot. At the end of the experiment, the 56 days aged plants were uprooted from pots. The host root system all with O. crenata attachments were washed carefully and the fol- lowing parameters were determined. O. crenata attachments were counted and classified according to their development stage (Abbes et al. 2011) to underground/non-emerged Oro- banche tubercles (NEO) and emerged Orobanche shoots (EON) per plant. Lentil shoot (SDW) and root (RDW) dry weight were also determined for the same plants. g In this study, we aimed to evaluate the response of a lentil germplasm collection to O. crenata parasitism under field and controlled conditions and investigate the potential meta- bolic differences between identified susceptible and resistant genotypes. Table 1. Lentil genotypes used to identify the resistance levels under field conditions during cropping seasons 2017–2018 and 2018/2019. Region Country of origin/Entry IG number Americas MEX (5645-ILL351, 502), ARG (4605, 268), CAN (4738), CHL (468, 361), URY (4778), ICA (10952, 10912), Europe ESP (4926, 5628-ILL915, 5653), FRA (6528), ITA (5418) DEU (4881), POL (705), UKR (82), UNK (4345, 6415), RUS (4830, 597, 4819), CZE (4409), YUG (2230- ILL624), GRC (304), HRV (4915), North and Sub- Saharan Africa ETH (5639-ILL207), DZA (4781), MAR (7726, Chakkouf, Bakria, Zaaria), SDN (1861), Asia IND (4164), IRN (223, 257), AFG (213), JOR (5384, 5562, 5244), LBN (5626-ILL840, 840, 191), PSE (4606), NPL (3485, 3487), PAK (6350), SYR (6870, 6848, 490), TUR (590, 71), ARM (619), Others LIRL-22-107, LIRL-21-187, 6002, 6021, 8009, 9951, 88527, 6025, LIRL-22-109, 9850, 8090, 7213, LC960254, 8195, 7982, 7984, 7685, 7701, 6783, 7668, 8622, 7934, 6015, 8068, 7723, 7532 Table 1. 2.1. Plant material and field trials In total, 80 lentil genotypes were subjected to field evaluation and screening for resistance to O. crenata (Table 1). Germ- plasm was provided by the International Center of Agricul- tural Research in dry areas (ICARDA) genebank. The trial was conducted during two consecutive cropping seasons 2017/2019 in a high O. crenata infested sick plot at ICARDA Merchouch research station – Morocco. Different genotypes JOURNAL OF PLANT INTERACTIONS 323 screening and evaluation showed significant differences (P ≤0.05) between the tested genotypes for D2F, D2OE, PI, BY, SY and HI. No significant differences were recorded for EON and EODW. The cropping season showed signifi- cant effect on D2F, D2OE, EON, EODW, SY and HI and no significant effect on PI and BY. Except for PI, the inter- action genotype*cropping season was significant for all other parameters (Table 2). Out of the 80 tested accessions, only five accessions showed a good resistance level to O. crenata. 2.3. Metabolites analyses Untargeted metabolomics profiling was performed using gas chromatography–mass spectrometry (GC–MS). The method used in this study for organic extraction and transesterifica- tion from shoots and roots of both infested and non-infested plant is sited by (Mutale-joan et al. 2020) with some modifi- cations. Samples were grinded in liquid nitrogen then 300 mg from each sample dissolved in 4 mL chloroform/ methanol mixture (2/1, v/v). 10 µL of internal standard Dodecane (Sigmaaldrich; Density, 0.75 g/mL) were added into the mixture, which were placed to a heat block (Labet International, Edison, USA) pre-set at 85°C and left for 2 h. After the mixture was placed to an ultra-sound bath (Branson ultrasonic Sonifier 450, Danbury, USA), the sonication was carried for 60 min. One milliliter of H2O was added to the vials and the mixtures were thoroughly vortexed. Then the organic phase was transferred into a new vial and the chloro- form was evaporated under a stream of nitrogen gas. For acid transesterification, 500 µL of methanol/sulfuric acid (6%, v/v) was added to dried organic material, then the mixture was heated, sonicated and dried as described above. 750 µL of chloroform and 250 µL of distilled water were added for phase separation. The organic phase was collected and con- served at −20°C for further analysis. The gas chromatography (GC) (Agilent 7890A Series) coupled to mass spectrometry (MS) was used for the identification of apolaire compounds. 2.1. Plant material and field trials A volume of 4 μL of each tested samples were injected into the 123-BD11 column (15 m × 320 μm × 0.1 μm) by 1/4 split mode using helium as carrier gas at 3 mL.min−1. Briefly, the temperature was set at 230 and 150°C in the ion source and the MS transfert line, respectively. The oven temperature was set to started at 30°C and to reach 360°C at the end. The identification of metabolite was carried by the compari- son of their mass spectra (MS) with NIST 2014 MS Library. The correlation matrix (Figure 1) shows that traits related to lentil productivity such as SY and HI were negatively cor- related with traits related to O. crenata infestation level D2OE (r = −0.20**), PI (r = −0.37**) and EON (r = −0.34**). Inter- estingly negative correlations were found also between SY and HI (r = −0.42**) and D2F (r = −0.56**) (Figure 1). However, a high positive correlation was found between D2F and D2OE, D2OE and EODW, SY and BY, BY and D2OE, EON and PI (Correlation coefficients varied between 0.17 and 0.68, p ≤ 0.001). The correlations between different traits were confirmed at a higher dimension using PCA which was used to select the best resistant genotypes. Five genotypes (ILL6415, ILL1861, LIRL21187, ILL7723, and ILL4830) were identified with a good level of resistance to O. crenata under field conditions. PCA revealed that the first three principal components (PC) explained 81% of the total original variation. The first PC, which explained 38.8% of the total variation, showed negative correlation with PI (r = −0.63) and positive corre- lation with BY (r = 0.57), SY (r = 0.89) and HI (r = 0.85). This PC corresponds to the list of genotypes with, high PI and low BY and SY such as ILL5645 and ILL82. The second PC, which described 24.6% of the total variability, is charac- terized with a positive correlation with EON (r = 0.76) and EODW (r = 0.76) and opposed the genotypes with high EON and EODW such as ILL5418 and ILL705 to those with low number such as ILL6415 and ILL7723. The third PC explained 17.6% of the total data variability and it is positively correlated with D2F (r = 0.62) and EODW (r = 0.64) which corresponds to genotypes with high D2F and D2OE (Figure 2). 2.4. Statistical analysis Statistical analyses were done using SPSS software and R script. Analysis of variance (ANOVA) for field data was done consid- ering a linear mixed model with blocks and repetitions as ran- dom factors and seasons and genotypes as fixed factors. Person correlation coefficients between all morphological traits were computed and tested for their statistical significance using prcomp function and Mix-Omics package. PCA and heatmap was generated using R studio, visualization of corrplot and ggplot packages, integrated into the R sofware. One way anova and Duncan’s test was studied using SPSS software. A cluster analysis, using all collected data was performed to cluster the different studied genotypes based on their resistance level. Four groups were identified (Figure 2). The first cluster contains 46 genotypes that presented a high susceptibility to O. crenata with high PI values ranging from 5.53 to 9 and low HI and seed production levels (SY ≤ 36.5 g m−2). The second cluster with only six genotypes, showed a moderate susceptibility to O. crenata expressed by high D2OE, a PI varying from 6.9 to 8.75, moderate emerged Orobanche number and dry weight. The level of seed production for the genotypes in this cluster varied from 6.22 to 39.1 g m−2 with a maximum HI of 0.12. Cluster three consisted of 22 genotypes showing intermediate values for the remaining morphological traits. Only six genotypes 3. Results 3.1. Field screening for resistance to O. crenata in lentil 3. Results 3.1. Field screening for resistance to O. crenata in lentil Results showed a high variability within the lentil germplasm collection in the response to O. crenata parasitism. Field Table 2. Analysis of variance of morphological traits of lentil genotypes under O.crenata infestation conditions. D2F D2OE PI EON EODW BY SY HI Genotypes (G) 19.9** 3.2** 1.9** 1.2ns 1.1ns 1.4* 2.3** 2.6** Cropping Season (CS) 197.5** 386.5** 0.8ns 103.8** 60.3** 0ns 10.31** 69.1** G*CS 6** 2.5** 0.8ns 1.67** 1.4* 1.5** 2** 2.3** D2F: Days to flowering, D2OE: Day to Orobanche emergence, IP: Parasitism index, EON: Emerged Orobanche number, EODW: Emerged Orobanche dry weight, BY: Biological yield, SY: Seed yield, HI: Harvest index;** significant at the 0.01 level;* significant at the 0.05 level, nsnot significant. 2F: Days to flowering, D2OE: Day to Orobanche emergence, IP: Parasitism index, EON: Emerged Orobanche number, EODW: Emerged O Biological yield, SY: Seed yield, HI: Harvest index;** significant at the 0.01 level;* significant at the 0.05 level, nsnot significant. 324 Y. EN-NAHLI ET AL. Y. EN-NAHLI ET AL. Y. EN-NAHLI ET AL. 324 Figure 1. Correlation analysis among morphological parameters of lentil in response to O.crenata infection under field conditions during the cropping season 2017–2018 and 2018–2019. D2F: Days to flowering; D2OE: Days to Orobanche emergence; IP: Parasitism index; EON: Emerged Orobanche number; EODW Emerged Orobanche dry weight; BY: Biological yield; SY: Seed yield; HI: Harvest index. ***Correlation is significant at the 0.001 level; ** Correlation is significan at the 0.01 level; * Correlation is significant at the 0.05 level. Figure 1. Correlation analysis among morphological parameters of lentil in response to O.crenata infection under field conditions during the cropping seasons 2017–2018 and 2018–2019. D2F: Days to flowering; D2OE: Days to Orobanche emergence; IP: Parasitism index; EON: Emerged Orobanche number; EODW: Emerged Orobanche dry weight; BY: Biological yield; SY: Seed yield; HI: Harvest index. ***Correlation is significant at the 0.001 level; ** Correlation is significant at the 0.01 level; * Correlation is significant at the 0.05 level. Figure 2. Biplot of the first two dimensions of the principal component analysis (PCA) for the 80 genotypes based on their morphological traits under O. creneta infection in field condition. 3.2. Pot experiment and confirmation of the resistance under controlled conditions Five genotypes from cluster 4, ILL1861, ILL4830, ILL4615, ILL7723 and LIRL21187, were selected to be subjected to a confirmation experiment and evaluation of the impact of the parasite on host development under controlled con- ditions. Result showed a highly significant difference between the genotypes (p < 0.001) under both infested and free Orobanche conditions. Compared to non-infested con- trol plants, biomass production (shoots and roots) was sig- nificantly decreased by O. crenata for all the tested genotypes except ILL6415 (Figure 3(A)). However, no significant differences were observed between the studied genotypes for the average number of TON (p > 0.05) that varied from 3.5 to 7.2, and the NEO (p > 0.05) wish varied from 3.2 to 5.9. Only EON showed sig- nificant differences between genotypes (p ≤0.05) wish varied from 0.4 to 0.7 (Table 4). The metabolites concentration found in the shoot and the root of infested and non-infested genotypes were used to perform a PCA and to build heat-maps to identify the pat- tern between the samples and gain clear details about the metabolic changes (Figures 4 and 5). The PC1 and PC2 of the shoot metabolites explain 78% and 17.6% of the total var- iance respectively. For both genotypes ILL6415 and ILL7723, the non-infested and infested pant functions were close to each other. Instead, PC1 and PC2 separate the function of the non-infested and infested Zaaria (Figure 4(B)). Differ- ently to the shoot, PC1 and PC 2 explain 36.3% and 25.3% of the total root metabolite variations. The PC plot separates markedly the functions of non-infested root of ILL6415, ILL7723 and Zaaria from the infested root functions (Figure 5(B)). Out of 19 abundant and identified metabolites detected, only linolenic acid, arachidic acid and abietic acid are markedly accumulated in the shoot of the resistant infested genotypes ILL6415. Four metabolite levels including stigmasterol, methyl 2-hydroxytetracosanoate, lignoceric acid and stigmastan-3,5-diene decreased compared with the non infested plants. On the other hand, the metabolite concentrations do not show significant changes between the treatments in the shoot of the resistant genotype ILL7723. While linolenic acid, g-sitosterol and melissic acid exhibit increased concentrations in the shoot of the infested Significant differences were observed between tested gen- otypes under both treatments (infested and non-infested) (p < 0.001) for the SDW (Table 5). Also, results showed that O. crenata significantly affected the RDW (p ≤0.05). 3. Results 3.1. Field screening for resistance to O. crenata in lentil Conversely to resistant genotypes, results showed an increase of the num- ber of metabolites in the infested roots of the susceptible check Zaaria (31 peaks) against only 13 observed in non- infested plants. The annotated metabolites in the shoot and the root belong to several biochemical groups such as fatty acid, sterol, alkane, alcene, organic compounds and others (Figure 4(C) and Figure 5(C)). with the highest resistance level were grouped in the fourth cluster. This group was characterized by relatively the lowest PI ranging from 2.77 and 5.87. The best recorded SY were observed for the genotypes of this cluster such as ILL7723, ILL4615, ILL1861and LIRL21187. Genotypes from cluster four showed the best resistance level against O. crenata infec- tation and relatively high seed production (Table 3). with the highest resistance level were grouped in the fourth cluster. This group was characterized by relatively the lowest PI ranging from 2.77 and 5.87. The best recorded SY were observed for the genotypes of this cluster such as ILL7723, ILL4615, ILL1861and LIRL21187. Genotypes from cluster four showed the best resistance level against O. crenata infec- tation and relatively high seed production (Table 3). 3.2. Pot experiment and confirmation of the resistance under controlled conditions The genotypes*treatment interaction was highly significant for SDW (p < 0.001) and not significant for RDW (p > 0.05). Compared to non infested plants, an important decrease of SDW (90%) was observed for genotypes Bakria, Zaaria and ILL4830. Moderate to low SDW decreases were observed for the genotypes ILL6415 (53.8%) and ILL7723 (66%). The same genotypes showed a relatively low RDW decrease with respectively 19.2% and 22.2% against a maximum of 72% recorded for Zaaria and ILL4830. 3. Results 3.1. Field screening for resistance to O. crenata in lentil D2F: Days to flowering; D2OE: Days to Orobanche emergence; IP: Parasitism index; EON: Emerged Orobanche number; EODW: Emerged Orobanche dry weight; BY: Biological yield; SY: Seed yield; HI: Harvest index; contrib: variables contribution to the PCA Cluster analysis based on Eucli- dean distance using the Ward method was performed to cluster the different studied genotypes based on their resistance level. Figure 2. Biplot of the first two dimensions of the principal component analysis (PCA) for the 80 genotypes based on their morphological traits under O. creneta infection in field condition. D2F: Days to flowering; D2OE: Days to Orobanche emergence; IP: Parasitism index; EON: Emerged Orobanche number; EODW: Emerged Orobanche dry weight; BY: Biological yield; SY: Seed yield; HI: Harvest index; contrib: variables contribution to the PCA Cluster analysis based on Eucli- dean distance using the Ward method was performed to cluster the different studied genotypes based on their resistance level. JOURNAL OF PLANT INTERACTIONS 325 Table 3. Mean, maximum and minimum of morphological traits of the four clusters grouping the 80 lentil genotypes under O. crenata infection. Cluster 1 Cluster 2 Cluster 3 Cluster 4 Min max mean Min max mean Min max mean Min Max mean D2F 80.7 103.0 89.9 72.4 211.0 73.7 73.0 92.0 83.2 85.0 101.0 90.9 D2OE 92.0 113.3 100.2 90.5 105.3 93.2 87.5 170.8 97.2 101.0 117 107.2 IP 5.5 9 8.1 6.9 8.5 7.0 5.1 8.0 7.3 2.8 5.9 5.1 EON 0.1 3.8 1.6 1.6 6.1 2.6 0.2 2.8 1.8 0.4 3.07 1.5 EODW 0.1 2.41 1.1 1.4 3.2 1.6 0.3 2.1 1.2 0.2 1.84 1.0 BY (g.m−2) 98.2 431.3 243.6 211 452.5 294.6 170.8 532.3 250.4 365.8 723.7 396.3 SY (g.m−2) 0.7 36.5 10.2 6.2 39.1 34.3 7.7 64 32.0 30.4 103.8 46.7 HI 0.0 0.1 0.03 0.02 0.1 0.04 0.1 0.2 0.1 0.1 0.2 0.1 D2F: Days to flowering, D2OE: Day to Orobanche emergence, IP: Parasitism index, EON: Emerged Orobanche number, EODW: Emerged Orobanche dry weight, BY: Biological yield, SY: Seed yield, HI: Harvest index maximum and minimum of morphological traits of the four clusters grouping the 80 lentil genotypes under O. crenata infection. Cluster 1 Cluster 2 Cluster 3 Cluster 4 (Zaaria). 3. Results 3.1. Field screening for resistance to O. crenata in lentil For the resistant genotype ILL6415, a total of 109 metabolites were identified in the lipophilic phase of both infested and non-infested plants, in which 59 were observed only in non-infested plants and 54 metabolites were found in the infested plants. For the genotype ILL7723, 115 metabolites were detected in which 66 were annotated in the non-infested plants and 49 in the infested plants. For the susceptible check Zaaria, 92 metabolites in total were recorded including 48 metabolites in non- infested plants, and 44 in the infested plants. Results showed that compared to non infested plants the number of identified metabolites decreased in shoots of infested plants. In total, 33, 33 and 13 metabolites were recorded in the infested shoots of ILL6415, ILL7723 and Zaaria, respectively against 38, 45 and 35 recorded in the non- infested shoots. Similar decreases were observed in the infested roots for both resistant genotypes ILL6415 (17 peaks), ILL7723 (16 peaks) respectively against 21 metab- olites recorded in the non-infested roots. Conversely to resistant genotypes, results showed an increase of the num- ber of metabolites in the infested roots of the susceptible check Zaaria (31 peaks) against only 13 observed in non- infested plants. The annotated metabolites in the shoot and the root belong to several biochemical groups such as fatty acid, sterol, alkane, alcene, organic compounds and others (Figure 4(C) and Figure 5(C)). (Zaaria). For the resistant genotype ILL6415, a total of 109 metabolites were identified in the lipophilic phase of both infested and non-infested plants, in which 59 were observed only in non-infested plants and 54 metabolites were found in the infested plants. For the genotype ILL7723, 115 metabolites were detected in which 66 were annotated in the non-infested plants and 49 in the infested plants. For the susceptible check Zaaria, 92 metabolites in total were recorded including 48 metabolites in non- infested plants, and 44 in the infested plants. Results showed that compared to non infested plants the number of identified metabolites decreased in shoots of infested plants. In total, 33, 33 and 13 metabolites were recorded in the infested shoots of ILL6415, ILL7723 and Zaaria, respectively against 38, 45 and 35 recorded in the non- infested shoots. Similar decreases were observed in the infested roots for both resistant genotypes ILL6415 (17 peaks), ILL7723 (16 peaks) respectively against 21 metab- olites recorded in the non-infested roots. 3.3. Qualitative untargeted metabolomic analysis To investigate the impact of O. crenata parasitism on the metabolomic profile of susceptible and resistant lentil gen- otypes and to gain more information and knowledge about the chemical and biochemical mechanisms involved in the resistance mechanisms, a metabolic profiles analysis was performed using GC–MS for three lentil genotypes charac- terized by different resistance levels; two resistant geno- types (ILL6415, ILL 7723) and one susceptible genotype 326 Y. EN-NAHLI ET AL. 326 Y. EN-NAHLI ET AL. Figure 3. Growth variation between infected and no-infected plants for the five selected genotypes and the susceptible checks (A) GC–MS chromatograms of th shoot of the resistant genotype (ILL6415), (B): non-infected (C): Infected. Figure 3. Growth variation between infected and no-infected plants for the five selected genotypes and the susceptible checks (A) GC–MS chromatograms of the shoot of the resistant genotype (ILL6415), (B): non-infected (C): Infected. l t d t d th tibl h k (A) GC MS h t f th Figure 3. Growth variation between infected and no-infected plants for the five selected genotypes and the susceptible checks (A) GC–MS chromatograms of the shoot of the resistant genotype (ILL6415), (B): non-infected (C): Infected. Table 4. The attachment number of O. crenata in selected lentil genotypes and the checks cultivars. arachidic acid significantly increased in the infested root of ILL6415, when a significant reduction of palmitic acid, oleic acid, lignoceric acid and methyl 2-hydroxy-tetraco- sanoate were found in the same infested roots. Stearic acid, telfairic acid and montanic acid were more abundant in the infested root of ILL7723 than the non-infested root, for the same genotype only melissic acid and palmitoloic acid were reduced in the infested root compared to the non- infested root. For the susceptible genotype Zaaria, tricosa- noic acid and pentacosanoic acid were significantly accumu- lated in the infested root (Figure 5(A)). Table 4. The attachment number of O. crenata in selected lentil genotypes and the checks cultivars. 3.3. Qualitative untargeted metabolomic analysis Total Orobanche Number per Plant (TON) Emerged Orobanche Shoots (EON) Non-Emerged Orobanche Tubercles (NEO) ILL 6415 4.1 ± 0.8 b 0.4 ± 0.2 b 3.3 ± 1.0 a ILL1861 7.1 ± 0.8 a 0.6 ± 0.3 a 5.1 ± 1.4 a LIRL21187 5.1 ± 1.9 ab 0.7 ± 0.3 ab 3.9 ± 2.3 a ILL7723 5.8 ± 2.5 a 0.7 ± 0.4 a 3.8 ± 2.4 a ILL4830 7.2 ± 3.4 ab 0.4 ± 0.2 ab 5.9 ± 2.9 a Zaaaria 4.3 ± 1.8 ab 0.6 ± 0.3 ab 3.2 ± 1.5 a Bakria 3.5 ± 1.8 b 0.6 ± 0.3 b 2.8 ± 0.9 a Total 4.8 ± 2.0 0.6 ± 0.1 3.7 ± 1.8 Data are means ± SE. Means with the same letters within a column are not sig- nificantly different at p > 0.05. TON: Total Orobanche number, EON: emerged Orobanche number, NEO: underground Orobanche number. Data are means ± SE. Means with the same letters within a column are not sig- nificantly different at p > 0.05. TON: Total Orobanche number, EON: emerged Orobanche number, NEO: underground Orobanche number. Data are means ± SE. Means with the same letters within a column are not sig- nificantly different at p > 0.05. TON: Total Orobanche number, EON: emerged Orobanche number, NEO: underground Orobanche number. 4.1. Field evaluation susceptible genotypes Zaaria compared with the non- infested plants (Figure 4(A)). The holoparasitic weed O.crenata is known for its devastat- ing effect on productivity of many crop species, especially legume crops such as faba bean, chickpea, grass pea and lentil Moreover, concentrations of g-sitosterol, stigmastan-3,5- diene, telfairic acid, docosanoic acid, stigmasterol and JOURNAL OF PLANT INTERACTIONS 327 Table 5. Mean ± standard error (SE) of shoot (SDW) and root dry weight (RDW) of the different infested and non-infested genotypes under controlled conditions. Shoot dry weight (SDW) (g) Root dry weight (RDW) (g) non-infected infected decreases (%) non-infected infected decreases (%) ILL 6415 2.7 ± 0.8 bc 1.2 ± 0 .0 d 53.8 1.0 ± 1.3 a 0.8 ± 0.9 ab 19.2 ILL1861 2.7 ± 0.8 cd 0.4 ± 0.0 bcd 84 1.2 ± 0.8 a 1.1 ± 0.2 a 66 LIRL21187 3.5 ± 1.4 ab 0.9 ± 0.0 d 73 0.6 ± 0.3 a 0.4 ± 0.1 ab 29.4 ILL7723 1.7 ± 0.3 bcd 0.6 ± 0.2 ab 66 0.7 ± 0.6 a 0.5 ± 0.0 ab 22.2 ILL4830 2.4 ± 0.5 bcd 0.2 ± 0.1 d 90 0.7 ± 0.5 a 0.2 ± 0.0 b 66.1 Bakria 5.0 ± 1.6 a 0.5 ± 0.1 abc 90 0.9 ± 0.2 a 0.4 ± 0.2 ab 48.9 Zaaria 2.7 ± 1.3 bc 0.2 ± 0.0 cd 90 0.5 ± 0.2 a 0.1 ± 0.0 b 72.0 Data are means ± SE Means with the same letters within a column are not significantly different at p > 0.05 Figure 4. Heat map and principal component analysis (PCA) of metabolite levels detected in infested and non-infested lentil genotypes (centered and scaled) of shoot metabolites (A and B). Metabolite concentrations were row normalized to highlight differences among treatments. Relative abundance ranges from blue (lower than the average percentage value) to red (higher than the average percentage value). The Compounds identified in the different apolar extracts derived from infested and non-infested shoot were grouped in structurally related families (C). Figure 4. Heat map and principal component analysis (PCA) of metabolite levels detected in infested and non-infested lentil genotypes (centered and scaled) of shoot metabolites (A and B). Metabolite concentrations were row normalized to highlight differences among treatments. Relative abundance ranges from blue (lower than the average percentage value) to red (higher than the average percentage value). 4.1. Field evaluation 2019), is associated with genes that are highly affected by the environmental con- ditions (Yaish et al. 2011). It is tightly controlled by some complex genetic and metabolic pathways such as salicylic acid and gibberellin pathways as well as some other phyto- hormones involved in plant growth (Dezar et al. 2011; Jing et al. 2020). The root parasitic plants are metabolically dependent on their hosts (Clermont et al. 2019), which suggest that the early metabolism adjustments associated with early flowering will stimulate the release of germination stimulants in the rhizosphere of the host root system result- ing in an early attachment and development of the parasite on the host plant. such early infestation results with an early parasitism impact affecting the host metabolism and thus its physiological and phenological behavior which explain the correlation found in the current study between D2F, D2OE and SY (Amri et al. 2021). Parasitism Index was positively correlated with EON and EODW, which yield through the prolongation of reproductive phase as well as seed filling period (Sundaram et al. 2019), is associated with genes that are highly affected by the environmental con- ditions (Yaish et al. 2011). It is tightly controlled by some complex genetic and metabolic pathways such as salicylic acid and gibberellin pathways as well as some other phyto- hormones involved in plant growth (Dezar et al. 2011; Jing et al. 2020). The root parasitic plants are metabolically dependent on their hosts (Clermont et al. 2019), which suggest that the early metabolism adjustments associated with early flowering will stimulate the release of germination stimulants in the rhizosphere of the host root system result- ing in an early attachment and development of the parasite on the host plant. such early infestation results with an early parasitism impact affecting the host metabolism and thus its physiological and phenological behavior which explain the correlation found in the current study between D2F, D2OE and SY (Amri et al. 2021). Parasitism Index was positively correlated with EON and EODW, which The score plot, the biplot and cluster analysis are graphical representations used for a better visualization of PCA results, and allow the identification of genotypes with the desirable characteristics. In general, whatever the genotypes are located close to the trait that’s mean a higher value for the correspond- ing trait. 4.1. Field evaluation The Compounds identified in the different apolar extracts derived from infested and non-infested shoot were grouped in structurally related families (C). (Amri et al. 2012; Millán et al. 2015; Nefzi et al. 2016; Abdal- lah et al. 2020). In our study, we evaluated the performance of a lentil germplasm collection under O. crenata open field infested conditions. The 80 tested genotypes showed signifi- cant differences in their response to O. crenata parasitism, this variation could be associated with the genetic variation within the population. Out of the 80 tested genotypes, ILL4615, ILL7723, ILL1861, ILL4830, ILL9850 and LIRL21187 showed a good resistance level. Similar results were reported in previous studies, using different lentil populations and studying their behavior against the O. crenata parasitism (Ennami et al. 2017; Mbasani-Mansi et al. 2019). Regarding our results, early flowering was posi- tively correlated to D2OE (r = 0.68***) and negatively corre- lated with SY (r = −0.20***). The early flowering, which has been described to have a positive effect on plant potential Y. EN 328 Y. EN-NAHLI ET AL. gure 5. Heat map and principal component analysis (PCA) of metabolite levels detected in infested and non-infested lentil genotypes (centered and scaled) of ot metabolites. Metabolite concentrations were row normalized to highlight differences among treatments. Relative abundance ranges from blue (lower than e average percentage value) to red (higher than the average percentage value). The Compounds identified in the different apolar extracts derived from infested d non-infested roots were grouped in structurally related families (C). Figure 5. Heat map and principal component analysis (PCA) of metabolite levels detected in infested and non-infested lentil genotypes (centered and scaled) of root metabolites. Metabolite concentrations were row normalized to highlight differences among treatments. Relative abundance ranges from blue (lower than the average percentage value) to red (higher than the average percentage value). The Compounds identified in the different apolar extracts derived from infested and non-infested roots were grouped in structurally related families (C). reflects the severe negative effect of O. crenata parasitism on lentil growth and seed production. Similar results were reported in previous studies performed on faba bean (Abbes et al. 2011; Trabelsi et al. 2015; Trabelsi et al. 2016), lentil (Ennami et al. 2017), chickpea (Nefzi et al. 2016) and grass pea (Abdallah et al. 2020). yield through the prolongation of reproductive phase as well as seed filling period (Sundaram et al. 4.3. Qualitative untargeted metabolomic analysis In this part of the study, the two resistant genotypes ILL 6415 and ILL7723 with the susceptible genotype Zaaria were selected to conduct a qualitative metabolomic analysis to explore the biochemical mechanisms involved in the resist- ance against O. crenata. The principal components analysis (PCA) is commonly used in non-targeted metabolomics studies to perform metabolite correlation networks (Arbona et al. 2013). Based on PCA for shoot metabolites performed for both resistant genotypes ILL6415 and ILL7723 and compared to the control samples Orobanche parasitism was found to have a less effect on metabolites changes compared to the susceptible genotype Zaaria (Figure 4(B)). However, the parasitism was found to have a markedly effect on metabolites change in the root metabolite for all genotypes compared to their respective non- infested control plants (Figure 5(B)). The changes in metabo- lomic profile was reported also by Clermont et al. (2019) between the facultative parasite T. versicolor and the obligate holoparasite P. aegyptiaca with the host species M. Truncatula and A. thaliana, respectively. Similarly, other authors reported that the parasitism by P. aegyptiaca and O. foetida has affected respectively tomato (Amir 2016) and faba bean (Trabelsi et al. 2017; Abbes et al. 2020) metabolites when compared to non infested plants. 5. Conclusion The broomrape O. crenata is one of the major problems limiting the production and the development of lentil in Morocco and many other countries in the region. Identifi- cation and development of resistant germplasm remains the best option to control this parasite. In this study, poten- tial sources of resistance were identified out of 80 genotypes screened and evaluated under high O. crenata infested field and controlled conditions. Both genotypes ILL6415 and ILL7723 showed the highest level of resistance to the cre- nate broomrape. Such resistance was associated with com- plex physiological and biochemical mechanisms such as an increase of some specific metabolite biosynthesis that contribute in improving the host immunity and fight against the parasite. These mechanisms, if combined with other potential physical and/or chemical mechanisms, through classical breeding and/or genetic engineering approches, could help in improving the resistance to O. crenata in lentil. The results demonstrated that O. crenata parasitism may modify the shoot and the root metabolites of the host plants, especially for susceptible genotypes. Indeed, out of the detected metabolites, the increase of α-linolenic acid in the shoot of the resistant genotype could be related to a specific biochemical pathway of resistance, this essential fatty acid is an important component of the cell membrane that maintain the membrane integrity and functionality, prevents the membrane rigidification under stress conditions and enhance the production of ROS via the activation of Ca2 +-ATPase (Delavault et al. 2017; Jia et al. 2020). Besides, α- linolenic acid is a precursor of jasmonic acid (JA) synthesis, a key rules in mediating resistant responses of plants under biotic and abiotic stresses by eliciting the production of alka- loid, terpenoid, coumarins, phytoalexins and taxane com- pound that are widely known by their functional value to plant under stress and regulating plant growth and 4.2. Pot experiment The pot experiments were conducted under controlled con- ditions to confirm field results and assess the underground infestation which was difficult to consider under field con- ditions. Data related to EON, NEO SDW and RDW recorded for different tested genotypes showed that the growth and biomass production have decreased in infested plants for all the genotypes compared to the non-infested plants. These results showed that out of the five tested genotypes, only two genotypes ILL6415 and ILL7723 showed good resistance level under controlled conditions which confirm the results observed under open field conditions. Such resist- ance was expressed by the lowest shoot and root dry weight reduction and a low number of total O. crenata shoots and tubercules. similar results were reported in previous studies performed on faba bean and lentil (Ennami et al. 2017; Abdallah et al. 2020) who reported a large variation in infes- tation intensity under pots conditions and field trials. 4.1. Field evaluation The genotypes ILL4605, ILL4830, LIR22107, ILL6415 and ILL7723 clustered together in cluster 4 showed the lowest PI levels and the highest SY and BY. The same genotypes are located to the negative side of PC2 which means they have low values of EON and EODW. On the other hand, genotypes such as ILL82, ILL304, ILL5385 clustered together in cluster 1, showed the highest PI and lowest SY and BY, and presented as the most susceptible genotypes to O. crenata. JOURNAL OF PLANT INTERACTIONS 329 development (Delavault et al. 2017). However, the accumu- lation of arachidic acid in the shoot and the root of the resist- ant genotype ILL6415 may serve as a defensive agent to fight the parasite attack, because several phytohormones and sec- ondary metabolites are derived from this compound (Schar- enberg et al. 2019). This long-chain fatty acid could be related to the wax, cutin and suberin production pathways, which help the plant to reduce water loss and protect the plant surface (Mutale-joan et al. 2020). Similar accumulation in α-linolenic acid and arachidic acid were reported by Jia et al. (2020) in drought-tolerant Populus simoniicv and drought-susceptible P. deltoides under drought conditions stress. Otherwise, clear difference was observed in root sterol content between the resistant and susceptible genotypes and between infested and non-infested plants. Wang et al. (2012) suggested that plant cells involve mechanical defense using sterols to make a physical barrier against the nutrient efflux to prevent nutrient and loss against bacterial and pathogens attack. In contrast to previous studies that focused more on polar metabolite variations including starch, amino acid and some secondary metabolite in response to parasit- ism in different plants (Abbes et al. 2009; Amir 2016; Cler- mont et al. 2019), the current study put the light-on fatty acids and sterols as important metabolites that can serve as regulatory pathways to conduct defense mechanisms in lentil and support the suggestion of the ability of the host plant to regulate phloem composition depending onthe host–parasite interaction (Jokinen and Irving 2019). Further, much remains unknown about the host–parasite biochemical interactions and a lot of work is still needed in exploring novel metabolic pathways and associated gene expression, genomic and proteomic analysis. 4.2. Pot experiment References Abbes Z, Bouallegue A, Trabelsi I, Trabelsi N, Taamalli A, Amri M, Mhadhbi H, Kharrat M. 2020. Investigation of some biochemical mechanisms involved in the resistance of faba bean (Vicia faba L.) varieties to Orobanche spp. Plant Prot Sci. 56(4):317–328. doi:10. 17221/103/2019-PPS. Shiv Kumar Holds a Ph.D. in Plant Breeding from the GB Pant Univer- sity of Agriculture and Technology, Pantnagar, India. His area of exper- tise includes crop improvement through resistance breeding, widening the genetic base through pre-breeding, and development of genetic and genomic resources in food legumes. He is leading ICARDA’s Food legumes program which aims to deliver improved germplasm of lentil, kabuli chickpea, faba bean and grass pea to national partners in South Asia, Sub-Saharan Africa, West Asia, and North Africa. He works on developing short duration climate smart varieties of lentil and grass pea with high iron and zinc content for sustainable intensification of cereal based cropping systems. Abbes Z, Kharrat M, Delavault P, Chaïbi W, Simier P. 2009. Nitrogen and carbon relationships between the parasitic weed Orobanche foe- tida and susceptible and tolerant faba bean lines. Plant Physiol Biochem. 47(2):153–159. doi:10.1016/j.plaphy.2008.10.004. Abbes Z, Kharrat M, Delavault P, Simier P, Chaïbi W. 2007. Field evalu- ation of the resistance of some faba bean (Vicia faba L.) genotypes to the parasitic weed Orobanche foetida poiret. Crop Prot. 26 (12):1777–1784. doi:10.1016/j.cropro.2007.03.012. Outmane Bouhlal is a Ph.D. candidate at the International Center for Agricultural Research in the Dry Areas (ICARDA) and the University of El-Jadida - Morocco. He is working on nutritional quality and drought tolerance in barley. Abbes Z, Sellami F, Amri M, Kharrat M. 2011. Variation in the resist- ance of some faba bean genotypes to Orobanche crenata. Pak J Bot. 43(4):2017–2021. Abbes Z, Trabelsi I, Kharrat M, Amri M. 2019. Intercropping with fenu- greek (trigonella foenum-graecum) enhanced seed yield and reduced Orobanche foetida infestation in faba bean (Vicia faba). Biol Agric Hortic. 35(4):238–247. doi:10.1080/01448765.2019.1616614. Rachid Mentag holds a PhD in plant biotechnology from University Laval – Canada. He has expertise in plant biotechnology and molecular biology, Plant pathology and Plant-pathogen interaction. Actually, he is working as senior research scientist at INRA-Morocco with research focus on host genetic diversity of food legume crops including faba bean, lentil and chickpea. He has expertise on parasitic weeds manage- ment in legume crops with more focus on parasite-host interaction and host specificity. Disclosure statement No potential conflict of interest was reported by the author(s). Author contribution YE, RM, MA., designed the research. YE, KH, HE, MA: per- formed the experiments. YE, KH, OB, RM, AD, ZA, NES, MA, contributed materials/analysis tools. YE, MA, wrote the paper. YE, HE, AD, ZA, NES, SK, RM, MA, revised the paper. All authors approved the final manuscript. YE, RM, MA., designed the research. YE, KH, HE, MA: per- formed the experiments. YE, KH, OB, RM, AD, ZA, NES, MA, contributed materials/analysis tools. YE, MA, wrote the paper. YE, HE, AD, ZA, NES, SK, RM, MA, revised the paper. All authors approved the final manuscript. Nour Eddine Es-Safiholds a PhD in organic chemistry from Mohammed V University in Rabat, Morocco. He undertook postdoc- toral at INRA-France. He is currently working at Mohammed V Uni- versity, Rabat-Morocco. His research focuses on natural products and their structural elucidation, biological activities, and role in food technology. Moez Amri holds a PhD in biological sciences and Plant breeding and HDR in Agricultural Science from the University of Carthage – Tunisia. He is an international scientist skilled in plant breeding with proven record in genetic enhancement of food legume crops as and their inte- gration into the cropping systems for healthy soils and better nutritious food. His area of expertise includes crop improvement in particular food legumes breeding and development of superior high yielding germplasm with resistance to major biotic and abiotic stresses. He is also conducting research activities on parasitic weeds management in field crops with more focus on genetic resistance and parasite-host interaction. ORCID Shiv Kumar http://orcid.org/0000-0001-8407-3562 Ahmed Douaik http://orcid.org/0000-0001-7374-4674 Zouhaier Abbes http://orcid.org/0000-0003-4419-4639 Moez Amri http://orcid.org/0000-0002-4707-0618 Hicham El Arroussi, Senior Scientist, R&D Manager of physiology and biotechnology of microalgae at Moroccan Fondation for Advanced Science, Innovation and Research (MAScIR). Affiliate professor at Mohammed VI Polytechnic University (UM6P). He has expertise on natural resources, microalgae production and valorization in different applications such as applied environment, agriculture and bioenergy. Moez Amri http://orcid.org/0000-0002-4707-0618 Acknowlegements This work was undertaken as part of research activities of crop improvement program at Mohammed VI Polytechnic University (UM6P) with contribution from ICARDA and Moroccan Foundation for Advanced Science, Inno- vation and Research (MAScIR). Y. EN-NAHLI ET AL. 330 Higher Institute of Sciences and Technology of Environment, Borj Cedria and National Institute of Agricultural Research of Tunisia. Notes on contributors Youness EN-Nahli is a Ph.D. candidate at African Integrated Plant and Soil Research Group (AiPlaS), University Mohammed VI Polytechnic (UM6P) – Morocco, the International Center for Agricultural Research in the Dry Areas (ICARDA) and Mohammed V University - Rabat. He is conducting his research activities on screening and evaluation of len- til germplasm against broomrapes, identification of potential resources of resistance and associated genes/QTLs and investigation of physio- logical and biochemical mechanisms involved such resistance and genes-pathway’s expression. References Grain legumes [internet]. New York, NY: Springer; [accessed 2021 Apr 20]; p. 85–109. p j Bai J, Wei Q, Shu J, Gan Z, Li B, Yan D, Huang Z, Guo Y, Wang X, Zhang L, et al. 2020. Exploration of resistance to Phelipanche aegyp- tiaca in tomato. Pest Manage Sci. 76(11):3806–3821. doi:10.1002/ps. 5932. Mutale-joan C, Redouane B, Najib E, Yassine K, Lyamlouli K, Laila S, Zeroual Y, Hicham EA. 2020. Screening of microalgae liquid extracts for their bio stimulant properties on plant growth, nutrient uptake and metabolite profile of solanum lycopersicum L. Sci Rep. 10 (1):1–12. doi:10.1038/s41598-020-59840-4. Çarman K. 1996. Some physical properties of lentil seeds. J Agricult Eng Res. 63(2):87–92. doi:10.1006/jaer.1996.0010. Clermont K, Wang Y, Liu S, Yang Z, DePamphilis CW, Yoder JI. 2019. Comparative metabolomics of early development of the parasitic plants Phelipanche aegyptiaca and triphysaria versicolor. Metabolites. 9:6. doi:10.3390/metabo9060114. Nefzi F, Trabelsi I, Amri M, Triki E, Kharrat M, Abbes Z. 2016. Response of some chickpea (Cicer arietinum L.) genotypes to Orobanche foetida poir. parasitism. Chilean J Agricult Res. 76 (2):170–178. doi:10.4067/S0718-58392016000200006. Cvejić S, Radanović A, Dedić B, Jocković M, Jocić S, Miladinović D. 2020. Genetic and genomic tools in sunflower breeding for broom- rape resistance. Genes (Basel). 11(2):152. doi:10.3390/ genes11020152. Pérez-De-Luque A, Jorrín J, Cubero JI, Rubiales D. 2005. Orobanche crenata resistance and avoidance in pea (Pisum spp.) operate at different developmental stages of the parasite. Weed Res. 45 (5):379–387. doi:10.1111/j.1365-3180.2005.00464.x. g Delavault P, Montiel G, Brun G, Pouvreau J, Thoiron S., Simier P. 2017. Communication between host plants and parasitic plants. Adv Bot Res. 82:55–82. Pérez-De-Luque A, Lozano MD, Moreno MT, Testillano PS, Rubiales D. 2007. Resistance to broomrape (Orobanche crenata) in faba bean (Vicia faba): cell wall changes associated with prehaustorial defensive mechanisms. Ann Appl Biol. 151(1):89–98. doi:10.1111/j. 1744-7348.2007.00164.x. Dezar CA, Giacomelli JI, Manavella PA, Ré DA, Alves-Ferreira M, Baldwin IT, Bonaventure G, Chan RL. 2011. HAHB10, a sunflower HD-Zip II transcription factor, participates in the induction of flowering and in the control of phytohormone-mediated responses to biotic stress. J Exp Bot. 62(3):1061–1076. doi:10.1093/jxb/erq339. Scharenberg F, Stegemann T, Çiçek SS, Zidorn C. 2019. Sequestration of pyridine alkaloids anabasine and nicotine from nicotiana (solana- ceae) by Orobanche ramosa (orobanchaceae). Biochem Syst Ecol. 86(May):103908. doi:10.1016/j.bse.2019.05.016. Ennami M, Briache FZ, Gaboun F, Abdelwahd R, Ghaouti L, Belqadi L, Westwood J, Mentag R. 2017. References Host differentiation and variability of Orobanche crenata populations from legume species in Morocco as revealed by cross-infestation and molecular analysis. Pest Manage Sci. 73(8):1753–1763. doi:10.1002/ps.4536. Sehgal A, Sita K, Rehman A, Farooq M, Kumar S, Yadav R, Nayyar H, Singh S, Siddique KHM. 2021. Chapter 13 - lentil. In: Sadras VO, Calderini DF, editor. Crop physiology case histories for major crops [internet]. [place unknown]: Academic Press; [accessed 2021 Jun 23]; p. 408–428. Erskine W, Sarker A, Kumar S. 2011. Crops that feed the world 3. Investing in Lentil Improvement Toward a Food Secure World. Food Secur.. 3:127–139. doi:10.1007/s12571-011-0124-5. Shah Z, Shah SH, Peoples MB, Schwenke GD, Herridge DF. 2003. Crop residue and fertiliser N effects on nitrogen fixation and yields of legume-cereal rotations and soil organic fertility. Field Crops Res. 83(1):1–11. doi:10.1016/S0378-4290(03)00005-4. Hacham Y, Hershenhorn J, Dor E, Amir R. 2016. Primary metabolic profiling of Egyptian broomrape (Phelipanche aegyptiaca) compared to its host tomato roots. J Plant Physiology. 205:11–19. doi:10.1016/j. jplph.2016.08.005. Singh KM, Singh AK. 2014. Lentil in India: an overview. SSRN Electronic Journal. MPRA Paper 59319, University Library of Munich, Germany. j Hasanuzzaman M, Nahar K, Alam M, Roychowdhury R., Fujita M. 2013. Physiological, biochemical, and molecular mechanisms of heat stress tolerance in plants. Int J Mol Sci. 14(5):9643–9684. doi:10.3390/ijms14059643. Sundaram P, Samineni S, Sajja SB, Roy C, Singh SP, Joshi P, Gaur PM. 2019. Inheritance and relationships of flowering time and seed size in kabuli chickpea. Euphytica. 215:9. doi:10.1007/s10681-019-2464-8. j Idrissi O, Houasli C, Amamou A, Nassrelhaq N. 2020. Lentil genetic improvement in Morocco: state of art of the program, major achieve- ments and perspectives. Moroccan J Agricult Sci [Internet]. 1(1):9– 13. https://techagro.org/index.php/MJAS/article/view/816/831. Taha K, Berraho EB, El Attar I, Dekkiche S, Aurag J, Béna G. 2018. Rhizobium laguerreae is the main nitrogen-fixing symbiont of culti- vated lentil (Lens culinaris) in Morocco. Syst Appl Microbiol. 41 (2):113–121. doi:10.1016/j.syapm.2017.09.008. Jia H, Wang L, Li J, Sun P, Lu M, Hu J. 2020. Comparative metabolo- mics analysis reveals different metabolic responses to drought in tol- erant and susceptible poplar species. Physiol Plant. 168(3):531–546. doi:10.1111/ppl.13036. Trabelsi I, Abbes Z, Amri M, Kharrat M. 2015. Performance of faba bean genotypes with Orobanche foetida poir. and Orobanche crenata forsk. infestation in Tunisia. Chilean J Agricult Res. 75(1):27–34. doi:10.4067/S0718-58392015000100004. Jing T, Zhang N, Gao T, Wu Y, Zhao M, Jin J, Wenkai D, Wilfried Schwab CS. 2020. References Abdallah F, Kumar S, Amri A, Mentag R, Kehel Z, Mejri RK, Triqui ZEA, Hejjaoui K, Baum M, Amri M. 2020. Wild Lathyrus species as a great source of resistance for introgression into cultivated grass pea (Lathyrus sativus L.) against broomrape weeds (Orobanche crenata forsk. and Orobanche foetida poir.). Crop Science. 61(1):263–276. doi:10.1002/csc2.20399. Kamal Hejjaoui Ph.D student conducting research on lentil breeding at the international Center for Agricultural Research in Dry Areas (ICARDA) with focus on screening and identification of superior high yielding lentil germplasm with resistance to heat and drought. Abu-Irmaileh and Labrada. 2017. The problem of Orobanche spp in Africa and Near East. http://www.fao.org/agriculture/crops/ thematic-sitemap/theme/biodiversity/weeds/issues/oro/en/ [Internet]. [accessed 2021 Jun 11]. http://www.fao.org/agriculture/ crops/thematic-sitemap/theme/biodiversity/weeds/issues/oro/en/. Ahmed Douaik currently works at the National Institute of Agricultural Research (INRA-Morocco). He is skilled in Statistics, Spatial Analysis, and Soil Science. He holds a BSc in Agricultural Sciences from Hassan II Institute of Agricultural Sciences and Veterinary Medicine (IAV- Hassan II), Morocco, an MSc in Biometrics from University of Liège, Gembloux, Belgium, and a PhD in Space-Time Statistics from Ghent University, Ghent, Belgium. y Amri M, Abbes Z, Trabelsi I, Ghanem ME, Mentag R, Kharrat M. 2021. Chlorophyll content and fluorescence as physiological parameters for monitoring Orobanche foetida poir. infection in faba bean. PLOS ONE. 16(5):e0241527. doi:10.1371/journal.pone.0241527. Amri M, Abbes Z, Youssef SB, Bouhadida M, Salah HB, Kharrat M. 2012. Detection of the parasitic plant, Orobanche cumana on sunflower (Helianthus annuus L.) in Tunisia. Afr J Biotechnol. 11 (18):4163–4167.. Zouhaier Abbes holds a PhD in biology from Université de Tunis El Manar – Tunisia and University of Nantes – France. He is a plant physi- ologist skilled in parasite-host plant interaction and identification of potential biochemical, physical and physiological resistance mechan- isms. he has also expertise in agricultural, genetics, biochemistry, mol- ecular biology and environmental science. He is currently working at Amri M, Trabelsi I, Abbes Z, Kharrat M. 2019. Release of a new faba bean variety “chourouk” resistant to the parasitic plants Orobanche foetida and O. crenata in Tunisia. Int J Agricult Biol. 21(3):499–505.. JOURNAL OF PLANT INTERACTIONS 331 using molecular markers. Physiol Mol Biol Plants. 25(4):965–974. doi:10.1007/s12298-019-00673-5. Arbona V, Manzi M, de Ollas C, Gómez-Cadenas A. 2013. Metabolomics as a tool to investigate abiotic stress tolerance in plants. Int J Mol Sci. 14(3):4885–4911. doi:10.3390/ijms14034885. Millán T, Madrid E, Cubero JI, Amri M, Castro P, Rubio J. 2015. Chickpea. In: De Ron AM, editor. References UGT85A53 promotes flowering via mediating abscisic acid glucosylation and FLC transcript in camellia sinensis. Ann Med. 0(0):1–14. Trabelsi I, Abbes Z, Amri M, Kharrat M. 2016. Study of some resistance mechanisms to Orobanche spp. infestation in faba bean (Vicia faba L.) breeding lines in Tunisia. Plant Prod Sci. 19(4):562–573. doi:10. 1080/1343943X.2016.1221734. Jokinen JI, Irving LJ. 2019. Effects of light level and nitrogen supply on the red clover-orobanche minor host-parasite interaction. Plants. 8 (6):1–12. doi:10.3390/plants8060146. Trabelsi I, Yoneyama K, Abbes Z, Amri M, Xie X, Kisugi T, Kim HI, Kharrat M, Yoneyama K. 2017. Characterization of strigo- lactones produced by Orobanche foetida and Orobanche crenata resistant faba bean (Vicia faba L.) genotypes and effects of phos- phorous, nitrogen, and potassium deficiencies on strigolactone production. S Afr J Bot. 108:15–22. doi:10.1016/j.sajb.2016.09. 009. Kharrat M, Abbes Z, Amri M. 2010. A New faba bean small seeded var- iety najeh tolerant to Orobanche registered in the Tunisian catalo- gue. Tunisian J Plant Protect. 125:1. Kumar S, Barpete S, Kumar J, Gupta P, Sarker A. 2013. Global lentil production: constraints and strategies. SATSA Mukhapatra – Annual Techn Issue. 17:1–13. Wang K, Senthil-Kumar M, Ryu CM, Kang L, Mysore KS. 2012. Phytosterols play a key role in plant innate immunity against bac- terial pathogens by regulating nutrient efflux into the apoplast. Plant Physiol. 158(4):1789–1802. doi:10.1104/pp.111.189217. Kumar S, Rajendran K, Kumar J, Hamwieh A, Baum M. 2015. Current knowledge in lentil genomics and its application for crop improve- ment. Front Plant Sci. 6. doi:10.3389/fpls.2015.00078. Mbasani-Mansi J, Ennami M, Briache FZ, Gaboun F, Benbrahim N, Triqui ZEA, Mentag R. 2019. Characterization of genetic diversity and population structure of Moroccan lentil cultivars and landraces Yaish MW, Colasanti J, Rothstein SJ. 2011. The role of epigenetic pro- cesses in controlling flowering time in plants exposed to stress. J Exp Bot. 62(11):3727–3735. doi:10.1093/jxb/err177.
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Cannabinoid CB2 receptors in the mouse brain: relevance for Alzheimer’s disease
Journal of neuroinflammation
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© The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. López et al. Journal of Neuroinflammation (2018) 15:158 https://doi.org/10.1186/s12974-018-1174-9 López et al. Journal of Neuroinflammation (2018) 15:158 https://doi.org/10.1186/s12974-018-1174-9 RESEARCH Open Access Cannabinoid CB2 receptors in the mouse brain: relevance for Alzheimer’s disease Alicia López1,2, Noelia Aparicio1,3, M. Ruth Pazos1,3, M. Teresa Grande3, M. Asunción Barreda-Manso1,3, Irene Benito-Cuesta3, Carmen Vázquez1, Mario Amores1, Gonzalo Ruiz-Pérez3, Elena García-García1, Margaret Beatka4,5, Rosa M. Tolón1,3, Bonnie N. Dittel4, Cecilia J. Hillard5 and Julián Romero1,3* Cannabinoid CB2 receptors in the mouse brain: relevance for Alzheimer’s disease Alicia López1,2, Noelia Aparicio1,3, M. Ruth Pazos1,3, M. Teresa Grande3, M. Asunción Barreda-Manso1,3, Irene Benito-Cuesta3, Carmen Vázquez1, Mario Amores1, Gonzalo Ruiz-Pérez3, Elena García-García1, Margaret Beatka4,5, Rosa M. Tolón1,3, Bonnie N. Dittel4, Cecilia J. Hillard5 and Julián Romero1,3* Abstract Background: Because of their low levels of expression and the inadequacy of current research tools, CB2 cannabinoid receptors (CB2R) have been difficult to study, particularly in the brain. This receptor is especially relevant in the context of neuroinflammation, so novel tools are needed to unveil its pathophysiological role(s). Methods: We have generated a transgenic mouse model in which the expression of enhanced green fluorescent protein (EGFP) is under the control of the cnr2 gene promoter through the insertion of an Internal Ribosomal Entry Site followed by the EGFP coding region immediately 3′ of the cnr2 gene and crossed these mice with mice expressing five familial Alzheimer’s disease (AD) mutations (5xFAD). Results: Expression of EGFP in control mice was below the level of detection in all regions of the central nervous system (CNS) that we examined. CB2R-dependent-EGFP expression was detected in the CNS of 3-month-old AD mice in areas of intense inflammation and amyloid deposition; expression was coincident with the appearance of plaques in the cortex, hippocampus, brain stem, and thalamus. The expression of EGFP increased as a function of plaque formation and subsequent microgliosis and was restricted to microglial cells located in close proximity to neuritic plaques. AD mice with CB2R deletion exhibited decreased neuritic plaques with no changes in IL1β expression. Conclusions: Using a novel reporter mouse line, we found no evidence for CB2R expression in the healthy CNS but clear up-regulation in the context of amyloid-triggered neuroinflammation. Data from CB2R null mice indicate that they play a complex role in the response to plaque formation. Keywords: Cannabinoid CB2 receptor, Transgenic mice, Enhanced green fluorescent protein, Amyloid, Neuroinflammation, Microglia Keywords: Cannabinoid CB2 receptor, Transgenic mice, Enhanced green fluorescent protein, Amyloid, Neuroinflammation, Microglia Background nervous system (CNS) [12, 18]. According to these early data, the abundance of CB2R message in human blood cells was highest in B-lymphocytes, followed by natural killer cells, macrophages, and cluster of differ- entiation (CD)8 and CD4 T-lymphocytes [12]. It has been long appreciated that cannabinoids such as Δ9- tetrahydrocannabinol (THC) exert effects on the immune system [40]. A primary target for the cannabinoids to alter immune system function, the cannabinoid receptor, subtype 2 (CB2R), was identified molecularly in 1993 [23]. Autoradiographic and in situ hybridization studies indicated a high level of expression of the CB2R in cellular elements of the immune system but these methods did not detect CB2R expression in the central The presence of CB2Rs in the CNS has been the subject of intense debate during the last decade. Some reports [13, 35] showed the expression of CB2Rs in neuronal elements of the uninjured brain, based primarily on im- munohistochemical approaches. Other studies, however, limited the presence of CB2R in the CNS to glial cells and, specifically, to microglia [6]. Seminal studies by Cabral and colleagues suggested that CB2R could be expressed by microglial cells and that the expression level varied as a function of cell activation [9]. Subsequent studies * Correspondence: j.romero.prof@ufv.es 1Laboratorio de Apoyo a la Investigación, Hospital Universitario Fundación Alcorcón, C/ Budapest 1, 28922 Alcorcón, Madrid, Spain 3Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Pozuelo de Alarcón, Madrid, Spain Full list of author information is available at the end of the article Methods Generation of CB2 EGFP/f/f and CB2 −/−mice Generation of CB2 EGFP/f/f and CB2 / mice Mice were generated at Genoway facilities (Lyon, France). A targeting strategy was designed consisting in the inser- tion of an enhanced Green Fluorescent Protein (EGFP) reporter gene, preceded by an Internal Ribosomal Entry Site (IRES) sequence in the 3′ untranslated region (UTR) of the cnr2 mouse gene. This approach results in the expression of the reporter gene under the control of the endogenous mouse cnr2 promoter and transcript from the same bicistronic mRNA as the CB2R protein. Further, the entire exon 3, including the 3′ UTR and knocked-in reporter, is flanked by loxP sites, allowing the conditional inactivation of the cnr2 gene in cells expressing Cre recombinase (Fig. 1a). However, concerns regarding the lack of specificity of antibodies against the CB2R protein have been raised [3] (Additional file 1), which call into question some of these results. It is clear that additional tools are needed to unambiguously demonstrate the cellular expression of CB2R throughout the body, but most particularly within the CNS. We here introduce a novel transgenic model designed to unveil the func- tional distribution of cannabinoid CB2R and present data regarding the expression of these receptors in the mouse, with special attention to the CNS. Fur- thermore, we used this new mouse model to analyze Three isolated sequences encompassing the murine cnr2 gene regions surrounding the targeted exon 3 were used for the construction of the targeting vector. These sequences included (i) a 3462 bp-sized fragment a b 30 kda 36 kda c d e Fig. 1 Generation of a novel mouse model. a Genomic structure of the construct employed for the generation of CB2 EGFP/f/f and CB2 −/−mice. Hatched rectangles represent cnr2 coding sequences, gray rectangles indicate non-coding exon portions, solid lines represent chromosome sequences. The neomycin-positive selection cassette (Neo) IRES sequence and reporter gene (EGFP) are indicated. loxP sites are represented by blue triangles and FRT sites by double red triangles. The initiation (ATG) and Stop (Stop) codons are indicated. For the generation of knock-in mice (CB2 EGFP/f/f), recombined mice were bred with ubiquitous FLP-recombinase expressing mice, enabling the deletion of the FRT-flanked region. b For the generation of knock-out mice (CB2 −/−), recombined mice were bred with ubiquitous Cre-recombinase expressing mice, resulting in the deletion of the loxP-flanked region. López et al. Journal of Neuroinflammation (2018) 15:158 Page 2 of 11 the changes in the brain expression pattern of this re- ceptor in the context of AD. confirmed this hypothesis [19, 31]. Regarding human sam- ples, we found expression of CB2R was restricted to peri- vascular microglia in control brains [24] but that CB2R protein were dramatically increased in different patho- logical conditions. Observations made in Alzheimer’s dis- ease (AD), multiple sclerosis, Down’s syndrome, and immunodeficiency virus-induced encephalitis confirmed that the presence of CB2R is greatly enhanced in areas of neuroinflammation, predominantly in microglial cells (see [6], for a review). Immunofluorescence and neuritic plaque staining Immunofluorescence and neuritic plaque staining Mice (N = 4–6 mice per group) were deeply anesthetized and transcardially perfused with cold PBS (pH 7.4) followed by freshly prepared cold 4% paraformaldehyde in PBS (pH 7.4). Tissue samples were collected and post- fixed in the same fixative overnight. Afterwards, tissues were dehydrated by sequential transfer to 10 and 30% su- crose solutions. Finally, tissues were cryoprotected with Tissue-Tek and frozen in dry ice. Thirty-micrometer- thick sections were obtained in a cryostat and pre- served in cryoprotectant solution until use. Homozygous mice identified by PCR were further verified by Southern blot analysis (Fig. 1c). All mice used in this study were fourth- or fifth-generation offspring from intercrosses of C57BL/6J mice. Mice were housed and bred in the animal facilities of Universidad Rey Juan Carlos (Alcorcón, Madrid, Spain) or the Medical College of Wisconsin (Milwaukee, WI, USA). Experimental pro- tocols met the European and Spanish regulations for protection of experimental animals (86/609/EEC and RD 1201/2005 and 53/2013) or were approved by the Insti- tutional Animal Care and Use Committee of the Medical College of Wisconsin. Male mice were used in all experi- ments included in the present report with the exception of flow cytometry experiments (see below). se ved c yop otecta t so ut o u t use. Floating tissue sections were washed with Tris Buffer Saline (TBS) before overnight incubation at 4 °C with the primary antibodies used for identification of the cellular types. For EGFP identification, overnight incubation with an anti-GFP antibody (1:1500; Abcam) was followed by in- cubation with an Alexa 488 anti-chicken antibody conju- gate (Invitrogen) carried out at 37 °C for 2 h, rendering green fluorescence. Afterwards, sections were incubated with a rabbit polyclonal anti-ionized calcium-binding adaptor molecule 1 (Iba1) (1:1000 dilution, Wako, Osaka, Japan), diluted in TBS containing 1% bovine serum albu- min (BSA; Sigma, St. Louis, USA) and 1% Triton x-100 (Sigma). After the incubation, sections were washed in TBS followed by incubation with an Alexa 546 anti-rabbit antibody conjugate (Invitrogen, Eugene, OR, USA) at 37 ° C for 2 h, rendering red fluorescence. Immunofluorescence and neuritic plaque staining Additional tissue sections were incubated with mouse monoclonal anti- GFAP-Cy3 antibody (1:1500 dilution, Sigma) in the same buffer for 2 h at 37 °C or with mouse monoclonal anti- neuron-specific nuclear protein (NeuN) antibody (1: 1000 dilution, Merck Millipore, Darmstadt, Germany) followed by incubation with Alexa 594 anti-mouse anti- body conjugate (Invitrogen) as described above. Generation of CB2 EGFP/f/f/5xFAD and CB2 −/−/5xFAD mice Mice co-expressing five familial Alzheimer’s disease muta- tions (5xFAD) were purchased from Jackson Laboratories (Bar Harbor, ME, USA; [25]) on the C57BL/6J background and were mated with CB2 EGFP/f/f and CB2 −/−mice and backcrossed for at least five generations to generate CB2 EGFP/f/f/5xFAD and CB2 −/−/5xFAD mice. Animals employed in the present experiments were 3 to 6 months old; this period was chosen based on previously published data [25, 36] in order to allow for the appearance of amyloid deposits. In order to study amyloid plaque deposits, a subset of CB2 EGFP/f/f/5xFAD mice received an i.p. dose of 10 mg/ kg of methoxy-XO4 (a Congo Red derivative known to selectively stain amyloid plaques; Tocris Bioscience; [4]) 24 h prior to sacrifice. Brains were processed and sec- tions were obtained and preserved for immunostaining as described above. Methods c Representative Southern blot showing the expected wild-type (WT) and recombined (Rec) hybridization signals at 9302 and 5794 bp, respectively, in embryonic stem cells from non-transfected (right column) and successfully transfected clones (left column). d Representative Western blot showing EGFP expression in spleen tissue homogenates from CB2 EGFP/f/f (left lane) and CB2 −/−mice (right lane). e The basal expression level of CB2 receptor mRNA is not modified as a consequence of the insertion of the genetic construct used for the generation of the knock-in mice (CB2 EGFP/f/f), as revealed by qRT-PCR in spleen samples and comparison with WT mice a b b a e c d 30 kda 36 kda d c e Fig. 1 Generation of a novel mouse model. a Genomic structure of the construct employed for the generation of CB2 EGFP/f/f and CB2 −/−mice. Hatched rectangles represent cnr2 coding sequences, gray rectangles indicate non-coding exon portions, solid lines represent chromosome sequences. The neomycin-positive selection cassette (Neo) IRES sequence and reporter gene (EGFP) are indicated. loxP sites are represented by blue triangles and FRT sites by double red triangles. The initiation (ATG) and Stop (Stop) codons are indicated. For the generation of knock-in mice (CB2 EGFP/f/f), recombined mice were bred with ubiquitous FLP-recombinase expressing mice, enabling the deletion of the FRT-flanked region. b For the generation of knock-out mice (CB2 −/−), recombined mice were bred with ubiquitous Cre-recombinase expressing mice, resulting in the deletion of the loxP-flanked region. c Representative Southern blot showing the expected wild-type (WT) and recombined (Rec) hybridization signals at 9302 and 5794 bp, respectively, in embryonic stem cells from non-transfected (right column) and successfully transfected clones (left column). d Representative Western blot showing EGFP expression in spleen tissue homogenates from CB2 EGFP/f/f (left lane) and CB2 −/−mice (right lane). e The basal expression level of CB2 receptor mRNA is not modified as a consequence of the insertion of the genetic construct used for the generation of the knock-in mice (CB2 EGFP/f/f), as revealed by qRT-PCR in spleen samples and comparison with WT mice López et al. Journal of Neuroinflammation (2018) 15:158 Page 3 of 11 containing exon 2 and downstream intronic sequences, (ii) a 2980 bp-sized fragment containing the coding part of exon 3 and upstream intronic sequences, and (iii) a 3657 bp-sized fragment containing the non-coding part of exon 3 and downstream sequences. Methods The linearized targeting construct was transfected into C57BL/6J embryonic stem cells. Homologous recombinant cells were identified by Southern analysis and five clones were used to generate chimeric mice. Chimeras were bred with C57BL/6J Flp- and Cre-deleter females, in order to generate Neo-excised EGFP reporter knock-in (CB2 EGFP/f/f) mice (Fig. 1a) and constitutive knock-out (CB2 −/−) mice (Fig. 1b), respectively. Homozygous mice identified by PCR were further verified by Southern blot analysis (Fig. 1c). All mice used in this study were fourth- or fifth-generation offspring from intercrosses of C57BL/6J mice. Mice were housed and bred in the animal facilities of Universidad Rey Juan Carlos (Alcorcón, Madrid, Spain) or the Medical College of Wisconsin (Milwaukee, WI, USA). Experimental pro- tocols met the European and Spanish regulations for protection of experimental animals (86/609/EEC and RD 1201/2005 and 53/2013) or were approved by the Insti- tutional Animal Care and Use Committee of the Medical College of Wisconsin. Male mice were used in all experi- ments included in the present report with the exception of flow cytometry experiments (see below). software to generate the geometric mean of eGFP expression in each immune cell population. containing exon 2 and downstream intronic sequences, (ii) a 2980 bp-sized fragment containing the coding part of exon 3 and upstream intronic sequences, and (iii) a 3657 bp-sized fragment containing the non-coding part of exon 3 and downstream sequences. The linearized targeting construct was transfected into C57BL/6J embryonic stem cells. Homologous recombinant cells were identified by Southern analysis and five clones were used to generate chimeric mice. Chimeras were bred with C57BL/6J Flp- and Cre-deleter females, in order to generate Neo-excised EGFP reporter knock-in (CB2 EGFP/f/f) mice (Fig. 1a) and constitutive knock-out (CB2 −/−) mice (Fig. 1b), respectively. Flow cytometry Single cell suspensions were prepared from the spleens of wild type, CB2 EGFP/f/f, and CB2 EGFP/f/+ mice of both sexes as described previously [27]. Cells were incubated with combinations of anti-mouse fluorescently-conjugated antibodies as follows: anti-B220 PE, anti-CD4 APC- eFluor780, anti-CD8 eFluor450, anti-CD11b eFluor450, anti-CD11c PE, anti-Ly6C APC, anti-Ly6G APC/Cy7, and anti-NK1.1 APC. Flow cytometry was used to identify B cells (B220+CD4−CD8−), CD4 T cells (CD4+NK1.1−), CD8 T cells (CD8+ NK1.1−), NKT cells (CD4+NK1.1+), NK cells (CD4−NK1.1+), macrophages (CD11b+Ly6C+/−Ly6G−), dendritic cells (CD11b+CD11chi), and granulocytes (CD 11b+Ly6C+Ly6G+). Sample acquisition was performed on a BD Biosciences LSR II, and data was analyzed using FlowJo Sections were mounted in aqueous solution (Vectashield, Vector Laboratories, Burlingame, CA, USA), coverslipped, and sealed. Slides were studied and photographed with up- right microscopes (Nikon 90i, Nikon, Tokyo, Japan; and Axioimager M2, Zeiss, Oberkochen, Germany) and using a DXM1200F camera and C1 and LSM710 confocal systems [36]. Image analysis was carried out as described [36] with Metamorph (Molecular Devices, Sunnyvale, CA, USA) and ImageJ software (Research Services Branch, National Insti- tute of Mental Health, Bethesda, MD, USA). López et al. Journal of Neuroinflammation (2018) 15:158 Page 4 of 11 Page 4 of 11 Page 4 of 11 López et al. Journal of Neuroinflammation (2018) 15:158 Western blotting from mouse brain. The transcript amounts were cal- culated using the second derivate maximum mode of the LC-software version 4.0. The specific transcript quantities were normalized to the transcript amounts of the reference gene 18S. All further calculations and statistical analyses were carried out with these values referred to as relative expression ratios. g Protein fractions were collected from a Tri-pure extrac- tion of hippocampal and spleen tissues, according to the manufacturer’s instructions (Roche). Lysates (20 μg/lane or 10 μg/lane for hippocampal and spleen protein sam- ples respectively) were separated by SDS-PAGE and transferred onto PVDF membranes (BioRad). After blocking in Tris-Tween buffered saline (TTBS; 10 mM Tris pH 7.5, 150 mM NaCl, 0.1% Tween 20 plus 5% nonfat dried milk), they were incubated overnight at 4 °C, as appropriate, with anti-GFP (1:500, Abcam, Cambridge, UK). Membranes were incubated with corresponding horseradish peroxidase-conjugated sec- ondary antibody (1:8000) and were developed using a chemiluminescent reagent (ECL detection reagent GE Healthcare, Buckinghamshire, UK). Developed signals were recorded on X-ray film (Agfa) for densi- tometric analysis (ImageJ, NIH, MD, USA). N = 4–6 mice per group were used for protein quantification by Western blot. Statistics Results are expressed as mean ± SEM. Statistical analysis were made using student’s t test for comparisons between two groups, analysis of variance (ANOVA), and two-way ANOVA with Tukey’s post-test for multiple comparisons. A p value < 0.05 was considered as statistically signifi- cant (see Additional file 3: Table S1). Data were ana- lyzed with Graph Pad Prism software version 6.0 (San Diego, CA, USA). ELISA Aβ1-42 p p To characterize the newly generated CB2 EGFP/f/f mice, we performed Western blotting on spleen samples. A single band corresponding to the EGFP molecular weight was evident in CB2 EGFP/f/f mice and was undetectable in spleen samples from CB2 −/−mice (Fig. 1d). We determined whether the strategy for the generation of the knock-in mice modified the expression levels of CB2R gene. Our results show that no changes were evident in CB2R mRNA expression levels between WT and CB2 EGFP/f/f mice in spleen (Fig. 1e; p = 0.474), thus ruling out a putative impact of the transgene on basal expression of the receptor. β Human ELISA kits (Invitrogen, Camarillo, CA, USA) were used for the quantification of Aβ1-42 in the brain soluble fractions, following the instructions provided by the manufacturer. Levels were normalized to the total amount of protein. Results Basal expression of EGFP in CB2 EGFP/f/f mouse spleen is coincident with previously described CB2 receptor patterns of expression in immune cells Real-time quantitative PCR for CB2 and IL1β Journal of Neuroinflammation (2018) 15:158 Page 5 of 11 a b c d e f Fig. 2 EGFP presence and distribution in CB2 EGFP/f/ spleens determined using flow cytometry (a–c) and immunofluorescence (d–f). a–c Determination of cell-specific expression of EGFP in splenocytes harvested from WT (a), CB2 EGFP/f/+ (b), and CB2 EGFP/f/f (c) mice. The numbers next to the histograms are the mean fluorescence intensity (MFI). d–f CB2-dependent-EGFP expression in B-lymphocytes in the spleen of CB2 EGFP/f/f. EGFP expression was evident in follicles of the white pulp. Scale bars, 100μm (d–g) a c b c b a c f d e d e Fig. 2 EGFP presence and distribution in CB2 EGFP/f/ spleens determined using flow cytometry (a–c) and immunofluorescence (d–f). a–c Determination of cell-specific expression of EGFP in splenocytes harvested from WT (a), CB2 EGFP/f/+ (b), and CB2 EGFP/f/f (c) mice. The numbers next to the histograms are the mean fluorescence intensity (MFI). d–f CB2-dependent-EGFP expression in B-lymphocytes in the spleen of CB2 EGFP/f/f. EGFP expression was evident in follicles of the white pulp. Scale bars, 100μm (d–g) contrast, intense EGFP signal could be seen in brain regions of CB2 EGFP/f/f/5xFAD mice known to be rich in beta-amyloid neuritic plaques, such as hippocampus (Fig. 3b). Other regions such as cortex, thalamus, and brain stem also exhibited EGFP signal (data not shown), in concordance with the previously reported distribution of neuritic plaques [25]. EGFP+ cells exhibited an ameboid shape and were mostly found in clusters (Fig. 3c), suggesting they could be activated microglial cells. No signal could be observed in the hippocampus of CB2 −/−/5xFAD mice (Fig. 3d) or in any other brain region examined (data not shown). pattern than the lymphocytes (Fig. 2). Given that the spleen contains numerous macrophage and dendritic cell populations, it is likely that CB2R, and thus EGFP, will be differentially expressed among them [7, 15]. Finally, of the myeloid subset, granulocytes exhibited the highest amount of EGFP expression. These data are consistent with the published reports of CB2R distribution among these cell types [12] indicating that the CB2 EGFP/f/f mouse is an excellent tool by which to determine steady state CB2R expression in various spleen cell populations using EGFP fluorescence. g y g mouse is an excellent tool by which to determine steady state CB2R expression in various spleen cell populations using EGFP fluorescence. Real-time quantitative PCR for CB2 and IL1β ea t e qua t tat e C o CB2 a d β Total RNA was isolated using Tripure Isolation Reagent (Roche, Mannheim, Germany) according to the protocol of the supplier. RNA was dissolved in RNase-free water and quantified by absorption at 260 nm. Aliquots were sub- jected to 1% denaturing agarose gel electrophoresis and GelRed Nucleic Acid Gel Stain (Biotium, Fremont, CA, USA) staining to verify the quantity and quality of RNA. Single-stranded complementary DNA (cDNA) was synthe- sized from 1 mg of total RNA using LightCycler Taqman Master (Roche Diagnostics). PCR primers and TaqMan probes were designed by Tib Molbiol (Berlin, Germany) (see Additional file 2: Figure S1). For normalization, 18S primers and probe number 55 from Universal ProbeLi- brary (Roche) were utilized. Gene expression was quanti- fied using LightCycler FastStart DNA Master HybProbe and LightCycler Taqman Master (Roche) and Quantimix Easy Probes kit (Biotools, Madrid, Spain) in a LightCycler thermocycler (Roche). The concentration of primers and probes were 0.5 and 0.2 μM, respectively. PCR assays were performed using 2 μl of the cDNA reaction. All assays were carried out twice as independent PCR runs for each cDNA sample. Mean values were used for further calculation. A negative (no template) control was measured in each of the PCR runs. Standard curves were calculated for quanti- fication purposes using fivefold serial dilutions of cDNA p p We used flow cytometry to identify and quantify the EGFP expression of splenocyte cell populations from wild type, CB2 EGFP/f/+, and CB2 EGFP/f/f mice (Fig. 2a–c). Using wild type mice, we found that background EGFP immunofluorescence was low in all immune cell populations examined (Fig. 2a). EGFP expression levels in splenic immune cells were compared in heterozygous (Fig. 2b) and homozygous (Fig. 2c) CB2 EGFP/f/f mice. In all immune cell populations investigated, the homozygous CB2 EGFP/f/f mice exhibited approximately double the mean fluorescence intensity (MFI) of the heterozygous mice. EGFP expression was highest in the B cell population, which is consistent with reports that B cells have the highest CB2 receptor expression among these cell types [12]. Among the T cell populations, CD4 T cells and NK T cells expressed a similar low level of EGFP expression, while CD8 T cells expressed ~ threefold higher levels (Fig. 2). NK cells expressed negligible levels of EGFP (Fig. 2). Monocytes/macrophages and dendritic cells expressed EGFP in a broader expression López et al. Basal expression of EGFP in CB2 EGFP/f/f mice is Basal expression of EGFP in CB2 EGFP/f/f mice is Real-time quantitative PCR for CB2 and IL1β We analyzed the expression of EGFP in spleens of CB2 EGFP/f/f mice by immunofluorescence and found discrete cell populations showing detectable signal. EGFP+ B cells were detected, limited to the marginal zone of the white pulp follicles, mostly located in the follicular corona (Fig. 2d–f). g As shown in Fig. 3e, EGFP immunoreactivity above background could be observed as early as 3 months of age in the CB2 EGFP/f/f/5xFAD mice, and EGFP- labeled cells increased in density with age in these mice (Fig. 3e–h). EGFP+ were found in clusters throughout the brain parenchyma and their distribution and increased density with age paralleled that of neuritic plaques, identified using methoxy-XO4, a dye for amyloid deposits (Fig. 3i–l). Interestingly, no EGFP signal could be observed in regions not exhibiting neuritic plaques (asterisks in Fig. 3g–k). The number of EGFP+ cells was dramatically increased at 4 and 6 months of age, which also paralleled the increase in the appearance of amyloid deposits (Fig. 3h: F3,18 = 58.46, p < 0.0001; Fig. 3l: F3,23 = 64.70, p < 0.0001). undetectable in the CNS but is induced as a consequence of amyloid deposition undetectable in the CNS but is induced as a consequence of amyloid deposition In the CNS, microscopic analysis of the brain and spinal cord of 3-, 4-, or 6-month-old CB2 EGFP/f/f mice showed no detectable EGFP immunoreactivity above background in glial or neuronal elements of any region examined, which included hippocampus (Fig. 3a), cortex, cerebellum, thalamus, brain stem, and spinal cord (not shown). In Page 6 of 11 López et al. Journal of Neuroinflammation (2018) 15:158 a b c d e f g i j k h l Fig. 3 In vivo EGFP induction in the context of AD, as revealed by immunofluorescence. a Un-manipulated, healthy CB2 EGFP/f/f mice showed no significant EGFP signal in hippocampus (a). b, c EGFP signal could be noticed in the brain of CB2 EGFP/f/f/5xFAD mice; these cells showed ameboid shape. d No EGFP signal could be observed in any brain region of CB2 −/−/5xFAD mice, including those enriched in amyloid plaques such as hippocampus. e–l EGFP signal in CB2 EGFP/f/f/5xFAD mice increased with age and paralleled that of amyloid deposits. EGFP was evident in brain samples of CB2 EGFP/f/f/5xFAD mice starting at 3 months of age (e) and progressively increasing with age (4 months, f, and 6 months, g) and matched with the pattern of distribution of amyloid-enriched plaques stained with methoxy-XO4 in those same samples (figure i–k). Note that neighboring brain regions devoid of amyloid deposits exhibited a complete absence of EGFP signal (asterisks in g, k). h, l Densitometric quantification of EGFP+ cells (h) and amyloid plaques (k) shows a parallel increase in neuritic plaques and EGFP expression. Data are expressed as mean ± SEM. *p < 0.05 vs CB2 EGFP/f/f mice, # vs CB2 EGFP/f/f/5xFAD-3mo mice, and “a” vs CB2 EGFP/f/f/5xFAD-4mo mice. N = 5 for immunofluorescence labeling. Scale bars, 10 μm (c) and 50 μm. DG (dentate gyrus); SBC (subiculum); CA1 (CA1 region of Ammon’s horn) c a b d b c h g f e f g e l k i j j i k Fig. 3 In vivo EGFP induction in the context of AD, as revealed by immunofluorescence. a Un-manipulated, healthy CB2 EGFP/f/f mice showed no significant EGFP signal in hippocampus (a). b, c EGFP signal could be noticed in the brain of CB2 EGFP/f/f/5xFAD mice; these cells showed ameboid shape. undetectable in the CNS but is induced as a consequence of amyloid deposition d No EGFP signal could be observed in any brain region of CB2 −/−/5xFAD mice, including those enriched in amyloid plaques such as hippocampus. e–l EGFP signal in CB2 EGFP/f/f/5xFAD mice increased with age and paralleled that of amyloid deposits. EGFP was evident in brain samples of CB2 EGFP/f/f/5xFAD mice starting at 3 months of age (e) and progressively increasing with age (4 months, f, and 6 months, g) and matched with the pattern of distribution of amyloid-enriched plaques stained with methoxy-XO4 in those same samples (figure i–k). Note that neighboring brain regions devoid of amyloid deposits exhibited a complete absence of EGFP signal (asterisks in g, k). h, l Densitometric quantification of EGFP+ cells (h) and amyloid plaques (k) shows a parallel increase in neuritic plaques and EGFP expression. Data are expressed as mean ± SEM. *p < 0.05 vs CB2 EGFP/f/f mice, # vs CB2 EGFP/f/f/5xFAD-3mo mice, and “a” vs CB2 EGFP/f/f/5xFAD-4mo mice. N = 5 for immunofluorescence labeling. Scale bars, 10 μm (c) and 50 μm. DG (dentate gyrus); SBC (subiculum); CA1 (CA1 region of Ammon’s horn) CB2R induction is limited to plaque-associated microglial cells EGFP+ cells were located in association with neuritic plaques (as revealed by staining with methoxy-XO4) and exhibited morphological features of microglia (Fig. 4). Co- localization studies with Iba-1, a commonly used marker of cells of myeloid lineage, were carried out. Low magnifica- tion (a to d) images showed a match in the pattern of distri- bution among EGFP+ and Iba1+ cells in the subiculum of 6-month-old CB2 EGFP/f/f/5xFAD mice; in addition, our data show that CB2-dependent EGFP expression takes place selectively in Iba1+ cells located in the vicinity of neuritic plaques (Fig. 4e–l). Microglial cells not associated with these pathological structures showed no EGFP staining (see Fig. 5a–d). For example, note the microglial cell at the arrow in Fig. 5b is neither EGFP positive nor associated with a plaque. Differences in the morphological features of EGFP+ and EGFP−microglial cells were evident, with EGFP+ cells exhibiting an ameboid-like shape (Fig. 5a and b), typical of activated microglia, while EGFP−cells showed a highly ramified morphology, characteristic of quiescent, non-activated, microglia (arrow in Fig. 5b). EGFP+ cells were located in association with neuritic plaques (as revealed by staining with methoxy-XO4) and exhibited morphological features of microglia (Fig. 4). Co- localization studies with Iba-1, a commonly used marker of cells of myeloid lineage, were carried out. Discussion We have established a novel transgenic mouse model (CB2 EGFP/f/f) that allows for identification of cells that are actively transcribing the cnr2 gene. The use of an IRES allows for coupling of EGFP expression to cnr2 gene transcription without loss or modification of the CB2 protein, which is a different approach from another reporter mouse line in which the cnr2 gene is replaced by EGFP, resulting in a CB2R knock out [29, 30]. The present reporter mice are expected to provide crucial information on the distribution, expression, and pathophysiological roles of the CB2R, while maintaining its appropriate cellular expression. By crossing these mice with 5xFAD mice, we have expanded our knowledge regarding the relevance of CB2R in amyloid pathology. The main conclusions of this study are that, if CB2R are expressed by neurons or glia in the CNS of healthy, un-manipulated mice, they are expressed at very low turnover rates undetectable in the CNS but is induced as a consequence of amyloid deposition Low magnifica- tion (a to d) images showed a match in the pattern of distri- bution among EGFP+ and Iba1+ cells in the subiculum of 6-month-old CB2 EGFP/f/f/5xFAD mice; in addition, our data show that CB2-dependent EGFP expression takes place Page 7 of 11 López et al. Journal of Neuroinflammation (2018) 15:158 a b c d e f g h i j k l Fig. 4 Restricted EGFP expression in microglial cells located in peri-plaque areas of the CB2 EGFP/f/f/5xFAD mouse hippocampus. a–l Low-magnification photographs of EGFP+ microglial cells (a, b) in close association to beta-amyloid neuritic plaques (c, d). Medium- (e–h) and high-magnification (i–l) photographs of EGFP+ microglial cells. Detailed co-localization immunofluorescent analysis reveals a complete overlap between EGFP+ cells and Iba1+ cells, indicative of their macrophage/microglia nature, and a selective association to amyloid-enriched plaques (stained with methoxy-XO4). Scale bars, 100 μm (a–d), 25 μm (e–h), and 25 μm (i–l). SBC (subiculum) d b c a h e g i j Fig. 4 Restricted EGFP expression in microglial cells located in peri-plaque areas of the CB2 EGFP/f/f/5xFAD mouse hippocampus. a–l Low-magnification photographs of EGFP+ microglial cells (a, b) in close association to beta-amyloid neuritic plaques (c, d). Medium- (e–h) and high-magnification (i–l) photographs of EGFP+ microglial cells. Detailed co-localization immunofluorescent analysis reveals a complete overlap between EGFP+ cells and Iba1+ cells, indicative of their macrophage/microglia nature, and a selective association to amyloid-enriched plaques (stained with methoxy-XO4). Scale bars, 100 μm (a–d), 25 μm (e–h), and 25 μm (i–l). SBC (subiculum) Furthermore, we also studied whether other cell types in the CNS, such as neurons or astrocytes expressed EGFP in CB2 EGFP/f/f/5xFAD mice. To that end, co-localization studies with a neuronal marker (NeuN; Fig. 5e–h) or with a marker of astrocytes (GFAP; Fig. 5i–l) were carried out. Our data indicate that neither of these cell types express EGFP; thus, cnr2-dependent EGFP expression is limited to microglial cells in CB2 EGFP/f/f/5xFAD mice. (Fig. 6c: F1,23 = 0.03775, p = 0.8476). Finally, a significant increase in interleukin-1 beta (IL1β) was observed as a consequence of the amyloid pathology (Fig. 6d: F1,23 = 49.12, p < 0.0001) but CB2R genotype had no effect (F1,33 = 0.2229, p = 0.6400). Changes associated with CB2R deletion include decreases in plaque deposition and no changes in gliosis or IL1β expression Second, under chronic neuroinflammatory stimuli (such as those derived from the deposition of the amyloid peptide in the brain parenchyma), the expression of CB2R is induced in microglial cells, and this induction takes place specifically in activated microglial cells surrounding neuritic plaques. These data confirm and expand previously published lit- erature and support the contention that the presence of CB2R may be a diagnostic marker of neuroinflammation in the context of AD [5, 6] and other pathological condi- tions with a neuroinflammatory component [19, 20]. 5xFAD mice brain tissues showed that cnr2-dependent EGFP expression is present in microglial (Iba1+) cells located in the vicinity of amyloid-enriched neuritic pla- ques (as revealed with methoxy-XO4 in vivo staining). There was a remarkable lack of detectable EGFP expres- sion in non-plaque areas. These data strongly support the hypothesis that CB2R gene expression is increased primar- ily in microglia that surround neuritic plaques. The time-course of the appearance of neuritic plaques in the subiculum of CB2 EGFP/f/f/5xFAD mice closely matched that previously described [25, 36]. Importantly, EGFP was detectable in plaque-associated microglia at 3 months of age, corresponding to the age when amyloid deposits are first present in the brain parenchyma. These data are indicative of the need to reach a threshold of inflammatory stimuli in the cellular milieu before the induction of CB2R expression takes place in the CNS. The present data suggest that threshold is reached coin- cident with appearance of the amyloid deposits. This suggests (i) that the induction of the expression of CB2 receptors takes place after a period of sustained inflam- mation and (ii) that CB2 receptors may be postulated as early markers of AD pathology. In this sense, it is im- portant to note that disease-linked symptoms in 5xFAD mice are not evident before 6 months of age; thus, the As previously suggested by us and by others [5, 19, 26], the expression of CB2R is induced under neuroinflamma- tory conditions in the human brain, being restricted to microglial cells closely associated to foci of neuroinflam- mation. Data obtained from samples of humans affected by several neurodegenerative conditions with accompany- ing neuroinflammation (i.e., AD, MS, HIV-encephalitis) revealed a consistent pattern of CB2R induction in micro- glia [6]. Our present data expand and confirm these obser- vations. Changes associated with CB2R deletion include decreases in plaque deposition and no changes in gliosis or IL1β expression We analyzed the impact of cnr2 gene deletion on plaque formation, soluble amyloid levels and neuroinflammation (Fig. 6). We found a small but significant decrease in hippo- campal neuritic plaque density (measured by staining with methoxy-XO4; Fig. 6a: p < 0.0338) in the CB2 −/−mice that was not paralleled by changes in soluble levels of Aβ1-42 in the hippocampus (measured by ELISA; Fig. 6b: p < 0.6413). Hippocampal microgliosis was assessed by counting Iba1+ cells in tissue sections. As expected, the 5xFAD mice exhibited a significant increase in Iba1+ cells (Fig. 6c: F1,23 = 85.84, p < 0.0001); however, there was no difference in this measure between the wild type and CB2 −/−mice Page 8 of 11 López et al. Journal of Neuroinflammation (2018) 15:158 a b c d e f g h i j k l Fig. 5 EGFP expression is limited to plaque-associated microglial cells but is absent in neurons and astrocytes in CB2 EGFP/f/f/5xFAD mice. a–c Z-stack showing that EGFP expression (a) was evident in microglial cells (b) located in close association to amyloid-enriched neuritic plaques, as revealed by methoxy-XO4 (c). However, microglial cells not linked with these pathological structures (arrow in b) showed reduced EGFP signal. d Orthogonal view in Z axis of the cluster of microglial EGFP+ cells shown in (a–c). Note the intimate contact established by microglial processes into the neuritic plaque. e–l Neurons (NeuN+ cells; e–h) nor astrocytes (GFAP+ cells; i–l) showed no EGFP signal. Scale bars, 25 μm c g i Fig. 5 EGFP expression is limited to plaque-associated microglial cells but is absent in neurons and astrocytes in CB2 EGFP/f/f/5xFAD mice. a–c Z-stack showing that EGFP expression (a) was evident in microglial cells (b) located in close association to amyloid-enriched neuritic plaques, as revealed by methoxy-XO4 (c). However, microglial cells not linked with these pathological structures (arrow in b) showed reduced EGFP signal. d Orthogonal view in Z axis of the cluster of microglial EGFP+ cells shown in (a–c). Note the intimate contact established by microglial processes into the neuritic plaque. e–l Neurons (NeuN+ cells; e–h) nor astrocytes (GFAP+ cells; i–l) showed no EGFP signal. Scale bars, 25 μm because no specific EGFP signaling could be detected in any region of the mouse brain or spinal cord. Changes associated with CB2R deletion include decreases in plaque deposition and no changes in gliosis or IL1β expression We used a well-known mouse model of amyloid pathology (5xFAD) to calibrate the impact that the ap- pearance of neuritic plaques in the brain parenchyma has on the expression of CB2R. The analysis of CB2 EGFP/f/f/ López et al. Journal of Neuroinflammation (2018) 15:158 Page 9 of 11 Fig. 6 Consequences of CB2 deletion in the context of AD. The genetic inactivation of CB2 in CB2 −/−/5xFAD mice led to a significant decrease in plaque density in hippocampus (a), without any changes in soluble amyloid production (b), or microgliosis (c). No changes were observed in the expression of IL1β as a consequence of gene deletion (d) in CB2 −/−/5xFAD mice as compared to those in CB2 EGFP/f/f/5xFAD mice. Data are expressed as mean ± SEM. *p < 0.05. Student’s t-test (a, b) and two-way ANOVA followed by Tukey’s post hoc test (c, d). N = 5 for immunofluorescence labeling measurements and N = 6 for experiments on soluble amyloid quantification and IL1β expression Fig. 6 Consequences of CB2 deletion in the context of AD. The genetic inactivation of CB2 in CB2 −/−/5xFAD mice led to a significant decrease in plaque density in hippocampus (a), without any changes in soluble amyloid production (b), or microgliosis (c). No changes were observed in the expression of IL1β as a consequence of gene deletion (d) in CB2 −/−/5xFAD mice as compared to those in CB2 EGFP/f/f/5xFAD mice. Data are expressed as mean ± SEM. *p < 0.05. Student’s t-test (a, b) and two-way ANOVA followed by Tukey’s post hoc test (c, d). N = 5 for immunofluorescence labeling measurements and N = 6 for experiments on soluble amyloid quantification and IL1β expression Surprisingly in light of earlier studies, CB2 −/−/5xFAD mice exhibited a small but significant decrease in neuritic plaque density in hippocampus compared to wild type 5xFAD mice that was not accompanied by a decrease in soluble Aβ1-42 levels, reduced microgliosis, or changes in IL1β expression. We do not have a conclusive explanation for this observation, though it is suggestive of a role for CB2R in microglial functions related to amyloid removal such as, for instance, phagocytosis [33]. In addition, conflicting results have been reported by several groups regarding the consequences of CB2 deletion on microgliosis, with both decreased and unchanged microgliosis being reported [2, 16, 30]. Competing interests Competing interests In summary, the present findings confirm and expand previous data showing the selective induction of CB2R in neuritic plaque-associated microglia and postulate these receptors as diagnostic and therapeutic targets in AD. The newly developed transgenic mouse model will be in- strumental for elucidating their role(s) in neuroinflam- matory conditions. The authors declare that they have no competing interests. Author details 1 1Laboratorio de Apoyo a la Investigación, Hospital Universitario Fundación Alcorcón, C/ Budapest 1, 28922 Alcorcón, Madrid, Spain. 2Universidad Rey Juan Carlos, Móstoles, Spain. 3Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Pozuelo de Alarcón, Madrid, Spain. 4Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI 53226, USA. 5Department of Pharmacology and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA. 1Laboratorio de Apoyo a la Investigación, Hospital Universitario Fundación Alcorcón, C/ Budapest 1, 28922 Alcorcón, Madrid, Spain. 2Universidad Rey Juan Carlos, Móstoles, Spain. 3Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Pozuelo de Alarcón, Madrid, Spain. 4Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI 53226, USA. Changes associated with CB2R deletion include decreases in plaque deposition and no changes in gliosis or IL1β expression Further experiments are needed to clarify the reasons for these discrepancies regarding the impact of CB2R deletion on the formation of amyloid-enriched plaques. induction of the cnr2 gene expression is previous to phenotypic changes due to amyloid pathology, indicating that CB2R may provide diagnostic and therapeutic tar- gets for the treatment of early stage AD [28]. CB2R functions in microglia as well as in other types of immune cells have been studied [8, 20]. In the context of AD neuroinflammation, there is evidence that CB2R ago- nists induce anti-inflammatory actions [1, 10, 21, 22, 26, 34], promote microglial migration and proliferation [37], and enhance amyloid removal [33, 38]. Furthermore, there is evidence that the activation of CB2R also decreases the production of amyloid peptides in a mouse model of AD [2], though conflicting results have been reported [29]. These effects make microglial CB2R interesting targets in amyloid-induced neuroinflammation as microglia play critical roles in the progression of the disease by modulat- ing, for instance, amyloid removal, cytokine production or exosome-mediated peptide degradation [14]. Several recent studies indicate that CB2R agonists affect neuronal function [11, 32, 39]. In particular, CB2R Page 10 of 11 López et al. Journal of Neuroinflammation (2018) 15:158 Page 10 of 11 Page 10 of 11 agonists have been reported to affect hippocampal plas- ticity, effects that are lost in CB2 −/−mice. These results are difficult to reconcile in light of the lack of detectable EGFP in the hippocampus of the present transgenic mice and in another reporter model [29]. It is possible that the turnover of the CB2R in neurons is slower than the turnover of EGFP protein or the detectable amount of EGFP expression may be lower than the CB2R expression levels required to achieve a functional response in vivo. Alternatively, it is possible that CB2R expression is upregulated by the processes involved in the preparation of tissues for study ex vivo. Availability of data and materials The datasets used and/or analyzed during the current study are available from the corresponding author on a reasonable request. Received: 11 January 2018 Accepted: 23 April 2018 Additional file 2: Figure S1. Sequences of the primers employed in the present studies. (DOCX 13 kb) Additional file 2: Figure S1. Sequences of the primers employed in the present studies. (DOCX 13 kb) Funding This work was supported by the Ministerio de Economía y Competitividad (SAF2013/42797-R and SAF2016/75959-R, JR), Ministerio de Educación of Spain (PR2009-0169, JR), Comunidad de Madrid (S2010/BMD-2308, JR), Universidad Francisco de Vitoria (2017, JR), and the Research Component of the Advancing a Healthier Wisconsin Endowment at the Medical College of Wisconsin (CJH), the National Institute on Drug Abuse (DA041212, CJH), and the National Multiple Sclerosis Society (RG 4432-A-5, BND). Our data are discordant compared to those reported in the Allen Mouse Brain Atlas [17]. Information pro- vided by this platform reveals low but detectable levels of CB2-mRNA in olfactory and cortical subplate areas, as shown by single cell in situ hybridization (ISH). How- ever, neither CB2 EGFP/f/f nor CB2 EGFP/f/f/5xFAD mice showed specific EGFP signal in either of these regions. We do not have an explanation for this discrepancy other than the mentioned mismatch between detection limits, in this case referred to single cell-ISH (Allen Atlas) and EGFP immunostaining (present data). Ethics approval l Experimental protocols met the European and Spanish regulations for protection of experimental animals (86/609/EEC and RD 1201/2005 and 53/ 2013) or were approved by the Institutional Animal Care and Use Committee of the Medical College of Wisconsin. Publisher’s Note S i N i Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. References Additional file 3: Table S1. Statistical analysis of the data provided in the manuscript. (DOCX 17 kb) Additional file 3: Table S1. Statistical analysis of the data provided in the manuscript. (DOCX 17 kb) Additional file 3: Table S1. Statistical analysis of the data provided in the manuscript. (DOCX 17 kb) 1. Aso E, Juvés S, Maldonado R, Ferrer I. CB2 cannabinoid receptor agonist ameliorates Alzheimer-like phenotype in AβPP/PS1 mice. J Alz Dis. 2013; 35:847-858. 1. Aso E, Juvés S, Maldonado R, Ferrer I. CB2 cannabinoid receptor agonist ameliorates Alzheimer-like phenotype in AβPP/PS1 mice. J Alz Dis. 2013; 35:847-858. 2. Aso E, Andrés-Benito P, Carmona M, Maldonado R, Ferrer I. Cannabinoid receptor 2 participates in amyloid-β processing in a mouse model of Alzheimer’s disease but plays a minor role in the therapeutic properties of a cannabis-based medicine. J Alz Dis. 2016;51:489-500. Acknowledgements A.L.V. (BES-2014-070233) and C.V. (BES-2011-043393) are recipients of FPI predoctoral fellowships from the Ministerio de Economía y Competitividad. N.A. and G.R-P. are recipients of predoctoral fellowships from Universidad Francisco de Vitoria. I.B-C. is a recipient of a postdoctoral fellowship from Comunidad Autónoma de Madrid (PEJD-2017-POST/BMD-4478). Authors’ contributions C d d CJH and JR conceived and designed the experiments. AL, NA, MRP, MTG, MABM, IBC, CV, MA, GRP, EGG, MB, RMT, BND, and JR performed the experiments. RMT, BND, CJH, and JR analyzed the data. BND, CJH, and JR wrote the manuscript. All authors read and approved the manuscript. Additional files Additional file 1: CB2 Western blots. Test of different CB2 primary antibodies in spleen samples (with high CB2 expression levels in normal conditions) harvested from CB2EGFP mice (lines 1, 2, and 3) and CB2KO mice (lines 4, 5, and 6). GFP and beta-actin immunodetection was employed as internal controls. (PPTX 6471 kb) 5Department of Pharmacology and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA. Received: 11 January 2018 Accepted: 23 April 2018 Received: 11 January 2018 Accepted: 23 April 2018 López et al. Journal of Neuroinflammation (2018) 15:158 7. Borges da Silva H, Fonseca R, Pereira RM, Cassado Ados A, Álvarez JM, D’Império Lima MR. Splenic macrophage subsets and their function during blood-borne infections. Front Immunol. 2015;6:480. 27. Ray A, Basu S, Gharalbeth RZ, Cook LC, Kumar R, Lefkowitz EJ, Walker CR, Morrow CD, Franklin CL, Gelger TL, Salzman NH, Fodor A, Dittel BN. Gut microbial dysbiosis due to helicobacter drives an increase in marginal zone B cells in the absence of IL-10 signaling in macrophages. J Immunol. 2015; 195:3071–85. 8. Cabral GA, Ferrerira GA, Jamerson MJ. Endocannabinoids and the immune system in health and disease. Handb Exp Pharmacol. 2015;231:185–211. 8. Cabral GA, Ferrerira GA, Jamerson MJ. Endocannabinoids and the immune system in health and disease. Handb Exp Pharmacol. 2015;231:185–211. 28. Savonenko AV, Melnikova T, Wang Y, Ravert H, Gao Y, Koppel J, Lee D, Pletnikova O, Cho E, Sayyida N, Hiatt A, Troncoso J, Davies P, Dannals RF, Pomper MG, Horti AG. Cannabinoid CB2 receptors in a mouse model of Ab amyloidosis: immunohistochemical analysis and suitability as a PET biomarker of neuroinflammation. PLoS One. 2015;10 https://doi.org/10.1371/ journal.pone.0129618. eCollection 2015 9. Carlisle SJ, Marciano-Cabral F, Staab A, Ludwick C, Cabral GA. Differential expression of the CB2 cannabinoid receptor by rodent macrophages and macrophage-like cells in relation to cell activation. Int Immunopharmacol. 2002;2:69–82. 10. Esposito G, Iuvone T, Savani C, Scuderi C, De Filippis D, Papa M, DiMarzo V, Steardo L. Opposing control of cannabinoid receptor stimulation on amyloid-beta-induced reactive gliosis: in vitro and in vivo evidence. J Pharmacol Exp Ther. 2007;322:1144–52. 29. Schmöle AC, Lundt R, Gennequin B, Schrage H, Beins E, Krämer A, Zimmer T, Limmer A, Zimmer A, Otte DM. Expression analysis of CB2-GFP BAC transgenic mice. PLoS One. 2015a;10 https://doi.org/10.1371/journal.pone. 0138986. eCollection 2015 11. Foster DJ, Wilson JM, Remke DH, Mahmood MS, Uddin MJ, Wess J, Patel S, Marnett LJ, Niwswender CM, Jones CK, Xiang Z, Lindsley CW, Rook JM, Conn PJ. Antipsychotic-like effects of M4 positive allosteric modulators are mediated by CB2 receptor-dependent inhibition of dopamine release. Neuron. 2016;91:1244–52. 30. Schmöle AC, Lundt R, Ternes S, Albayram Ö, Ulas T, Schultze JL, Bano D, Nicotera P, Alferink J, Zimmer A. Cannabinoid receptor 2 deficiency results in reduced neuroinflammation in an Alzheimer’s disease mouse model. Neurobiol Ag. 2015b;36:710–9. 12. Galiègue S, Mary S, Marchand J, Dussossoy D, Carrière D, Carayon P, Bouaboula M, Shire D, Le Fur G, Casellas P. López et al. Journal of Neuroinflammation (2018) 15:158 Expression of central and peripheral cannabinoid receptors in human immune tissues and leukocyte subpopulations. Eur J Biochem. 1995;232:54–61. 31. Stella N. Cannabinoid and cannabinoid-like receptors in microg astrocytes, and astrocytomas. Glia. 2010;58:1017–30. 32. Stempel AV, Stumpf A, Zhang HY, Özdögan T, Pannasch U, Theis AK, Otte DM, Wojtalla A, Racz I, Ponomarenko A, Xi ZX, Zimmer A, Schimtz D. Cannabinoid type 2 receptors mediate a cell type-specific plasticity in the hippocampus. Neuron. 2016;90:795–809. 13. Gong JP, Onaivi ES, Ishiguro H, Liu QR, Tagliaferro PA, Brusco A, Uhl GR. Cannabinoid CB2 receptors: immunohistochemical localization in rat brain. Brain Res. 2006;1071:10–23. 33. Tolón RM, Núñez E, Pazos MR, Benito C, Castillo AI, Martínez-Orgado JA, Romero J. The activation of cannabinoid CB2 receptors stimulates in situ and in vitro beta-amyloid removal by human macrophages. Brain Res. 2009; 1283:148–54. 14. Heneka MT, Golenbock DT, Latz E. Innate immunity in Alzheimer’s disease. Nat Immunol. 2015;16:229–36. 15. Hey YY, O’Neill HC. Murine spleen contains a diversity of myeloid and dendritic cells distinct in antigen presenting function. J Cell Mol Med. 2012;16:2611–9. 34. Van der Stelt M, Mazzola C, Esposito G, Matias I, Petrosino S, De Filippis D, Micale V, Steardo L, Drago F, Iuvone T, Di Marzo V. Endocannabinoids and beta-amyloid-induced neurotoxicity in vivo: effect of pharmacological elevation of endocannabinoid levels. Cell Mol Life Sci. 2006;63:1410–24. 16. Koppel J, Vingtdeux V, Marambaud P, D’Abramo C, Jimenez H, Stauber M, Friedman R, Davies P. CB2 receptor deficiency increases amyloid pathology and alters tau processing in a transgenic mouse model of Alzheimer’s disease. Mol Med. 2014;20:29–36. 35. Van Sickle MD, Duncan M, Kingsley PJ, Mouihate A, Urbani P, Mackie K, Stella N, Makriyannis A, Piomelli D, Davison JS, Marnett LJ, Di Marzo V, Pittman QJ, Patel KD, Sharkey KA. Identification and functional characterization of brainstem cannabinoid CB2 receptors. Science. 2005;310:329–32. 17. Lein ES, et al. Genome-wide atlas of gene expression in the adult mouse brain. Nature. 2007;445:168–76. 18. Lynn AB, Herkenham M. Localization of cannabinoid receptors and nonsaturable high-density cannabinoid binding sites in peripheral tissues of the rat: implications for receptor-mediated immune modulation by cannabinoids. J Pharmacol Exp Ther. 1994;268:1612–23. 36. Vazquez C, Tolón RM, Grande MT, Caraza M, Moreno M, Koester EC, Villaescusa B, Ruiz-Valdepeñas L, Fernández-Sánchez FJ, Cravatt BF, Hillard CJ, Romero J. Endocannabinoid regulation of amyloid-induced neuroinflammation. Neurobiol Ag. 2015;36:3008–19. 19. Maresz K, Carrier EJ, Ponomarev ED, Hillard CJ, Dittel BN. López et al. Journal of Neuroinflammation (2018) 15:158 Modulation of the cannabinoid CB2 receptor in microglial cells in response to inflammatory stimuli. J Neurochem. 2005;95:437–45. 37. Walter L, Franklin A, Witting A, Wade C, Xie Y, Kunos G, Mackie K, Stella N. Nonpsychotropic cannabinoid receptors regulate microglial cell migration. J Neurosci. 2003;23:1398–405. 20. Maresz K, Pryce G, Ponomarev ED, Marsicano G, Croxford JL, Shriver LP, Ledent C, Cheng X, Carrier EJ, Mann MK, Giovannoni G, Pertwee RG, Yamamura T, Buckley NE, Hillard CJ, Lutz B, Baker D, Dittel BN. Direct supression of CNS autoimmune inflammation via the cannabinoid receptor CB1 on neurons and CB2 on autoreactive T cells. Nat Med. 2007;13:492–7. 38. Wu J, Bie B, Yang H, Xu JJ, Brown DL, Naguib M. Activation of the CB2 receptor system reverses amyloid-induced memory deficiency. Neurobiol Ag. 2013;34:791–804. 39. Zhang HY, Gao M, Liu QR, Bi GH, Li X, Gardner EL, Wu J, Xi ZX. Cannabinoid CB2 receptors modulate midbrain dopamine neuronal activity and dopamine-related behavior in mice. Proc Natl Acad Sci U S A. 2014;111: E5007–15. 21. Martín-Moreno AM, Reigada D, Ramírez G, Mechoulam R, Innamorato N, Cuadrado A, de Ceballos ML. Cannabidiol and other cannabinoids reduce microglial activation in vitro and in vivo: relevance to Alzheimer’s disease. Mol Pharmacol. 2011;79:964–73. 40. Zimmerman AM, Titishov N, Mechoulam R, Zimmerman S. Effect of stereospecific cannabinoids on the immune system. Adv Exp Med Biol. 1991;288:71–80. 22. Martín-Moreno AM, Brera B, Spuch C, Carro E, García-García L, Delgado M, Pozo MA, Innamorato NG, Cuadrado A, de Ceballos ML. Prolonged oral cannabinoid administration prevents neuroinflammation, lowers beta- amyloid levels and improves cognitive performance in Tg APP2576 mice. J Neuroinflamm. 2012;9:8. 23. Munro S, Thomas KL, Abu-Shaar M. Molecular characterization of a peripheral receptor for cannabinoids. Nature. 1993;365:61–5. 24. Nuñez E, Benito C, Pazos MR, Barbachano A, Fajardo O, González S, Tolón RM, Romero J. Cannabinoid CB2 receptors are expressed by perivascular microglial cells in the human brain: an immunohistochemical study. Synapse. 2004;53:208–13. 25. Oakley H, Cole SL, Logan S, Maus E, Shao P, Craft J, Guillozet-Bongaarts A, Ohno M, Disterhoft J, Van Eldik L, Berry R, Vassar R. Intraneuronal beta- amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation. J Neurosci. 2006;26:10129–40. 26. Ramírez BG, Blázquez C, Gómez del Pulgar T, Guzmán M, de Ceballos ML. Prevention of Alzheimer's disease pathology by cannabinoids: neuroprotection mediated by blockade of microglial activation. López et al. Journal of Neuroinflammation (2018) 15:158 Abbreviations 5xFAD: Mice co-expressing five familial Alzheimer’s disease mutations; AD: Alzheimer’s disease; BSA: Bovine serum albumin; CB2R: Cannabinoid receptor, subtype 2; CD4: Cluster of differentiation 4; CNS: Central nervous system; EGFP: Enhanced green fluorescent protein; ELISA: Enzyme-linked immunosorbent assay; GFAP: Glial fibrillary acidic protein; i.p.: Intraperitoneal; Iba1: Ionized calcium-binding adaptor molecule 1; IL1β: Interleukin-1 beta; IRES: Internal Ribosomal Entry Site; ISH: In situ hybridization; NeuN: Neuron- specific nuclear protein; PBS: Phosphate buffered saline; PVDF: Polyvinylidene fluoride; qRT-PCR: Quantitative real-time polymerase chain reaction; SDS- PAGE: Sodium dodecyl sulfate polyacrylamide gel electrophoresis; THC: Δ9- tetrahydrocannabinol; TTBS: Tris-Tween buffer saline; UTR: Untranslated region 3. Atwood BK, Mackie K. CB2: a cannabinoid receptor with an identity crisis. Br J Pharmacol. 2010;160:467–79. 4. Bacskai BJ, Klunk WE, Mathis CA, Hyman BT. Imaging amyloid-β deposits in vivo. J Cereb Blood Flow Metab. 2002;22:1035-1041. 5. Benito C, Nunez E, Tolon RM, Carrier EJ, Rabano A, Hillard CJ, Romero J. Cannabinoid CB2 receptors and fatty acid amide hydrolase are selectively overexpressed in neuritic plaque-associated glia in Alzheimer’s disease brains. J Neurosci. 2003;23:11136–41. 6. Benito C, Tolon RM, Pazos MR, Nuñez E, Castillo AI, Romero J. Cannabinoid CB2 receptors in human brain inflammation. Br J Pharmacol. 2008;153:277–85. Page 11 of 11 López et al. Journal of Neuroinflammation (2018) 15:158 J Neurosci. 2005;23:1904–13.
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Potential of Egg shell powder as replacement of Lime in soil stabilization
International journal of advanced engineering research and sciences
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I. INTRODUCTION Improvement of soil properties is necessary in the modern scenario as soils with the required properties are not readily available for construction activities. There have been a lot of issues reported when structures were constructed on weak and soft soils like problems of shear failure, excessive settlement, differential settlement etc. The alternatives left with us are making the soil at site suitable for the expected load by improving its properties or adopting a deep foundation. Adoption of deep foundation is not at all an economically viable solution. Hence improvement of soil properties and in-situ treatment of soil are gaining importance these days. Soil stabilization is an economically feasible solution to one of the major construction problems. Researchers all over the world have studied various materials which can be used in conjunction with soil to improve soil properties. (Basha, 2005) studied the stabilization of soil with Rice husk ash and cement. (Brooks, 2009) conducted stabilization studies on stabilization using fly ash and rice husk ash. (Kamon, 1991 ) conducted researches on stabilization of soil using lime and industrial wastes. (Paul, 2014) conducted studies on soil stabilization using egg shell powder and quarry dust. (Anoop S P, 2017) conducted studies on improving soil using lime and elephant dung Anoop S P1, Hizana Beegom1, Jwoleena P Johnson1, Midhula J1, Tharis Muhammed T N1, Prasanth S2 Keywords— Lime, Soil stabilization, Egg shell, improvement, Geotechnical, replacement Keywords— Lime, Soil stabilization, Egg shell, improvement, Geotechnical, replacement [Vol-4, Issue-8, Aug- 2017] ISSN: 2349-6495(P) | 2456-1908(O) [Vol-4, Issue-8, Aug- 2017] ISSN: 2349-6495(P) | 2456-1908(O) International Journal of Advanced Engineering Research and Science (IJAERS) https://dx.doi.org/10.22161/ijaers.4.8.15 Anoop S P1, Hizana Beegom1, Jwoleena P Johnson1, Midhula J1, Tharis Muhammed T N1, Prasanth S2 1Under graduate students in Civil Engineering, UKF College of Engineering & Technology, Kollam, Kerala, India 2Assistant Professor in Civil Engineering, UKF College of Engineering, Kollam, Kerala, India 1Under graduate students in Civil Engineering, UKF College of Engineering & Technology, Kollam, Kerala, India 2Assistant Professor in Civil Engineering, UKF College of Engineering, Kollam, Kerala, India Abstract— This paper presents a study on the properties of soil stabilized by using lime and egg shell powder. Tests were conducted to assess the potential of egg shell powder in replacing lime, which can make the overall stabilization process economical and eco-friendly. Results obtained show that all the treated mixes gave much better strength than untreated soil. Egg shell powder was introduced in quantities of 0.5%, 1%, 1.5% and 2% of the weight of soil. Tests were conducted replacing up to 50% of the lime used for stabilization. It was observed that 25% replacement of lime by egg shell powder gave better strength properties and can be adopted for practical purposes. strips. Of all the various studies conducted around the world, the most commonly used and effective stabilizer was found to be lime. Lime is a not an industrial waste or a by-product, the manufacture of lime requires heating in the order of 750° C, which contribute to the fact that stabilization of large areas of soil with lime alone will increase the cost required for stabilization. In this study an attempt is made to replace lime with egg shell powder and to find out the extent up to which lime can be replaced by egg shell powder without compromising on the strength. Egg shell powder is an ideal material to replace lime in the stabilization process due to its similar chemical composition. The chief ingredient in egg shell powder is calcium carbonate as in the case of lime. Egg shells are disposed from hotels, restaurants etc in huge quantities and they are currently facing disposal problems. Use of egg shell powder in soil stabilization reduces the disposal problems associated with egg shell generations. Moreover, powdering of egg shell can be done easily. Egg shell powder generation does not involve generation of CO2 as in the case of lime where heating is done up to 750°C. Hence use of egg shell powder in soil stabilization will make the overall stabilization process economical, sustainable and eco-friendly. Potential of Egg shell powder as replacement of Lime in soil stabilization Anoop S P1, Hizana Beegom1, Jwoleena P Johnson1, Midhula J1, Tharis Muhammed T N1, Prasanth S2 [Vol-4, Issue-8, Aug- 2017] ISSN: 2349-6495(P) | 2456-1908(O) Table.1: Mixes used in this study Mix designation Details C Untreated soil C + 4L Clay + 4% weight of soil replaced by lime C+3.5L+0.5ESP Clay + 3.5% lime replacement and 0.5% weight replaced by egg shell powder C+3L+1 ESP Clay + 3% lime replacement and 1% weight replaced by egg shell powder C+2.5L+1.5ESP Clay + 2.5% lime replacement and 1.5% weight replaced by egg shell powder C+2L+2 ESP Clay + 2% lime replacement and 2% weight replaced by egg shell powder Table.1: Mixes used in this study Mix designation Details C Untreated soil C + 4L Clay + 4% weight of soil replaced by lime C+3.5L+0.5ESP Clay + 3.5% lime replacement and 0.5% weight replaced by egg shell powder C+3L+1 ESP Clay + 3% lime replacement and 1% weight replaced by egg shell powder C+2.5L+1.5ESP Clay + 2.5% lime replacement and 1.5% weight replaced by egg shell powder C+2L+2 ESP Clay + 2% lime replacement and 2% weight replaced by egg shell powder Fig.2: Variation of atterberg limits with Egg shell powder 0 5 10 15 20 25 30 35 40 0 1 2 3 Atterberg limits (%) Egg shell powder (%) Liquid limit Plastic limit Fig.2: Variation of atterberg limits with Egg shell powder Compaction tests showed an increase in the dry density upto 25% replacement of lime by egg shell powder. Above 25% replacement of lime by egg shell powder, dry density started to decrease. Egg shell powder is not that compatible a material as lime and hence when added in large quantities to replace lime, soil properties could not be improved. The variations in dry density on the addition of egg shell powder to lime modified mix is shown in Fig 3. Compaction tests showed an increase in the dry density upto 25% replacement of lime by egg shell powder. Above 25% replacement of lime by egg shell powder, dry density started to decrease. Egg shell powder is not that compatible a material as lime and hence when added in large quantities to replace lime, soil properties could not be improved. The variations in dry density on the addition of egg shell powder to lime modified mix is shown in Fig 3. [Vol-4, Issue-8, Aug- 2017] ISSN: 2349-6495(P) | 2456-1908(O) International Journal of Advanced Engineering Research and Scienc https://dx.doi.org/10.22161/ijaers.4.8.15 Fig.1: Egg shell powder T re co 0 st li so in International Journal of Advanced Engineering Research and Science (IJAERS) https://dx.doi.org/10.22161/ijaers.4.8.15 Fig.1: Egg shell powder IV. RESULTS AND DISCUSSIONS The soil mixes mentioned above were tested and the results obtained are summarized in table 2. Unconfined compressive strength of in situ soil was found to be only 0.45 kg/cm2 which indicate the necessity for soil stabilization. When the soil was mixed with optimum lime content, there was a drastic change in the strength of soil sample. The strength almost doubled upon introduction of lime. Table.2: Results of experimental tests on untreated and modified soil mixes Table.2: Results of experimental tests on untreated and modified soil mixes Sample Liqu id limit (%) Plasti c limit (%) OM C (%) γd (g/cc ) Mean UCC (kg/c m2) Untreated soil 24 11 18 1.76 0.45 C+ 4L 30 12.41 20 1.8 0.88 C+3.5L+0.5ESP 33 12.71 20 1.83 0.85 C+3L+1ESP 34 13.08 22 1.87 0.92 C+2.5L+1.5ESP 35 13.1 22 1.77 0.81 C+2L+2ESP 35 13.01 22 1.77 0.68 Fig.1: Egg shell powder Fig.1: Egg shell powder The materials mentioned above were mixed in various proportions for studying its effect on the soil stabilization process. First of all, the untreated soil was tested and its strength was obtained to understand whether there is need for stabilization. To this untreated soil mix, optimum lime content calculated as per ASTM D 6276 standards was added. The optimum lime content was found to be 4% of the weight of soil. Then egg shell powder was introduced as a replacement to lime in the stabilization process. The proportions of lime and egg shell powder were varied keeping the total replacement amount a constant. The various mixes used in this study are mentioned in table 1. There were not much variations in the atterberg limits of the soil sample on addition of egg shell powder. Egg shell powder was not found to alter the flow and consistency behavior of the soil sample. The variation of atterberg limits with the addition of egg shell powder is shown graphically in Fig 2. II. MATERIALS AND MIXES The materials used for this study consist of Soil, Lime and Egg shell powder. Soft clayey soil from Chathanoor area of Kollam district in Kerala was used for the study. Lime was purchased from the local markets and Egg shells were collected from hotels and restaurants in Parippally. The egg shells, thus collected were crushed and made into powder form. This was then sieved through 75 micron IS sieve so as to bring it to the size range of fine grained soil. The egg shell powder used for the study is shown in Fig 1 Page | 86 Page | 86 www.ijaers.com REFERENCES [1] Amu, O. O., A. B. Fajobi, and B. O. Oke. "Effect of eggshell powder on the stabilizing potential of lime on an expansive clay soil." Journal of Applied Sciences 5.8 (2005): 1474-1478. [1] Amu, O. O., A. B. Fajobi, and B. O. Oke. "Effect of eggshell powder on the stabilizing potential of lime on an expansive clay soil." Journal of Applied Sciences 5.8 (2005): 1474-1478. [2] Bowles, Joseph E. "Physical and geotechnical properties of soils." (1979). [2] Bowles, Joseph E. "Physical and geotechnical properties of soils." (1979). [3] Petry, Thomas M., and Dallas N. Little. "Review of stabilization of clays and expansive soils in pavements and lightly loaded structures—history, practice, and future." Journal of Materials in Civil Engineering 14.6 (2002): 447-460. [3] Petry, Thomas M., and Dallas N. Little. "Review of stabilization of clays and expansive soils in pavements and lightly loaded structures—history, practice, and future." Journal of Materials in Civil Engineering 14.6 (2002): 447-460. Fig.3: Variation of dry density of soil on adding egg shell powder All the soil mixes were tested for their unconfined compressive strength. The results show that there is an increase in unconfined compressive strength upto 25% replacement of lime by egg shell powder. Above this level of replacement, the strength was found to decline. Addition of small dosages of egg shell powder improved the strength of lime modified mix. As the replacement percentage increased, the strength started to fall as shown in figure 4. This may be due to the fact that egg shell powder is not an efficient material as lime and increasing egg shell powder will reduce the total lime content. Addition of small dosages of egg shell powder increased the rate of pozzolanic reaction occurring and hence gave a higher strength. All the modified mixes gave much better strength than untreated soil as shown in Fig 4. Fig.4: Variation of UCC with Egg shell powder 0 0.2 0.4 0.6 0.8 1 0 1 2 3 unconfined compressive strength Egg shell powder (%) Modified soil Untreated soil Fig.4: Variation of UCC with Egg shell powder III. TESTS CONDUCTED Experimental tests were conducted on untreated soil as well on lime and egg shell powder modified mixes in order to study the effect of addition of egg shell powder. The various tests conducted were atterberg limits, compaction and unconfined compression test. All these tests were carried out as per IS 2720 standards. Experimental tests were conducted on untreated soil as well on lime and egg shell powder modified mixes in order to study the effect of addition of egg shell powder. The various tests conducted were atterberg limits, compaction and unconfined compression test. All these tests were carried out as per IS 2720 standards. 3. Page | 87 Page | 87 www.ijaers.com International Journal of Advanced Engineering Research and Science (IJAERS) [Vol-4, Issue-8, Aug- 2017] https://dx.doi.org/10.22161/ijaers.4.8.15 ISSN: 2349-6495(P) | 2456-1908(O) Fig.3: Variation of dry density of soil on adding egg shell powder REFERENCES [1] Amu, O. O., A. B. Fajobi, and B. O. Oke. "Effect of eggshell powder on the stabilizing potential of lime on an expansive clay soil." Journal of Applied Sciences 5.8 (2005): 1474-1478. [2] Bowles, Joseph E. "Physical and geotechnical properties of soils." (1979). [3] Petry, Thomas M., and Dallas N. Little. "Review of stabilization of clays and expansive soils in pavements and lightly loaded structures—history, practice, and future." Journal of Materials in Civil Engineering 14.6 (2002): 447-460. 1 1.2 1.4 1.6 1.8 2 0 1 2 3 Max Dry Density (g/cc) Egg shell powder (%) International Journal of Advanced Engineering Research and Science (IJAERS) https://dx.doi.org/10.22161/ijaers.4.8.15 Fig.3: Variation of dry density of soil on adding egg shell powder [1] Amu, O. eggshell on an e Sciences [2] Bowles, propertie [3] Petry, Th stabilizat pavemen practice, Engineer 1 1.2 1.4 1.6 1.8 2 0 1 2 3 Max Dry Density (g/cc) Egg shell powder (%) International Journal of Advanced Engineering Research and Science (IJAERS https://dx.doi.org/10.22161/ijaers.4.8.15 Fig.3: Variation of dry density of soil on adding egg shell powder [1] Amu, eggsh on a Scien [2] Bowl prope [3] Petry stabil pavem practi Engin 1 1.2 1.4 1.6 1.8 2 0 1 2 3 Max Dry Density (g/cc) Egg shell powder (%) International Journal of Advanced Engineering Research and Science (IJAERS) https://dx.doi.org/10.22161/ijaers.4.8.15 V. CONCLUSIONS Egg shell powder was found to be a very good alternative in replacing the costly lime used for soil stabilization. The use of egg shell powder in soil stabilization will reduce the disposal problems of egg shell as well as make the stabilization process economically and sustainable. From the study, it was seen that egg shell powder can replace upto 25% of the lime used for stabilization process. This replacement also increased the strength of treated soil. Thus it can be concluded that egg shell powder is an ideal material to replace lime in the soil stabilization process owing to its similar chemical compositions and properties Page | 88 Page | 88 www.ijaers.com
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Inferring soil salinity in a drip irrigation system from multi-configuration EMI measurements using Adaptive Markov Chain Monte Carlo
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Hydrol. Earth Syst. Sci., 21, 5375–5383, 2017 https://doi.org/10.5194/hess-21-5375-2017 © Author(s) 2017. This work is distributed under the Creative Commons Attribution 3.0 License. Hydrol. Earth Syst. Sci., 21, 5375–5383, 2017 https://doi.org/10.5194/hess-21-5375-2017 © Author(s) 2017. This work is distributed under the Creative Commons Attribution 3.0 License. 4Brandenburg University of Technology, Research Center Landscape Development and Mining Landscapes, 03046 Cottbus Germany 5Agrosphere (IBG-3), Institute of Bio- and Geosciences, Forschungszentrum Jülich, GmbH, 52425 Jülich, German anow at: Department of Civil Engineering, International Islamic University, Islamabad 44000, Pakistan 5Agrosphere (IBG-3), Institute of Bio- and Geosciences, Forschungszentrum Jülich, GmbH, 52425 Jülich, Germany anow at: Department of Civil Engineering, International Islamic University, Islamabad 44000, Pakistan Correspondence to: Khan Zaib Jadoon (khanzaib.jadoon@iiu.edu.pk) Received: 12 June 2016 – Discussion started: 8 August 2016 Revised: 16 July 2017 – Accepted: 23 July 2017 – Published: 26 October 2017 Abstract. A substantial interpretation of electromagnetic in- duction (EMI) measurements requires quantifying optimal model parameters and uncertainty of a nonlinear inverse problem. For this purpose, an adaptive Bayesian Markov chain Monte Carlo (MCMC) algorithm is used to assess multi-orientation and multi-offset EMI measurements in an agriculture field with non-saline and saline soil. In MCMC the posterior distribution is computed using Bayes’ rule. The electromagnetic forward model based on the full solution of Maxwell’s equations was used to simulate the apparent elec- trical conductivity measured with the configurations of EMI instrument, the CMD Mini-Explorer. Uncertainty in the pa- rameters for the three-layered earth model are investigated by using synthetic data. Our results show that in the scenario of non-saline soil, the parameters of layer thickness as com- pared to layers electrical conductivity are not very informa- tive and are therefore difficult to resolve. Application of the proposed MCMC-based inversion to field measurements in a drip irrigation system demonstrates that the parameters of the model can be well estimated for the saline soil as compared to the non-saline soil, and provides useful insight about pa- rameter uncertainty for the assessment of the model outputs. 1 Introduction Electromagnetic induction (EMI) with low frequency is a powerful tool to map the hydrological processes in the va- dose zone due to the sensitivity to water content and soil salinity (Robinson et al., 2009). The use of EMI is largely motivated by the need for robust and compact system de- sign, ease of use, rapid acquisition, and capability to provide a large set of georeferenced measurements, which can be as- sociated with the spatial variability of subsurface at the field scale (Corwin, 2008). The EMI instrument is used to measure soil apparent electrical conductivity (ECa), providing distri- bution of averaged electrical conductivity over a particular depth range. The depth of investigation of ECa depends on the coil spacing, the coil orientation, and the frequency of the energizing field. Mester et al. (2011) reported that in the low induction number condition, the coil orientation, offset, and frequency have major, moderate and minor effects on the penetration depth, respectively. Soil moisture, salinity, and texture cannot be directly observed with EMI measurements. However, in non-saline soils, cation exchange capacity, and soil moisture and texture are factors responsible for ECa vari- ations (Rhoades et al., 1976; Sudduth et al., 2003), whereas Khan Zaib Jadoon1,a, Muhammad Umer Altaf2,3, Matthew Francis McCabe2, Ibrahim Hoteit3, Nisar Muhammad1, Davood Moghadas4, and Lutz Weihermüller5 Khan Zaib Jadoon1,a, Muhammad Umer Altaf2,3, Matthew Francis McCabe2, Ibrahim Hoteit3, Nisar Muhammad1, Davood Moghadas4, and Lutz Weihermüller5 Khan Zaib Jadoon1,a, Muhammad Umer Altaf2,3, Matthew Francis McCabe2, Ibrahim Hote Davood Moghadas4, and Lutz Weihermüller5 1Department of the Civil Engineering, COMSATS Institute of Information Technology, Abbottabad 22060, Pakistan 2Water Desalination and Reuse Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia 3Earth Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia 4Brandenburg University of Technology, Research Center Landscape Development and Mining Landscapes, 03046 Cottbus, Germany 5 4Brandenburg University of Technology, Research Center Landscape Development and Mining Landscapes, 03046 Cottbus, Germany 5 K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradients 5376 in saline soil, the ECa measurement is generally dominated by the soil salinity, and the reason is the accumulation of more salt concentration in the topsoil due to the loss of water through evaporation (Corwin and Lesch, 2005a, b; Ershadi et al., 2014). The success of EMI measurements to assess soil salinity depends on the establishment of site-specific petro- physical relationships to relate ECa with the soil salinity esti- mated by electrical conductivity of the saturated paste extract (ECe) (Cook and Walker, 1992). three-layer model via a Bayesian Markov chain Monte Carlo (MCMC) approach. They showed that combining multiple configuration EMI measurements significantly reduced total error, was best able to capture the shallow interface, and re- duced regions of uncertainty at depth. Conventional estimation of a single best-fit model with lin- ear uncertainty does not usually trace ambiguity in the mod- els, and may lead to a misguiding or imprecise interpreta- tion. In this work, an adaptive Bayesian MCMC algorithm was used for inverting multi-orientation and multi-offset EMI measurements, in which the parameter posterior distribution represents the complete solution of the Bayesian inversion problem, including prediction of optimal parameter values and the associated uncertainty. Synthetic scenarios are first analyzed for a three-layered earth model to evaluate the un- certainty in model parameters for saline and non-saline soil using the characteristics of the CMD Mini-Explorer EMI sys- tem. Field measurements of the CMD Mini-Explorer are then used to quantify parameter uncertainties in the three-layered earth model and soil salinity distributions in an agricultural field irrigated with drip irrigation system. Several inversion algorithms have been developed for EMI measurements to improve the resolution of subsurface fea- tures and the assessment of soil properties (Hendrickx et al., 2002; Santos et al., 2010; Triantafilis and Monteiro Santos, 2013). The majority of these inversion algorithms solve a 1- D earth model for electromagnetic wave propagation. The model of McNeill (1980) has been extensively used for low induction number and Maxwell’s equations have been uti- lized for high-conductive soil (ECa > 100 mS m−1) where the low induction number assumption is not valid. For ex- ample, Li et al. (2013) used Geonics EM38 to measure ECa in a rice paddy and inverted these using the McNeill (1980) forward model to estimate the variation of soil salinity in a field condition. 2 Materials and methods EMI systems are sensitive to the field-specific calibration procedure, which limits the accuracy of ECa measurements. In inversion modeling, however, precise measurement of ECa is a prerequisite to characterize subsurface soil properties. For decades, the development and use of quantitative EMI inversions were mainly hampered by the lack of efficient cal- ibration methods; von Hebel et al. (2014) used electrical re- sistivity tomography to calibrate EMI measurements before inversion to estimate three-dimensional images of subsurface electrical conductivity. Recently, Jadoon et al. (2015) cali- brated EMI measurements via vertical electrical conductivity profile measured by capacitance sensors in different pits and later performed inversion for calibrated multi-configuration EMI measurements to estimate the effect of soil salinity dis- tribution in an acacia tree farm. K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradients They reported that the yield reduced by 33 % in an irregularly shaped patch of strong saline topsoil. 2.1 Electromagnetic forward model Forward EMI response for a given layered earth model is usually calculated by the McNeill (1980) model, which is generated using the cumulative electrical conductivity distri- bution over a certain depth range, and is valid under condi- tion of low induction number. The alternative method used to calculate the forward EMI response is to solve the Maxwell equation for the magnetic field measured over a horizon- tal layered medium (Keller and Frischknecht, 1966; Ander- son, 1979). Preliminary analysis indicated that the electro- magnetic forward model, which is based on high induction number assumption, returned more reliable apparent electri- cal conductivity values than the standard sensitivity curves of McNeill (1980). Furthermore, increased computational power made it possible to characterize the subsurface by utilizing forward models based on the Maxwell equation (Santos et al., 2010). The effective depth of exploration is independent of ECa in a low induction number condition, whereas in high induction number condition an inverse re- lationship was found between the depth of exploration and ECa (Callegary et al., 2007). For a combination of a vertical and horizontal dipole source–receiver with an offset ρ over a multilayered earth, the electromagnetic forward model can be written as EMI inversion algorithms are generally robust and provide useful estimates of subsurface properties in terms of opti- mal model parameters. Analysis of uncertainty in model pa- rameters is however often left unaddressed. Parameter un- certainty can be associated with measurement errors (acqui- sition geometry, instrumental calibration and human error), modeling errors (assumptions in the electromagnetic forward model and petrophysical relationships), prior assumptions or constraints, parametrization, and estimation methods. Pa- rameter uncertainty analysis can serve two main purposes: to identify the model parameters of dominant importance, and to provide confidence in the estimated model parame- ters (Scharnagl et al., 2011). For instance, Minsley (2011) used synthetic data considering the characteristics of the shallow ground-based EMI system, geophex GEM-2 (Huang and Won, 2003), to quantify the parameter uncertainty of a ECHCP a (x,ρ) = −4ρ ωµ0 Im   ∞ Z 0 R0J0(ρλ)λ2dλ  , (1) (1) www.hydrol-earth-syst-sci.net/21/5375/2017/ www.hydrol-earth-syst-sci.net/21/5375/2017/ Hydrol. Earth Syst. Sci., 21, 5375–5383, 2017 K. Z. 2.1 Electromagnetic forward model (7) ϵ = y −M(α). (7) Assuming the components of the observational noise to be independent and Gaussian of mean zero and variance σ 2, the likelihood function can then be decomposed as Assuming the components of the observational noise to be independent and Gaussian of mean zero and variance σ 2, the likelihood function can then be decomposed as 2.2 Bayesian inference Bayesian inference is used to express the uncertainties in the system parameters based on a suitable likelihood function and a prior. Given a set of unknown parameters, the so-called posterior distribution of the model parameters, which is the distribution of the parameters conditioned on available ob- servations, is calculated as the product of the prior distribu- tion and the likelihood function (Arulampalam et al., 2002; Sivia, 2006). Bayesian inversion has gained a lot of interest in recent years and has been applied in different applications, including climate, ocean and geophysical modeling (Malin- verno, 2002; Zedler et al., 2012; Olson et al., 2012; Altaf et al., 2014; Sraj et al., 2014). p({yi}n i=1|α) = n Y i=1 1 √ 2πσ 2 exp  −(yi −Mi(α))2 2σ 2  . (8) (8) Here we consider σ 2 as an additional unknown (hyper) pa- rameter and try to estimate its distribution as part of the in- ference process. The (joint) posterior distribution is then ex- pressed as Here we consider σ 2 as an additional unknown (hyper) pa- rameter and try to estimate its distribution as part of the in- ference process. The (joint) posterior distribution is then ex- pressed as p(α,σ 2|{yi}n i=1) ∝ n Y i=1 1 √ 2πσ 2 exp  −(yi −Mi(α))2 2σ 2  p(α)p(σ 2). (9) Suppose a set of observations ({yi}n i=1) is available and assume a certain model to predict the data. Let α be the set of unknown parameters in the model; then according to Bayes’ rule, (9) The choice of the prior is a key step in the inference pro- cess. Here, an informative uniform prior for all five (three conductivities and two thickness) parameters is considered, with αk in the range [αmax k αmin k ]; i.e., p(α|{yi}n i=1) ∝p({yi}n i=1|α) p(α), (5) (5) where p(α) is the prior distribution of α that represents the a priori knowledge about α (i.e., before considering the data). where p(α) is the prior distribution of α that represents the a priori knowledge about α (i.e., before considering the data). The p({yi}n i=1|α) denotes the likelihood function: the proba- bility of predicting the data given α. The p(α|{yi}n i=1) is the posterior probability: the probability of recovering α given the data ({yi}n i=1). where p(α) is the prior distribution of α that represents the a priori knowledge about α (i.e., before considering the data). 2.1 Electromagnetic forward model Jadoon et al.: Diffusive extinction depth and soil moisture gradients 5377 10 1 10 2 1.5 1.0 0.5 0 Depth (m) Conductivity ( ) 10 1 10 2 10 3 10 4 1.5 1.0 0.5 0 Depth (m) Conductivity ( ) 15 mS m– 1 25 40 1800 1000 80 mS m– 1 mS m– 1 mS m– 1 mS m– 1 mS m– 1 mS m– 1 mS m–1 (a) (b) Figure 1. Three-layer synthetic earth model of electrical conductiv- ity for (a) non-saline soil and (b) saline soil in the top horizon. ECVCP a (x,ρ) = −4 ωµ0 Im   ∞ Z 0 R0J1(ρλ)λdλ  . (2) (2) In these expressions, ECVCP a and ECHCP a represent appar- ent electrical conductivity – measured in vertical and hori- zontal coplanar mode, µ0 represents permeability of the free space, λ indicates the radial wave number, J0 and J1 cor- respond to the zero-order and first-order Bessel functions, x is the depth of layer, ω is the angular frequency, and Im the quadrature component. The reflection factor R0 is ob- tained recursively, starting from the lowest layer N +1, with RN+1 = 0: Rn(hn,σn) = 0n−0n+1 0n+0n+1 + Rn+1 exp(−20n+1hn+1) 1 + 0n−0n+1 0n+0n+1 Rn+1 exp(−20n+1hn+1) , (3) 0n = q λ2 + ωµ0jσn, (4) (3) 0n = q λ2 + ωµ0jσn, (4) Figure 1. Three-layer synthetic earth model of electrical conductiv- ity for (a) non-saline soil and (b) saline soil in the top horizon. where σ0 = 0, hn is the height, and σn is the electrical con- ductivity for the nth layer. This is based on the assumption that each layer is uniform with infinite horizontal extent. EMI measurements were carried out under high induction number conditions (ECa > 100 mS m−1) utilizing the full solution of Maxwell’s equation to model the forward EMI response. where σ0 = 0, hn is the height, and σn is the electrical con- ductivity for the nth layer. This is based on the assumption that each layer is uniform with infinite horizontal extent. EMI measurements were carried out under high induction number conditions (ECa > 100 mS m−1) utilizing the full solution of Maxwell’s equation to model the forward EMI response. Let ϵ be a random variable representing the discrepancy be- tween our model M(α) and the observations, which we refer to as the observational noise: ϵ = y −M(α). 2.2 Bayesian inference The p({yi}n i=1|α) denotes the likelihood function: the proba- bility of predicting the data given α. The p(α|{yi}n i=1) is the posterior probability: the probability of recovering α given the data ({yi}n i=1). p(αk) = ( 1 αmax k −αmin k for αmin k < αk ≤αmax k , 0 otherwise. (10) The p({yi}n i=1|α) denotes the likelihood function: the proba- bility of predicting the data given α. The p(α|{yi}n i=1) is the posterior probability: the probability of recovering α given the data ({yi}n i=1). (10) For the noise variance σ 2, we consider a Jeffreys prior (Sivia, 2006): Let us consider the forward model M, for the evaluation of the observations y as a function of the parameters such that p(αk) = ( 1 σ 2 for σ 2 > 0, 0 otherwise. (11) (11) y = M(α). (6) www.hydrol-earth-syst-sci.net/21/5375/2017/ Hydrol. Earth Syst. Sci., 21, 5375–5383, 2017 K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradients K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradien 5378 10 15 20 25 30 35 40 V 32 V 71 V 118 H 32 H 71 H 118 CMD Mini−Explorer confgurations EC (mS m– 1) a Observed Modeled Range (a) 0 400 800 1200 1600 2000 V 32 V 71 V 118 H 32 H 71 H 118 CMD Mini−Explorer configurations EC (mS m– 1) a Observed Modeled Range (b) Figure 2. Observed electrical conductivity obtained from the forward response of the six different configuration of CMD Mini-Explorer (red star), estimated (modeled) earth electrical conductivity (blue asterisk) and the range of ECa simulated by MCMC for (a) non-saline and (b) saline soil scenarios. 10 15 20 25 30 35 40 V 32 V 71 V 118 H 32 H 71 H 118 CMD Mini−Explorer confgurations EC (mS m– 1) a Observed Modeled Range (a) 0 400 800 1200 1600 2000 V 32 V 71 V 118 H 32 H 71 H 118 CMD Mini−Explorer configurations EC (mS m– 1) a Observed Modeled Range (b) 32 V 71 V 118 H 32 H 71 H 1 CMD Mini−Explorer configurations Figure 2. Observed electrical conductivity obtained from the forward response of the six different configuration of CMD Mini-Explorer (red star), estimated (modeled) earth electrical conductivity (blue asterisk) and the range of ECa simulated by MCMC for (a) non-saline and (b) saline soil scenarios. Figure 3. 2.3 Synthetic and field measurements Two sets of experimental setups were considered to test the MCMC approach and to evaluate the estimated model pa- rameters and associated uncertainties using synthetic data for CMD Mini-Explorer configurations. Figure 1a and b show a three-layer earth model setups of low and high conductiv- ity for non-saline soil and saline soil salinity, respectively. In both setups, thicknesses for the three-layer earth model were conceptualized by a plow horizon (0.25 m thick), with an in- termediate subsoil layer (0.50 m thick) and underlying con- solidated layer up to 1.5 m depth. The plowing horizon gener- ally has less soil moisture as compared to the deeper horizon because of evaporation and infiltration processes. The sce- nario of non-saline soil therefore used a plowing horizon with low electrical conductivity of 15 mS m−1 as compared to the intermediate and consolidated soil layers (Fig. 1a). In the saline soil scenario, salt accumulates on the surface of soil due to evaporation of water. As a result, the electrical conduc- tivity of plowing horizon is considered higher 1800 mS m−1 as compared to the deeper layers (Fig. 1b). In the agricul- tural field, the increase in the soil salinity is generally due to the use of poor water quality or the excessive use of fertiliz- ers. The forward response of both scenarios was calculated in HCP and VCP via Eqs. (1) and (2), respectively, for EMI configuration setups using the characteristics of CMD Mini- Explorer of three receiver coils respectively placed at 0.32, 0.71 and 1.18 m distance from the receiver. Figure 3. Summary of the MCMC simulation for the synthetic three-layer earth model of non-saline soil. (a) True (red line) and es- timated parameter (blue dashed line) for the vertical electrical con- ductivity profile, and the gray background with the 95 % confidence interval of kernel distribution estimation (KDE). Panels (b–f) show the KDE of the marginalized posterior distributions for the three layer conductivities (σ1, σ2, and σ3) and the two layer thicknesses (h1 and h2). The most commonly used computational strategy to nu- merically solve a multidimensional parameters Bayesian in- ference problem is the Markov chain Monte Carlo (MCMC) method. We have applied an adaptive Metropolis MCMC al- gorithm to sample the posterior distribution, as described in details in Haario et al. 2.2 Bayesian inference Summary of the MCMC simulation for the synthetic three-layer earth model of non-saline soil. (a) True (red line) and es- timated parameter (blue dashed line) for the vertical electrical con- ductivity profile, and the gray background with the 95 % confidence interval of kernel distribution estimation (KDE). Panels (b–f) show the KDE of the marginalized posterior distributions for the three layer conductivities (σ1, σ2, and σ3) and the two layer thicknesses (h1 and h2). www.hydrol-earth-syst-sci.net/21/5375/2017/ 3.1 Synthetic data Figure 2a and b depict the observed, estimated (modeled) and range of ECa as they result from the chain of MCMC simu- lation for six configurations of the synthetic case with saline and non-saline soil. The x axis represents VCP and HCP with three coil spacing (ρ32, ρ71, ρ118). In a non-saline sce- nario, the layer electrical conductivity increases with depth (Fig. 1a), and this is reflected in the observed and modeled ECa in the VCP and HCP with increasing trend for larger spacing (Fig. 2a). The ECa value for the VCP and HCP with maximum spacing of 1.8 m between transmitter and receiver corresponds to deeper horizon; in the case of saline soil sce- nario the layer conductivity decreases (Fig. 1b) and as a result ECa values in VCP and HCP configuration exhibit a decreas- ing trend (Fig. 2b). The electromagnetic forward model is sensitive to high electrical conductive soil, so the modeled ECa values for the saline soil scenario match well with the observed as compared to the non-saline scenario. The mis- match between the observed and modeled ECa values for non-saline soil is due to the weak sensitivity of the forward electromagnetic model to the low electrical conductivity. Figure 4. Summary of the MCMC simulation for the synthetic three-layer earth model of saline soil. (a) True (red line) and es- timated parameter (blue dashed line) for the vertical electrical con- ductivity profile, and the gray background with the 95 % confidence interval of kernel distribution estimation (KDE). Panels (b–f) show the KDE of the marginalized posterior distributions for the three layer conductivities (σ1, σ2, and σ3) and the two layer thicknesses (h1 and h2). Figure 3a shows the true parameter values (red line) with the estimated parameters using MCMC (blue dashed line) for the non-saline soil scenario. The MCMC samples were used to obtain the marginalized posterior distributions based on kernel density estimation (KDE) (Parzen, 1962). The 95 % confidence interval of the KDE for each parameter is shown by the shaded gray background (Fig. 3a). The re- sulting marginalized posterior probability density functions (PDFs) of the three conductivities and two thicknesses are shown in Fig. 3b–f. The estimated parameters (Fig. 3b–f) show a single peak, corresponding to the best parameter val- ues. The electrical conductivities of the three model layers (σ1, σ2, and σ3) are reasonably well estimated as compared to the layer thicknesses. 3.1 Synthetic data Different uniform prior distributions were also tested for the layer thicknesses, but the MCMC so- lution converged close to the prior instead of the true layer thicknesses. The topography of the objective function was too flat in this case to allow consequent changes in the direc- tion of layer thicknesses. This suggests that the electromag- netic model is not sensitive to the layer thicknesses for the low-conductive soil layer. the observed data. All the results presented below are based on 104 MCMC samples. Parameter range for h1 and h2 was fixed between 0.05 and 0.6 m in each scenario. In the non- saline scenario, parameter range for σ1, σ2, and σ3 was con- sidered between 5 and 100 mS m−1 and the saline soil sce- nario range was fixed between 5 and 3000 mS m−1. A uni- form prior distribution function was considered in both sce- narios. Field measurements were also carried out in a farm, where Acacia trees were irrigated with saline groundwater. The farm is located at a distance of 6 km from the Red Sea coast at Al-Qadeimah, Makkah province, Saudi Arabia. EMI mea- surements were collected at an interval of 2 m over a 40 m long transect, along which three Acacia trees were irrigated using drip irrigation. At each location, EMI measurements using CMD Mini-Explorer system gives six different val- ues of apparent electrical conductivity (using two coil ori- entations and three offsets); each responds to different depth ranges. Ten pits were dug along the same transect and in each pit the bulk electrical conductivity σb profile was measured at 15 locations within a depth range of 0.05–1.5 m via 5TE capacitance sensors (Decagon Devices, Pullman, USA). EMI and 5TE measurements were performed 8 h after the drip ir- rigation system was stopped, so that the soil moisture is not concentrated below the drippers and to give enough time to reduce the soil moisture impact due to evaporation, root wa- ter uptake, and infiltration (Jadoon et al., 2015). Figure 4 illustrates the true and estimated depth profile of electrical conductivity for saline scenario, and the KDE of the marginalized posterior distributions for the three layer conductivities (σ1, σ2, and σ3) and the two layer thicknesses (h1 and h2). The shaded gray background shows the 95 % of the KDE for each parameter (Fig. 4a). The vertical electrical conductivity profile is well recovered by MCMC. K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradients K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradients 5379 Figure 4. Summary of the MCMC simulation for the synthetic three-layer earth model of saline soil. (a) True (red line) and es- timated parameter (blue dashed line) for the vertical electrical con- ductivity profile, and the gray background with the 95 % confidence interval of kernel distribution estimation (KDE). Panels (b–f) show the KDE of the marginalized posterior distributions for the three layer conductivities (σ1, σ2, and σ3) and the two layer thicknesses (h1 and h2). 2.3 Synthetic and field measurements (2001) and Roberts and Rosenthal (2009) In both scenarios, six configurations, three for each HCP and VCP with different spacings, were taken as an output for forward models. Let α = (σ1,σ2,σ3,h1,h2)T be a vector of model parameters. σ1, σ2, and σ3 are layer conductivities, and h1 and h2 thicknesses. Bayesian inference was used to estimate these five parameters that minimize the errors be- tween observed and modeled HCP and VCP. An adaptive MCMC method was used to sample the posterior distribu- tions and consequently update α distributions according to Hydrol. Earth Syst. Sci., 21, 5375–5383, 2017 www.hydrol-earth-syst-sci.net/21/5375/2017/ 3.1 Synthetic data The elec- trical conductivity of the top two layers are well estimated as compared to the consolidated layer with low electrical con- ductivity. Furthermore, for the six tested configurations of www.hydrol-earth-syst-sci.net/21/5375/2017/ Hydrol. Earth Syst. Sci., 21, 5375–5383, 2017 K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradients K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradients 5380 Figure 5. (a) Electrical conductivity (mS m−1) measured by the 5TE capacitance sensors from 10 soil pits along transect and the location of the soil pits is indicated by black triangles (Jadoon et al., 2015); (b) the soil electrical conductivity obtained by using Markov chain Monte Carlo simulation for multi-configuration electromagnetic induction measurements. Figure 5. (a) Electrical conductivity (mS m−1) measured by the 5TE capacitance sensors from 10 soil pits along transect and the location of the soil pits is indicated by black triangles (Jadoon et al., 2015); (b) the soil electrical conductivity obtained by using Markov chain Monte Carlo simulation for multi-configuration electromagnetic induction measurements. 0 20 40 60 80 100 H 32 H 71 H 118 V 32 V 71 V 118 CMD Mini−Explorer conf igurations EC (mS m– 1) a Measured Modeled Range (a) 0 400 800 1200 1600 2000 2400 V 32 V 71 V 118 H 32 H 71 H 118 CMD Mini−Explorer configurations EC (mS m– 1) a Measured Modeled Range (b) Figure 6. Measured six different configuration of CMD Mini-Explorer (red star), estimated (modeled) earth electrical conductivity (blue asterisk) and the range of ECa simulated by MCMC for (a) non-saline soil at pit 4 and (b) saline soil at pit 9 location. 0 400 800 1200 1600 2000 2400 V 32 V 71 V 118 H 32 H 71 H 118 CMD Mini−Explorer configurations EC (mS m– 1) a Measured Modeled Range (b) 0 20 40 60 80 100 H 32 H 71 H 118 V 32 V 71 V 118 CMD Mini−Explorer conf igurations EC (mS m– 1) a Measured Modeled Range (a) Figure 6. Measured six different configuration of CMD Mini-Explorer (red star), estimated (modeled) earth electrical conductivity (blue asterisk) and the range of ECa simulated by MCMC for (a) non-saline soil at pit 4 and (b) saline soil at pit 9 location. reduction of soil moisture impact due to root water uptake, evaporation and infiltration (Jadoon et al., 2015). 3.1 Synthetic data CMD Mini-Explorer, the HCP and VCP configuration with spacing 1.18 m are mostly sensitive to the consolidated layer while the remaining four configurations are more sensitive to the upper horizon. A large range of the parameter space was explored by MCMC (Fig. 4b–e), illustrating the sensitivity of the electromagnetic model to the considered parameters. Figure 5 shows the soil electrical conductivity measured in ten pits along a transect and the modeled soil elec- trical conductivity as estimated by the MCMC using the multi-configuration EM induction measurements. Pit loca- tions along the transect are indicated by black triangle and cubic interpolation of 150 5TE sensor measurements were used to construct the two-dimensional profile of measured soil electrical conductivity σ (Fig. 5a). The groundwater used to irrigate the acacia trees has an electrical conductivity of 4200 mS m−1. The three patterns of high electrical conduc- tivity is due to the infiltration front and soil salinity near the three acacia trees. In total, 21 multi-configuration EMI measurements were performed along a transect and cali- brated with in situ measurements collected using capacitance sensors (Jadoon et al., 2015). The three-layer earth model was considered for Bayesian inference of the five param- eters (σ1,σ2,σ3,h1,h2) and their uncertainty based on the 15 000 MCMC samples. For all MCMC simulations, the pa- rameter search space was set relatively large, with the range of low and high values of electrical conductivity of soil; 0 < σ1 < 3000 mS m−1, 0 < σ2 < 3000 mS m−1, 0 < σ3 < 3000 mS m−1, 0.05 < h1 < 0.6 m, and 0.05 < h1 < 0.6 m. In the depth section of soil electrical conductivity resulting from the EMI MCMC simulations, the effect of infiltration pat- K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradients Spatial distribution of soil salinity (ECe) obtained using Bayesian inversion of multi-configuration EMI measurements along a transect. Depth (m) Position (m) 0 10 20 30 40 0 0.5 1 1.5 ECe (dS m– 1) 0 200 400 terns and the soil salinity due to the drip irrigation near the three acacia trees is clear (Fig. 5b). The estimated soil elec- trical conductivity values by MCMC are in a good agreement with the sensor measurements performed in pits (Fig. 5a). p p g Figure 6a and b show the measured, estimated (modeled) and range of ECa as they result from the MCMC chain for the six multi-configurations of CMD Mini-Explorer for saline and non-saline soil. Three coil spacings for each VCP and HCP are represented on the x axis. EMI measurement is shown for non-saline and saline soil at locations 4 and 9 of the pit (Fig. 5a), respectively. The soil was completely dry for non-saline soil as no irrigation was applied, whereas in the case of saline soil the moisture in the soil varied be- tween 0.005 and 0.19 at the time of EMI and sensor mea- surements. In non-saline soil, the measured six ECa values range between 5 and 60 mS m−1 and the modeled ECa be- tween 23 and 38 mS m−1 (Fig. 6a). The range of ECa esti- mated from the last 10 000 MCMC samples is in the range of 0–75 mS m−1. As observed in the synthetic non-saline soil scenario, the electromagnetic forward model was not sensi- tive to the low electrical conductive soil. Similarly, the fit be- tween the measured and modeled ECa is not in good agree- ment with the real measurements (Fig. 6a). Furthermore, the misfit may be due to the large search parameter space in the MCMC simulations. In the case of saline soil, the electrical conductivity of the top 50 cm soil is high due to the saline infiltration and soil salinity. This effect can be seen in the de- creasing trend of the measured ECa for the VCP and HCP Figure 9. Spatial distribution of soil salinity (ECe) obtained using Bayesian inversion of multi-configuration EMI measurements along a transect. measurements with larger coil spacing (Fig. 6b). The mea- sured and modeled ECa are in good agrement and this is due to the high sensitivity of the electromagnetic forward model to high electrical conductive soil. K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradients (b–f) The KDE of the marginalized posterior dis- tributions for the three layer conductivities (σ1, σ2, and σ3) and two layer thicknesses (h1 and h2). Depth (m) Position (m) 0 10 20 30 40 0 0.5 1 1.5 ECe (dS m– 1) 0 200 400 Figure 9. Spatial distribution of soil salinity (ECe) obtained using Bayesian inversion of multi-configuration EMI measurements along a transect. Figure 7. Summary of the MCMC simulation for three-layer earth model by considering CMD Mini-Explorer measurement over a non-saline soil. (a) True (red line) and estimated parameter (blue dashed line) for the vertical electrical conductivity profile, and the gray background with the 95 % confidence interval of kernel distri- bution estimation (KDE). (b–f) The KDE of the marginalized pos- terior distributions for the three layer conductivities (σ1, σ2, and σ3) and two layer thicknesses (h1 and h2). Figure 8. Summary of the MCMC simulation for three-layer earth model by considering CMD Mini-Explorer measurement over a saline soil. (a) True (red line) and estimated parameter (blue dashed line) for the vertical electrical conductivity profile, and the gray background with the 95 % confidence interval of kernel distribution estimation (KDE). (b–f) The KDE of the marginalized posterior dis- tributions for the three layer conductivities (σ1, σ2, and σ3) and two layer thicknesses (h1 and h2). Figure 7. Summary of the MCMC simulation for three-layer earth model by considering CMD Mini-Explorer measurement over a non-saline soil. (a) True (red line) and estimated parameter (blue dashed line) for the vertical electrical conductivity profile, and the gray background with the 95 % confidence interval of kernel distri- bution estimation (KDE). (b–f) The KDE of the marginalized pos- terior distributions for the three layer conductivities (σ1, σ2, and σ3) and two layer thicknesses (h1 and h2). Figure 8. Summary of the MCMC simulation for three-layer earth model by considering CMD Mini-Explorer measurement over a saline soil. (a) True (red line) and estimated parameter (blue dashed line) for the vertical electrical conductivity profile, and the gray background with the 95 % confidence interval of kernel distribution estimation (KDE). (b–f) The KDE of the marginalized posterior dis- tributions for the three layer conductivities (σ1, σ2, and σ3) and two layer thicknesses (h1 and h2). Depth (m) Position (m) 0 10 20 30 40 0 0.5 1 1.5 ECe (dS m– 1) 0 200 400 Figure 9. 3.2 Experimental data Measurements were carried out in a farm, where acacia trees were irrigated with saline groundwater. The farm is located at a distance of 6 km from the Red Sea coast at Al-Qadeimah, Makkah province, Saudi Arabia. EMI measurements were collected at an intervals over a 40 m long transect, along which three acacia trees were irrigated using drip irrigation. At each location, EMI measurements using the CMD Mini- Explorer system provides six different values of apparent electrical conductivity (using two coil orientations and three offsets); each responds to different depth ranges. Ten pits were dug along the same transect and in each pit the verti- cal σb profile was measured at 15 locations within a depth range of 0.05–1.5 m via 5TE capacitance sensors (Decagon Devices, Pullman, USA). 5TE and EMI measurements were carried out on the same day 8 h after the drip irrigation sys- tem was stopped, so that the soil moisture concentration be- low the drippers is avoided, and enough time is given for the www.hydrol-earth-syst-sci.net/21/5375/2017/ Hydrol. Earth Syst. Sci., 21, 5375–5383, 2017 www.hydrol-earth-syst-sci.net/21/5375/2017/ K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradients 5381 Figure 7. Summary of the MCMC simulation for three-layer earth model by considering CMD Mini-Explorer measurement over a non-saline soil. (a) True (red line) and estimated parameter (blue dashed line) for the vertical electrical conductivity profile, and the gray background with the 95 % confidence interval of kernel distri- bution estimation (KDE). (b–f) The KDE of the marginalized pos- terior distributions for the three layer conductivities (σ1, σ2, and σ3) and two layer thicknesses (h1 and h2). Figure 8. Summary of the MCMC simulation for three-layer earth model by considering CMD Mini-Explorer measurement over a saline soil. (a) True (red line) and estimated parameter (blue dashed line) for the vertical electrical conductivity profile, and the gray background with the 95 % confidence interval of kernel distribution estimation (KDE). (b–f) The KDE of the marginalized posterior dis- tributions for the three layer conductivities (σ1, σ2, and σ3) and two layer thicknesses (h1 and h2). Figure 7. Summary of the MCMC simulation for three-layer earth model by considering CMD Mini-Explorer measurement over a non-saline soil. (a) True (red line) and estimated parameter (blue dashed line) for the vertical electrical conductivity profile, and the gray background with the 95 % confidence interval of kernel distri- bution estimation (KDE). (b–f) The KDE of the marginalized pos- terior distributions for the three layer conductivities (σ1, σ2, and σ3) and two layer thicknesses (h1 and h2). terns and the soil salinity due to the drip irrigation near the three acacia trees is clear (Fig. 5b). The estimated soil elec- trical conductivity values by MCMC are in a good agreement with the sensor measurements performed in pits (Fig. 5a). Figure 6a and b show the measured, estimated (modeled) and range of ECa as they result from the MCMC chain for the six multi-configurations of CMD Mini-Explorer for saline and non-saline soil. Three coil spacings for each VCP and HCP are represented on the x axis. EMI measurement is shown for non-saline and saline soil at locations 4 and 9 of the pit (Fig. 5a), respectively. The soil was completely dry Figure 8. Summary of the MCMC simulation for three-layer earth model by considering CMD Mini-Explorer measurement over a saline soil. (a) True (red line) and estimated parameter (blue dashed line) for the vertical electrical conductivity profile, and the gray background with the 95 % confidence interval of kernel distribution estimation (KDE). K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradients 5382 separation Hρ118 and Vρ118 is behind the overestimation of the soil electrical conductivity. The marginalized poste- rior PDFs of the three conductivities and two thicknesses are shown in Fig. 7b–f. The PDFs of the parameters (Fig. 7b–f) exhibit a single peak, corresponding to the best parameters. The peak of the σ3 is flat between 30 and 38 mS m−1 and it seems that the topography of the objective function does not change within this range of conductivity in each iteration of the MCMC simulation. (σ1, σ2, and σ3) and two layer thicknesses (h1 and h2) using MCMC. Such analysis helps to provide insight about param- eter estimates and uncertainties. The experimental results showed that the MCMC simula- tions can improve the reliability of the electromagnetic for- ward model to estimate the subsurface electrical conductiv- ity profiles. Analysis shows that the electromagnetic forward model is less sensitive to the non-saline soil as compared to the saline soil. The proposed approach is flexible and can be implemented for various low-frequency ground-based EMI systems and can provide subsurface electrical conductivity distribution and uncertainty of model parameters. Future re- search will focus on implementing the Bayesian inference approach on time-lapse EMI measurements in different agri- cultural fields to monitor the soil dynamics, and estimate the model parameters and their uncertainties. Figure 8 plots the vertical profile of electrical conductivity for the saline soil measured by capacitance sensors (red line), the value of the MCMC estimated parameters (blue dashed line), and the KDE of the marginalized posterior distributions for the three layer conductivities and the two layer thick- nesses. CMD Mini-Explorer measurements at pit 9 for saline soil was used for the analysis. The shaded area in Fig. 8a indi- cates the 95 % KDE distribution limits. The whole measured vertical profile of soil electrical conductivity falls within the shaded area, suggesting that the electrical conductivity is well estimated. The marginalized posterior PDFs of the three conductivities and two thicknesses, as shown in Fig. 8b–f, exhibit a single peak for all parameters except the layer thick- ness h2 which is flat, suggesting that the data were not infor- mative to refine our prior knowledge about h2. The posterior PDFs of the first two conductivities (σ1 and σ2) and layer thickness h1 exhibit a clear Gaussian shape with an obvious maximum a posteriori (MAP) estimate. References Altaf, M. U., Butler, T., Mayo, T., Luo, X., Dawson, C., Heemink, A. W., and Hoteit, I.: A Comparison of Ensemble Kalman Filters for Storm Surge Assimilation, Mon. Weather Rev., 142, 2899– 2914, 2014. Anderson, W. L.: Numerical integration of related Hankel trans- forms of orders 0 and by adaptive digital filtering, Geophysics, 44, 1287–1305, 1979. Arulampalam, M. S., Maskell, S., Gordon, N., and Clapp, T.: A tutorial on particle filters for online nonlinear/non-Gaussian Bayesian tracking, IEEE T. Signal Proces., 50, 174–188, 2002. K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradients For the conductivity parameter σ3, we notice a posterior with a well-defined peak, but no standard PDF shape. Data availability. The data were acquired at a privately owned farm in Saudi Arabia and are not available to the public. Competing interests. The authors declare that they have no conflict of interest. Acknowledgements. This research was funded by the Water Desalination and Reuse Center, King Abdullah University of Science and Technology (KAUST), Saudi Arabia. Acknowledgements. This research was funded by the Water Desalination and Reuse Center, King Abdullah University of Science and Technology (KAUST), Saudi Arabia. p Figure 9 shows the spatial distribution of the soil salin- ity as estimated from EMI measurement using MCMC. Soil salinity ECe is related to bulk electrical conductivity σb via a linear relationship (ECe = 13.74σb +0.001) established by Jadoon et al. (2015) for the same site. Infiltration front and high soil salinity range between 0.01 and 0.5 m at three lo- cations where acacia trees are irrigated with brackish wa- ter. The results show that the Bayesian inversion of multi- configuration EMI measurements successfully estimates the soil salinity caused by the brackish water infiltration. In the field, acacia tree roots concentrated in the top 70 cm of soil and the low soil salinity below 30 cm shows that acacia are capable of extracting salt solutions and reducing subsoil salinity. Edited by: Monica Riva Reviewed by: one anonymous referee Edited by: Monica Riva Reviewed by: one anonymous referee K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradients Figure 7 plots the vertical profile of electrical conductivity for non-saline soil as measured by capacitance sensors (red line), the value of the MCMC estimated parameters (blue dashed line), and the KDE of the marginalized posterior dis- tributions for the three layer conductivities and the two layer thicknesses. The CMD Mini-Explorer measurements at pit 4 for non-saline soil were used for the analysis. In Fig. 7a the measured vertical profile of soil electrical conductivity falls within the shaded area in the top 95 % KDE distribution limit 0–0.7 m depth and below this depth the modeled soil electrical conductivity is overestimated. The mismatch be- tween the measured and modeled ECa for the maximum coil www.hydrol-earth-syst-sci.net/21/5375/2017/ Hydrol. Earth Syst. Sci., 21, 5375–5383, 2017 K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradients 5383 Parzen, E.: On Estimation of a Probability Density Function and Mode, Ann. Math. Stat., 33, 1065–1076, 1962. J. J., and Ehsani, M. R., CRC Press, Taylor and Francis Group, Boca Raton, Folrida, 17–44, 2008. Corwin, D. L. and Lesch, S. M.: Apparent soil electrical conduc- tivity measurements in agriculture, Comput. Electron. Agr., 46, 11–43, 2005a. Rhoades, J. D., Raats, P. A. C., and Prather, R. J.: Effects of Liquid- phase Electrical Conductivity, Water Content, and Surface Con- ductivity on Bulk Soil Electrical Conductivity, Soil Sci. Soc. Am. J., 40, 651–655, 1976. Corwin, D. L. and Lesch, S. M.: Characterizing soil spatial variabil- ity with apparent soil electrical conductivity: I. Survey protocols, Comput. Electron. Agr., 46, 103–134, 2005b. Roberts, G. O. and Rosenthal, J. S.: Examples of Adaptive MCMC, J. Comput. Graph. Stat., 18, 349–367, 2009. Robinson, D. A., Lebron, I., Kocar, B., Phan, K., Sampson, M., Crook, N., and Fendorf, S.: Time-lapse geophysical imaging of soil moisture dynamics in tropical deltaic soils: An aid to inter- preting hydrological and geochemical processes, Water Resour. Res., 45, W00D32, https://doi.org/10.1029/2008WR006984, 2009. Ershadi, A., McCabe, M. F., Evans, J. P., Chaney, N. W., and Wood, E. F.: Multi-site evaluation of terrestrial evaporation models us- ing FLUXNET data, Agr. Forest Meteorol., 187, 46–61, 2014. Haario, H., Saksman, E., and Tamminen, J.: An adaptive Metropolis algorithm, Bernoulli, 7, 223–242, 2001. Hendrickx, J. M. H., Borchers, B., Corwin, D. L., Lesch, S. M., Hilgendorf, A. C., and Schlue, J.: Inversion of soil conductivity profiles from electromagnetic induction measurements: Theory and experimental verification, Soil Sci. Soc. Am. J., 66, 673–685, 2002. Santos, F. A. M., Triantafilis, J., Taylor, R. S., Holladay, S., and Bruzgulis, K. E.: Inversion of Conductivity Profiles from EM Us- ing Full Solution and a 1-D Laterally Constrained Algorithm, J. Environ. Eng. Geoph., 15, 163–174, 2010. Huang, H. P. and Won, I. J.: Real-time resistivity sounding using a hand-held broadband electromagnetic sensor, Geophysics, 68, 1224–1231, 2003. Scharnagl, B., Vrugt, J. A., Vereecken, H., and Herbst, M.: In- verse modelling of in situ soil water dynamics: investigat- ing the effect of different prior distributions of the soil hy- draulic parameters, Hydrol. Earth Syst. Sci., 15, 3043–3059, https://doi.org/10.5194/hess-15-3043-2011, 2011. Jadoon, K. Z., Moghadas, D., Jadoon, A., Missimer, T. M., Al- Mashharawi, S. K., and McCabe, M. 4 Conclusion Callegary, J. B., Ferre, T. P. A., and Groom, R. W.: Vertical spa- tial sensitivity and exploration depth of low-induction-number electromagnetic-induction instruments, Vadose Zone J., 6, 158– 167, 2007. In this paper, an adaptive Bayesian MCMC algorithm has been implemented for the model assessment and uncertainty analysis of multi-orientation and multi-offset EMI mea- surements. The algorithm has been tested for CMD Mini- Explorer with both synthetic and field measurements con- ducted in an agriculture field over a non-saline and saline soil. Using Bayesian inference, marginalized posterior PDFs were computed for three subsurface electrical conductivities Cook, P. G. and Walker, G. R.: Depth profiles of electrical- conductivity from linear-combinations of electromagnetic induc- tion measurements, Soil Sci. Soc. Am. J., 56, 1015–1022, 1992. Corwin, D. L.: Past, present, and future trends of soil electrical conductivity measurement using geophysical methods, in: Hand- book of Agricultural Geophysics, edited by: Allred, B., Daniels, www.hydrol-earth-syst-sci.net/21/5375/2017/ Hydrol. Earth Syst. Sci., 21, 5375–5383, 2017 K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradients F.: Estimation of soil salin- ity in a drip irrigation system by using joint inversion of mul- ticoil electromagnetic induction measurements, Water Resour. Res., 51, 3490–3504, 2015. Sivia, D. S.: Data Analysis: A Bayesian Tutorial, Oxford Science Publications, Oxford, UK, 2006. Sraj, I., Mandli, K. T., Knio, O. M., Dawson, C. N., and Hoteit, I.: Uncertainty quantification and inference of Manning’s friction coefficients using DART buoy data during the Tohoku tsunami, Ocean Model., 83, 82–97, 2014. Keller, G. and Frischknecht, F.: Electrical methods in geophysical prospecting. International Series of Monographs in Electromag- netic Waves 10, Pergamon Press, Oxford, New York, 1966. Sudduth, K. A., Kitchen, N. R., Bollero, G. A., Bullock, D. G., and Wiebold, W. J.: Comparison of electromagnetic induction and direct sensing of soil electrical conductivity, Agron. J., 95, 472– 482, 2003. Li, H. Y., Shi, Z., Webster, R., and Triantafilis, J.: Mapping the three-dimensional variation of soil salinity in a rice-paddy soil, Geoderma, 195, 31–41, 2013. Malinverno, A.: Parsimonious Bayesian Markov chain Monte Carlo inversion in a nonlinear geophysical problem, Geophys. J. Int., 151, 675–688, 2002. Triantafilis, J. and Monteiro Santos, F. A.: Electromagnetic con- ductivity imaging (EMCI) of soil using a DUALEM-421 and in- version modelling software (EM4Soil), Geoderma, 211, 28–38, 2013. McNeill, J. D.: Electromagnetic terrain conductivity measurement at low induction numbers, Tech note TN-6, Geonics Ltd., Mis- sissauga, ON, Canada, 10, 1319–1330, 1980. von Hebel, C., Rudolph, S., Mester, A., Huisman, J. A., Kumbhar, P., Vereecken, H., and van der Kruk, J.: Three-dimensional imag- ing of subsurface structural patterns using quantitative large- scale multiconfiguration electromagnetic induction data, Water Resour. Res. 50, 2732–2748, 2014. Mester, A., van der Kruk, J., Zimmermann, E., and Vereecken, H.: Quantitative Two-Layer Conductivity Inversion of Multi- Configuration Electromagnetic Induction Measurements, Vadose Zone J., 10, 1319–1330, 2011. Zedler, S. E., Kanschat, G., Korty, R., and Hoteit, I.: A new ap- proach for the determination of the drag coefficient from the up- per ocean response to a tropical cyclone: a feasibility study, J. Oceanogr., 68, 227–241, 2012. Minsley, B. J.: A trans-dimensional Bayesian Markov chain Monte Carlo algorithm for model assessment using frequency-domain electromagnetic data, Geophys. J. Int., 187, 252–272, 2011. Olson, R., Sriver, R., Goes, M., Urban, N. M., Matthews, H. D., Haran, M., and Keller, K.: A climate sensitivity estimate using Bayesian fusion of instrumental observations and an Earth System model, J. Geophys. Res.-Atmos., 117, D04103, https://doi.org/10.1029/2011JD016620, 2012. www.hydrol-earth-syst-sci.net/21/5375/2017/ Hydrol. K. Z. Jadoon et al.: Diffusive extinction depth and soil moisture gradients Earth Syst. Sci., 21, 5375–5383, 2017
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English
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Improving Sexual Function by Using Focal Vibrations in Men with Spinal Cord Injury: Encouraging Findings from a Feasibility Study
Journal of clinical medicine
2,019
cc-by
8,185
Received: 23 March 2019; Accepted: 10 May 2019; Published: 11 May 2019 Abstract: Erectile dysfunction (ED) is a frequent and disabling condition in patients with spinal cord injury (SCI). Spasticity can negatively affect sexual intercourse, as it may interfere with positioning, mobility, and muscle activation and strength, leading to ED. The aim of our study was to evaluate the feasibility and efficacy of muscle vibration (MV) applied to the pelvic muscles in improving ED in men with SCI. Ten adult men with traumatic SCI were submitted to 15 sessions of MV, applied on the perineum and the suprapubic and sacrococcygeal areas, using a pneumatic vibrator. MV was performed three times a week for five consecutive weeks, each session lasting 30 min. Muscle tone and sexual function were assessed before and after MV using the Modified Ashworth Scale (MAS) and International Index of Erectile Function (IIEF). We assessed the cremasteric and bulbocavernosus reflexes, as well as the electrophysiological bulbocavernosus reflex (eBCR) and pudendal nerve somatosensory-evoked potential (PSEP). MV was safe and well tolerated. All the patients reported an improvement in MAS and IIEF, with better reflexive responses, and a significant increase in eBCR and PSEP amplitude. In conclusion, MV of the pelvic floor is a promising method to reduce segmental spasticity and improve ED in men with incomplete SCI. However, our findings require confirmation through a randomized clinical trial with a larger sample size and longer trial period to examine long-term after effects. Keywords: sexual dysfunction; spinal cord injury; focal muscles vibrations; international index of erectile function Journal of Clinical Medicine Journal of Clinical Medicine Journal of Clinical Medicine Journal of Clinical Medicine J. Clin. Med. 2019, 8, 658; doi:10.3390/jcm8050658 www.mdpi.com/journal/jcm Improving Sexual Function by Using Focal Vibrations in Men with Spinal Cord Injury: Encouraging Findings from a Feasibility Study Rocco Salvatore Calabrò 1,*, Antonino Naro 1, Massimo Pullia 1, Bruno Porcari 1, Michele Torri Gianluca La Rosa 1, Alfredo Manuli 1, Luana Billeri 1, Placido Bramanti 1 and Fabrizio Quattri Rocco Salvatore Calabrò 1,*, Antonino Naro 1, Massimo Pullia 1, Bruno Porcari 1, Michele Torrisi 1, Gianluca La Rosa 1, Alfredo Manuli 1, Luana Billeri 1, Placido Bramanti 1 and Fabrizio Quattrini 2 1 Department of Robotic Neurorehabilitation, IRCCS Centro Neurolesi Bonino Pulejo, 98124 Messina, Italy; g.naro11@alice.it (A.N.); massimo.pullia@irccsme.it (M.P.); bruno.porcari@irccsme.it (B.P.); michele.torrisi@irccsme.it (M.T.); gianluca.larosa@irccsme.it (G.L.R.); alfredo.manuli@irccsme.it (A.M.); luana.billeri@irccsme.it (L.B.); dino.brama@gmail.com (P.B.) 1 Department of Robotic Neurorehabilitation, IRCCS Centro Neurolesi Bonino Pulejo, 98124 Messina, Italy; g.naro11@alice.it (A.N.); massimo.pullia@irccsme.it (M.P.); bruno.porcari@irccsme.it (B.P.); michele.torrisi@irccsme.it (M.T.); gianluca.larosa@irccsme.it (G.L.R.); alfredo.manuli@irccsme.it (A.M.); luana.billeri@irccsme.it (L.B.); dino.brama@gmail.com (P.B.) * Correspondence: salbro77@tiscali.it; Tel.: +3909060128166 * Correspondence: salbro77@tiscali.it; Tel.: +3909060128166 1. Introduction Ove there is one penile tumescence pathway (lumbar and sacral spinal segment  pelvic plexus  cavern nerve  penis) and three penile detumescence pathways (1: lumbar spinal segment  superior plexu cavernous nerve  penis; 2: lumbar spinal segment  paravertebral sympathetic chain pelvic/cavernous nerve  penis; 3: lumbar spinal segment  paravertebral sympathetic chain Figure 1. Diagram of the nervous pathways regulating erection. Reflexogenic erection depends on a circuitry made of the dorsal nerve of the penis/pudendal nerve, which conveys sensory input, a parasympathetic center in the sacral spinal cord, and the pelvic plexus/cavernous nerve, which convoys efferent output to the penis. Sensory input reaches the brain via ascending spinal pathways. The brain can initiate psychogenic erection by various stimuli received by or generated within the brain. It also controls lumbar sympathetic and sacral parasympathetic outflow to the penis. Overall, there is one penile tumescence pathway (lumbar and sacral spinal segment →pelvic plexus →cavernous nerve →penis) and three penile detumescence pathways (1: lumbar spinal segment →superior plexus →cavernous nerve →penis; 2: lumbar spinal segment →paravertebral sympathetic chain →pelvic/cavernous nerve →penis; 3: lumbar spinal segment →paravertebral sympathetic chain → pudendal nerve →penis). + and −indicate penile tumescence or detumescence effect, respectively. Figure 1. Diagram of the nervous pathways regulating erection. Reflexogenic erection depends o circuitry made of the dorsal nerve of the penis/pudendal nerve, which conveys sensory inpu parasympathetic center in the sacral spinal cord, and the pelvic plexus/cavernous nerve, wh convoys efferent output to the penis. Sensory input reaches the brain via ascending spinal pathwa The brain can initiate psychogenic erection by various stimuli received by or generated within brain. It also controls lumbar sympathetic and sacral parasympathetic outflow to the penis. Over there is one penile tumescence pathway (lumbar and sacral spinal segment  pelvic plexus  caverno nerve  penis) and three penile detumescence pathways (1: lumbar spinal segment  superior plexus cavernous nerve  penis; 2: lumbar spinal segment  paravertebral sympathetic chain pelvic/cavernous nerve  penis; 3: lumbar spinal segment  paravertebral sympathetic chain Figure 1. Diagram of the nervous pathways regulating erection. Reflexogenic erection depends on a circuitry made of the dorsal nerve of the penis/pudendal nerve, which conveys sensory input, a parasympathetic center in the sacral spinal cord, and the pelvic plexus/cavernous nerve, which convoys efferent output to the penis. Sensory input reaches the brain via ascending spinal pathways. 1. Introduction Spinal cord injury (SCI) can severely impair erection, ejaculation, and perception of orgasm, with a consequent change in patients’ sexual behavior [1,2]. About 20% of patients with complete SCI complain of severe erectile dysfunction (ED), i.e., the inability to achieve or maintain an erection sufficient for satisfactory sexual performance [1–3]. ED severity varies in men with incomplete SCI, depending on the location and degree of damage of the neural pathways subtending erection [1–3]. Erection is a neurovascular event characterized by the tumescence of the cavernous bodies that rely upon integration of neural and humoral mechanisms at various levels of the nervous system. It requires the participation of autonomic and somatic (i.e., the dorsal nerve of the penis) nerves and the integration of numerous spinal and supraspinal sites, including the medial preoptic area of the J. Clin. Med. 2019, 8, 658; doi:10.3390/jcm8050658 www.mdpi.com/journal/jcm 2 of 12 2 of J. Clin. Med. 2019, 8, 658 J. Clin. Med. 2019, 8, hypothalamus, and septal region (Figure 1). The penis receives innervation from sacral parasympathetic (pelvic), thoracolumbar sympathetic (hypogastric and lumbar chain), and somatic (pudendal) nerves. The major excitatory input to the penis is provided by the parasympathetic nervous system (S2–S4), responsible for vasodilatation of the penile vasculature and erection. The sympathetic nervous system (T10–L2) seems to play a pivotal role in the detumescence of the penis [4]. hypothalamus, and septal region (Figure 1). The penis receives innervation from sac parasympathetic (pelvic), thoracolumbar sympathetic (hypogastric and lumbar chain), and soma (pudendal) nerves. The major excitatory input to the penis is provided by the parasympathe nervous system (S2–S4), responsible for vasodilatation of the penile vasculature and erection. T sympathetic nervous system (T10–L2) seems to play a pivotal role in the detumescence of the penis [4 Figure 1. Diagram of the nervous pathways regulating erection. Reflexogenic erection depends circuitry made of the dorsal nerve of the penis/pudendal nerve, which conveys sensory inpu parasympathetic center in the sacral spinal cord, and the pelvic plexus/cavernous nerve, wh convoys efferent output to the penis. Sensory input reaches the brain via ascending spinal pathw The brain can initiate psychogenic erection by various stimuli received by or generated within brain. It also controls lumbar sympathetic and sacral parasympathetic outflow to the penis. J. Clin. Med. 2019, 8, 658 J. Clin. Med. 2019, 8, 658 3 of 12 Most of the patients with SCI require specific, multidisciplinary management for ED, including pharmacological and surgical approaches, counseling, and rehabilitation with physical therapy treatment [4,8,9]. For instance, the oral administration of PDE-5 inhibitors represents one of the best choices in men with SCI, if the basic mechanisms responsible for erection, including both normal vasculature and S2–S4 reflex arc, are preserved [10]. Injectable and intra-urethral agents are relegated to second line therapy after oral PDE-5 inhibitors are ineffective, although the local delivery of medications (i.e., PGE1 and papaverine) remains useful in about 25%–30% of ED patients. Penile prosthesis offers a valid therapeutic alternative for patients who fail vasoactive drugs and vacuum-constrictive devices and who are not candidates for vascular reconstruction procedures [4]. However, such approaches may be unacceptable to the patient, unavailable, or inapplicable [4,8,9]. Growing research is focusing on instrumental approaches to manage ED. It is worth noting that among the problems facing patients with SCI, spasticity significantly contributes to ED [11–14]. Spasticity develops gradually over several months after SCI, is strictly associated with hyperreflexia and excessive muscle spasms, and involves also pelvic floor muscles [11–14]. Thus, spasticity may affect: (1) positioning and mobility that are necessary for sexual intercourse, and (2) activation, strength, time of force development, and control of the pelvic floor muscles that are involved in erectile and ejaculation functions, with spasms during penetration [11–14]. Therefore, the reduction of spasticity may be a therapeutic option to improve ED. A useful tool to reduce segmental spasticity is represented by muscle vibration (MV), as suggested by reports on patients with stroke, multiple sclerosis, and cerebral palsy [15–18]. Vibrations have been already used to manage different pelvic floor dysfunctions due to diverse pathologies, but only employing whole body vibration (not addressing ED) or penile vibration used for ejaculation [19–27]. There is converging evidence that MV provides the central nervous system with strong proprioceptive inputs (preferentially through Ia afferents) that reach the somatomotor cortices. This may help to modify the corticospinal excitability, to favor intracortical inhibitory systems, and to induce better muscle synergy pattern by acting on the excitability of spinal motoneurons and interneurons. MV may directly act at the spinal level, reducing abnormalities of the spinal excitability (as the activation of primary Ia spindle afferents result in inhibition of the monosynaptic reflex) and restoring abnormal reciprocal and presynaptic inhibition mechanisms [15–18]. 2.1. Study Population We screened SCI outpatients visiting the Behavioral and Robotic Neurorehabilitation Unit of our institute between January and June 2018 for patients complaining of ED. Ten patients with neurogenic ED were enrolled in this open label pilot study, according to the following inclusion criteria: (1) age 18–65 years; (2) diagnosis of incomplete SCI, with American Spinal Injury Association (ASIA) level C-D, no involvement of sacral spinal segment and SCI occurred at least six months before the study enrollment (i.e., chronic phase); (3) an International Index of Erectile Function (IIEF) score <18 (that is, severe, moderate, or mild-to-moderate ED) [28–30]; (4) to be sexually active and fully continent before SCI; and (5) withdrawal from previous treatment (for at least three months before the study inclusion), such as erectogenic aids, nutraceutics, antispastics, and psychoactive drugs. J. Clin. Med. 2019, 8, 658 Altogether, these effects lead to a reduction in spasticity [15–18]. Hypothesizing that the MV-induced reduction of pelvic floor spasticity may improve ED, we evaluated the feasibility and efficacy of low-amplitude/high-frequency MV delivered to specific muscles of the pelvic floor and sacral area in improving ED in males with incomplete SCI. 1. Introduction The brain can initiate psychogenic erection by various stimuli received by or generated within the brain. It also controls lumbar sympathetic and sacral parasympathetic outflow to the penis. Overall, there is one penile tumescence pathway (lumbar and sacral spinal segment →pelvic plexus →cavernous nerve →penis) and three penile detumescence pathways (1: lumbar spinal segment →superior plexus →cavernous nerve →penis; 2: lumbar spinal segment →paravertebral sympathetic chain →pelvic/cavernous nerve →penis; 3: lumbar spinal segment →paravertebral sympathetic chain → pudendal nerve →penis). + and −indicate penile tumescence or detumescence effect, respectively. pudendal nerve  penis). + and − indicate penile tumescence or detumescence effect, respectively. SCI may cause structural changes within the pelvic floor, neuropathic pain, spasticity, a problems with bladder and bowel continence with the consequent shame of unwanted sme Altogether, these concerns can worsen ED significantly. Changes in body image representati SCI may cause structural changes within the pelvic floor, neuropathic pain, spasticity, and problems with bladder and bowel continence with the consequent shame of unwanted smells. Altogether, these concerns can worsen ED significantly. Changes in body image representation, depression, anxiety, and fatigue also contribute to worsen ED [5,6]. g , g y g y g p depression, anxiety, and fatigue also contribute to worsen ED [5,6]. Whether achieved, reflexogenic, psychogenic, or mixed, erection is often short lasting a non-sufficient to maintain satisfactory sexual relations [5,6]. Frequency and quality of sexual activ inevitably decline after SCI. This obviously represents a serious concern in people with SCI, as sex activity is an important factor in quality of life and self-esteem [5,6]. Diminished or absent sexual activ Whether achieved, reflexogenic, psychogenic, or mixed, erection is often short lasting and non-sufficient to maintain satisfactory sexual relations [5,6]. Frequency and quality of sexual activity inevitably decline after SCI. This obviously represents a serious concern in people with SCI, as sexual activity is an important factor in quality of life and self-esteem [5,6]. Diminished or absent sexual activity does not mean absent sexuality, as the need for sexual expression and intimacy remains [7]. 2.2. Intervention The patients were assessed at baseline using clinical and electrophysiological tests. MV was performed three times a week for five consecutive weeks, each session lasting 30 min. The stimulation 4 of 12 ineum. J. Clin. Med. 2019, 8, 658 2.2. Intervent a Velcro strap, and (Fi 2 3) was delivered to the perineum, suprapubic, and sacrococcygeal areas using a pneumatic vibrator powered by compressed air (Vibraplus, @-Circle; San Pietro in Casale, Bologna, Italy). The device is equipped with cup-like probes of 2 cm2 fixed to the suprapubic and sacrococcygeal areas by a Velcro strap, and a pen-like probe held by the therapist who carried out MV over the perineum. (Figures 2 and 3). performed three times a week for five consecutive weeks, each session lasting 30 min. The stimulation was delivered to the perineum, suprapubic, and sacrococcygeal areas using a pneumatic vibrator powered by compressed air (Vibraplus, @-Circle; San Pietro in Casale, Bologna, Italy). The device is equipped with cup-like probes of 2 cm2 fixed to the suprapubic and sacrococcygeal areas by a Velcro strap, and a pen-like probe held by the therapist who carried out MV over the perineum. (Figures 2 3) pped with cup-like probes of 2 cm fixed to the suprapubic and sacrococcygeal areas by a Velcro str a pen-like probe held by the therapist who carried out MV over the perineum. (Figures 2 and 3) device is equipped with cup-like probes of 2 cm2 fixed to the suprapubic and sacrococcygeal areas by a Velcro strap, and a pen-like probe held by the therapist who carried out MV over the perineum. (Figures 2,3). Figure 2. Placement of the suprapubic and perineum probes prior to body fixation by Velcro-straps. Figure 3. Placement of the probes and pudendal nerve somatosensory-evoked potential (PSEP) setup. Figure 2. Placement of the suprapubic and perineum probes prior to body fixation by Velcro-straps. Figure 2. Placement of the suprapubic and perineum probes prior to body fixation by Velcro-straps. Figure 3 Placement of the probes and pudendal nerve somatosensory-evoked potential (PSEP) Figure 3. Placement of the probes and pudendal nerve somatosensory-evoked potential (PSEP) setup. Figure 2. Placement of the suprapubic and perineum probes prior to body fixation by Velcro-straps. Figure 2. Placement of the suprapubic and perineum probes prior to body fixation by Velcro-straps. Figure 2. Placement of the suprapubic and perineum probes prior to body fixation by Velcro-straps. Figure 2. 2.2. Intervention Placement of the suprapubic and perineum probes prior to body fixation by Velcro-straps. Figure 2. Placement of the suprapubic and perineum probes prior to body fixation by Velcro-straps. g p p p p p y y p Figure 3. Placement of the probes and pudendal nerve somatosensory-evoked potential (PSEP) setup. Figure 3 Placement of the probes and pudendal nerve somatosensory evoked potential (PSEP) Figure 3. Placement of the probes and pudendal nerve somatosensory-evoked potential (PSEP) setup. Figure 3 Placement of the probes and pudendal ner e somatosensory e oked potential (PSEP) Figure 3. Placement of the probes and pudendal nerve somatosensory-evoked potential (PSEP) setup. Figure 3. Placement of the probes and pudendal nerve somatosensory evoked potential (PSEP) setup. Vibration stimuli were delivered at a frequency (f) of 150 Hz, with an amplitude (A) (i.e., of the peak-to-peak sinusoidal displacement of the underneath structures; on average 4 ± 0.5 mm) sufficient to evoke a progressive contraction of the perineal muscles in each of the participants, as assessed by the therapist who carried out the MV. The resulting intensity of stimulation was calculated by the formula (2πf) 2A. 2.3. Outcome Measures Changes in IIEF (the primary end-point) were used to estimate the effectiveness of MV in improving ED. The IIEF [28–30] consists of 15 questions aimed at highlighting ED and its effects on the 5 of 12 J. Clin. Med. 2019, 8, 658 sex life in the 4 weeks preceding the test. The questionnaire evaluates 5 different fields of male sexuality within the different cultures. A: Erectile Function (Q1–5; 15, score 1–30), B: Orgasmic Function (Q9, 10; score 0–10), C: Sexual Desire (Q11, 12; score 2–10), D: Intercourse Satisfaction (Q6–8; score 0–15), and E: overall Satisfaction (Q13, 14, score 2–10). The total score ranges from 5–75, and is interpreted as follows: <10 severe, 11–16 moderate, 17–21 mild-to-moderate, 22–25 mild ED, and 26–30 no dysfunction. The secondary end-points consisted in the improvement in pelvic floor muscle Modified Ashworth Scale (MAS), pelvic floor pain rated on a Visual Analogue Scale (VAS), groin and penile sensation, cremasteric and bulbocavernosus (BCR) reflexes, electrophysiological bulbocavernosus reflex (eBCR), and pudendal nerve somatosensory-evoked potential (PSEP). MAS measures resistance during passive soft-tissue stretching and is used as a simple measure of spasticity (score 0: no tone–4: complete rigidity). VAS is a measurement instrument that tries to measure a characteristic (such as pain) or attitude that is believed to range across a continuum of values and cannot easily be directly measured (score 0: no pain–10: worst pain). Before MAS and VAS administration, the patient underwent a complete physical examination, including general appearance, secondary sexual characteristics, cardiovascular system (blood pressure, peripheral pulses), genitourinary system, penis inspection (circumcision, deformity, plaques, phimosis, hypoesthesia), testes examination (size and consistency), rectal examination (sphincter tone and prostate examination), and groin and penile sensation (using Semmes–Weinstein monofilament sensory testing). To this end, the penis was sectored in six parts: the right and left halves of the shaft, the glans, the scrotum, and the left and right groin. The patient was blindfolded and each region was stimulated 3 times at random intervals. If all of the stimuli were experienced all 3 times correctly in all of the sectors, we concluded the patient had sensation. The peripheral and central neural pathways underlying exteroceptive stimulation of the genital regions, the sacral spinal reflex mechanisms, the pudendal somatosensory and somatomotor pathways were studied using clinical (cremasteric reflex, BCR) and electrophysiological tests (eBCR, PSEP). 2.3. Outcome Measures The cremasteric reflex is a superficial reflex found in human males that is related to emission and psychogenic erection (whereas BCR is more related to reflex erection). It is elicited when the inner part of the thigh is stroked. This action stimulates sensory fibers of the ilioinguinal nerve, consequently activating the motor fibers originating in the thoracolumbar segment (i.e., L1–L2) of the genital branch of the genitofemoral nerve, which causes the cremaster muscle to contract and elevate the testis. Like other superficial reflexes, it is simply graded as present or absent. The absence of cremasteric reflex suggests an upper motor neuron lesion above L1–L2. The BCR consists of the contraction of the bulbocavernosus muscle in response to squeezing the glans penis (or clitoris), and is mediated through the pudendal nerve. In case of a complete lesion, the presence of BCR is indicative of intact S2–S4 spinal reflex arcs and loss of supraspinal inhibition, determining an upper motor neuron lesion; its absence indicates a lower motor neuron lesion. The BCR further helps distinguish conus medullaris from cauda equina syndromes [31]. The eBCR was recorded from the bulbocavernosus muscles using concentric needle electrodes and elicited by delivering brief electric shocks (square-wave of 200 µs pulse-width) through a bipolar direct-current electric stimulator (Nihon Kohden; Tokyo, Japan), equipped with ring-electrodes (placed one at the corona and one approximately 3 cm proximal to the corona). In this way, it is possible to explore the neural pathway involving the dorsal nerve of the penis-pudendal nerve and Onuf’s nucleus (S2–S4), through which pelvic muscles can dramatically increase penile rigidity of an erect penis. The stimulation intensity was seven times the individual’s sensory threshold, which is sufficient to ensure a steady reflex response [31,32]. The scanning time was 5 ms/division, bandwidth range was 10 Hz to 2 kHz, and persistence time was 100 ms. Electrode impedance was kept always <5 kΩ. We measured the latency (calculated based on the beginning of the stimulus and the start of reflex response) and peak-to-peak amplitude of eBCR. Latency reflects the integrity of the entire afferent and efferent arcs of the BCR. Amplitude reflects the increased or reduced excitability of the medullaris neurons in the epiconus. This may be useful to demonstrate an association of upper and lower motor J. Clin. Med. 2.4. Statistical Analysis First, the Kolmogorov–Smirnov test and Shapiro–Wilk test were used to assess the normality of distribution and the homogeneity of variance of the data, respectively (all p > 0.2). A one-way ANOVA was used to analyze the differences in clinical and electrophysiological parameters over time. A value of p ≤0.05 was considered statistically significant. A Bonferroni correction for multiple comparison was applied. The comparison of eBCR and PSEP parameters was performed using a Kruskal–Wallis rank. The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. 2.3. Outcome Measures 2019, 8, 658 6 of 12 neuron lesions in the lower sacral segments, which may be sometime difficult to demonstrate clinically. eBCR response was rated as abnormal if the latency exceeded 3 times the standard deviations from the mean (about 40 ms). The integrity of the sensory pathway from penis to brain cortex (including dorsal nerve of penis, pudendal nerve, sacral/lumbar spinal cord) was assessed by measuring PSEP latency and amplitude. The former reflects the integrity of the entire afferent pathway from penis to cortex. The latter is a general marker of increased or reduced cortical excitability. The PSEP responses were recorded by using the same stimulation setup as per eBCR test (Figure 3) [33]. The recording was done with surface electrodes placed in the midline of the scalp, 2 cm behind the vertex region. A reference electrode was placed in the midline of the forehead at the Fz region according to the 10–20 International System (Figure 3). The intensity of the stimulus was three times the individual’s sensory threshold. The frequency of the square wave was 5 pulses/s and was averaged across 200 waves, obtaining a P41 wave. The scanning time was set to 0.2 ms/division, and the relevant persistence time was 100 ms, with a bandwidth ranging from 10 Hz to 5 kHz. Electrode impedance was kept always <5 kΩ. Emotional status was evaluated by the Hamilton Depression Rating Scale (HDRS), a 17–21-item scale measuring the severity of depressive and somatization symptoms, where a score of ≥15 is generally regarded as indicative of a diagnosis of depression. All patients were assessed at baseline (T0), after the treatment (T1), and three months after the end of the MV protocol (T4). 2.5. Ethical Approval All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. The Local Ethics Committee approved the present study (IRCCSME ID: 32/2017). Informed consent was obtained from all individual participants included in the study. 3. Results All patients enrolled in the study were affected by incomplete SCI (ASIA C-D). The patients had some sensory and motor preservation (C) or useful motor function (D). Specifically, a patient would be an ASIA C if more than half of the muscles evaluated had a grade of less than 3/5 on the Muscle Research Council scale. If not, the person would be an ASIA D. All patients complained of mild/moderate to severe ED, as per IIEF score, with regard to erectile and orgasmic functions. None of the patients complained of significant depressive symptoms (HDRS < 15). Further, four of them complained of urinary incontinence. All patients presented with weak or absent BCR, absent monolateral or bilateral cremasteric reflex, lack or presence of sensation, mild-to-moderate spasticity (MAS 1–2) and mild pain (VAS 1–3) of pelvic floor muscles, marked reduction of eBCR and PSEP amplitude and a clear increase of PSEP latency. eBCR latency was within the normal range. The clinical-demographic characteristics of the samples are reported in Table 1. J. Clin. Med. 2019, 8, 658 7 of 12 Table 1. Clinical-demographic characteristic of the sample at baseline. Table 1. Clinical-demographic characteristic of the sample at baseline. Legend: SCI—spinal cord injury; ASIA—American Spinal Injury Association; * urinary incontinence; BCR—bulbocavernosus reflex; eBCR—electrophysiological bulbocavernosus reflex; MAS—Modified Ashworth Scale; VAS—visual Analogue Scale; IIEF—International Index of Erectile Function; PSEP—pudendal nerve somatosensory-evoked potential. J. Clin. Med. 2019, 8, 658 J. Clin. Med. 2019, 8, 658 8 of 12 All patients well tolerated MV, and completed the protocol without any adverse event. All participants showed a significant improvement in IIEF total score (F(2,18) = 88, p <0.0001), erectile (F(2,18) = 65, p < 0.0001) and orgasmic function (F(2,18) = 78, p < 0.0001) (Figure 4). All significant changes were present at both T1 and T4 compared to baseline (T0) (Figure 4). J. Clin. Med. 2019, 8, x FOR PEER REVIEW 10 of 14 All patients well tolerated MV, and completed the protocol without any adverse event. All participants showed a significant improvement in IIEF total score (F(2,18) = 88, p <0.0001), erectile (F(2,18) = 65 p < 0 0001) and orgasmic function (F(2 18) = 78 p < 0 0001) (Figure 4) All significant changes were MAS and subjective pain assessment (VAS) significantly decreased (F(2,18) = 49 p < 0.0001, and F(2,18) = 12 p < 0.0001, respectively). All patients with weak BCR and cremasteric reflex showed a better clinical response. The patients were labeled as “with preserved sensation” if all the stimuli provided to the six groin and penile sectors with the monofilament were experienced all three times correctly. Even though six-out-of-ten patients did not get “preserved sensation”, they experienced sensory stimuli all three times correctly in 3/4-out-of-six sectors, on average. 65, p < 0.0001) and orgasmic function (F(2,18) 78, p < 0.0001) (Figure 4). All significant changes were present at both T1 and T4 compared to baseline (T0) (Figure 4). MAS and subjective pain assessment (VAS) significantly decreased (F(2,18) = 49 p < 0.0001, and F(2,18) = 12 p < 0.0001, respectively). All patients with weak BCR and cremasteric reflex showed a better clinical response. The patients were labeled as “with preserved sensation” if all the stimuli provided to the six groin and penile sectors with the monofilament were experienced all three times correctly. Even though six-out-of-ten patients did not get “preserved sensation”, they experienced ti li ll th ti tl i 3/4 t f i t Concerning the electrophysiological measures, we found a significant increase in eBCR (F(2,18) = 7.8, p = 0.004) and PSEP amplitude (F(2,18) = 9, p = 0.002). The latency of eBCR and PSEP did not vary. All these changes were significant at both T1 and T4 compared to the baseline (T0) (Figure 4). 3. Results Age (y) dd (m) SCI Level ASIA Level BCR eBCR Cremasteric Reflex Sensory Preservation PSEP MAS VAS IIEF amp (µV) lat (ms) lat (ms) amp (µV) Total A B 65 8 T12–L1 D no 5 34 present/asymmetric yes 48 3 2 2 16 2 1 38 10 L1–L2 D weak 6 35 present/asymmetric no / 0 1 0 18 6 2 62 12 T9–D12 C no 6 34 absent no 44 1 1 2 17 * 5 2 26 14 T10–L1 C yes 11 34 present/asymmetric yes 41 3 2 2 18 8 3 45 6 L1–L2 D no 6 36 present/asymmetric yes 43 4 2 3 13 * 9 0 48 10 L1–L3 C no 8 33 absent no 39 2 1 0 16 * 9 1 45 4 L1–L3 C weak 11 36 present/asymmetric no 38 1 1 2 14 12 2 22 13 T12–L2 C no 4 34 absent no / 0 1 1 14 5 3 39 3 T12–L1 D no 5 34 present/asymmetric yes 36 3 3 3 11 6 3 48 12 T8–D10 C weak 8 34 absent no 42 1 1 0 18 * 7 0 Legend: SCI—spinal cord injury; ASIA—American Spinal Injury Association; * urinary incontinence; BCR—bulbocavernosus reflex; eBCR—electrophysiological bulbocavernosus reflex; MAS—Modified Ashworth Scale; VAS—visual Analogue Scale; IIEF—International Index of Erectile Function; PSEP—pudendal nerve somatosensory-evoked potential. 4. Discussion To the best of our knowledge, this is the first attempt to improve ED by means of focal MV to pelvic muscles in men with SCI, since previous works applied whole body vibration to potentiate weak pelvic floor muscles and reduce urinary incontinence [19–27]. The most significant finding of our feasibility study consisted of the fact that the patients reported an improvement in erection during sexual activity, inter-course completion, and reaching ejaculation and orgasm (as per IIEF). A reduction in pelvic floor muscle spasticity and pain (as per MAS and VAS), and better reflexive responses were also found, besides a significant amplitude increase in eBCR and PSEP. Clinical changes lasted up to three months. It is likely that the improvement in ED depended on MV-induced reduction of spasticity. However, spasticity of the muscles targeted by MV (including the bulbocavernosus, ischiocavernosus, external sphincter, and superficial transverse perineal) can regularly enhance the rigidity of erections and the veno-occlusive mechanism [34–36]. It is hypothesizable that MV may potentiate the mechanisms of reciprocal innervation through the presynaptic inhibition at segmental level, consequently improving muscle synergies and counterbalancing the segmental hyperreflexia [37–41], as suggested by the increase in eBCR amplitude. MV after effects may also depend on supraspinal mechanisms. In fact, focal MV can modify sensorimotor cortex excitability [42–44], as suggested by the PSEP amplitude increase. This may in turn contribute to reduce segmental hyper-excitability by harnessing the abovementioned mechanisms of reciprocal innervation. Studies employing transcranial magnetic stimulation demonstrated that focal MV increases or decreases motor evoked potential amplitude and short intracortical inhibition strength in the vibrated muscles, while opposite changes occur in the neighboring muscles [33,45–47]. In this way, pelvic MV may contribute to regulate the contraction and excitability dynamics of the pelvic floor muscles involved in erection. Sensory inputs from penile skin, prepuce and glans conveyed by the dorsal penis nerve may also contribute to improve erection [22,25], given that we vibrated the lower trunk muscles, which partially contribute to sexual function dynamics. In addition, the improvement in erection may depend on the effects of MV on the specific properties of the muscles and surrounding connectivity tissues (including viscoelasticity), as well as on vessel vasodilatation. Vibrations can stimulate the release of neurotransmitters and nitric oxide (NO) from the parasympathetic and non-adrenergic non-cholinergic fibers of cavernous nerve terminals of the pudendal nerve, thus evoking a reflexogenic erection [3,8,9,15,25]. 4. Discussion To summarize, MV may contribute to reduce segmental spasticity and improve muscle synergies, thus improving erection, through both bottom-up (i.e., sensory inputs resetting sensorimotor hyperexcitability) and top-down mechanisms (re-afferent descending volleys from sensorimotor cortex to spinal centers). As additional findings, patients reported some improvement in genital sensation, even though this did not reach statistical significance. Further assessment is mandatory to verify whether MV may represent a non-surgical modality to improve sensation in neurological patients [23]. Moreover, four patients reported urinary continence improvement. As we did not specifically address this issue, we can only speculate that the contemporary use of pen- and cup-like probes to stimulate the perineum and the lower trunk muscles allowed the deep floor muscles to be reached, which provide support for pelvic organs, urinary continence, and intestinal emptying. J. Clin. Med. 2019, 8, 658 sensory stimuli all three times correctly in 3/4-out-of-six sectors, on average. Concerning the electrophysiological measures, we found a significant increase in eBCR (F(2,18) = 7.8, p = 0.004) and PSEP amplitude (F(2,18) = 9, p = 0.002). The latency of eBCR and PSEP did not vary. All these changes were significant at both T1 and T4 compared to the baseline (T0) (Figure 4). g g p g these changes were significant at both T1 and T4 compared to the baseline (T0) (Figure 4). Figure 4. Clinical and electrophysiological aftereffects of pelvic muscle vibration at T0 (baseline), T1 (post-treatment) and T4 (3 months after the end of the treatment). Significance (*) was tested between T1 and T0 and T4 and T0 (***p < 0.001). Vertical bars indicate s.d. IIEF—International Index of Erectile Function (A—erectile function, B—orgasmic function); eBCR—electrophysiological bulbocavernosus Figure 4. Clinical and electrophysiological aftereffects of pelvic muscle vibration at T0 (baseline), T1 (post-treatment) and T4 (3 months after the end of the treatment). Significance (*) was tested between T1 and T0 and T4 and T0 (*** p < 0.001). Vertical bars indicate s.d. IIEF—International Index of Erectile Function (A—erectile function, B—orgasmic function); eBCR—electrophysiological bulbocavernosus reflex; MAS—Modified Ashworth Scale; VAS—visual Analogue Scale for pain esteem; PSEP—pudendal nerve somatosensory-evoked potential. Figure 4. Clinical and electrophysiological aftereffects of pelvic muscle vibration at T0 (baseline), T1 (post-treatment) and T4 (3 months after the end of the treatment). Significance (*) was tested between T1 and T0 and T4 and T0 (***p < 0.001). Vertical bars indicate s.d. IIEF—International Index of Erectile Function (A—erectile function, B—orgasmic function); eBCR—electrophysiological bulbocavernosus Figure 4. Clinical and electrophysiological aftereffects of pelvic muscle vibration at T0 (baseline), T1 (post-treatment) and T4 (3 months after the end of the treatment). Significance (*) was tested between T1 and T0 and T4 and T0 (*** p < 0.001). Vertical bars indicate s.d. IIEF—International Index of Erectile Function (A—erectile function, B—orgasmic function); eBCR—electrophysiological bulbocavernosus reflex; MAS—Modified Ashworth Scale; VAS—visual Analogue Scale for pain esteem; PSEP—pudendal nerve somatosensory-evoked potential. J. Clin. Med. 2019, 8, 658 9 of 12 5. Limitations and Conclusions There are some limitations in the study to acknowledge. First, the small sample size does not let us generalize our results. However, this is a feasibility study intended to prove the safety and the potential efficacy of MV in improving ED following SCI. Further studies with a larger sample size, including females, should be conducted to confirm the benefits of MV. Second, since improvement in erection may be ascribed to psychogenic arousal and not solely to reflexogenic mechanisms, the effectiveness of MV needs to be confirmed by comparing real and sham MV. Third, as the patients were followed only J. Clin. Med. 2019, 8, 658 10 of 12 up to three months after the end of the treatment, studies with a longer follow-up period are needed to establish whether and to what extent the MV after effects last. Last, since patients’ inclusion criteria may have influenced MV outcomes, we enrolled only men with incomplete SCI. It would be interesting to use this protocol also in individuals with complete SCI and in those with lesions involving the sacral spinal segments. p g Notably, we excluded from this study patients taking erectogenic aids, nutraceutics, antispastics, and psychoactive drugs. This was necessary to maintain a homogeneous group and avoid confounding effects due to these drugs. Antispastic and erectogenic aids naturally interfere with the neurophysiological and vasculogenic mechanisms triggered by MV. For instance, baclofen can itself cause ED, probably by over-stimulating the central and spinal inhibitory mechanisms overseeing erectile function [9,48]; PDE-5 inhibitors may interfere with MV due to the common effect on NO release from nerve terminals and endothelial cells in the corpus cavernosum. Many nutraceutics target bodily vasculogenic and metabolic mechanisms, potentially altering the erectile processes when coupled with MV. Side effects of some psychoactive drugs may impact erection, biasing MV effects [49]. Thus, other studies are necessary to better clarify the neurophysiological basis of MV effects concerning ED treatment, also by testing MV-drug interaction and NO blood levels. y g g In conclusion, pelvic floor MV seems promising to improve ED in men with incomplete SCI. Given that we designed a pilot study, larger sample randomized clinical trials, including additional neurophysiological measures, are necessary to confirm MV as an add-on treatment to the conventional ED pharmacological, rehabilitative, and counseling approaches. Author Contributions: “Conceptualization, R.S.C. and A.N.; methodology, R.S.C. and A.N.; software, G.L.R.; validation, B.P., M.T. 5. Limitations and Conclusions and M.P.; formal analysis, A.N.; investigation, L.B.; resources, A.M.; data curation, A.M and L.B.; writing—original draft preparation, A.N.; writing—review and editing, R.S.C.; visualization, R.S.C.; supervision, P.B. and F.Q.; project administration, F.Q.; funding acquisition, P.B.”, please turn to the CRediT taxonomy for the term explanation. Authorship must be limited to those who have contributed substantially to the work reported. Conflicts of Interest: The authors declare that they have no competing interests. Author Contributions: “Conceptualization, R.S.C. and A.N.; methodology, R.S.C. and A.N.; software, G.L.R.; validation, B.P., M.T. and M.P.; formal analysis, A.N.; investigation, L.B.; resources, A.M.; data curation, A.M and L.B.; writing—original draft preparation, A.N.; writing—review and editing, R.S.C.; visualization, R.S.C.; supervision, P.B. and F.Q.; project administration, F.Q.; funding acquisition, P.B.”, please turn to the CRediT taxonomy for the term explanation. Authorship must be limited to those who have contributed substantially to the work reported. Conflicts of Interest: The authors declare that they have no competing interests. References Efficacy and safety of sildenafil citrate (Viagra®) in men with erectile dysfunction and spinal cord injury: A review. Urology 2002, 60, 49–57. [CrossRef] 11. Lieber, R.L.; Steinman, S.; Barash, I.A.; Chambers, H. Structural and functional changes in spastic skeletal muscle. Muscle Nerve 2004, 29, 615–627. [CrossRef] [PubMed] 12. Slot, O.; Drewes, A.; Andreasen, A.; Olsson, A. Erectile and ejaculatory function of males with spinal cord injury. Int. Disabil. Stud. 1989, 11, 75–77. [CrossRef] 13. Anderson, K.D.; Borisoff, J.F.; Johnson, R.D.; Stiens, S.A.; Elliott, S.L. Long-term effects of spinal cord injury on sexual function in men: implications for neuroplasticity. Spinal Cord 2007, 45, 338–348. [CrossRef] [PubMed] 14. Alexander, M.; Courtois, F.; Elliott, S.; Tepper, M. Improving Sexual Satisfaction in Persons with Spinal Cord Injuries: Collective Wisdom. Top Spinal Cord Inj. Rehabil. 2017, 23, 57–70. [CrossRef] [PubMed] , ; , ; , ; pp , p g p Injuries: Collective Wisdom. Top Spinal Cord Inj. Rehabil. 2017, 23, 57–70. [CrossRef] [PubMed] 15. Naro, A.; Leo, A.; Russo, M.; Casella, C.; Buda, A.; Crespantini, A.; Calabrò, R.S. Breakthroughs in the spasticity management: Are non-pharmacological treatments the future? J. Clin. Neurosci. 2017, 39, 16–27. [CrossRef] [PubMed] 16. Poenaru, D.; Cinteza, D.; Petrusca, I.; Cioc, L.; Dumitrascu, D. Local Application of Vibration in Motor Rehabilitation - Scientific and Practical Considerations. Maedica (Buchar) 2016, 11, 227–231. [PubMed] 17. Chang, E.; Ghosh, N.; Yanni, D.; Lee, S.; Alexandru, D.; Mozaffar, T. A Review of Spasticity Treatments: Pharmacological and Interventional Approaches. Crit. Rev. Physic. Rehabil. Med. 2013, 25, 11–22. [CrossRef] 18. Calabrò, R.S.; Naro, A.; Russo, M.; Milardi, D.; Leo, A.; Filoni, S.; Bramanti, P. Is two better than one? Muscle vibration plus robotic rehabilitation to improve upper limb spasticity and function: A pilot randomized controlled trial. PLoS ONE 2017, 12, e0185936. [CrossRef] 19. Lauper, M.; Kuhn, A.; Gerber, R.; Luginbühl, H.; Radlinger, L. Pelvic Floor Stimulation: What are the good vibrations? Neurourol. Urodyn. 2008, 28, 405–410. [CrossRef] [PubMed] 20. Farzinmehr, A.; Moezy, A.; Koohpayehzadeh, J.; Kashanian, M. A Comparative Study of Whole Body Vibration Training and Pelvic Floor Muscle Training on Women’s Stress Urinary Incontinence: Three-Month Follow-Up. J. Family Reprod. Health 2015, 9, 147–154. 21. Crevenna, R.; Cenik, F.; Margreiter, M.; Marhold, M.; Komanadj, T.S.; Keilani, M. Whole body vibration therapy on a treatment bed as additional means to treat postprostatectomy urinary incontinence. Wien. Med. Wochenschr. 2016, 167, 139–141. [CrossRef] [PubMed] 22. Brackett, N. References 1. Mahoney, C.; Smith, A.; Marshall, A.; Reid, F. Pelvic floor dysfunction and sensory impairment: Current evidence. Neurourol. Urodyn. 2016, 36, 550–556. [CrossRef] 2. Ramos, A.S.; Samsó, J.V. Specific aspects of erectile dysfunction in spinal cord injury. Int. J. Impot. Res. 2004, 16, 42–45. [CrossRef] [PubMed] 3. Everaert, K.; Waard, W.I.; Hoof, T.V.; Kiekens, C.; Mulliez, T.; Dherde, C. Neuroanatomy and neurophysiology related to sexual dysfunction in male neurogenic patients with lesions to the spinal cord or peripheral nerves. Spinal Cord 2010, 48, 182–191. [CrossRef] [PubMed] 4. Calabro, R.S.; Polimeni, G.; Bramanti, P. Current and Future Therapies of Erectile Dysfunction in Neurological Disorders. Recent Pat. CNS Drug Discov. 2011, 6, 48–64. [CrossRef] 5. Aikman, K.; Oliffe, J.L.; Kelly, M.T.; Mccuaig, F. Sexual Health in Men with Traumatic Spinal Cord Injuries: A Review and Recommendations for Primary Health-Care Providers. Am. J. Mens Health 2018, 12, 2044–2054. [CrossRef] 6. Previnaire, J.G.; Soler, J.M.; Alexander, M.S.; Courtois, F.; Elliott, S.; Mclain, A. Prediction of sexual function following spinal cord injury: A case series. Spinal Cord Ser. Cases 2017, 3. [CrossRef] [PubMed] 7. Kennedy, S.; Over, R. Psychophysiological assessment of male sexual arousal following spinal cord injury. Arch Sex Behav. 1990, 19, 15–27. [CrossRef] [PubMed] 6. Previnaire, J.G.; Soler, J.M.; Alexander, M.S.; Courtois, F.; Elliott, S.; Mclain, A. Prediction of sexual f following spinal cord injury: A case series. Spinal Cord Ser. Cases 2017, 3. [CrossRef] [PubMed] 6. Previnaire, J.G.; Soler, J.M.; Alexander, M.S.; Courtois, F.; Elliott, S.; Mclain, A. Prediction of sexual function following spinal cord injury: A case series. Spinal Cord Ser. Cases 2017, 3. [CrossRef] [PubMed] 7. Kennedy, S.; Over, R. Psychophysiological assessment of male sexual arousal following spinal cord injury. 7. Kennedy, S.; Over, R. Psychophysiological assessment of male sexual arousal following spinal cord Arch Sex Behav. 1990, 19, 15–27. [CrossRef] [PubMed] 8. Calabro, R.S.; Polimeni, G.; Ciurleo, R.; Casella, C.; Bramanti, P. Neurogenic Ejaculatory Disorders: Focus on Current and Future Treatments. Recent Pat. CNS Drug Discov. 2011, 6, 205–221. [CrossRef] [PubMed] 9. Calabrò, R.S.; Daleo, G.; Sessa, E.; Leo, A.; Cola, M.C.; Bramanti, P. Sexual Dysfunction Induced by Intrathecal Baclofen Administration: Is This the Price to Pay for Severe Spasticity Management? J. Sex. Med. 2014, 11, 1807–1815. [CrossRef] [PubMed] J. Clin. Med. 2019, 8, 658 11 of 12 10. Derry, F.; Hultling, C.; Seftel, A.D.; Sipski, M.L. References Penile vibratory stimulation for men with spinal cord injury. Video. Hum. Reprod. Update 1999, 5, 551–552. [CrossRef] 23. Guess, M.K.; Connell, K.A.; Chudnoff, S.; Adekoya, O.; Richmond, C.; Nixon, K.E.; Melman, A. The Effects of a Genital Vibratory Stimulation Device on Sexual Function and Genital Sensation. Female Pelvic Med. Reconstr. Surg. 2017, 23, 256–262. [CrossRef] 24. Laessøe, L.; Nielsen, J.B.; Biering-Sørensen, F.; Sønksen, J. Antispastic effect of penile vibration in men with spinal cord lesion. Arch. Phys. Med. Rehabil. 2004, 85, 919–924. 25. Tajkarimi, K.; Burnett, A. Viberect® device use by men with erectile dysfunction: Safety, ease of use, tolerability, and satisfaction survey. J. Sex. Med. 2011, 8, 441–444. 26. Tantawy, S.A.; Elgohary, H.M.; Abdelbasset, W.K.; Kamel, D.M. Effect of 4 weeks of whole-body vibration training in treating stress urinary incontinence after prostate cancer surgery: A randomised controlled trial. Physiotherapy 2018. [CrossRef] 27. Rodrigues, M.P.; Paiva, L.L.; Ramos, J.G.; Ferla, L. Vibratory perineal stimulation for the treatment of female stress urinary incontinence: A systematic review. Int. Urogynecol. J. 2018, 29, 555–562. [CrossRef] [PubMed] 28. Rosen, R.C.; Riley, A.; Wagner, G.; Osterloh, I.H.; Kirkpatrick, J.; Mishra, A. The international index of erectile function (IIEF): A multidimensional scale for assessment of erectile dysfunction Urology 1997 49 822 830 27. Rodrigues, M.P.; Paiva, L.L.; Ramos, J.G.; Ferla, L. Vibratory perineal stimulation for the treatment o stress urinary incontinence: A systematic review. Int. Urogynecol. J. 2018, 29, 555–562. [CrossRef] [P 27. Rodrigues, M.P.; Paiva, L.L.; Ramos, J.G.; Ferla, L. Vibratory perineal stimulation for the treatment of female stress urinary incontinence: A systematic review. Int. Urogynecol. J. 2018, 29, 555–562. [CrossRef] [PubMed] 28. Rosen, R.C.; Riley, A.; Wagner, G.; Osterloh, I.H.; Kirkpatrick, J.; Mishra, A. The international index of erectile function (IIEF): A multidimensional scale for assessment of erectile dysfunction. Urology 1997, 49, 822–830. [CrossRef] 28. Rosen, R.C.; Riley, A.; Wagner, G.; Osterloh, I.H.; Kirkpatrick, J.; Mishra, A. The international index of erectile function (IIEF): A multidimensional scale for assessment of erectile dysfunction. Urology 1997, 49, 822–830. [CrossRef] 29. Rosen, R.C.; Cappelleri, J.C.; Gendrano, N., 3rd. The International Index of Erectile Function (IIEF): A state-of-the-science review. Int. J. Impot. Res. 2002, 14, 226–244. [CrossRef] [PubMed] 30. Cappelleri, J.C.; Rosen, R.C.; Smith, M.D.; Mishra, A.; Osterloh, I.H. Diagnostic evaluation of the erectile function domain of the international index of erectile function. Urology 1999, 54, 346–351. [CrossRef] 31. Previnaire, J.G. The importance of the bulbocavernosus reflex. References Spinal Cord Ser Cases 2018, 4, 2. [CrossRef] [P bM d] 30. Cappelleri, J.C.; Rosen, R.C.; Smith, M.D.; Mishra, A.; Osterloh, I.H. Diagnostic evaluation of the erectile function domain of the international index of erectile function. Urology 1999, 54, 346–351. [CrossRef] 31. Previnaire, J.G. The importance of the bulbocavernosus reflex. Spinal Cord Ser Cases 2018, 4, 2. [CrossRef] [PubMed] 32. Podnar, S. Neurophysiologic studies of the penilo-cavernosus reflex: normative data. Neurourol. Urodyn. 2007, 26, 864–869. [CrossRef] [PubMed] 12 of 12 J. Clin. Med. 2019, 8, 658 33. Kaiser, T.; Jost, W.H.; Osterhage, J.; Derouet, H.; Schimrigk, K. Penile and perianal pudendal nerve somatosensory evoked potentials in the diagnosis of erectile dysfunction. Int. J. Impot. Res. 2001, 13, 89–92. [CrossRef] [PubMed] 34. Dorey, G.; Speakman, M.; Feneley, R.; Swinkels, A.; Dunn, C.; Ewings, P. Randomised controlled trial of pelvic floor muscle exercises and manometric biofeedback for erectile dysfunction. Br. J. Gen. Pract. 2004, 54, 819–825. [PubMed] 35. Cohen, D.; Gonzalez, J.; Goldstein, I. The Role of Pelvic Floor Muscles in Male Sexual Dysfunction and Pelvic Pain. Sex. Med. Rev. 2016, 4, 53–62. [CrossRef] [PubMed] 36. Lavoisier, P.; Roy, P.; Dantony, E.; Watrelot, A.; Ruggeri, J.; Dumoulin, S. Pelvic-floor muscle rehabilitation in erectile dysfunction and premature ejaculation. Physical Therapy 2014, 94, 1731–1743. [CrossRef] [PubMed] 36. Lavoisier, P.; Roy, P.; Dantony, E.; Watrelot, A.; Ruggeri, J.; Dumoulin, S. Pelvic-floor muscle rehabilitation in erectile dysfunction and premature ejaculation. Physical Therapy 2014, 94, 1731–1743. [CrossRef] [PubMed] 37. Nielsen, J.; Petersen, N.; Crone, C. Changes in transmission across synapses of Ia afferents in spastic patients. B i 1995 118 995 1004 [C R f] [P bM d] 37. Nielsen, J.; Petersen, N.; Crone, C. Changes in transmission across synapses of Ia afferents in spastic patients. Brain 1995, 118, 995–1004. [CrossRef] [PubMed] 38. Mileva, K.N.; Bowtell, J.L.; Kossev, A.R. Effects of low-frequency whole-body vibration on motor-evoked potentials in healthy men. Exper. Physiol. 2008, 94, 103–116. [CrossRef] [PubMed] 39. Rocchi, L.; Suppa, A.; Leodori, G.; Celletti, C.; Camerota, F.; Rothwell, J.; Berardelli, A. Plasticity Induced in the Human Spinal Cord by Focal Muscle Vibration. Front. Neurol. 2019, 9, 1170. [CrossRef] 40. Morita, H.; Crone, C.; Christenhuis, D.; Petersen, N.T.; Nielsen, J.B. Modulation of presynaptic inhibition and disynaptic reciprocal Ia inhibition during voluntary movement in spasticity. Brain 2001, 124, 826–837. [CrossRef] 41. Trompetto, C.; Marinelli, L.; Mori, L.; Pelosin, E.; Currà, A.; Molfetta, L.; Abbruzzese, G. © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). References Pathophysiology of spasticity: implications for neurorehabilitation. BioMed Res. Internat. 2014, 2014, 354906. [CrossRef] 42. Saggini, R.; Bellomo, R.G.; Cosenza, L. Vibration in Neurorehabilitation: a narrative review. Med. Res. Arch. 2017, 5, 11. 43. Rosenkranz, K.; Rothwell, J.C. Differential effect of muscle vibration on intra-cortical inhibitory circuits in humans. J. Physiol. 2003, 551, 649–660. [CrossRef] [PubMed] 44. Sadeghi, M.; Sawatzky, B. Effects of vibration on spasticity in individuals with spinal cord injury: A scoping systematic review. Am. J. Physic. Med. Rehabil. 2014, 93, 995–1007. [CrossRef] [PubMed] 5. Kossev, A.; Siggelkow, S.; Schubert, M.; Wohlfarth, K.; Dengler, R. Muscle vibration: Different effect transcranial magnetic and electrical stimulation. Muscle Nerve 1999, 22, 946–948. [CrossRef] 46. Valls-Sole, J.; Alvarez, R.; Tolosa, E.S. Vibration-induced presynaptic inhibition of the soleus H reflex is temporarily reduced by cortical magnetic stimulation in human subjects. Neurosci. Lett. 1994, 170, 149–152. [CrossRef] 47. Siggelkow, S.; Kossev, A.; Schubert, M.; Kappels, H.H.; Wolf, W.; Dengler, R. Modulation of motor evoked potentials by muscle vibration: the role of vibration frequency. Muscle Nerve 1999, 22, 1544–1558. [CrossRef] 48. Saval, A.; Chiodo, A.E. Sexual dysfunction associated with intrathecal baclofen use: A report of two cases. J S i C d M d 2008 31 103 105 [C R f] 47. Siggelkow, S.; Kossev, A.; Schubert, M.; Kappels, H.H.; Wolf, W.; Dengler, R. Modulation of motor evoked potentials by muscle vibration: the role of vibration frequency. Muscle Nerve 1999, 22, 1544–1558. [CrossRef] potentials by muscle vibration: the role of vibration frequency. Muscle Nerve 1999, 22, 1544–1558. [CrossRef] 48. Saval, A.; Chiodo, A.E. Sexual dysfunction associated with intrathecal baclofen use: A report of two cases. J. Spin. Cord Med. 2008, 31, 103–105. [CrossRef] 48. Saval, A.; Chiodo, A.E. Sexual dysfunction associated with intrathecal baclofen use: A report of two cases. J. Spin. Cord Med. 2008, 31, 103–105. [CrossRef] 49. Gitlin, M. Sexual dysfunction with psychotropic drugs. Expert Opin. Pharmacother. 2003, 4, 2259–2269. [CrossRef] © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
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Lipid Nanoparticle Encapsulating mRNAs Encoding Human OX40L/IL-23/IL-36gamma mRNA-2752
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Qeios · Definition, February 2, 2020 Open Peer Review on Qeios Lipid Nanoparticle Encapsulating mRNAs Encoding Human OX40L/IL-23/IL- 36gamma mRNA-2752 National Cancer Institute Qeios ID: 8212U4 · https://doi.org/10.32388/8212U4 Source National Cancer Institute. Lipid Nanoparticle Encapsulating mRNAs Encoding Human OX40L/IL-23/IL-36gamma mRNA-2752. NCI Thesaurus. Code C157247. A lipid nanoparticle encapsulating mRNAs encoding for the human co-stimulatory protein tumor necrosis factor ligand superfamily member 4 (TNFSF4; OX40 Ligand; OX40L), the pro-inflammatory cytokines interleukin-23 (IL-23) and interleukin-36gamma (IL- 36gamma), with potential immunomodulatory and anti-tumor activities. Upon intratumoral (IT) injection of the lipid nanoparticle encapsulated mRNAs encoding human OX40L/IL-23/IL-36gamma mRNA-2752, the lipid nanoparticle binds to the plasma membrane of cells and releases the mRNAs into the cell. The OX40L mRNA is then translated by the cellular protein translation machinery to produce OX40L protein, which is then expressed on the plasma membrane of the cells that internalized the OX40L mRNA. OX40L binds to and activates signaling pathways downstream of its cognate receptor tumor necrosis factor receptor superfamily member 4 (TNFRSF4; OX40), which is expressed on activated T-cells. OX40L/OX40 binding promotes increased cytokine production, which can induce proliferation of memory and effector T-lymphocytes against the nearby tumor cells. The co-administration of IL-23 and IL-36gamma further stimulates anti-tumor immune responses. Altogether, this may enhance T-cell mediated anti-tumor immune responses thereby killing of the tumor cells. OX40L, a cell surface glycoprotein and member of the tumor necrosis factor (TNF) ligand superfamily, provides a co-stimulatory signal for the proliferation and survival of activated T-cells. IL- 36gamma activates innate immune cells and promotes T-helper 1 (Th1) responses, whereas IL-23 has been implicated in Th1/Th17 immunity as well as in the modulation of antigen-presenting cells (APCs). Qeios ID: 8212U4 · https://doi.org/10.32388/8212U4 1/1
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Depressão Pós-parto para além do Diagnóstico: Representações Sociais e Subjetividade
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Resumo Este artigo tem como objetivo apresentar reflexões teóricas acerca dos processos subjetivos de uma mulher diagnosticada com depressão pós-parto. Ele se insere em uma busca por romper com a visão reducionista da depressão pós-parto, calcada no modelo biomédico, que a reduz a seus aspectos biológicos-sintomatológicos, resgatando as dimensões sociais, histórico-políticas e singulares, frequentemente preteridas, presentes em sua construção. Para isto, utilizou-se da teoria da subjetividade de González Rey, em uma perspectiva histórico- cultural, em um diálogo com a teoria das representações sociais e autores críticos ao modelo biomédico, como Foucault e Illich. O controle por normas exercido na biopolítica, assim como o controle pelo diagnóstico resultante da medicalização da vida, configuram-se enquanto elementos importantes para refletir acerca da produção subjetiva da depressão pós-parto. Foi feito um estudo de caso, a partir de uma perspectiva qualitativa de base construtivo-interpretativa. No processo de construção de informação, discutimos que a depressão pós-parto expressa a disparidade entre a maternidade idealizada socialmente e aquela subjetivamente produzida de forma singular. Assim, a depressão pós-parto é uma produção subjetiva complexa que, para além de apenas aspectos biológicos e hormonais, é configurada pela subjetividade individual da puérpera em questão, e pela subjetividade social marcada pelo discurso médico e a medicalização da vida, que padronizam as experiências socialmente aceitáveis de maternidade e patologizam as demais, gerando frequentes quadros de frustração e culpa. Ademais, argumentamos que os modelos de assistência atualmente prestados, que partem de protocolos rígidos e que têm a norma como referência, não oportunizam uma reflexão crítica que viabilize o desenvolvimento de recursos subjetivos frente a essa experiência. Desse modo, defende-se a necessidade de espaços que acolham as experiências das puérperas de maneira a oportunizar a reflexão crítica acerca dos aspectos envolvidos na construção subjetiva singular da depressão pós-parto; viabilizando, assim, o desenvolvimento de recursos subjetivos. Palavras-chave: depressão pós-parto; maternidade; subjetividade; representações sociais. Daniel Magalhães Goulart (Lattes) (OrcID) Professor Adjunto do curso de Psicologia do Centro Universitário de Brasília (UniCEUB). Mestre em Educação pela Universidade de Brasília. Membro do grupo de pesquisa “A subjetividade na saúde e na educação”, coordenado pelo Dr. González Rey, na Universidade de Brasília. e-ISSN: 2359-0777 SUBJETIVIDADES Subjetividades Relatos de Pesquisa Rafaella Pinheiro Cesario (Lattes) (OrcID) Rafaella Pinheiro Cesario (Lattes) (OrcID) Rafaella Pinheiro Cesario (Lattes) (OrcID) Graduanda em psicologia pelo Centro Universitário de Brasília (UniCEUB). Membro do grupo de pesquisa “A subjetividade na saúde e na educação”, coordenado pelo Dr. González Rey em 2015. Pesquisadora-bolsista da Iniciação Científica 2015-2016 com foco nos processos subjetivos envolvidos na depressão pós-parto. ( ) ( ) Graduanda em psicologia pelo Centro Universitário de Brasília (UniCEUB). Membro do grupo de pesquisa “A subjetividade na saúde e na educação”, coordenado pelo Dr. González Rey em 2015. Pesquisadora-bolsista da Iniciação Científica 2015-2016 com foco nos processos subjetivos envolvidos na depressão pós-parto. D i l M lhã G l t (L tt ) (O ID) DEPRESSÃO PÓS-PARTO PARA ALÉM DO DIAGNÓSTICO: REPRESENTAÇÕES SOCIAIS E SUBJETIVIDADE Postpartum Depression beyond Diagnosis: Social Representations and Subjectivity Depresión Post-parto para allá del Diagnóstico: Representaciones Sociales y Subjetivas Dépression Post-partum au-delà du Diagnostic: Des Représentations Sociales et de la Subjectivité Abstract This article aims to present theoretical reflections about the subjective processes of a woman diagnosed with postpartum depression. It is part of a quest to break with the reductionist vision of postpartum depression, based on the biomedical model, which reduces it to its biological and symptomatological aspects, rescuing the social, historical-political and singular dimensions, often overlooked, present in its construction. For this, González Rey’s theory of subjectivity was used in a historical-cultural perspective, in a dialogue with the theory Rafaella Pinheiro Cesario e Daniel Magalhães Goulart of social representations and authors critical to the biomedical model, such as Foucault and Illich. The control by norms exerted in the biopolitics, as well as the control by the diagnosis resulting from the medicalization of the life, are configured as important elements to reflect about the subjective production of the postpartum depression. A case study was carried out from a qualitative perspective with constructive-interpretative basis. In the process of information construction, we argue that postpartum depression expresses the disparity between socially idealized and subjectively produced motherhood. Thus, postpartum depression is a complex subjective production that, in addition to only biological and hormonal aspects, is shaped by the individual subjectivity of the puerperal woman in question, and by the social subjectivity marked by the medical discourse and the medicalization of life, which standardize the socially acceptable experiences of maternity and pathologize the others, generating frequent frustrations and guilts. In addition, we argue that the assistance models currently provided, which depart from rigid protocols and that have the norm as a reference, do not offer a critical reflection that enables the development of subjective resources in front of this experience. Thus, we defend the need for spaces that welcome the experiences of puerperal women in a way that allows the critical reflection on the aspects involved in the singular subjective construction of postpartum depression; thus enabling the development of subjective resources. Keywords: postpartum depression; maternity; subjectivity; social representations. Resumen Este artículo objetiva presentar reflexiones teóricas acerca de los procesos subjetivos de una mujer diagnosticada con depresión post-parto. Está basado en una búsqueda por romper la visión reduccionista de la depresión post-parto, calcada en el modelo biomédico, que la reduce a sus aspectos biológicos-sintomatológicos, rescatando las dimensiones sociales, histórico-políticas y singulares, frecuentemente ignoradas, presente en su construcción. Para eso, fue utilizada la teoría de la subjetividad de González Rey, en una perspectiva histórico-cultural, en un dialogo con la teoría de las representaciones sociales y autores críticos al modelo biomédico, como Foucault e Illich. El control por reglas ejercido en la biopolítica, así como el control por el diagnostico resultante de la medicalización de la vida, se configuran mientras elementos importantes para reflexionar acerca de la producción subjetiva de la depresión post-parto. Fue hecho un estudio de caso, a partir de una perspectiva cualitativa de base constructivo-interpretativo. En el proceso de construcción de información, discutimos que la depresión post-parto expresa la divergencia entre maternidad idealizada socialmente y aquella subjetivamente producida de forma singular. Así, la depresión post-parto es una producción subjetiva compleja que, para allá de solo aspectos biológicos y hormonales, es configurada por la subjetividad individual de la puérpera en cuestión, y por la subjetividad social marcada por el discurso médico y la medicalización de la vida, que estandarizan las experiencias maternales socialmente aceptables y ‘patologizan’ las demás, generando frecuentes cuadros de frustración y culpa. Además, argumentamos que los modelos de asistencia actualmente presentados, que parten de protocolos rígidos y que tienen la norma como referencia, no dan la oportunidad para una reflexión crítica que viabilice el desarrollo de recursos subjetivos ante esa experiencia. De este modo, se defiende la necesidad de espacios que reciban las experiencias de las puérperas de manera a dar oportunidad a la reflexión crítica acerca de los aspectos envueltos en la construcción subjetiva singular de la depresión post-parto, viabilizando, así, el desarrollo de recursos subjetivos. Palabras clave: depresión post-parto; maternidad; subjetividad; representaciones sociales. Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 Résumé Cet article a le but de présenter des réflexions théoriques sur les processus subjectifs d’une femme touchée par la dépression post-partum. Le présent travail cherche rompre avec la vision réductionbiniste de la dépression post-partum, laquelle est basé dans le modèle biomédical, ce qui la réduit aux aspects biologiques et symptomatiques. Donc, on essaye de récupérer les dimensions sociales, historiques, politiques et singuliers, lesquels sont fréquemment négligées. Pour ceci, on a utilisé la théorie de la subjectivité de González Rey, dans une perspective historique-culturel, dans un dialogue avec la théorie des représentations sociales et aussi avec des auteurs critiques au modèle biomédical, comme Foucault et Illich. Le contrôle par normes exercé dans la bio-politique, et le contrôle par le diagnostic qui résulte dans la médicalisation de la vie, constituent des éléments importants à réfléchir sur la production subjective de la dépression post-partum. Une étude de cas a été faite, à partir d’une perspective qualitative de base constructive et interprétative. Dans le processus de construction d’information, on discute que la dépression post-partum expresse la disparité entre la maternité socialement idéalisée et celle qui a été produite subjectivement de façon singulier. Ainsi, la dépression post-partum est production subjective complexe qui, au-delà des aspects biologiques et hormonaux, elle est configurée par la subjectivité individuelle de la femme qui a récemment accouché et par la subjectivité sociale marquée par le discours médical et par la médicalisation de la vie. Ceux-ci normalisent l’expérience socialement acceptable de la maternité et transforme des autres en pathologies, ce qui gèrent des images fréquents de frustration et de culpabilité. En outre, on soutient que les modèles de l’aides actuellement fournies ne donne pas des possibilités de réflexions critiques qui permettent le développement des capacités subjectives face à cette expérience, car ils sont crées par des protocoles rigides qu’ont les normes comme références. Ainsi, on défend le besoin d’espaces qui Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 80 Depressão Pós-parto para além do Diagnóstico: Representações Sociais e Subjetividade accueillent les expériences des femmes puerpérales d’une manière qui soit possible faire des réflexions critiques sur les aspects impliqués dans la construction subjective singulière de la dépression post-partum; ce qui permet, donc, le développement de ressources subjectives. Mots-clés: dépression du post-partum; maternité; subjectivité; représentations sociales. Résumé A depressão pós-parto é uma categoria médica que delimita e normatiza um fenômeno que atinge cerca de 10 a 15% das puérperas com base em seus sintomas, tais como: estado de morbidez, irritabilidade, choro frequente, baixa energia e motivação, falta de prazer e de interesse sexual, sentimento de desamparo e culpa, perda de concentração, bem como ideias de morte ou suicídio ocorrendo por um período mínimo de duas semanas (Beck, 2002; Chandran, Tharyan, Muliyil & Abraham, 2002; Lobato, Moraes &Reichenheim, 2011; Rodrigues & Schiavo, 2011; Schardosim & Heldt, 2011). Contudo, a qualidade da experiência desse processo se configura como única; extrapolando, portanto, tal representação social de base sintomatológica, que não dá visibilidade à dimensão emocional, singular e político-social presentes na mesma; ocultando, assim, por detrás do diagnóstico, o sujeito que vivencia o fenômeno.ll No intuito de refletir sobre esse tema, foi feito um estudo de caso, a partir do qual foram tecidas reflexões utilizando a teoria da subjetividade em uma perspectiva cultural-histórica, que se orienta à geração de inteligibilidade sobre a complexidade das produções simbólico-emocionais nas condições da cultura (González Rey, 2004, 2005, 2015, 2016). Utilizou-se também contribuições da teoria das representações sociais, que permite enfocar a maneira como o conhecimento e as produções simbólicas acerca de determinados fenômenos são partilhados, constituindo a realidade comum, transformando ideias em práticas, de modo a intervir nos processos de subjetivação (Moscovici, 2003). Ambas as propostas teóricas contribuem para avançar em uma visão complexa acerca da depressão pós-parto, abrindo possibilidades para se refletir sobre suas dimensões singulares e político-sociais, frequentemente ignoradas.l Articulada a essa reflexão teórica, a noção de biopolítica, com seus dispositivos de poder, saber e cuidado de si, teorizados por Foucault (1980, 2004), é discutida em suas formas de controle e práticas. Além disso, aliado às formas de controle efetivadas pela biopolítica de Foucault, encontra-se o processo de medicalização da vida, e o consequente controle por meio do diagnóstico, dos quais fala Illich (1975), que se fazem presentes nas representações sociais dominantes e na delimitação do que é saudável e do que é patológico. Desse modo, tais contribuições teóricas se fazem importantes, uma vez que desempenham destacado papel nos processos de subjetivação da depressão pós-parto. Résumé Assim, defende-se a hipótese de que a depressão pós-parto é uma produção subjetiva complexa que, para além de apenas aspectos biológicos e hormonais, é configurada pela subjetividade individual da puérpera em questão, e pela subjetividade social marcada pelo discurso médico e a medicalização da vida, que padronizam as experiências socialmente aceitáveis de maternidade e patologizam as demais, oportunizando sentimentos de frustração e culpa que caracterizam a representação social dominante da depressão pós-parto.l O presente trabalho também reflete acerca da importância de uma rede de apoio que viabilize um espaço dialógico de apoio singularizado, tornando viável, por meio deste, uma reflexão crítica – o que implica um resgate dasdimensão simbólico- emocional, do espaço social e das representações e normas implicadas nessa produção, favorecendo o desenvolvimento de um novo modo de vivenciar a maternidade. Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 Teoria da Subjetividade e Representações Sociais: Uma Complexa Aproximação Moscovici (2003) define as representações sociais enquanto forma característica de conhecimento de nossa época, que corresponde, por um lado, a uma substância simbólica e, por outro, à prática que tal substância produz. Dessa maneira, as representações sociais são “um sistema de valores, ideias e práticas” (Moscovici, 2003, p. 21) que desempenham uma dupla função. Primeiramente, de estabelecer uma ordem, permitindo que as pessoas se orientem a partir delas em seu mundo material e social. Em segundo lugar, elas possibilitam a comunicação entre os membros de uma comunidade ao fornecer- lhes um código que nomeie e classifique os fenômenos de seu mundo (Moscovici, 2003). Uma aproximação teórico-epistemológica entre teoria da subjetividade e a teoria das representações sociais se faz possível mediante a interpretação desenvolvida por González Rey (2008, 2015) das representações sociais enquanto produções simbólicas produzidas e configuradas socialmente, mas que não prescindem dos processos emocionais que se articulam complexamente no nível do sujeito individual. Vale ressaltar que a teoria da subjetividade avança teoricamente nessa explicação, pois a subjetividade social vai além do conceito de representações sociais, visto que integra o indivíduo como parte indissociável desse processo, dado que considera não somente os processos simbólicos abordados pela teoria das representações sociais Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 81 Rafaella Pinheiro Cesario e Daniel Magalhães Goulart (Moscovici, 2003), mas a unidade dos processos simbólicos com os processos emocionais, que se articulam no caráter dinâmico e criador da subjetividade humana. Nesse sentido, para o autor, as representações sociais figuram como uma produção subjetiva social, que, como tal, se organizam simultaneamente nas práticas sociais e individuais (González Rey, 2003), de modo que as representações sociais não são vistas como causas lineares de comportamentos, mas como um sistema complexo que é fonte de sentidos subjetivos para qualquer atividade (González Rey, 2015), caracterizando a relação entre as práticas instituídas e as concepções, saberes e normas que instituem essa prática (Machado, Almeida & Saraiva, 2009). Nessa ótica, faz-se importante discutir as representações sociais dominantes da maternidade, uma vez que são concebidas como fontes de produções subjetivas associadas a determinado ideal, que termina por ser amplamente influente na experiência da puérpera. Esse processo leva, frequentemente, à normalização que se impõe desde fora, gerando uma dissociação entre a norma e a vivência singular desse processo, prejudicando a criação de parâmetros singulares de acordo com a própria experiência da pessoa. Teoria da Subjetividade e Representações Sociais: Uma Complexa Aproximação p p p p A representação social da depressão pós-parto é fortemente marcada pelo modelo biomédico, que se baseia em uma rígida dicotomia entre o normal e o patológico. Nesse processo, aquilo que diverge da norma, ou da representação social hegemônica, passa a ser compreendido como inatural a partir do pressuposto de uma única maneira “saudável” de vivenciar a experiência da maternidade (Arrais, 2005). O normal configura-se, por outro lado, a partir de um ponto de vista estatístico quantitativo e também em um protótipo qualitativo ideal a ser atingido (Canguilhem, 2002). Nessa ótica, ignora-se todo o aspecto cultural, social e singular presentes na produção da “doença”, como também a capacidade do indivíduo de criar seus próprios parâmetros em consonância com sua própria experiência. A teoria da subjetividade em uma perspectiva cultural-histórica adquire valor heurístico na discussão desse tema ao enfatizar o resgate do sujeito no cerne desse processo, permitindo teorizar sobre seu papel como constituinte e constituído por essas representações sociais, abrindo novas possibilidades de existência perante as exigências exercidas pela representação idealizada de maternidade. Inspirado por contribuições teóricas da psicologia soviética, tais como Vygotsky (1987, 2001) e Bozhovich (1968), bem como por diversas inovações conceituais dessa psicologia a partir da década de 1970 (Abuljanova, 1980; Chudnovsky, 1988; Lomov, 1978, 1984), González Rey elabora o conceito subjetividade enquanto sistema simbólico-emocional, que expressa a mobilidade e diversidade da experiência dos indivíduos e dos grupos sociais; representando, portanto, uma produção humana ontologicamente diferenciada sobre a experiência vivida (González Rey, 2007, 2015, 2016). Inspirado por contribuições teóricas da psicologia soviética, tais como Vygotsky (1987, 2001) e Bozhovich (1968), bem como por diversas inovações conceituais dessa psicologia a partir da década de 1970 (Abuljanova, 1980; Chudnovsky, 1988; Lomov, 1978, 1984), González Rey elabora o conceito subjetividade enquanto sistema simbólico-emocional, que expressa a mobilidade e diversidade da experiência dos indivíduos e dos grupos sociais; representando, portanto, uma produção humana ontologicamente diferenciada sobre a experiência vivida (González Rey, 2007, 2015, 2016). A subjetividade expressa, enquanto “fenômeno complexo produzido de forma simultânea no nível social e individual” (González Rey, 2003, p. 202), por meio dos sentidos subjetivos, os diversos aspectos “objetivos” da vida social imbricados em sua formação (González Rey, 2005). Os sentidos subjetivos representam unidades simbólico-emocionais (González Rey, 2009) produzidas em nossa experiência, em um fluxo inconsciente e dinâmico, expressando a qualidade da relação do sujeito em determinado momento da vida social (González Rey, 2005). Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 Teoria da Subjetividade e Representações Sociais: Uma Complexa Aproximação Essa definição, contudo, é contestada por González Rey, que define saúde como uma produçãos imbólica, cultural e Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 82 Depressão Pós-parto para além do Diagnóstico: Representações Sociais e Subjetividade historicamente organizada, por meio de processos institucionais e de práticas sociais imbricadas nos posicionamentos frente a essa importante dimensão da vida humana, tanto por parte das pessoas, como das sociedades (González Rey, 2004; Costa & Goulart, 2015). Assim, a categoria diagnóstica “depressão pós-parto” não pode ser dissociada da medicalização da vida, do controle exercido pela norma e pelo diagnóstico, assim como os aspectos subjetivos individuais que se fazem presentes na configuração subjetiva dessa experiência (Goulart & González Rey, 2016; Goulart, 2017). A partir de tal perspectiva, a saúde é vista não como produto, mas como processo que não corresponde a um estado de normalidade (González Rey, 2011). historicamente organizada, por meio de processos institucionais e de práticas sociais imbricadas nos posicionamentos frente a essa importante dimensão da vida humana, tanto por parte das pessoas, como das sociedades (González Rey, 2004; Costa & Goulart, 2015). Assim, a categoria diagnóstica “depressão pós-parto” não pode ser dissociada da medicalização da vida, do controle exercido pela norma e pelo diagnóstico, assim como os aspectos subjetivos individuais que se fazem presentes na configuração subjetiva dessa experiência (Goulart & González Rey, 2016; Goulart, 2017). A partir de tal perspectiva, a saúde é vista não como produto, mas como processo que não corresponde a um estado de normalidade (González Rey, 2011). A dicotomia normal-patológico expressa uma concepção de mundo como externo ao sujeito, como se não estivéssemos implicados nele de maneira orgânica por meio do nosso funcionamento (González Rey, 2004). O normal deixa de ser a capacidade do indivíduo de produzir suas próprias normas na sua relação concreta com seu meio de acordo com suas possibilidades e limitações - processo que Canguilhem (2002) denomina normatividade biológica - para ser uma normatividade social, marcadamente externa ao sujeito. , j Ao estabelecer a dicotomia saúde/doença e normal/patológico, o sujeito se depara com uma perspectiva rígida e arbitrária de vivenciar suas experiências, em que qualquer maneira que divirja da norma é marginalizada à esfera do patológico, não levando em consideração a implicação do sujeito em seus processos - o que pode levar à mortificação do eu (Goffman, 2001). Teoria da Subjetividade e Representações Sociais: Uma Complexa Aproximação Ademais, algumas características tidas como sintomas são eleitas e totalizadas, tornando-se definidoras do sujeito que passa a ser considerado doente (Moysés, 2001). Vale ressaltar que o conceito de normalidade é histórico e cultural, somente adquirindo sentido por meio dos discursos e representações ali presentes. Portanto, a condição de doença, do patológico, depende em si de seu contexto – é a partir da cultura que se denomina a norma. Considerando o explícito acima, a perspectiva aqui adotada permite alternativas teóricas e epistemológicas para compreender de forma complexa a configuração subjetiva da depressão pós-parto, uma vez que, de acordo com Morin (1983, p. 35), “o que me interessa é o fenômeno multidimensional (...) Tudo o que é humano é ao mesmo tempo físico, sociológico, econômico, histórico, demográfico; interessa, pois, que esses aspectos não sejam separados”. E conhecer um fenômeno, ou condição social, somente se faz possível por meio do “sistema disperso de suas consequências sobre a constituição subjetiva daqueles que a compartilham” (González Rey, 2005, p.14). Tal compreensão permite avançar em configurações subjetivas singulares do processo da maternidade, para além de suas normatizações sintomáticas e de seu divórcio com as dimensões sociais e culturais que o constituem, viabilizando investigar o tema de forma complexa. Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 Teoria da Subjetividade e Representações Sociais: Uma Complexa Aproximação Tais unidades se organizam em configurações subjetivasque, por sua vez, expressam formações simbólico-emocionais relativamente estáveis em relação a processos, acontecimentos e figuras significativos para a pessoa, ou grupo social. Tais conceitos se revelam importantes, pois permitem refletir acerca da produção singular da puérpera em permanente tensão com aspectos sociais dessa produção. A subjetividade é composta por níveis integrantes e inalienáveis expressos pela subjetividade individual e social, uma vez que o caráter relacional e institucional da vida humana resulta na configuração subjetiva dos sujeitos, assim como dos espaços sociais onde essas relações se configuram (González Rey, 2003). A subjetividade social expressa produções simbólico- emocionais configuradas nos diferentes espaços sociais, permitindo que grupos, instituições e culturas se identifiquem pelos seus aspectos subjetivos convergentes. A subjetividade social se apresenta nas representações sociais, nas normas, nas crenças, na moral que caracteriza os mais diversos espaços sociais em que vivemos. Esses são os mesmos elementos presentes na subjetividade individual, com a diferença de que a produção de sentido nesse nível é configurada pelos aspectos singulares de indivíduos concretos (González Rey, 2005). Encontra-se aí o valor heurístico da teoria da subjetividade: ao enfatizar a qualidade recursiva entre o social e individual, bem como o caráter gerador e ativo da subjetividade, inaugura uma nova concepção da categoria sujeito. Rompe-se com uma perspectiva individualizada de sujeito, de modo que ele passa a ser concebido a partir de sua relação com o social. Nesse sentido, o indivíduo é um momento da experiência social, pois os espaços sociais geram formas de subjetivação que se concretizam nos diferentes sujeitos a partir de suas produções, sempre em tensão com suas produções subjetivas individuais. Desse modo, a relação recursiva entre essas duas faces da subjetividade não se dá de forma linear e causal, pois a subjetividade implica uma produção humana que evidencia uma alternativa às imposições da realidade (González Rey, 2009). A subjetividade individual é sempre atravessada pela subjetividade social, entretanto, os sentidos subjetivos produzidos dependem dos modos que essa relação adquire (González Rey, 2003). Ser saudável, na ótica biomédica, é visto como não ter sintomas, instaurando a dicotomia saúde/doença e individual/ social. A Norma, o Poder e o Diagnóstico: Um Olhar Histórico 83 Rafaella Pinheiro Cesario e Daniel Magalhães Goulart Essa incursão histórica nos auxilia a compreender o processo pelo qual as práticas e representações sociais referentes à maternidade foram construídas, assim como a patologização daquilo que diverge do socialmente almejado, evidenciando a relação indissociável entre as produções singulares com seu contexto histórico, político e cultural. Ariés (1978), em A História Social da Criança e da Família, destaca que, até o século XVI, não há registros, icônicos nem escritos, que fizessem referência à criança, demonstrando que o conceito de infância e de maternidade, tal qual conhecemos, é uma construção social recente. A noção atual de família, consequentemente de maternidade, foi sendo concebida concomitantemente ao surgimento do conceito de infância, que, por sua vez, acompanhava mudanças sociais e econômicas (Ariés, 1978). A reflexão de Ariés explicita como as mudanças de conceito de família modificaram sua ontologia e práticas sociais. Por exemplo, de acordo com um tenente da polícia parisiense de 1780, das 21 mil crianças que nasceram em Paris, apenas mil foram amamentadas pelas mães, tendo mais de 19 mil delas partido para longe de suas mães para serem amamentadas. Tal atitude atribui-se, com frequência, à alta taxa de mortalidade infantil da época, que contribuía para um distanciamento em relação aos filhos. Essa prática social expressa uma representação social da maternidade, englobando aí suas obrigações, distintas das atuais (Badinter, 1985), evidenciando que mudanças nas tendências sociais que compõe a subjetividade social geram novas representações, que delimitam o que é socialmente aceito enquanto experiência da maternidade.i É A crítica de Rousseau (2004) sobre a prática de mandar os filhos para serem amamentados presente em Émile ilustrou o início de uma nova representação social da maternidade ao endossá-la e ao associar uma boa mãe àquela que se sacrifica em nome da maternidade. Foi através dessa mudança na representação de maternidade que se instaurou a “injunção obrigatória do amor materno” (Badinter, 1985), o que teve implicação na maneira como os indivíduos e grupos sociais vivenciam a experiência da maternidade. Assim, a noção de “instinto materno” pode ser vista como desdobramento de um dispositivo biopolítico que extrapola o âmbito da ciência, tornando-se a representação social dominante e normatizante acerca da maternidade. A Norma, o Poder e o Diagnóstico: Um Olhar Histórico Isto é expresso na própria definição do dicionário Aurélio em sua edição de 1867, que define a maternidade como: “(...) força biológica que atua, em geral, de modo inconsciente, mas com finalidade precisa, e independentemente de qualquer aprendizado (...) Tendência natural; aptidão inata” (Arrais, 2005, p. 41). Tal definição, ainda que contestada (Badinter, 1985), exemplifica como essa visão foi naturalizada, impregnando o senso comum e resultando na imposição arbitrária de uma experiência determinada, a priori, de uma vivência singular. Pode-se observar que, ao longo do tempo, expressando fatores sociais, econômicos e políticos, houve diversas mudanças acerca da representação social do ideal de maternidade a ser vivenciado. Tais práticas sociais “tomam corpo e tomam o próprio corpo em esquemas de comportamento, em conjuntos técnicos, em instituições que, atuando de forma articulada, operacionalizam a transmissão e a difusão de modos específicos de subjetivação” (Vasconcelos et. al., 2011, p. 10). A representação social da depressão pós-parto refere-se a um conjunto de sintomas que antagonizam a representação social dominante da maternidade, relacionada a um amor instintivo, realização e felicidades plenas, naturalizando a maternidade como instinto materno.i As experiências que se distanciam desse amor instintivo se configuram como forma anormal, adoecida, de vivenciar a maternidade (Arrais, 2005), visando localizar no indivíduo a sede do problema, o desvio do instituído, ignorando toda a dimensão social, cultural e política dessa produção. Desse modo, a concepção de um sujeito individualizado, ponto central da sociedade capitalista (Furtado, 2007), dicotomiza com suas produções singulares da dimensão social inexoravelmente presente em tais produções. Cabe, assim, à psicologia, à medicina, à família, entre outras instituições, o papel de agentes do poder disciplinar, que prezam pelo retorno à “normalidade”. Dessa forma, a dicotomia entre o ideal de maternidade e a experiência adoecida de maternidade, expressa pela depressão pós-parto, sustenta uma representação social dominante e práticas sociais que ignoram as diversas formas possíveis de vivenciar essa experiência, a depender da produção subjetiva de cada puérpera (Arrais, 2005). Nesse contexto, o tratamento e cuidado prestados a puérperas diagnosticadas com depressão pós-parto busca a eliminação dos sintomas e retorno à “normalidade” sem se atentar para as produções subjetivas que a levaram a ser enquadrada em tal diagnóstico. Os protocolos rígidos e inflexíveis tampouco proporcionam um espaço dialógico que oportunize à puérpera refletir sobre os próprios processos e gerar seus próprios caminhos singulares de produção de saúde. A Norma, o Poder e o Diagnóstico: Um Olhar Histórico A partir da perspectiva adotada, é importante fazer uma incursão histórica de modo a enfatizar a maneira como tal constituição histórica se faz presente nas produções sociais e individuais associadas à produção da depressão pós-parto. A partir do século XVIII, como desdobramento da Revolução Industrial Inglesa e da nova ordem econômica e política por ela instaurada, o capitalismo, instaurou-se também uma nova forma de normatização, uma vez que a saúde individual e o rendimento passaram a ser considerados indispensáveis ao bom funcionamento da engrenagem social (Foucault, 1980). Assim, institui-se um processo de normalização e controle, por meio de diversos dispositivos, que resultam em um importante elemento na produção de subjetividades, tanto individuais quanto sociais, bem como das representações sociais de maternidade, e, consequentemente, na produção da depressão pós-parto.i Nesse contexto, “a medicina passou a ser uma oficina de reparos e manutenção, destinada a conservar em funcionamento o homem usado como produto não humano” (Illich, 1975). Não só a medicina, mas a psicologia e também a própria família, passam a se encarregar da normalidade, reduzindo a complexidade e amplitude de formas de vivenciar fenômenos sociais à dicotomia normal/patológico. Essa apropriação dos discursos por parte da medicina implica não somente em uma produção de saber, mas em uma produção de poder, que cria espaços sociais de subjetivação engendrados por normas, discursos e práticas (Foucault, 1980, 2004). De acordo com Canguilhem (2002), o doente é doente por aceitar apenas uma norma. A norma em si não é o problema, e sim o fato de que diz respeito a valores morais naturalizados. A normatização da maternidade acarreta no consequente exílio daquilo que difere desse ideal na esfera do patológico, ignorandoa multiplicidade e singularidade dos processos subjetivos. Assim, a depressão pós-parto é, historicamente, produzida nessa relação de poder que termina por delimitar modos de viver e de existir no mundo (Vasconcelos, Zago, Machado & Ross, 2011). A consequente imposição da representação social hegemônica naturalizada gera processos de normatização que produzem intenso sofrimento àquelas que divergem desse ideal. A medicina e a psicologia passam a ocupar, na nossa sociedade moderna, um lugar social de dispositivos disciplinares que enxergam os fenômenos que divergem da norma através da lente da anormalidade, buscando corrigir tal patologia reintegrando-os à norma por meio de seus cuidados (Foucault, 2004). Desse modo, dificulta-se a possibilidade de gerar sentidos subjetivos relacionados à valorização da realidade existencial de cada uma. Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 A Norma, o Poder e o Diagnóstico: Um Olhar Histórico Percebe-se, portanto, um duplo processo de normalização, que se configura a partir da norma e da captura dos processos de singularização, consolidando o discurso biomédico como dispositivo disciplinar que desempenha um importante papel nos processos de subjetivação individuais e sociais. A redução de fenômenos complexos a uma dimensão biológica desdobra-se na medicalização da maternidade, produzindo consequências, tais como o controle social pelo diagnóstico, que leva as puérperas a portarem-se como objeto pelo qual o médico é responsável, e perdendo, assim, sua autonomia e liberdade, o que Illich denomina de iatrogenêse social (Illich, 1975). Ao normatizar e prescrever uma maneira padronizada de vivenciar a maternidade, a experiência vivida que sobrepuja a normatizada é diagnosticada, tornando a puérpera objeto de conhecimento e tratamento médico, que tem sempre como referencial a norma. Retira-se, assim, a puérpera de seu lugar de sujeito de sua experiência – o que, em consonância com o discurso capitalista-individualizante, localiza exclusivamente no indivíduo o problema e alimenta, desse modo, a Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 84 Depressão Pós-parto para além do Diagnóstico: Representações Sociais e Subjetividade culpa sentida. Ademais, a posição de paciente, objeto do saber médico, que nada sabe sobre si, minimiza a possibilidade de que desenvolva por si, a partir dos sentidos subjetivos que emergirem, seu próprio modo de vivenciar a maternidade. culpa sentida. Ademais, a posição de paciente, objeto do saber médico, que nada sabe sobre si, minimiza a possibilidade de que desenvolva por si, a partir dos sentidos subjetivos que emergirem, seu próprio modo de vivenciar a maternidade. Apesar dos saberes e poderes que sustentam essa dicotomia e que pretendem domar a subjetivação, tornando-a homogênea, as experiências singulares lhe extrapolam, perfazendo uma história de resistência (Cardoso, 2005) e demandando novos olhares para contemplar o fenômeno. Exalta-se a necessidade de resgatar a possibilidade de vivenciar a experiência da maternidade de diversas maneiras de acordo com a subjetividade (individual e social), interesses, valores, necessidades e possibilidades de cada mulher. Fica, assim, expressa a importância de criar novas zonas de sentido, ou seja, formas de inteligibilidade acerca da realidade produzidas na pesquisa e que não esgotam a questão, mas abrem possibilidades de aprofundamento na construção teórica (González Rey, 2007), a partir de uma visão complexa, explorando como os aspectos psicossociais, históricos, políticos, culturais e singulares se articulam na experiência da pessoa. Método A presente pesquisa teve como base a epistemologia qualitativa (González Rey, 1997, 2005), que defende o caráter construtivo-interpretativo do conhecimento, a legitimidade do singular na pesquisa científica e o conhecimento como processo de comunicação. Tal baliza epistemológica propõe a metodologia construtiva-interpretativa como referencial, cujo objetivo é a construção de modelos teóricos compreensivos referentes ao fenômeno pesquisado, e não uma apropriação linear de uma realidade.i Nessa perspectiva, a pesquisa científica visa à abertura de novas zonas de sentido sobre o fenômeno estudado, sem buscar esgotá-lo em todas suas possibilidades (González Rey, 2005). Consequentemente, o singular se torna fonte legítima de informações que contribuem para o modelo teórico resultante da pesquisa. De acordo com esse referencial, a produção subjetiva da participante em relação à depressão pós-parto não se dá de forma direta e explicitamente relacionada a esse fenômeno, mas encontra-se “dispersa na produção total da pessoa” (González Rey, 2005, p. 32), necessitando de interpretações e construções, de forma a articulá-las e produzir construções teóricas acerca do fenômeno. i Este artigo foi aprovado como parte de um projeto de iniciação científica, coordenado pelo professor Fernando González Rey e aprovado pelo Comitê de Ética em Pesquisa por meio do Parecer nº. 1.372.682. A pesquisa se desenvolveu com uma participante, com a qual se teve encontros pessoalmente e virtualmente no decorrer de quatro meses. O contato foi feito por meio de indicação de uma pessoa conhecida em comum, de modo que a escolha da participante se deu por ela ter se disponibilizado a participar do estudo. C. é uma mulher de 42 anos, nascida em uma cidade do interior de Minas Gerais, mas que vive em Brasília desde os seis anos de idade. Vive com o marido, com quem é casada há 11 anos, e sua filha de sete anos. Sua família de origem é composta por um pai, uma mãe e quatro irmãos, com quem ela mantém contato frequente. Ela é formada em Administração de Empresas e atualmente é servidora pública. Cinco anos antes da gravidez, C. havia sido diagnosticada com depressão, bem como com síndrome do pânico. Durante esse período, teve acompanhamento médico e psicológico, apresentando melhora gradual após tais intervenções. Somente a partir da gravidez, mais especificamente após o parto, C. voltou a vivenciar situações de intenso sofrimento psíquico. A Norma, o Poder e o Diagnóstico: Um Olhar Histórico O estudo de caso permite tal imersão profunda e complexa resgatando os sentidos subjetivos emergidos na singularidade dessa experiência. Desse modo, o presente estudo propõe investigar de que modo as representações sociais da maternidade e do próprio diagnóstico de depressão pós-parto, bem como os elementos singulares da história de vida da puérpera, articulam-se na produção subjetiva da depressão pós-parto da participante.i Pretende-se, assim, contribuir para a desmistificação da representação social da depressão pós-parto como modo patológico de vivenciar a maternidade, assim como dar subsídios para uma atenção integral à puérpera, voltando um olhar complexo a esse fenômeno complexo. A partir disso, dar legitimidade à singularidade dessa vivência, resgatando a puérpera como sujeito de sua experiência e devolvendo a ela a possibilidade de desenvolver por si, a partir dos sentidos subjetivos que emergirem de seu próprio modo de vivenciar a maternidade. Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 Construção da Informação No primeiro encontro da participante com a primeira autora deste texto, foi perguntado como, na concepção dela, havia se iniciado seu processo depressivo. Diante de tal questionamento, ela respondeu: Um dia, meu marido viajou, e aí tive uma crise de referência mesmo (...) Tipo, bom, eu achava isso (seu modo de pensar e agir na vida) correto, aí eu comecei assim: será que isso é correto mesmo? Aí eu passei a questionar tudo que eu acreditava, pra ver se era isso que eu queria pra ela (bebê). E eu comecei a pensar umas coisas muito doidas. Assim, eu ficava em pânico de influenciar a formação do que uma pessoa pensa. Parecia que eu não sentia... É muito poder, sabe? Aquilo me assustou muito. Tem isso, de se cobrar, mas mais que isso, o que ficou pra mim foi: quem eu sou? Quem eu sou para, agora, influenciar uma coisinha que não tem nada escrito? Quem eu sou? O que eu acredito de verdade? Quais são os meus valores? E era tudo... Quais são meus valores? E, quando eu me fiz essa pergunta, eu me desestruturei. Ela disse ainda: “Eu não sei se esse negócio de ser mãe te muda de posição na vida, que aí de repente você tem que dar conta do outro. Aí você fala, poxa, será que eu dou conta de mim? Aí tive uma crise de referência mesmo”. Tais trechos expressam claramente a insegurança de C. em relação a ser mãe. No entanto, as associações feitas entre ser mãe e questões mais gerais de sua pessoa podem ser consideradas como indicador de sentidos subjetivos relacionados à insegurança e baixa autoestima em relação à sua constituição como pessoa. Os trechos acima citados também são entendidos como indicadores de que a representação social dominante, da mãe como a principal figura responsável pelos filhos, se faz presente na produção subjetiva de C. com relação à maternidade, configurando um ideal que ela se cobra atingir. Além disso, em ambas as falas, estão presentes questões de gênero, que delimitam os papéis do que é considerado feminino, incluindo nesse escopo a mulher/mãe como principal figura responsável pelos filhos. Essa concepção tradicional de gênero se desdobra na assunção de que a formação da filha é estritamente sua responsabilidade; desconsiderando, nesse processo, por exemplo, os papéis desempenhados pelo pai da criança – seu marido. Método Além da dinâmica conversacional, foi utilizado o “complemento de frase”, instrumento que apresenta indutores curtos a serem preenchidos pelo sujeito (González Rey, 2005) com o intuito de estabelecer outra via de acesso aos sentidos subjetivos e à experiência singular da participante. Pelo fato de os indutores serem bastante curtos, é possível utilizar uma ampla gama deles, abordando diferentes temáticas, favorecendo expressões sobre diversas esferas da vida do participante. Método i Após completar oito anos de matrimônio e ter se estabelecido financeiramente, tendo “viajado o que queria viajar, passeado o que queria passear”, C. decidiu ter filhos. Foi uma decisão conjunta com seu parceiro, de modo que, poucos meses depois do planejamento, engravidou. Antes da gravidez, não se encontrava em depressão, tampouco apresentava sintomas da síndrome do pânico, tão frequentes outrora. Estes somente foram deflagrados no sexto mês de gravidez, agravando-se no pós-parto.i A construção do cenário de pesquisa, definido como a “criação de um clima de comunicação e de participação que facilita o envolvimento por parte das pessoas” (González Rey, 2005, p. 84), iniciou-se pelo contato virtual que explicava o tema da pesquisa, o que resultou no interesse de contribuir por parte da participante, que demonstrava desejo de dividir sua Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 85 Rafaella Pinheiro Cesario e Daniel Magalhães Goulart experiência. Os encontros presenciais ocorreram na casa da participante, o que proporcionou a ela conforto e liberdade por estar em um ambiente familiar, permitindo paulatinamente o estabelecimento de um vínculo por meio do diálogo. experiência. Os encontros presenciais ocorreram na casa da participante, o que proporcionou a ela conforto e liberdade por estar em um ambiente familiar, permitindo paulatinamente o estabelecimento de um vínculo por meio do diálogo. De acordo com a metodologia construtivo-interpretativa, os instrumentos caracterizam-se pela criação de recursos relacionais por parte do pesquisador, cujo objetivo é provocar a expressão do participante. Conforme expressa González Rey (2005, p. 42), o instrumento expressa uma “via legítima para estimular a reflexão e a construção do sujeito a partir de perspectivas diversas”, resultando no tecido de informações a partir do qual o pesquisador constrói novos questionamentos e instrumentos para avançar no modelo teórico em desenvolvimento. Para tanto, foi utilizado como instrumento a “dinâmica conversacional” (González Rey, 2005), que consiste em instigar o participante, por meio do diálogo, criando assim um “tecido de informação” significativo para a construção dos sentidos subjetivos relacionados ao fenômeno estudado. Ao longo desse processo, tanto os participantes como o pesquisador, integram suas experiências, suas dúvidas, suas tensões, suas emoções no processo, o que facilita a emergência de sentidos subjetivos ao longo das conversações, que vão tomando formas distintas, nas quais a riqueza da informação se expressa numa multiplicidade de formas diferentes que vão se organizando em representações teóricas construídas pelo pesquisador (González Rey, 2005). Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 Construção da Informação Esse aspecto nos leva a questionar a qualidade das relações pessoais que C. estabelece em sua vida, bem como a existência de uma rede social de apoio.i Ao abordar o tema do momento de nascimento da filha C. diz: Outra coisa, a coisa do amor... Essa questão também, a gravidez e a maternidade é muito romanceada, né? Nossa! A mulher grávida fica numa aura! Não, “e aí, quando você olha a carinha, você se apaixona, não sei o que”. Eu olhei a carinha e eu falei uhm... Você tem um instinto de “meu Deus, tá chorando, tenho que dar comida!”, um instinto de defesa. Mas eu ficava cobrando, assim, “eu tenho que sentir aquele amor”, né, que quando você olha já transforma. Eu não senti aquele amor. Assim, no meu caso, nem sei o que eu tava sentindo. Aí assim, “não tô amando esse bebê. Meu Deus, não tô amando esse bebê, que nem todo mundo ama”. Que culpa! Não tô amando, tô cuidando, mas... Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 86 Depressão Pós-parto para além do Diagnóstico: Representações Sociais e Subjetividade A culpa relatada por C. pode ser entendida como indicador da dissociação entre sua produção subjetiva individual e a idealização do que é ser mãe, ambas atravessadas pela representação social hegemônica da maternidade, que ela própria cultiva. É marcante como C. não se posiciona ativamente a partir de sua vivência singular, mas se submete a esse ideal, que passa a cobrar de si mesma. As representações sociais hegemônicas acerca da maternidade ilustram somente uma de suas inúmeras facetas, reduzindo-a, assim, à maneira romanceada que é retratada e a “injunção obrigatória do amor materno” (Badinter, 1985). Ao se deparar com uma maneira distinta de vivenciar a maternidade, C. se viu fragilizada e sem confiança para assumir a forma singularizada que estava vivenciando a maternidade. A posição de submissão de C. em relação à tal representação social hegemônica é indicador de uma produção de sentidos subjetivos associada à insegurança que sente em si mesma enquanto pessoa, reforçando e naturalizando esse ideal de maternidade socialmente construído. Nesse processo, ela se vê sem condições para emergir enquanto sujeito de sua experiência, não conseguindo abrir um campo de subjetivação alternativo à normatização social, que poderia lhe permitir um caminho de desenvolvimento subjetivo singularizado (González Rey, 2005). Ao longo dos encontros, C. relatou diversas situações que frustraram suas expectativas, distanciando-a do ideal materno. Construção da Informação A primeira experiência na qual se sentiu frustrada foi a gravidez. A gravidez - que, de acordo com o relato da participante, “é muito romanceada. Dizem que a mulher grávida fica numa aura (...) É tudo lindo” - foi uma experiência de bastante desconforto, sendo distinta do que ela imaginava: “engravidei, passei muito mal na gravidez, enjoei muito, não passou, fiquei com várias manchas, me questionando se dava conta... Não tinha nada a ver com aquela aura”. É interessante perceber que, apesar de C. por vezes racionalmente criticar essa representação “romanceada” da maternidade, tal crítica é dissonante da sua produção subjetiva de cobrar-se e culpar-se por não se adequar à norma social (Canguilhem, 2002), o que sugere que essa crítica expressa valores carentes de sentido subjetivo, representando apenas uma posição racional despersonalizada assumida perante as representações sociais dominantes presentes na subjetividade social (González Rey, 2005). A discrepância entre sua vivência e sua expectativa levou C. a se questionar não somente acerca de sua capacidade para ser mãe, mas acerca de si mesma, levando-a a se “desestruturar completamente”. C. buscou, então, “um médico para me ajudar”. É interessante que a primeira reação de C. ao se sentir desorganizada subjetivamente tenha sido buscar a ajuda especializada de um médico, e não o apoio de pessoas afetivamente próximas a ela. Tal ação pode ser interpretada como uma expressão do monopólio radical da medicina (Illich, 1975), uma vez que, ao vivenciar a maternidade de forma distinta da idealizada, C. a concebe como uma forma doente de experimentá-la, que requer, portanto, tratamento e cura. É interessante perceber que, mais do que buscar diferentes formas de compreender a sua própria experiência e, a partir de então, fomentar recursos subjetivos que a poderiam ajudar nesse momento, C. parece se submeter à lógica patologizante do modelo biomédico (Arrais, 2005; Illich, 1975), buscando se livrar daquilo que a está distanciando da normalidade. Os diagnósticos dados e relatados à participante, bem como as perguntas feitas, exacerbaram o pânico que já estava sentindo: “Eu fui aos médicos e eles perguntavam se a televisão estava conversando comigo, aí eu ficava com medo de assistir televisão. Eu sabia que isso era coisa de doido, e eu falava: ‘vai que a televisão conversa comigo!’”. A fala anterior é mais um indicador da insegurança de C. em si mesma, que, nesse processo, foi se generalizando e tomando corpo em diversas dimensões de sua vida. Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 Construção da Informação vive um intenso conflito entre o que idealizava para esse momento e as condições concretas nas quais ele se deu. Algo a ser destacado é que, para além da frustração e culpa oriundas da impossibilidade de ter um parto normal, não foi proporcionado a C. um espaço dialógico, por parte da equipe profissional que a atendeu, no qual seu sofrimento fosse acolhido e fosse possível construir, mediante a constituição de relações de confiança e vínculo, um espaço para ela se expressar. Tal espaço relacional estaria afinado a um tratamento que parta da experiência concreta da puérpera, e não de um protocolo padronizado definido de forma apriorística – o que não parece ter acontecido com C. ii filme de terror”. Percebe-se, portanto, que C. vive um intenso conflito entre o que idealizava para esse momento e as condições concretas nas quais ele se deu. Algo a ser destacado é que, para além da frustração e culpa oriundas da impossibilidade de ter um parto normal, não foi proporcionado a C. um espaço dialógico, por parte da equipe profissional que a atendeu, no qual seu sofrimento fosse acolhido e fosse possível construir, mediante a constituição de relações de confiança e vínculo, um espaço para ela se expressar. Tal espaço relacional estaria afinado a um tratamento que parta da experiência concreta da puérpera, e não de um protocolo padronizado definido de forma apriorística – o que não parece ter acontecido com C. ii A postura da equipe profissional expressa precisamente a rigidez das intervenções profissionais aprisionadas ao referencial da normalidade (Foucault, 1980). “E as enfermeiras disseram assim: não fica nervosa, senão seu leite vai secar”, aumentando ainda mais a pressão já sentida por C. em alcançar certo ideal de mãe. Nesse caso, faz-se necessário questionar a atenção que lhe foi prestada, que operou por meio de uma violência invisível e sutil, legitimada pela subjetividade social da instituição na qual é praticada, agravando seu quadro de sofrimento ao invés de apoiá-la e auxiliá-la a gerar novos recursos subjetivos. Dito e feito, meu leite secou. Com cinco dias, ela tentava mamar e eu chorava e chorava. Aí, chamei uma dessas enfermeiras que ajudam com o aleitamento e ela disse que eu não tinha leite. E aquilo ali me fez muito mal, assim, porque eu me senti muito mal. Construção da Informação E ela teve que tomar leite de soja e ficou com o peitinho crescido, por causa do hormônio da soja. E uma culpa, uma culpa... A culpa que C. refere sentir em sua experiência como mãe passa a representar, a partir de sua produção subjetiva, um fracasso total como pessoa. Nesse processo, ela ocupa cada vez mais o lugar de objeto de saber médico, ao qual ela deve estar submetida via prescrições e proscrições que, teoricamente, irão possibilitar o retorno a um “estado de normalidade” (Illich, 1975). Assim, muito mais do que possibilitar novos caminhos de desenvolvimento para C., as práticas em torno do diagnóstico de depressão pós-parto culminaram na intensificação de seu sofrimento, visto que reforçaram sua condição de passividade, insegurança e medo no processo de sua maternidade. Construção da Informação Essa coisa do aleitamento e aquela carteirinha do ministério da saúde: “o que fazer para seu filho crescer emocionalmente saudável? Amamente exclusivamente no peito por até seis meses. O que fazer para seu filho ter uma dentição saudável? Amamente”... É tudo muito sofrido, e eu fazia de tudo para ter o leite, e a sensação é essa, de desconexão total com o mundo. Eu tinha a sensação de ficar doida. Acumulava com a falta de sono e a mudança, que é muito brusca. Essa foi a terceira experiência que culminou no amplo sentimento de fracasso e culpa por parte de C. Sua fala é indicador de que, nesse caso, as práticas sociais hegemônicas relacionadas ao aleitamento, como determinados usos da Cartilha do Ministério da Saúde, podem também intensificar a idealização de ser mãe, conforme viemos discutindo (Cadoná & Strey, 2014). Entretanto, é importante ressaltar que tais práticas somente têm um efeito tão profundo sobre a experiência de C. em função de sua produção subjetiva individual. É precisamente esse o caráter paradoxal da biopolítica que Foucault (2004) discute: a proteção da vida por meio do controle de corpos, como nas campanhas de saúde a nível populacional, pode não somente favorecer a vida, mas limitá-la ao ponto de morte. Assim, aspectos destrutivos e impeditivos relativos à vida continuam sendo parte integral da biopolítica, embora justificado pela perspectiva de sua proteção. Outro aspecto que parece ter contribuído para a posição submissa de C. está relacionado à sua trajetória de vida familiar. Ao falar sobre sua família, C. relata, “minha família era bem tradicional... A gente ia à igreja todo domingo, e o que a bíblia pregava era o certo e o que era esperado de nós”. A pouca flexibilidade e espaço para questionamento perante as normas da igreja repercute, no caso de C., em um posicionamento passivo que, a partir das construções interpretativas anteriores, podemos articular à naturalização e submissão às diversas normas e representações hegemônicas presentes na subjetividade social. Nesse processo, quando C. não corresponde aos ideais cultivados, ela se sente imersa em culpa, como relatado abaixo: E uma culpa, uma culpa. Porque ela sempre foi miudinha. Ela era pequeninha e magrinha, e aí, meu Deus, era tudo por minha causa, porque ela não tinha mamado no peito e porque eu tinha tomado remédio. Porque ela não crescia. Aí, leite de vaca não deu certo. Construção da Informação Esta é uma evidência de como o processo de sofrimento de C. durante a gravidez e o pós-parto não é uma patologia limitada a seu déficit enquanto mãe, ou a esse momento específico, mas uma trajetória subjetiva inserida em um caminho de vida em que ela foi minando suas possibilidades de ação. i É possível identificar, por meio dos relatos de C., que dois processos simultâneos (seu sofrimento por não se adequar ao almejado e o diagnóstico que rotula sua experiência como forma “doente”de vivenciar a maternidade (Arrais, 2005) intensificam seu processo de tornar-se refém do descompasso entre ideal e real, sem condições de se posicionar ativamente a partir da sua própria experiência. Além de aumentar o medo e a impotência que a participante já estava sentindo, exemplificando a iatrogênese social discutida por Illich (1987), os diagnósticos foram vivenciados como processos externos a ela. Isto sinaliza a falta de um espaço dialógico que favorecesse a apropriação de sua condição singular e reflexões conjuntas com implicação emocional sobre seu próprio processo, o que poderia oportunizar a emergência de sentidos subjetivos que a permitissem desenvolver recursos frente aos imprevistos de sua experiência (González Rey, Goulart & Bezerra, 2016). Outro aspecto interessante e amplamente articulado às construções interpretativas realizadas até aqui, é que, ao falar sobre sua vivência, C. utilizava termos técnicos oriundos do jargão médico: “E aí, não sei se a depressão veio junto da dissociação, despersonalização e fragmentação de personalidade, essas coisas que eu tive”. O uso de tais categorias para falar de si mesma pode ser compreendido como indicador da carência de apropriação singularizada desse processo por parte de C., bem como a produção de sentidos subjetivos relacionados à naturalização do discurso biomédico. Mais além, o uso das categorias demonstra a naturalização da ótica médica enquanto única forma legitima de conceber sua vivência. i A segunda experiência que divergiu das expectativas de C., tendo resultado na intensificação do sentimento de culpa, foi resultado de sua expectativa frustrada de ter um parto normal: “tentei normal e não consegui. A bolsa estourou. Eu era toda bicho-grilo, vegetariana... Mas não consegui fazer parto normal. A filmagem do meu parto é eu em pânico, chorando. É um 87 Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 Rafaella Pinheiro Cesario e Daniel Magalhães Goulart filme de terror”. Percebe-se, portanto, que C. Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 Considerações Finais Com este artigo buscamos resgatar as dimensões históricas, políticas e sociais imbricados na produção da depressão pós- parto, de modo a romper com a visão reducionista, calcada no modelo biomédico, que se tem acerca do fenômeno. Também refletimos sobre a importância de novas estratégias de assistência por meio da oferta de espaços dialógicos que, não partindo de um ideal biomédico a priori, acolham a experiência vivida pela puérpera, contemplando os aspectos da subjetividade individual e da subjetividade social implicados na vivência de uma maternidade que é reconhecida como depressão pós-parto. Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 88 Depressão Pós-parto para além do Diagnóstico: Representações Sociais e Subjetividade Desse modo, oportuniza-se condições que favoreçam a emergência do sujeito que vivencia tal experiência, supostamente patológica, de forma a criar condições para uma reflexão crítica e viabilizar possibilidades de compreensão mais amplas e complexas. Esse processo pode fomentar o desenvolvimento de recursos subjetivos que favoreçam formas singularizadas de vivenciar a maternidade. O estudo de caso sugere que o que é denominado amiúde enquanto “depressão pós-parto” é uma produção subjetiva resultante da relação que se estabelece entre a subjetividade social, a partir da qual as representações sociais dominantes sobre maternidade normatizam e favorecem a idealização desse processo, e a subjetividade individual, que muitas vezes se limita a tais modelos normatizados. Assim, observou-se que a depressão pós-parto expressa a dissonância entre o ideal socialmente preconizado e a experiência singularmente vivenciada. No caso de C., a falta de espaços relacionais dialógicos, que marca tanto o âmbito das relações afetivas privadas como a esfera do apoio profissional, acaba por dificultar a produção de recursos subjetivos para lidar de maneira saudável com essa experiência, culminando na aceitação acrítica dos ideais cultivados socialmente. A medicalização da vida e a dicotomia normal-patológico relegam à esfera do patológico as experiências que extrapolam aquelas preconizadas pelas normas e representações sociais dominantes de maternidade. Partindo do referencial da normalidade, e reduzindo a depressão pós- parto a aspectos biológicos, a assistência prestada tem como objetivo a eliminação de sintomas, sem se preocupar, no entanto, com a trama subjetiva complexa que constitui esse fenômeno. As construções teóricas produzidas neste artigo não pretendem ser conclusivas no sentido de esgotarem outras possibilidades interpretativas sobre o fenômeno designado como depressão pós-parto. Considerações Finais Nesse sentido, ressaltamos a condição irrevogavelmente parcial e provisória do conhecimento científico, sempre limitado às condições contextuais de sua produção, e também permanentemente voltado à sua própria superação e à possibilidade de construção de novas formas de entendimento e ação no mundo. Referências Abuljanova, K. (1980). El sujeito de la actividad psíquica. Cidade do México: Roca. Arrais, A. (2005). As configurações subjetivas da depressão pós-parto: Para além da padronização patologizante. Tese de Doutorado, Programa de Pós graduação em Psicologia Clínica e Cultura, Universidade de Brasília, Brasília. Arrais, A. (2005). As configurações subjetivas da depressão pós-parto: Para além da padronização patologizante. Tese de Doutorado, Programa de Pós graduação em Psicologia Clínica e Cultura, Universidade de Brasília, Brasília. Ariés, P. (1978). História Social da Criança e da Família. Rio de Janeiro: Editora Zabar. Ariés, P. (1978). História Social da Criança e da Família. Rio de Janeiro: Editora Zabar. Badinter, E. (1985).Um amor conquistado: O mito do amor materno. Rio de Janeiro: Nova Fronteira. Beck, C. T. (2002). Revision of the postpartum depression predictors inventory. Journal Obstetric Gynecology Neonatal Nursing, 31(4), 394-402. Bozhovich, L. I. (1968). La personalidad y su formación en la edad infantile. Habana, Cuba: Pueblo y Educación. Cadoná, E., & Strey, M. (2014). A produção da maternidade nos discursos de incentivo à amamentação. Estudos Feministas, Florianópolis, 22(2), 304. Canguilhem, G. (2002). O normal e o patológico. Rio de Janeiro: Forense Universitária. Canguilhem, G. (2002). O normal e o patológico. Rio de Janeiro: Forense Universitária. Chandran, M., Tharyan, P., Muliyil, J., & Abraham, S. (2002). Post-partum depression in a cohort of women from rural area of Tamil Nadu, India: Incidence and risk factors. The British Journal of Psychiatry,181(6), 499-504. Cardoso, H. R., Jr. (2005). Para que serve uma subjetividade? Foucault, tempo e corpo. Psicologia: Reflexão e Crítica, 78(3), 343-349. DOI: 10.1590/S0102-79722005000300008 Costa, J. M., & Goulart, D. M. (2015). A saúde humana como produção subjetiva: Aproximando clínica e cultura. Psicologia & Sociedade, 27(1), 240-242. 89 Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 Chudnovsky, V. E. (1988). Problema subjectivnosti v svete sobremennyx zadach psikjologii vospitaniya. Vorpocy 89 Rafaella Pinheiro Cesario e Daniel Magalhães Goulart psikjologii, 4, 15-24. psikjologii, 4, 15-24. Foucault, M. (1980). A microfísica do poder. Rio de Janeiro: Edições Graal. Foucault, M. (1980). A microfísica do poder. Rio de Janeiro: Edições Graal. Foucault, M. (2004). Naissance de la biopolitique. Paris: Gallimard - Seuil. Foucault, M. (2004). Naissance de la biopolitique. Paris: Gallimard - Seuil. . Naissance de la biopolitique. Paris: Gallimard - Seuil. Furtado, O. (2007). O psiquismo e a subjetividade social. In A. M. M. Bock, M. G. M. Gonçalvez & O. Recebido em: 22/12/2016 Revisado em: 07/11/2017 Aceito em: 05/12/2017 Referências Furtado (Orgs.), Psicologia sócio-histórica: Uma perspectiva crítica em psicologia (3a ed., pp. 75-93). São Paulo: Cortez. Goffman, E. (2001). Manicômios, prisões e conventos. São Paulo: Editora Perspectiva. González Rey, F. (1997). Epistemologia cualitativa: Sus implicaciones metodológicas. Psicologia Revista, (5), 13-32. González Rey, F. (2003). Sujeito e subjetividade: Uma aproximação histórico-cultural. São Paulo: Thomson Learning. González Rey, F. (2004). Personalidade, saúde e modo de vida. São Paulo: Thomson. González Rey, F. (2005). Pesquisa qualitativa e subjetiva: Os processos de construção da informação. São Paulo: Thomson. González Rey, F. (2007). Psicoterapia, subjetividade e pós-modernidade. Uma aproximação histórico-cultural. São Paulo: Thomson Learning. González Rey, F. (2008). Subjetividad social, sujeto y representaciones sociales. Diversitas, 4(2), 225-243. González Rey, F. (2009). Epistemología y ontología: Un debate necesario para la psicología hoy. Diversitas, 5(2), 205-224. González Rey, F. (2011). Subjetividade e saúde: Superando a clínica da patologia. São Paulo: Cortez. González Rey, F. (2015). A new path for the discussion of social representations: Advancing the topic of subjectivity from a cultural-historical standpoint. Theory & Psychology, 25(4), 494-512. González Rey, F. (2016). Advancing the topics of social reality, culture, and subjectivity from a cultural-historical standpoint: Moments, paths, and contradictions. Journal of Theoretical and Philosophical Psychology, 36(3), 175-189. González Rey, F., Goulart, D. M., & Bezerra, M. S. (2016). Ação profissional e subjetividade: Para além do conceito de intervenção profissional na psicologia. Revista Educação (PUCRS. Online), 39(supl.), 54-65. Goulart, D. M. (2017). Educação, saúde mental e desenvolvimento subjetivo: Da patologização da vida à ética do sujeito. Tese de Doutorado, Programa de Pós-Graduação em Educação, Universidade de Brasília, Brasília. Goulart, D. M., & González Rey, F. (2016). Mental health care and educational actions: From institutional exclusion to subjective development. European Journal of Psychotherapy & Counselling, 18(4), 367-383. DOI: 10.1080/13642537.2016.1260617 Illich, I. (1975). A expropriação da saúde: Nêmesis da medicina. Rio de Janeiro: Editora Nova Fronteira. Lobato, G., Moraes, C., & Rreichenheim, M. E. (2011). Magnitude da depressão pós-parto no Brasil: Uma revisão sistemática. Revista Brasileira de Saúde Materno Infantil, 11(4), 369-379. Lomov, B. F. (1978). Kategorii obtscheniya i deyatelnosti v psykjologii. Voprocy Filosofii, 8, 34–47 Machado, A. M., Almeida, I., & Saraiva, L. F. O. (2009). Rupturas necessárias para uma prática inclusiva. In A. Anache & I. R. Silva (Eds). Educação inclusiva: Experiência profissionais em psicologia (pp.21-36). Brasília: Conselho Federal de Psicologia. Referências 90 Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 90 Depressão Pós-parto para além do Diagnóstico: Representações Sociais e Subjetividade Morin, E. (1983). O problema epistemológico da complexidade. Lisboa: Europa-America. Morin, E. (1983). O problema epistemológico da complexidade. Lisboa: Europa-America. Moscovici, S. (2003). Representações sociais: Investigações em psicologia social. Petrópolis: Vozes. Moysés, M. A. A. (2001). A institucionalização invisível – crianças que não aprendem na escola. Campinas: FAPESP/ Mercado de Letras. Rodrigues, O. M. P. R., & Schiavo, R. A. (2011). Stress na gestação e no puerpério: Uma correlação com a depressão pós- parto. Revista Brasileira de Ginecologia e Obstetrícia, 33(9), 252-257. Rousseau, J. J. (2004). Emílio ou da Educação. São Paulo: Martins Fontes. Schardosim, J. M., & Heldt, E. P. S. (2011). Escalas de rastreamento para depressão pós-parto: Uma revisão sistemática. Revista Gaúcha de Enfermagem, 32(1), 159-166. Vasconcelos, M., Zago, L. F., Machado, D. O., & Ross, C. R. (2011). Os limbos felizes da não-identidade: Tensões e implicações. Revista Mal-Estar e Subjetividade, 11(3), 1217-1264. Vygotsky, L. S. (1987). Thinking and speech. In R. Rieber & A. Carton (Eds.), The collected works of L. S. Vygotsky (Vol. 1, pp. 43–287). New York: Plenum. Vygotsky, L. S. (2001). Psicologia pedagógica. São Paulo: Martins Fontes. Vygotsky, L. S. (2001). Psicologia pedagógica. São Paulo: Martins Fontes. Endereço para correspondência Rafaella Pinheiro Cesario Email: rafapcesario@gmail.com Daniel Magalhães Goulart Email: danielgoulartbr@gmail.com Revista Subjetividades, Fortaleza, 18(1): 79-91, abril, 2018 91
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Statin therapy in multimorbid older patients with polypharmacy- a cross-sectional analysis of the Swiss OPERAM trial population
Frontiers in cardiovascular medicine
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Statin therapy in multimorbid older patients with polypharmacy- a cross-sectional analysis of the Swiss OPERAM trial population EDITED BY Lars Norgren, Örebro University, Sweden REVIEWED BY Sree Kondapally, St George’s University Hospitals NHS Foundation Trust, United Kingdom Valeria Conti, University of Salerno, Italy *CORRESPONDENCE Nicolas Rodondi nicolas.rodondi@insel.ch RECEIVED 07 June 2023 ACCEPTED 04 September 2023 PUBLISHED 21 September 2023 CITATION Adam L, Baretella O, Feller M, Blum MR, Papazoglou DD, Boland B, Aujesky D, Baggio S and Rodondi N (2023) Statin therapy in multimorbid older patients with polypharmacy- a cross-sectional analysis of the Swiss OPERAM trial population. F t C di M d 10 1236547 EDITED BY Lars Norgren, Örebro University, Sweden REVIEWED BY Sree Kondapally, St George’s University Hospitals NHS Foundation Trust, United Kingdom Valeria Conti, University of Salerno, Italy *CORRESPONDENCE Nicolas Rodondi nicolas.rodondi@insel.ch RECEIVED 07 June 2023 ACCEPTED 04 September 2023 PUBLISHED 21 September 2023 CITATION Adam L, Baretella O, Feller M, Blum MR, Papazoglou DD, Boland B, Aujesky D, Baggio and Rodondi N (2023) Statin therapy in multimorbid older patients with polypharmac a cross-sectional analysis of the Swiss OPERA trial population. F C di M d 10 1236547 EDITED BY Lars Norgren, Örebro University, Sweden REVIEWED BY Sree Kondapally, St George’s University Hospitals NHS Foundation Trust, United Kingdom Valeria Conti, University of Salerno, Italy 1Institute of Primary Health Care (BIHAM), University of Bern, Bern, Switzerland, 2Department of General Internal Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland, 3Division of Angiology, Gefässzentrum, Kantonsspital Baden, Baden, Switzerland, 4Geriatric Medicine, Cliniques Universitaires Saint-Luc, Brussels, Belgium, 5Health Science Research Institute, UCLouvain, Louvain, Belgium, 6Population Health Laboratory (#PopHealthLab), University of Fribourg, Fribourg, Switzerland Adam L, Baretella O, Feller M, Blum MR, Papazoglou DD, Boland B, Aujesky D, Baggio S and Rodondi N (2023) Statin therapy in multimorbid older patients with polypharmacy- a cross-sectional analysis of the Swiss OPERAM trial population. Background: Statin therapy in multimorbid older individuals with polypharmacy is controversial, particularly in primary prevention of cardiovascular disease. Thereby, physicians must weigh potential benefits against potential side effects, drug-drug interactions, and limited life expectancy. Aim: To assess the prevalence and determinants of potentially inappropriate statin therapy in multimorbid older patients. Front. Cardiovasc. Med. 10:1236547. Front. Cardiovasc. Med. 10:1236547. doi: 10.3389/fcvm.2023.1236547 Front. Cardiovasc. Med. 10:1236547. doi: 10.3389/fcvm.2023.1236547 Methods: We conducted a cross-sectional analysis of patients aged ≥70 years with multimorbidity and polypharmacy in the Swiss study center of OPERAM, a cluster- randomized trial on pharmacotherapy optimization to reduce drug-related hospital admissions. TYPE Original Research PUBLISHED 21 September 2023 DOI 10.3389/fcvm.2023.1236547 Frontiers in Cardiovascular Medicine KEYWORDS polypharmacy, multimorbidity, cardiovascular prevention, statin, -guideline adherence polypharmacy, multimorbidity, cardiovascular prevention, statin, -guideline adherence Statin therapy in multimorbid older patients with polypharmacy- a cross-sectional analysis of the Swiss OPERAM trial population We assessed potential underuse (no statin but formal indication) and potential overuse (statin but no formal indication, including predicted >60% one-year mortality based on the Walter Score) based on current guidelines for patients in secondary and primary cardiovascular prevention. We assessed the association of potential statin overuse and underuse with six patient characteristics (age, gender, number of diagnoses, number of medications, mental impairment, being housebound) in LASSO-selection analyses. Results: Of 715 multimorbid older adults (79.7 ± 6.5 years, 39.9% women), 337 (47%) were on statin. Statin therapy was appropriate in 474 (66.3%), underused in 130 (18.2%), and overused in 111 (15.5%) patients. In participants in secondary cardiovascular prevention (n = 437), being female (odds ratio [OR] 2.65, 95% confidence interval [CI] 1.67–4.22) was significantly associated with potential underuse while being housebound (OR 3.53, 95%CI 1.32–9.46) and taking ≥10 medications (OR 1.95,95%CI 1.05–3.67) were associated with potential overuse. In participants in primary cardiovascular prevention (n = 278), 28.1% were potentially under- (9%) or overusing (19%) a statin, with no identified risk factor. Conclusion: A third of hospitalized multimorbid older patients with polypharmacy potentially (either) overused or underused statin therapy. Among patients in secondary cardiovascular prevention, women were at risk for potential statin underuse. Housebound patients and those taking ≥10 medications were at risk for potential overuse of a statin. Physicians should carefully evaluate the indication for statin prescription in multimorbid older patients with polypharmacy. © 2023 Adam, Baretella, Feller, Blum, Papazoglou, Boland, Aujesky, Baggio and Rodondi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. polypharmacy, multimorbidity, cardiovascular prevention, statin, -guideline adherence Frontiers in Cardiovascular Medicine 01 frontiersin.org Adam et al. 10.3389/fcvm.2023.1236547 Avoidable hospital admissions in Multimorbid older people) to assess the prevalence and determinants of potentially inappropriate statin therapy in multimorbid older hospitalized patients. Avoidable hospital admissions in Multimorbid older people) to assess the prevalence and determinants of potentially inappropriate statin therapy in multimorbid older hospitalized patients. Introduction As people age, they are increasingly likely to suffer from more than one disease (multimorbidity): 60% of adults >65 suffer from more than three chronic diseases (1). These multimorbid patients may take different drugs to treat each disease (polypharmacy) (2), some of which may be inappropriate (3). Multimorbid patients are also at risk of underusing drugs (4). Both under- and overuse (inappropriate prescribing) may lead to avoidable hospital admissions and reduce the patient’s quality of life (5–7). Therefore, polypharmacy among the multimorbid older patients must be managed carefully to meet the needs of the aging population. Multimorbidity, older age, and polypharmacy are associated with cardiovascular risk factors and disease (8): more than 50% of multimorbid patients have cardiovascular disease (CVD) (9) and are often prescribed statins to reduce cardiovascular events (CVE) and mortality in primary and secondary prevention (10, 11). Methods We included participants from the Swiss study center (Bern University Hospital) of the cluster-randomized controlled OPERAM trial with detailed information on statin use, related factors and lipid values. A detailed protocol of OPERAM and its main results were published elsewhere (3, 23). We included only Swiss participants as the adjudication algorithm was based on local guidelines. Since the OPERAM trial studied a systematic drug review vs. usual care, we chose a cross-sectional study design at hospital admission, prior to the drug review, in order to receive the most accurate real life reflection. Statins are effective for secondary prevention of CVD even in old patients, with data until 82 years (12), but guidelines still suggest physicians consider individual factors that could influence their decision to start, change, or end statin therapy in older patients (13, 14). A small randomized controlled trial even showed that stopping statins in patients with life-limiting disease was safe, had no significant effect on mortality, and slightly increased quality of life (15, 16). Study population The OPERAM trial included multimorbid (more than three diagnosed chronic diseases) patients ≥70 years old with polypharmacy (five or more chronic medications). Patients were excluded from this analysis if they were missing information essential for assessing appropriateness of the statin therapy (e.g., missing lipid values for primary prevention). For primary prevention of atherosclerotic CVD, the current European Society of Cardiology and American Heart Association (AHA) guidelines recommend statins to match individual cardiovascular risk, setting the minimum bar at ≥5 to <10% 10- year risk of fatal and non-fatal atherosclerotic CVD (ASCVD) (17–19). Cardiovascular risk can be calculated with tools like the PROCAM-SCORE or SCORE2 (20, 21), which include age, gender, and known modifiable cardiovascular risk factors. Among older adults, the evidence of benefits of statins for primary prevention is less clear. The recent ESC guidelines for elderly recommend risk-factor treatment in older patients (≥70 years) with very high-risk for CVD (≥15% 10-year risk of CVD according to SCORE-OP2,) and apparently healthy older high- risk patients (7.5%–15% 10-year CVD risk, Class IIa recommendation) but there is insufficient evidence for low- density lipoprotein cholesterol (LDL-C) targets (22). The AHA guidelines neither suggest nor discourage statin prescription as primary prevention for this group of patients and they encourage physicians to individualize their recommendations, taking into account life expectancy, patient preferences, co-morbidities, and other factors (evidence level E) (13, 18, 19). Outcomes: statin therapy appropriateness Patients were classed according to ICD-10 coded diagnoses at baseline (Table 1) into patients with and without ASCVD. We classed patients with an ICD-10 code for ASCVD into secondary prevention and patients without ASCVD into primary prevention. Clinical ASCVD were defined as acute coronary syndromes, history of myocardial infarction, stable or unstable angina, coronary or other arterial revascularization, stroke, TIA, or peripheral arterial disease presumed to be of atherosclerotic origin, which occurred before study inclusion (24), and visceral atherosclerotic manifestations (Supplementary Table S2). Clinical ASCVD were defined as acute coronary syndromes, history of myocardial infarction, stable or unstable angina, coronary or other arterial revascularization, stroke, TIA, or peripheral arterial disease presumed to be of atherosclerotic origin, which occurred before study inclusion (24), and visceral atherosclerotic manifestations (Supplementary Table S2). ( pp y ) Patients who took a statin in accordance to current guidelines were classed as receiving appropriate statin therapy. Patients who took a statin without formal indication (overuse) or who did not receive statin therapy when statins were formally indicated (underuse) were classed as receiving “inappropriate statin therapy”. To assess appropriateness for patients in primary prevention, we calculated the PROCAM-Score, adapted for Switzerland (25), as it is the most used risk score in Switzerland (26). We collected lipid profiles either during index hospitalization (hospitalization at the time of inclusion in the OPERAM trial) or from the patient’s general practitioner (GP) whenever possible, preferably collected before lipid-lowering therapy initiation. If those values were unavailable, we used the last available lipid profile, either from their GP or from the OPERAM baseline visit. For patients with available lipid-values that were taken during statin therapy for Patients who took a statin in accordance to current guidelines were classed as receiving appropriate statin therapy. Patients who took a statin without formal indication (overuse) or who did not receive statin therapy when statins were formally indicated (underuse) were classed as receiving “inappropriate statin therapy”. To assess appropriateness for patients in primary prevention, we calculated the PROCAM-Score, adapted for Switzerland (25), as it is the most used risk score in Switzerland (26). We collected lipid profiles either during index hospitalization (hospitalization at the time of inclusion in the OPERAM trial) or from the patient’s general practitioner (GP) whenever possible, preferably collected before lipid-lowering therapy initiation. Frontiers in Cardiovascular Medicine Outcomes: statin therapy appropriateness If those values were unavailable, we used the last available lipid profile, either from their GP or from the OPERAM baseline visit. For patients with available lipid-values that were taken during statin therapy for Based on current evidence, physicians should carefully consider whether to prescribe drug treatment in multimorbid older patients with polypharmacy since data have shown that such patients are at risk for inappropriate prescription (underuse and overuse) (3). To date, there is little data on whether statins are appropriately prescribed to multimorbid older patients with polypharmacy, and risk factors associated with statin under- and over prescription. To overcome this research gap, we conducted a cross-sectional analysis of the OPERAM trial (OPtimising thERapy to prevent Frontiers in Cardiovascular Medicine frontiersin.org 02 Adam et al. 10.3389/fcvm.2023.1236547 TABLE 1 Baseline characteristics. TABLE 1 Baseline characteristics. All patients (n = 715) Primary prevention (n = 278)* Secondary prevention (n = 437)** Age [years] [means and sd] 79.7 ± 6.5 79.4 ± 6.6 79.9 ± 6.5 Sex [n and %] Men 429 (60.0) 148 (53.2) 281 (64.3) Women 286 (40.0) 130 (46.8) 156 (35.7) Smoking [n and %] 64 (9.0) 24 (8.6) 40 (9.2) Hypertension [n and %] 552 (77.2) 211 (75.9) 341 (78.0) Family history of myocardial infarction [n and %] 13 (8.2) 3 (5.4) 10 (9.8) Diabetes [n and %] 235 (32.9) 80 (28.8) 155 (35.5) No of medications [n and %] ≥10 399 (55.8) 139 (50.0) 260 (59.5) No. of diagnoses [n and %] 3–10 101 (14.1) 60 (21.6) 41 (9.4) ≥10 614 (85.9) 218 (78.4) 396 (90.6) Walter score >6 (scale 0–20) [n and %] 194 (27.1) 89 (32.0) 105 (24.0) Housebound [n and %] 36 (5.0) 15 (5.4) 21 (4.81) Dementia [n and %] 76 (10.6) 31 (11.5) 45 (10.3) Statin users [n and %] 377 (52.7) 82 (29.5) 295 (67.5) Sd: standard deviations. *No diagnosis of cardiovascular disease (CVD) prior to study inclusion. **With diagnosis of CVD prior to study inclusion. being housebound [defined as inability to leave the house unassisted e.g., for (primary) care visits], ≥5–9 chronic medications vs. ≥10 chronic medicationsco-morbidities (into ≥10 and <10 chronic diagnoses), and whether they suffered from dementia/cognitive impairment according to ICD-10 code. All these factors potentially influence the likelihood medication will be prescribed inappropriately (31). Predictors We considered all patients with a diagnosis of cardiovascular ischemic disease to be patients who needed secondary prevention for cardiovascular events. Thus, all patients with cardiovascular disease were considered to be underusing a statin if they were not taking a statin. For all patients, we calculated the Walter Score to determine individual 1-year mortality risk (28); we considered a score >6 (>60% 1-year mortality) to be potentially life limiting. Since current evidence suggests that statin therapy offers no benefit when prescribed for primary prevention to patients with a life-limiting disease, we classed all patients whose Walter Score was >6 as potentially being overusing statins if they were using statins at baseline (Figure 1) (15, 29). Outcomes: statin therapy appropriateness primary prevention, we estimated the possible LDL-C value prior to statin initiation using the mean reduction values by the statin taken (27) in order to be able to better estimate the cardiovascular risk. Frontiers in Cardiovascular Medicine Statistical analyses We stratified patients according to their indication for statin use, i.e., primary and secondary cardiovascular prevention. We first calculated descriptive statistics for all variables (percentages and n for categorical variables; means and standard deviations for continuous variables). We also calculated descriptive statistics for participants we included and excluded. Comparisons between included and excluded participants were performed using χ2 tests for categorical variables and t-tests for continuous variables. Second, we assessed the bivariate associations between potential over- and underuse of a statin with risk factors (i.e., age sex, houseboundedness, co-morbidities and cognitive impairment) using logistic regression models, with potential underuse and overuse as two separate outcomes. We reported odd ratios (OR) with 95% confidence intervals (CI). We calculated individual risk for cardiovascular events within the next 10 years based on the patient’s AGLA Score (PROCAM Score adapted for Switzerland) (25). Because several guidelines make no clear recommendation for primary prevention in patients aged >75 years (18, 19, 22, 30), we calculated cardiovascular risk scores for those patients as if they were 75 years old. Additionally, the Walter Score was used to estimate individual life expectancy (above) and two medical doctors (LA, OB) independently reviewed the patients’ chart to determine if they were on appropriate statin therapy. If the two reviewers disagreed, they consulted a third reviewer (MF). Figure 1 shows the study flow chart for adjudication, which we developed based on current guidelines. Third, we selected the variables with the strongest association with potential statin underuse and overuse using least absolute shrinkage and selection operator (LASSO) regression analyses. We chose this method because of the small numbers of patients in some subgroups. We used multiple logistic regression models with LASSO selection, with underuse and overuse as two separate outcomes. We also reported ORs with 95% CIs. We used Stata Version 16.0 (StataCorp. 2019. Stata Statistical Software: Release 16. College Station, TX: StataCorp LLC.). The following predictors were included into our analysis: age (classed into three categories: 70–75, 76–85 and >85 years), sex, Frontiers in Cardiovascular Medicine 03 frontiersin.org Adam et al. 10.3389/fcvm.2023.1236547 FIGURE 1 Adjudication algorithm according to AGLA score (25). Legend: abbreviations: ASCVD, LDL-C. FIGURE 1 Adjudication algorithm according to AGLA score (25). Legend: abbreviations: ASCVD, LDL-C. Frontiers in Cardiovascular Medicine Results All patients (n = 715) Primary prevention (n = 278) Secondary prevention (n = 437) Appropriate 474 (66.3%) 200 (71.9%) 274 (62.7%) Potential underuse* 130 (18.2%) 25 (9.0%) 105 (24.0%) Potential overuse** 111 (15.5%) 53 (19.1%) 58 (13.3%) LDL > 4.9 mmol/L 33 (62.3%) Results Of the 437 patients in secondary prevention, 274 (62.7%) were using a statin appropriately, 105 (24%) patients were underusing a statin, while 58 (13.3%) patients were considered to be potentially overusing a statin as their predicted mortality risk was >60% based on their Walter Score (≥6 points) (Table 2). The Swiss OPERAM study center included 822 hospitalized multimorbid patients ≥70 years with polypharmacy (≥5 medications); 17 patients (2.1%) withdrew their consent; and 90 patients (10.9%) were excluded because their available information did not allow us to adjudicate the appropriateness of statin therapy. We thus included 715 patients in our analysis (see the study flow chart in the Supplementary Figure S1). Included patients had a mean age of 79.7 years [±6.5 years standard deviation (SD)]; 60% were male (Table 1). In the secondary prevention group (n = 437), 295 patients (67.5%) used a statin and 105 (24%) patients had a Walter score >6, 68 (23%) of those using a statin (Supplementary Table S3). In the primary prevention group (n = 278), 82 patients (29.5%) used statins and 89 (32%) patients had a Walter Score >6. In secondary prevention, statin underuse was significantly associated with being very old (>85 years; OR 2.40; 95% CI 1.26– 4.57) and female (OR 2.79; 95% CI1.78–4.38) in bivariate models (Table 3). We confirmed the association between underuse and being female with LASSO regression (OR 2.65; 95%CI 1.67–4.22). Potential overuse was associated with being housebound (OR 3.58; 95% CI 1.38–9.28) and taking ≥10 medications (1.94; 95% CI 1.05–3.57) in bivariate analyses, which was confirmed after LASSO regression (OR 3.53 (1.32–9.46) and 1.95 (1.05–3.67)) (Table 4). In secondary prevention, statin underuse was significantly associated with being very old (>85 years; OR 2.40; 95% CI 1.26– 4.57) and female (OR 2.79; 95% CI1.78–4.38) in bivariate models (Table 3). We confirmed the association between underuse and being female with LASSO regression (OR 2.65; 95%CI 1.67–4.22). Potential overuse was associated with being housebound (OR 3.58; 95% CI 1.38–9.28) and taking ≥10 medications (1.94; 95% CI 1.05–3.57) in bivariate analyses, which was confirmed after LASSO regression (OR 3.53 (1.32–9.46) and 1.95 (1.05–3.67)) (Table 4). Additional baseline characteristics of included patients are presented in Table 1 and comparisons of the baseline characteristics of patients we included and patients we excluded because we could not properly adjudicate them in Supplementary Table S1. TABLE 2 Appropriateness of statin prescribing. TABLE 2 Appropriateness of statin prescribing. ot properly adjudicate them in Supplementary Table S1. LASSO: least absolute shrinkage and selection operator. **No subjects in this subgroup, removed. frontiersin.org ot properly adjudicate them in Supplementary Table S1. not properly adjudicate them in Supplementary Table S1 In the 278 patients in primary prevention, we determined estimated risk for CVE at 10-years was low (<10%) in 95 patients, intermediate (10%–20%) in 53 patients, and high (>20%) in 40 patients (Supplementary Table S3). Patients with a Walter Score >6 (n = 89) were classified as potential Statin- overusers without further risk calculation. p *Potential underuse: lack of statin therapy despite formal indication (Figure 1). **Potential overuse: statin use without formal indication or if Walter Score >6 (predicted one year mortality >60%). Appropriateness of statin therapy in secondary cardiovascular prevention: Frontiers in Cardiovascular Medicine 04 frontiersin.org Adam et al. 10.3389/fcvm.2023.1236547 Potential underuse Potential underuse Bivariable analysesa LASSO selectionb Primary prevention Secondary prevention Primary prevention Secondary prevention p. underuse, n = 25 p. underuse, n = 105 p. underuse, n = 25 p. underuse, n = 105 Age (years) 70–75 1 (Reference) 1 (Reference) 1 (Reference) 1 (Reference) 76–84 0.86 (0.35–2.09) 1.58 (0.89–2.80) * 1.32 (0.74–2.40) >85 0.41 (0.11–1.56) 2.40 (1.26–4.57) * 1.86 (0.94–3.70) Women 1.80 (0.78–4.16) 2.79 (1.78–4.38) * 2.65 (1.67–4.22) Housebound ** 0.32 (0.07–1.40) ** 0.29 (0.06–1.31) ≥10 diagnoses 0.86 (0.32–2.26) 1.94 (0.79–4.76) * 1.81 (0.71–4.60) ≥10 medications 0.53 (0.22–1.25) 0.84 (0.54–1.30) * 0.72 (0.45–1.16) Dementia 0.31 (0.04–2.37) 1.49 (0.76–2.92) * 1.23 (0.60–2.50) LASSO: least absolute shrinkage and selection operator. TABLE 4 Associations between potential statin overuse and study variables. TABLE 4 Associations between potential statin overuse and study variables. TABLE 4 Associations between potential statin overuse and study variables. Potential overuse Potential overuse Bivariable analysesa LASSO selectionb Primary prevention Secondary prevention Primary prevention Secondary prevention p. overuse, n = 53 p. overuse, n = 58 p.overuse, n = 53 p.overuse, n = 58 Age (years) 70–75 1 (Reference) 1 (Reference) 1 (Reference) 1 (Reference) 76- 84 1.31 (0.67–2.57) 0.83 (0.43–1.59) * * >85 0.55 (0.21–1.43) 1.04 (0.48–2.23) * * Women 0.70 (0.38–1.28) 0.43 (0.22–0.83) * 0.38 (0.19–0.76) Housebound 1.07 (0.29–3.92) 3.58 (1.38–9.28) * 3.53 (1.32–9.46) ≥10 diagnoses 0.56 (0.28–1.10) ** * ** ≥10 medications 1.39 (0.76–2.54) 1.94 (1.05–3.57) * 1.95 (1.05–3.67) Dementia 1.02 (0.40–2.63) 0.61 (0.21–1.77) * * LASSO: least absolute shrinkage and selection operator. Bold values denote the significant results. aSimple logistic regressions. Odds ratios and 95% confidence intervals are reported. bMultivariable logistic regressions with LASSO selection. Odds ratios and 95% confidence intervals are reported. *Dropped after Lasso selection. **No subjects in this subgroup, removed. Limitations Housebound patients in secondary prevention were at risk for overuse (defined as having a Walter Score >6) of a statin (OR 3.53), a finding that aligns with a Japanese study of eldery, housebound patient amongst whom potentially inappropriate prescribing was highly prevalent (42). This might be due to the fact that preventive medical visits are associated with a high effort by these patients and his/her proxies (42). A further factor could be that stopping an established statin therapy is currently a matter of discussion and doctors might be especially hesitant to stop a statin in a patient with established ASCVD despite advanced chronic illness and a high 1-year mortality risk (Walter Score > 6) (16). However, Kutner et al. found that stopping statins in patients with limited life expectancy was safe and slightly improved quality of life (15). In primary prevention, we found no pre-defined risk factor associated with higher risk of inappropriate statin therapy (neither potential underuse nor potential overuse), perhaps because it was more difficult to assess cardiovascular risk and define the necessity for statin therapy in the primary prevention group. Though older people are at higher cardiovascular risk, few RCTs have studied the potential benefits of statin therapy for primary prevention in the elderly. A recent meta-analysis of 28 RCTs that analyzed the benefits of statin therapy in 186,854 individuals (but only 8% aged >70 years) found that statin therapy benefited to patients over 70, but provided little evidence on patients in primary prevention (43). An age- stratified analysis of the JUPITER-trial and HOPE III study showed that taking Rosuvastatin would benefit patients >70 years regarding a composite outcome (pooled estimate HR 0.74) of nonfatal MI, stroke or cardiovascular death (44) but included only few patients >80 years. On the other hand, deprescribing statins in older patients is common in primary prevention in the very older people because clinicians might weigh the potential of side effects in frail patients higher than the potential long-term benefit (45). Appropriateness of statin therapy in primary cardiovascular prevention Discussion Among 715 multimorbid older (≥70 years) hospitalized patients, potentially inappropriate statin therapy was common (33.7%) due to potential underuse with (15.5%) and potential overuse (18.2%). Female gender was significantly associated with potential underuse in secondary prevention (OR 2.65). Being housebound (OR 3.53) and taking ≥10 medications (OR 1.95) were associated with potential overuse in secondary prevention. No specific risk factors were identified for potential over- or underuse in primary prevention. Of the 278 patients in primary prevention, 200 (71.9%) were on appropriate statin therapy when they were included in the OPERAM trial, based on our prespecified criteria (Figure 1); 25 (9%) had intermediate to high cardiovascular risk but did not take a statin so we considered them as potentially underusing a statin, while 53 patients (19.1%) were potentially overusing statin (Table 2); 23 of these potential overusers (43.4%) had a Walter Score >6. No factor among patients in primary prevention predicted a significantly higher risk for potential under—or overuse (Tables 3, 4) in bivariate analyses. We confirmed this finding with LASSO regressions. (Tables 3, 4). Though the benefits of statins for primary prevention in the older patients remain controversial, statin therapy in secondary prevention in older patients is supported by evidence (22). Frontiers in Cardiovascular Medicine 05 frontiersin.org Adam et al. Adam et al. 10.3389/fcvm.2023.1236547 10.3389/fcvm.2023.1236547 Despite the evidence, this cross-sectional study found that 24% of patients in secondary prevention were potentially underusing statins. In secondary prevention, women, particularly, were at risk of underuse (OR 2.65), a finding that aligns with previous studies (32–34). (16). In general, evidence towards statin therapy in older people in primary prevention is limited, as shown by the discrepancies in different guidelines concerning statin therapy in the elderly (46). Especially for multimorbid older patients guidelines or recommendations concerning (deprescribing) statins are lacking (47). Statin use is clearly established for prevention of further cardiovascular events in secondary prevention, in both men and women (35). On average, women live longer than men and are therefore more likely to suffer from CVE (36). CVD is the main cause of death for women in developed countries (37, 38), but health care systems may not adequately consider women’s cardiovascular risk (38). Though men and women have the same main cardiovascular risk factors, women may present differently in clinical exams, have different symptoms, and tests may not work as well for women as men (39, 40). Limitations In an international survey using case vignettes, GPs recommended to stop statins for primary prevention especially in frail patients, those with evident side effects and patients with limited life expectancy We were limited in our ability to estimate cardiovascular risk in primary prevention, so we used the PROCAM Score adapted for Switzerland, approved for maximally 75-year-old, to determine cardiovascular risk at 10 years and had two medical doctors independently judge the patient’s clinical situation on a case-by- case basis (including knowledge of patient’s preferences; this data was collected during the OPERAM trial) as current guidelines suggest (18). Our study was also limited because it was conducted at only one center. Though we tried to assess the statin indication for each individual patient, we did not know why treating physicians decided to prescribe or withhold a statin. Appropriateness of statin therapy in primary cardiovascular prevention Discussion Our findings align well with a population-based Italian study of older patients with polypharmacy, in which women were more likely to discontinue statin therapy (41). Our finding of ASCVD prevalence (61%) aligns with previous studies of this older multimorbid population (8). We found statin therapy was prescribed to 52.5% in the entire patient cohort, (29.5% of patients in primary prevention and 67.5% of patients in secondary prevention). A 2011–2015 UK cohort study of statin prescription in old patients (>80 years) in primary prevention yielded similar results (30%) (45). Other studies from the UK and the US found that between 63% and 80% of the older population are taking statins (45, 32). Strengths This is a cross-sectional analysis from the understudied, but especially in Western countries growing population of multimorbid older patients with polypharmacy. Assessing risk- factors for statin under- or overuse in this specific population of multimorbid eldery has not yet been done to our knowledge (48). We accounted for patient’s specific risk factors as well as patients’ individual life expectancy in a standardized way. Statins are among the most prescribed drugs for the prevention of first or recurrent cardiovascular events (49), which are highly prevalent in multimorbid older patients. This study provides evidence for risk factors that are associated with under- or overuse of a statin, alerting the clinician to frequently adapt and reassess statin therapy according to her/his patient’s current situation and need. frontiersin.org Conclusion A third of multimorbid older patients with polypharmacy either potentially overused or underused statins. Among participants in secondary cardiovascular prevention, women were at highest risk for potential underuse while housebound patients Frontiers in Cardiovascular Medicine 06 frontiersin.org Adam et al. 10.3389/fcvm.2023.1236547 Swiss government. This project was also partially funded by the Swiss National Scientific Foundation (SNSF 320030_188549) and by a grant from the Swiss National Science Foundation to study the usefulness of statins among older adults in primary prevention (IICT 33IC30-193052 to Nicolas Rodondi). The funder of the study had no role in study design, data collection, data analysis, data interpretation or writing of the report. LA work was supported through a “Young Talents in Clinical Research” Grant from the Gottfried and Julia Bangerter-Rhyner Foundation (YTCR_22/17). OB obtained a Protected Research Time (PRT) Grant from the University of Bern. were at risk for potential overuse of a statin. Physicians should carefully evaluate their need for statin prescriptions in this understudied population and adapt prescriptions as needed. Supplementary material The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fcvm.2023. 1236547/full#supplementary-material Data availability statement The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation. 4. Kuijpers MA, van Marum RJ, Egberts AC, Jansen PA, Group OS. Relationship between polypharmacy and underprescribing. Br J Clin Pharmacol. (2008) 65 (1):130–3. doi: 10.1111/j.1365-2125.2007.02961.x Acknowledgment The studies involving humans were approved by Kantonale Ethikkomission Bern (KEK Nr. 2016-01200). The studies were conducted in accordance with the local legislation and institutional requirements. The participants provided their informed consent to participate in the OPERAM-trial. We thank Kali Tal for her editorial assistance. Author contributions The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. LA, MF, MB, BB, DA; NR contributed to conception and design of the study. LA, OB, DP organized the database. LA, MF, MB, DP, SB performed the statistical analysis. LA wrote the first draft of the manuscript. All authors contributed to the article and approved the submitted version. 8. Aubert CE, Streit S, Da Costa BR, Collet TH, Cornuz J, Gaspoz JM, et al. Polypharmacy and specific comorbidities in university primary care settings. Eur J Intern Med. (2016) 35:35–42. doi: 10.1016/j.ejim.2016.05.022 Funding This work is part of the project “OPERAM: OPtimising thERapy to prevent Avoidable hospital admissions in the Multimorbid elderly” supported by the European Union’s Horizon 2020 research and innovation program under the grant agreement No 634238, and by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number 15.0137. The opinions expressed and arguments employed herein are those of the authors and do not necessarily reflect the official views of the European Commission and the 7. Klarin I, Wimo A, Fastbom J. The association of inappropriate drug use with hospitalisation and mortality: a population-based study of the very old. Drugs Aging. (2005) 22(1):69–82. doi: 10.2165/00002512-200522010-00005 6. Jensen LD, Andersen O, Hallin M, Petersen J. Potentially inappropriate medication related to weakness in older acute medical patients. Int J Clin Pharm. (2014) 36(3):570–80. doi: 10.1007/s11096-014-9940-y Publisher’s note All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher. 5. Jin H, Tang C, Wei Q, Chen L, Sun Q, Ma G, et al. Age-related differences in factors associated with the underuse of recommended medications in acute coronary syndrome patients at least one year after hospital discharge. BMC Cardiovasc Disord. (2014) 14:127. doi: 10.1186/1471- 2261-14-127 2. Dalleur O, Boland B, De Groot A, Vaes B, Boeckxstaens P, Azermai M, et al. Detection of potentially inappropriate prescribing in the very old: cross-sectional analysis of the data from the BELFRAIL observational cohort study. BMC Geriatr. (2015) 15:156. doi: 10.1186/s12877-015-0149-2 1. Barnett K, Mercer SW, Norbury M, Watt G, Wyke S, Guthrie B. Epidemiology of multimorbidity and implications for health care, research, and medical education: a cross- sectional study. Lancet. (2012) 380(9836):37–43. doi: 10.1016/S0140-6736(12)60240-2 References 5. Jin H, Tang C, Wei Q, Chen L, Sun Q, Ma G, et al. Age-related differences in factors associated with the underuse of recommended medications in acute coronary syndrome patients at least one year after hospital discharge. BMC Cardiovasc Disord. (2014) 14:127. doi: 10.1186/1471- 2261-14-127 1. Barnett K, Mercer SW, Norbury M, Watt G, Wyke S, Guthrie B. Epidemiology of multimorbidity and implications for health care, research, and medical education: a cross- sectional study. Lancet. (2012) 380(9836):37–43. doi: 10.1016/S0140-6736(12)60240-2 2. Dalleur O, Boland B, De Groot A, Vaes B, Boeckxstaens P, Azermai M, et al. Detection of potentially inappropriate prescribing in the very old: cross-sectional analysis of the data from the BELFRAIL observational cohort study. BMC Geriatr. (2015) 15:156. doi: 10.1186/s12877-015-0149-2 3. Blum MR, Sallevelt B, Spinewine A, O’Mahony D, Moutzouri E, Feller M, et al. Optimizing therapy to prevent avoidable hospital admissions in multimorbid older adults (OPERAM): cluster randomised controlled trial. Br Med J. (2021) 374:n1585. doi: 10.1136/bmj.n1585 4. Kuijpers MA, van Marum RJ, Egberts AC, Jansen PA, Group OS. Relationship between polypharmacy and underprescribing. Br J Clin Pharmacol. (2008) 65 (1):130–3. doi: 10.1111/j.1365-2125.2007.02961.x Frontiers in Cardiovascular Medicine 07 frontiersin.org Adam et al. 10.3389/fcvm.2023.1236547 10.3389/fcvm.2023.1236547 on clinical practice guidelines. Circulation. (2019) 139(25):e1046–e81. doi: 10.1161/ CIR.0000000000000624 9. Violan C, Bejarano-Rivera N, Foguet-Boreu Q, Roso Llorach A, Pons-Vigues M, Martin Mateo M, et al. The burden of cardiovascular morbidity in a European mediterranean population with multimorbidity: a cross-sectional study. BMC Fam Pract. (2016) 17(1):150. doi: 10.1186/s12875-016-0546-4 30. US Preventive Services Task Force; Mangione CM, Barry MJ, Nicholson WK, Cabana M, Chelmow D, et al. Statin use for the primary prevention of cardiovascular disease in adults: US preventive services task force recommendation statement. JAMA. (2022) 328(8):746–53. doi: 10.1001/jama.2022.13044 10. Ebrahim S, Taylor FC, Brindle P. Statins for the primary prevention of cardiovascular disease. Br Med J. (2014) 348:g280. doi: 10.1136/bmj.g280 11. Koskinas KC, Siontis GCM, Piccolo R, Mavridis D, Raber L, Mach F, et al. Effect of statins and non-statin LDL-lowering medications on cardiovascular outcomes in secondary prevention: a meta-analysis of randomized trials. Eur Heart J. (2018) 39 (14):1172–80. doi: 10.1093/eurheartj/ehx566 31. Bare M, Lleal M, Ortonobes S, Gorgas MQ, Sevilla-Sanchez D, Carballo N, et al. Factors associated to potentially inappropriate prescribing in older patients according to STOPP/START criteria: MoPIM multicentre cohort study. BMC Geriatr. (2022) 22 (1):44. doi: 10.1186/s12877-021-02715-8 12. References Rationale and design of optimising therapy to prevent avoidable hospital admissions in multimorbid older people (OPERAM): a cluster randomised controlled trial. BMJ open. (2019) 9(6):e026769. doi: 10.1136/bmjopen-2018-026769 43. Cholesterol Treatment Trialists C. Efficacy and safety of statin therapy in older people: a meta-analysis of individual participant data from 28 randomised controlled trials. Lancet. (2019) 393(10170):407–15. doi: 10.1016/S0140-6736(18)31942-1 44. Ridker PM, Lonn E, Paynter NP, Glynn R, Yusuf S. Primary prevention with statin therapy in the elderly: new meta-analyses from the contemporary JUPITER and HOPE-3 randomized trials. Circulation. (2017) 135(20):1979–81. doi: 10.1161/ CIRCULATIONAHA.117.028271 24. Powers WJ, Rabinstein AA, Ackerson T, Adeoye OM, Bambakidis NC, Becker K, et al. 2018 guidelines for the early management of patients with acute ischemic stroke: a guideline for healthcare professionals from the American heart association/ American stroke association. Stroke. (2018) 49(3):e46–e110. doi: 10.1161/STR. 0000000000000158 45. Gulliford M, Ravindrarajah R, Hamada S, Jackson S, Charlton J. Inception and deprescribing of statins in people aged over 80 years: cohort study. Age Ageing. (2017) 46(6):1001–5. doi: 10.1093/ageing/afx100 25. AGLA Risikorechner. https://www.agla.ch/de/rechner-und-tools/agla- risikorechner 46. Hawley CE, Roefaro J, Forman DE, Orkaby AR. Statins for primary prevention in those aged 70 years and older: a critical review of recent cholesterol guidelines. Drugs Aging. (2019) 36(8):687–99. doi: 10.1007/s40266-019-00673-w 26. Dallongeville J, Banegas JR, Tubach F, Guallar E, Borghi C, De Backer G, et al. Survey of physicians’ practices in the control of cardiovascular risk factors: the EURIKA study. Eur J Prev Cardiol. (2012) 19(3):541–50. doi: 10.1177/ 1741826711407705 47. van der Ploeg MA, Floriani C, Achterberg WP, Bogaerts JMK, Gussekloo J, Mooijaart SP, et al. Recommendations for (discontinuation of) statin treatment in older adults: review of guidelines. J Am Geriatr Soc. (2020) 68(2):417–25. doi: 10. 1111/jgs.16219 27. Law MR, Wald NJ, Rudnicka AR. Quantifying effect of statins on low density lipoprotein cholesterol, ischaemic heart disease, and stroke: systematic review and meta-analysis. Br Med J. (2003) 326(7404):1423. doi: 10.1136/bmj.326.7404.1423 48. Aeschbacher-Germann M, Kaiser N, Speierer A, Blum MR, Bauer DC, Del Giovane C, et al. Lipid-lowering trials are not representative of patients managed in clinical practice: a systematic review and meta-analysis of exclusion criteria. J Am Heart Assoc. (2023) 12(1):e026551. doi: 10.1161/JAHA.122.026551 28. Walter LC, Brand RJ, Counsell SR, Palmer RM, Landefeld CS, Fortinsky RH, et al. Development and validation of a prognostic index for 1-year mortality in older adults after hospitalization. JAMA. (2001) 285(23):2987–94. doi: 10.1001/jama. 285.23.2987 29. References Recommendations for management of dyslipidemia in 2016 in Switzerland. Rev Med Suisse. (2016) 12(508):430–4. 18. Mach F, Baigent C, Catapano AL, Koskinas KC, Casula M, Badimon L, et al. 2019 ESC/EAS guidelines for the management of dyslipidaemias: lipid modification to reduce cardiovascular risk. Eur Heart J. (2020) 41(1):111–88. doi: 10.1093/ eurheartj/ehz455 38. Woodward M. Cardiovascular disease and the female disadvantage. Int J Environ Res Public Health. (2019) 16(7):1165. doi: 10.3390/ijerph16071165 39. Reynolds HR, Srichai MB, Iqbal SN, Slater JN, Mancini GB, Feit F, et al. Mechanisms of myocardial infarction in women without angiographically obstructive coronary artery disease. Circulation. (2011) 124(13):1414–25. doi: 10. 1161/CIRCULATIONAHA.111.026542 19. Stone NJ, Robinson JG, Lichtenstein AH, Bairey Merz CN, Blum CB, Eckel RH, et al. 2013 ACC/AHA guideline on the treatment of blood cholesterol to reduce atherosclerotic cardiovascular risk in adults: a report of the American college of cardiology/American heart association task force on practice guidelines. Circulation. (2014) 129(25 Suppl 2):S1–45. doi: 10.1093/eurheartj/ehz455 40. Hochman JS, Tamis JE, Thompson TD, Weaver WD, White HD, Van de Werf F, et al. Sex, clinical presentation, and outcome in patients with acute coronary syndromes. Global use of strategies to open occluded coronary arteries in acute coronary syndromes IIb investigators. N Engl J Med. (1999) 341(4):226–32. doi: 10. 1056/NEJM199907223410402 20. Assmann G, Cullen P, Schulte H. Simple scoring scheme for calculating the risk of acute coronary events based on the 10-year follow-up of the prospective cardiovascular munster (PROCAM) study. Circulation. (2002) 105(3):310–5. doi: 10. 1161/hc0302.102575 41. Rea F, BiffiA, Ronco R, Franchi M, Cammarota S, Citarella A, et al. Cardiovascular outcomes and mortality associated with discontinuing statins in older patients receiving polypharmacy. JAMA Netw Open. (2021) 4(6):e2113186. doi: 10.1001/jamanetworkopen.2021.13186 21. group Sw, collaboration ESCCr. SCORE2 risk prediction algorithms: new models to estimate 10-year risk of cardiovascular disease in Europe. Eur Heart J. (2021) 42 (25):2439–54. doi: 10.1093/eurheartj/ehab309 22. Visseren FLJ, Mach F, Smulders YM, Carballo D, Koskinas KC, Back M, et al. 2021 ESC guidelines on cardiovascular disease prevention in clinical practice. Eur Heart J. (2021) 42(34):3227–337. doi: 10.1093/eurheartj/ehab484 42. Onda M, Imai H, Takada Y, Fujii S, Shono T, Nanaumi Y. Identification and prevalence of adverse drug events caused by potentially inappropriate medication in homebound elderly patients: a retrospective study using a nationwide survey in Japan. BMJ Open. (2015) 5(8):e007581. doi: 10.1136/bmjopen-2015-007581 23. Adam L, Moutzouri E, Baumgartner C, Loewe AL, Feller M, M’Rabet-Bensalah K, et al. References Shepherd J, Blauw GJ, Murphy MB, Bollen EL, Buckley BM, Cobbe SM, et al. Pravastatin in elderly individuals at risk of vascular disease (PROSPER): a randomised controlled trial. Lancet. (2002) 360(9346):1623–30. doi: 10.1016/S0140- 6736(02)11600-X 32. Ngo-Metzger Q, Zuvekas S, Shafer P, Tracer H, Borsky AE, Bierman AS. Statin use in the U.S. for secondary prevention of cardiovascular disease remains suboptimal. J Am Board Fam Med. (2019) 32(6):807–17. doi: 10.3122/jabfm.2019.06.180313 33. Sarraju A, Spencer-Bonilla G, Chung S, Gomez S, Li J, Heidenreich P, et al. Statin use in older adults for primary cardiovascular disease prevention across a spectrum of cardiovascular risk. J Gen Intern Med. (2021) 37(11):2642–9. doi: 10. 1007/s11606-021-07107-7 13. Stone NJ, Intwala S, Katz D. Statins in very elderly adults (debate). J Am Geriatr Soc. (2014) 62(5):943–5. doi: 10.1111/jgs.12788_1 14. Rabar S, Harker M, O’Flynn N, Wierzbicki AS, Guideline Development G. Lipid modification and cardiovascular risk assessment for the primary and secondary prevention of cardiovascular disease: summary of updated NICE guidance. Br Med J. (2014) 349:g4356. doi: 10.1136/bmj.g4356 34. Rachamin Y, Grischott T, Rosemann T, Meyer MR. Inferior control of low- density lipoprotein cholesterol in women is the primary sex difference in modifiable cardiovascular risk: a large-scale, cross-sectional study in primary care. Atherosclerosis. (2021) 324:141–7. doi: 10.1016/j.atherosclerosis.2021.02.024 15. Kutner JS, Blatchford PJ, Taylor DH Jr., Ritchie CS, Bull JH, Fairclough DL, et al. Safety and benefit of discontinuing statin therapy in the setting of advanced, life- limiting illness: a randomized clinical trial. JAMA Intern Med. (2015) 175 (5):691–700. doi: 10.1001/jamainternmed.2015.0289 35. Saeed A, Kampangkaew J, Nambi V. Prevention of cardiovascular disease in women. Methodist Debakey Cardiovasc J. (2017) 13(4):185–92. doi: 10.14797/mdcj- 13-4-185 36. Leening MJ, Ferket BS, Steyerberg EW, Kavousi M, Deckers JW, Nieboer D, et al. Sex differences in lifetime risk and first manifestation of cardiovascular disease: prospective population based cohort study. Br Med J. (2014) 349:g5992. doi: 10. 1136/bmj.g5992 16. van der Ploeg MA, Streit S, Achterberg WP, Beers E, Bohnen AM, Burman RA, et al. Patient characteristics and general practitioners’ advice to stop statins in oldest- old patients: a survey study across 30 countries. J Gen Intern Med. (2019) 34 (9):1751–7. doi: 10.1007/s11606-018-4795-x 37. Gholizadeh L, Davidson P. More similarities than differences: an international comparison of CVD mortality and risk factors in women. Health Care Women Int. (2008) 29(1):3–22. doi: 10.1080/07399330701723756 17. Aubert CE, Gencer B, Rodondi N. References Grundy SM, Stone NJ, Bailey AL, Beam C, Birtcher KK, Blumenthal RS, et al. 2018 AHA/ACC/AACVPR/AAPA/ABC/ACPM/ADA/AGS/APhA/ASPC/NLA/ PCNA guideline on the management of blood cholesterol: executive summary: a report of the American college of cardiology/American heart association task force 49. Karmali KN, Lloyd-Jones DM, Berendsen MA, Goff DC Jr., Sanghavi DM, Brown NC, et al. Drugs for primary prevention of atherosclerotic cardiovascular disease: an overview of systematic reviews. JAMA Cardiol. (2016) 1(3):341–9. doi: 10.1001/jamacardio.2016.0218 Frontiers in Cardiovascular Medicine frontiersin.org 08
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From Building Information Modelling to Digital Twins: Digital Representation for a Circular Economy
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A. Koutamanis (✉) Delft University of Technology, Delft, the Netherlands e-mail: a.koutamanis@tudelft.nl © The Author(s) 2024 C. De Wolf et al. (eds.), A Circular Built Environment in the Digital Age, Circular Economy and Sustainability, https://doi.org/10.1007/978-3-031-39675-5_1 Chapter 1 From Building Information Modelling to Digital Twins: Digital Representation for a Circular Economy Alexander Koutamanis Abstract Building information modelling (BIM) has ushered in the era of symbolic building representation: building elements and spaces are described not by graphical elements but by discrete symbols, each with properties and relations that explicitly integrate all information. Digital twinning promises even more: a digital replica in complete sync with the building and its behaviour. Such technologies have obvious appeal for circularity because they accommodate the rich information it requires and link circularity goals to other activities in AECO (architecture, engineering, con- struction and operation of buildings). Present implementations of BIM may fall short of the promise, and digital twinning may be hard to achieve, but they remain crucial not only for circularity but for all AECO disciplines. To realise the potential of such representations, information should be treated not as a product of integration but as the integrator of all activities. Similarly, digitalisation should be at the core of business models and deployment plans, not an additional or even optional layer at a high cost. This calls for a coherent approach that includes the full capture of building information, supports the detailed exploration of circular operations, uses the results to constrain decisions and actions and does so throughout the life cycle. Keywords Information · Digitalisation · Representation · Building information modelling (BIM) · Digital twinning 1.1 Building Information Modelling and Digital Twinning Rhetoric has three modes of persuasion: pathos, ethos and logos. Circularity is derived from pathos: appeals to emotions and ideals, expressing beliefs about the environment and materiality. It is reinforced by ethos: arguments from authorities and other credible sources, such as scientists and industry leaders. When it comes to 3 3 4 A. Koutamanis A. Koutamanis A. Koutamanis 4 implementing circularity, however, it is the logos that matters most: the reasoning that underlies business models, material flow calculations, feasibility assessments, implementation requirements, deployment plans, etc. Information is the basic resource for making such analyses and projections reliable and transparent: valid, meaningful data that describe past and future states of the world, providing input to and accommodating output from decision processes. This chapter focuses on the critical, fundamental role of information in the context of circularity. It explains the two most relevant general-purpose technolo- gies, building information modelling (BIM) and digital twinning, and links them to passports and logbooks proposed specifically for circularity. It then moves on to current and proposed uses of the technologies in AECO (architecture, engineering, construction and operation of buildings), including with respect to circularity, and concludes with guidelines for developing circularity business models and practical applications. 1.1.1 BIM BIM is a frequently misrepresented and therefore misunderstood technology. Many poor definitions describe not the phenomenon itself but its applications and effects (Sacks et al. 2018), often from the perspective of existing analogue practices. The production of drawings and other conventional documents to incrementally improve efficiency or reduce errors takes up a disproportionate amount of the BIM literature but does not explain how BIM is structured and how its structure helps to achieve certain objectives. Instead, it makes BIM appear as a mere step in AECO computerisation. The truth is more revolutionary: BIM marks the transition to symbolic representation (Koutamanis 2022). While earlier technologies like computer-aided design (CAD) focused on the graphic implementation mechanisms of building representations, BIM makes explicit the symbols described by these mechanisms. Symbolic representation is already the norm in many computer applications. In a digital text, the capital ‘A’ is not a group of three strokes, as in handwriting, but the Unicode symbol U+0041, explicitly entered through a keyboard and stored as such, regardless of how it appears on the screen. Any change to the symbol does not come from changing the three strokes but from changing the properties of the symbol (e.g. a different font or size) or switching to a different symbol (e.g. U+1D434 for the mathematical capital ‘A’). Symbolic representation underlies a lot of machine intelligence. In digital texts, knowing each letter allows computers to recognise words and sentences and subsequently understand grammar and syntax. Similarly, in BIM, a window is not the group of line segments one sees in a graphic view like a floor plan but a symbol explicitly entered in a specific location of a wall. One can reposition the window in the wall, but changing its type or even its size may require switching to a different symbol. The interfaces of BIM software tend to depart from facsimiles of analogue drawing, which confuse users into 5 1 From Building Information Modelling to Digital Twins. . . 5 Fig. 1.1 Symbols, properties and connections Fig. 1.1 Symbols, properties and connections thinking that they are drawing and obscure the symbolic structure of the model. We should think of BIM models not as 2D or 3D drawings with additional data but as graphs of interconnected symbols. In fact, connections are between specific symbol properties (Fig. 1.1.1 BIM 1.1): the co-termination of two walls links the endpoints of their axes, while the orientation of a wall is inherited by the windows it hosts. External constraints, such as the maximum height of a roof in planning regula- tions, are also linked to relevant symbol properties, while other constraints affect relations between two symbols, such as when windows are not allowed in certain wall parts. As a result, all primary information resides in the properties and relations of the symbols in a model. This allows for the derivation of further information through functions, e.g. calculations of fire resistance on the basis of the material composition of a building component. It also supports the production of various views of the model, including conventional drawings. As for machine intelligence, the potential is already evident in the behaviours of symbols: a window sticks to the hosting wall, and the shape of a room follows the bounding building elements. Integration, a key selling point of BIM, comes from this symbolic structure. With all information residing in symbols, there are no multiple representations from different disciplines that must be combined to obtain a full description. Instead, all actors have access to different symbols, properties and relations in a model, in adjustable worksets that give them specific rights and responsibilities. This integra- tion of information and its dynamic relation to authorship and custodianship also mean that information processing and AECO activities can be accommodated in BIM. The same holds for continuity through phases and stages: a symbolic repre- sentation can contain the entire history of a building. 6 A. Koutamanis A. Koutamanis BIM is often called ‘object-oriented’. This is misleading because the term has a different meaning in computer science but also because we should not equate symbols with real things. In English, the letter ‘a’ corresponds to five different sounds (phonemes). Knowing how to pronounce the letter depends on the context (the word). When considering representations in building, the correspondence between symbols and things can be even fuzzier. A window may be considered a discrete component, but a wall is an assemblage with variable composition and indeterminate form. Its material layers often continue into other walls, forming construction networks that are not captured by wall symbols in BIM. A main reason for this is geometric bias: continuous walls are segmented into separate symbols by the geometry of their axes. 1.1.1 BIM Despite such fuzziness and resulting ambiguities, the symbolic representation underlying BIM remains the obvious choice for AECO computerisation, with a potential similar to that of the Latin alphabet or the Hindu-Arabic numerals. The graph of symbols and their relations is a transparent, consistent and efficient foun- dation for any application. The capacity for integration and continuity means that information efforts can be consolidated into a single representation that caters for all aspects, goals and disciplines. 1.1.2 Digital Twinning While the use of BIM has yet to reach a satisfactory level or achieve significant efficiencies, AECO has already adopted a new buzzword: digital twinning. In contrast to BIM, digital twinning has yet to consolidate into a recognisable technol- ogy. Quite frequently, any virtual model seems to qualify as a digital twin, purely on the basis of intent. However, a digital twin is more than a model: it is a digital replica of something physical. It describes the form, behaviour and performance of the thing, including uses, users and direct context – all that is required for precise and accurate analyses and forecasts of future states of the physical twin. Information in a digital twin is dynamic and reciprocal: sensors in the physical twin that monitor temperature, light, sound, occupancy, vibration, etc., send their data to the digital twin, where they become attached to relevant properties of the appropriate symbols. The products of the digital twin travel in the reverse direction, guiding actuators in operational adaptations, e.g. the functioning of heating systems, and informing users through displays (Fig. 1.2). In other words, the twins are connected in both directions in near real time and are capable of communication and synchronisation (Chen 2017; Liu et al. 2018). Consequently, we can distinguish between representations (static models, as in BIM), shadows (representations which are updated by data from the physical things) and twins (full two-way synchronisa- tion) (Fuller et al. 2020; Sepasgozar 2021). Digital twins of buildings are invariably based on BIM (Boje et al. 2020; Sacks et al. 2020; Begić and Galić 2021; Mêda et al. 2021; Shahat et al. 2021; Tagliabue et al. 2021; Alibrandi 2022; Shaharuddin et al. 2022). At the same time, it is stressed 1 From Building Information Modelling to Digital Twins. . . 7 Fig. 1.2 Connections between symbols in a digital twin and things in a physical twin 1 From Building Information Modelling to Digital Twins. . . 1 From Building Information Modelling to Digital Twins. . . 7 Fig. 1.2 Connections between symbols in a digital twin and things in a physical twin that digital twinning is more than BIM, as it includes sociotechnical and process aspects, especially in use (Boje et al. 2020; Davila Delgado and Oyedele 2021; Sepasgozar 2021). This makes it significantly more demanding than as-built BIM in terms of reliability, precision and completeness. 1.1.3 Passports and Logbooks BIM and digital twinning are general-purpose technologies. There are also stand- alone information technologies specifically developed for circularity in AECO. These are referred to by terms such as building or material passport or logbook. Chapter 5 by Honic et al. in this book describes the potential of such technologies and relevant life cycle and standardisation challenges in detail. Therefore, from the perspective of this chapter, it suffices to emphasise that BIM, as an integrated information environment, is more than a useful source of data (Durmišević 2018; Bertin et al. 2020). There is a significant overlap between BIM and material or building passports (Charef and Emmitt 2021), even when the latter are based on other sources for product composition breakdown. The advantage of BIM is that it makes materials situated and connected to life cycle processes (Honic et al. 2019). This supports design for deconstruction and disassembly (Minunno et al. 2018; Xing et al. 2020; Marzouk and Elmaraghy 2021; O’Grady et al. 2021) and other circularity goals. Translating manufacturers’ disas- sembly instructions into simulations in BIM improves legibility and completeness, especially concerning resources that may be available or required. It also verifies the disassembly procedures and validates designs with respect to them. Including the location of a component among its metaproperties in a passport does not offer the same advantages. In conclusion, passports and logbooks are amenable to the integrating power of BIM and digital twins, which can accommodate product information (Kebede et al. 2022), life cycle energy data (Shah et al. 2023) and other key information in their properties and relations. In BIM, information collections such as material passports can become views of the model, similarly to bills of quantities. Linking their goals and constraints to all activities in design, construction and operation through BIM returns connections to information sources that help make material flow registration and analysis realistic and reliable (Miatto et al. 2022). 1.1.2 Digital Twinning Furthermore, it is questionable whether BIM can accommodate and process the big data produced by sensors in the built environment. Rather than a foundation, BIM is a predecessor to digital twinning, based on the same symbolic approach to representation (Boje et al. 2020; Koutamanis et al. 2021). More than on BIM, digital twinning relies on the Internet of Things (IoT): the networks that connect sensors, actuators and displays in a building, making it ‘smart’, i.e. automating certain operations, such as opening doors and regulating ventilation systems. In addition to such local automation, the IoT also collects data from all sources to capture the history and the overall conditions in a building. This improves local operations by connecting them to global goals and constraints. The IoT is not just an enabler but a necessity because digital twinning presupposes a building heavily populated by IoT for bidirectional communication and synchroni- sation, including feedback to users and operators (Farsi et al. 2020; Fuller et al. 2020; Lu et al. 2020; Sepasgozar 2021). The collection of data for digital twinning could be much more extensive than in most smart buildings, resulting in a lack of suitable physical twins and possibly rendering digital twinning a pipe dream. Alternatively, one could tolerate low-fidelity solutions as early deployment stages and encourage incremental development (Mêda et al. 2021). However, experience with BIM matu- rity levels suggests that such tolerance is self-defeating because it provides alibis for not taking the trouble to use the technology properly while continuing processes that actually undermine it. The degree of validation and verification required in digital twinning makes any attempt to pass off static models as twins as misguided as calling 2D drawings BIM. A. Koutamanis A. Koutamanis 8 8 1.2 BIM in the Built Environment There is general agreement that digital uptake in AECO is slow and limited, even though investment in digitisation may not be that low (Turk 2021; Koutamanis 2022). Nevertheless, BIM was received with unprecedented willingness and opti- mism as a solution to major inefficiencies and malperformances (Sacks et al. 2018; Ernstsen et al. 2021), but rapid adoption was not accompanied by a scope wide and coherent enough to effect fundamental changes. There are persistent complaints about BIM costs, complexity and social and organisational aspects that contrast with its arguably unrealistic promotion (Miettinen and Paavola 2014; Oesterreich and Teuteberg 2019) and put smaller enterprises at a disadvantage (Dainty et al. 2017; Murguia et al. 2023). BIM is commonly deployed in hybrid situations, where it 1 From Building Information Modelling to Digital Twins. . . 9 1 overlaps with other technologies (Davies 2017). This conflicts with the holistic character of BIM and reduces its potential. As AECO remains attached to existing, document-based practices, BIM is generally restricted to office use and the produc- tion of such documents. Out of the office, the reliance of AECO on low-cost human labour does little to promote digitalisation. Even in office use, BIM has not always facilitated innovation. Its emphasis on integration and interoperability is not linked to models of labour division and specialisation (Turk 2020). It is also questionable that complex assemblages such as buildings can be broken down into hierarchical ontologies by merely observing real-world buildings and following pre-existing, paper-based standards (Koutamanis et al. 2021). Unfortunately, such limitations are seldom experienced, as most applications and models tend to remain selective, partial and restricted to specific tasks, such as clash detection between load-bearing structures and building services. g g BIM has yet to make its presence felt beyond design and construction, in the costly and resource-intensive use stage (Gao and Pishdad-Bozorgi 2019; Abideen et al. 2022; Benn and Stoy 2022; Durdyev et al. 2022; Matos et al. 2022; Pinti et al. 2022; Tsay et al. 2022). Making and especially maintaining as-is models appears to be beyond the scope or capacities of most organisations, which are already overwhelmed by the amount of existing information and the multiplicity of channels through which they exchange information. 1.3 BIM and Digital Twinning for a Circular Economy BIM, while not perfect, remains preferable to its predecessors and indicative of the symbolic direction building representations are taking. Implemented properly, it offers information integration and continuity, unambiguous interpretation by both humans and machines and full and reliable support of complex analyses. This supports goals such as circularity and the information-intensive processes they require. At the same time, present limitations in BIM create interest in technological advances. Digital twinning promises the additional capacity to accommodate and process all states of the physical twin, past and present (Rafael Sacks et al. 2020). This helps transform static evaluations into dynamic life cycle processes, combining, e.g. end-of-life assessment with adaptable planning (Chen et al. 2021). This transi- tion from static to dynamic is demanding but seems justified by feasibility evalua- tions, which confirm a significant potential for improved life cycle assessment and control (Tagliabue et al. 2021). Neither BIM nor digital twinning are goals for AECO; they are means towards domain-specific performances. Moreover, circularity may be viewed as an imposed, external societal constraint. As with any such constraint, it may conflict with established practices and be poorly served by existing tools, which are attuned to other priorities. To remove such obstacles, the general capacities of digital twinning, BIM and digitalisation should be taken for granted, and attention should be on 10 A. Koutamanis A. Koutamanis A. Koutamanis specific, critical issues (Çetin et al. 2021). General intentions, such as reducing inefficiencies, improving communication, optimising design performance or just providing visualisations (Wong and Fan 2013; Akinade et al. 2017; Minunno et al. 2018; Charef and Emmitt 2021), can be relevant but do not amount to a specific, coherent approach. 1.3.1 Registration of Relevant Information The first step in a coherent approach to circularity with BIM or digital twins is to learn to rely on symbolic representation. Any full model or twin can easily cover circularity information needs without additional investment, but in practice repre- sentations can be selective or opportunistic and hence incomplete or inconsistent. Deferring the information burden to any particular goal and its stakeholders (as with passports) is not a viable option. Instead, all AECO stakeholders should insist on joint, permanent working environments, not disconnected repositories or documen- tation for different phases. There can be no half-hearted BIM or digital twin deployment: economising on investment means severely limited potential and low returns. The first reason why a digital solution cannot be made for circularity solely is cost: the value of what it supports can hardly be justified by the returns, certainly in the perception of most AECO stakeholders with different priorities. General-purpose solutions such as BIM are clearly preferable because they support most such priorities. If circular goals can be added to them, then circularity stakeholders can reap the benefits, while others are stimulated to include circularity in their considerations. The perennial question in AECO is not so much who makes a BIM model but who maintains it, especially in the life cycle of a building. If this does not happen collaboratively by conjoining the core processes of all actors, and preferably auto- matically, there is little hope for success. Collaborative solutions also lower the participation threshold for smaller enterprises and offer enticing benefits in terms of digital support and room for fruitful specialisation. In return, the enterprises con- tribute to the completeness and up-to-dateness of information simply by using it. The second reason for a lack of digital solutions for circularity is selectivity: any information solution motivated primarily or exclusively by circularity inevitably remains restricted to circularity factors and aspects. It may even suffer from inattentional blindness, which causes omissions of important data simply because we concentrate on other matters (Chabris and Simons 2010). One can naturally work with conscious concentration towards a full, inclusive solution, but then the results would amount to something akin to BIM or digital twins, i.e. a comprehensive solution that could only justify costs and improve returns by being open to other goals and priorities, too. 1 From Building Information Modelling to Digital Twins. . . 11 1.3.2 Exploration of Circular Operations The second step towards circularity with BIM or digital twins is to utilise their capacities for exploring deconstruction and disassembly (Akanbi et al. 2019; van den Berg et al. 2021). In the same way that we simulate construction processes, we can also simulate the expected maintenance, refurbishment, renovation and deconstruc- tion processes with the accuracy and precision required for feasibility, effectiveness and efficiency. This provides direct support for construction-related circularity goals (narrow and regenerate through efficiency improvement) and a useful background for others (slow and close through reliable life cycle projections). It also stresses the necessity of detail and realism. For deconstruction in particular, we should acknowl- edge that it is not a mere reversal of construction. As Van den Berg explains in Chap. 11 in the relevant chapter in this volume, information is a key issue in organising reverse logistics. As-is representations are essential for the identification and harvesting of reusable resources from existing buildings because as-built models (i.e. construction documentation) are neither sufficient nor reliable enough. Closing loops requires certainty about the state of components and materials, as well as about their physical context, which has changed from an accommodating construction site to a finished, functioning building. This calls for solutions that are full and realistic, including all details of deconstruction in space and time, e.g. how cranes and scaffolds would function in the existing building. Van den Berg (Chap. 11) describes a number of focused explorations and demonstrations that must graduate from opportunistic demonstrations of potential to standard facilities in BIM and digital twinning. 1.3.3 Constraining Design, Construction and Operation 1.3.4 Life Cycle Registration and Guidance The final step is an extension of the previous three: use 4D symbolic representations to monitor the detailed history of a building, preferably in near-real time. As symbol properties and relations can register the activities and effects of maintenance, refurbishment, etc., material flows are measured and managed not by questionable proxies but with primary, precise and accurate data (Minunno et al. 2018; Chen and Huang 2020; Marzouk and Elmaraghy 2021). Up-to-date information is essential for the planning of circularity operations: narrowing, slowing, closing and regenerating can be based not just on initial assumptions and projections but on constantly refinable and dynamic decision frameworks that include permanent validation and verification facilities for making sense of the existing building conditions for decon- struction (Van den Berg, Chap. 11). The bidirectional relation between digital twins and buildings is clearly advantageous in this respect, as it covers not only monitoring but also adaptations in the behaviour of the physical twins, e.g. adjusting the heating and ventilation of a building in order to reduce the extent of material ageing in specific components. 1.3.3 Constraining Design, Construction and Operation Based on the second step, we should explicitly describe circularity dependencies and constraints in properties and relations of symbols (e.g. constraints on interfacing between components for effective deconstruction). Relations are of particular impor- tance in this respect because they link interfacing between components to symbol behaviours. They can ensure that the building design and construction allow for deconstruction (Sanchez et al. 2021), e.g. avoid additions that spoil interfaces designed for disassembly, such as equalising layers of in situ concrete over demount- able floor slabs. If symbols refuse to accept such additions to their properties or relations, similarly to a door not accepting positioning outside a wall, the scope for human error becomes much smaller. This is particularly important in the use phase, where changes are only too frequently improvised, in both refurbishment and maintenance. The representation can also anticipate circularity operations, such as the replacement of some components when they fall below a certain performance level, by including among the symbol triggers that adjust the timing of loops. A. Koutamanis A. Koutamanis 12 1.4 Current Applications of BIM and Digital Twinning to Circularity Judging the efficacy of a technology or approach requires realistic applications that can be analysed with respect to both means and ends. However, most publications on circularity and digital twinning, as well as many on circularity and BIM, are programmatic or aspirational. They focus on aspects such as technology and plat- form development, enablers and challenges (Copeland and Bilec 2020; Fuller et al. 2020; Ganiyu et al. 2020; Rafael Sacks et al. 2020; Davila Delgado and Oyedele 2021; Sepasgozar 2021; Shahat et al. 2021; Ammar et al. 2022; Charef 2022). Actual case studies are thin on the ground and mostly presented as plans or untested prototypes. The best examples illustrate that highly specific subjects and goals are beneficial for both the setup of a digital twin and analyses in it (Funari et al. 2021). Laboratory case studies, however limited, represent useful steps forward, especially for learning and testing (Rocca et al. 2020; Marzouk and Elmaraghy 2021). The narrow scope of digital twinning case studies is inherent to any early stage. With the sensitising of architects, engineers, authorities and clients to environmental issues and the life cycles of materials, ambition and attention inevitably become dispersed over a wide range of subjects and possibilities, from key applications in AECO to promising digital technologies (Hillebrandt et al. 2019; Çetin et al. 2021), arguably at the cost of coherence, consistency and effectivity. There is no uniform solution that applies to all aspects and goals. Each component, material or building has different potential, not just generically but in every instance and situation. 13 1 From Building Information Modelling to Digital Twins. . . 1 From Building Information Modelling to Digital Twins. . . However, even advanced and convincing cases with a narrow and well-defined scope, such as bridge maintenance, still fall short of a full digital twin (Mahmoodian et al. 2022). Other studies are hampered by the small samples available, as longitu- dinal or long-term data are required for consistent and reliable results (Rita et al. 2022). This is particularly true of attempts to go beyond the microscale of materials and elements and extend to the macroscales of neighbourhoods and cities, so as to identify and promote synergies (Bejtullahu and Morishita-Steffen 2021). Such extensions inevitably shift attention from new designs to the existing stock. Existing buildings, especially historical ones, involve knowledge not easy to codify in systems developed for today. So, it is not only information we are lacking, it is also decision-making and design tools (Durmišević 2018; Bianchini et al. 2021). g g ( ) One of the key problems with case analysis is that evaluation tends to be weak, based on opinion rather than objective criteria. Information collected through ques- tionnaires, interviews and similar means (Charef and Emmitt 2021; Çetin et al. 2022) should not be taken at face value. It contains opinions, subjective estimates and uncorroborated reported results that indicate belief or strategic support for potential rather than tangible, verifiable results. As time-use studies demonstrate, personal estimates can be heavily biased by goals and emotions: stressed people overestimate how they spend their time and produce sums of more than 24 hours per day (Robinson and Godbey 1999). This calls for yet another use of BIM and digital twins: the collection of reliable, comprehensive and consistent data, which can be processed through generally accepted methods towards case analyses and bench- marks. Without such objective information processing, it is impossible to arrive at clear evidence that not only convinces but also shows what can be improved and how. 1.5 Business Models for BIM and Digital Twinning in a Circular Built Environment 1.5 Business Models for BIM and Digital Twinning in a Circular Built Environment Business models address organisational aspects, such as who, what, when and how in key tasks that contribute towards delivering desired results and outcomes. Infor- mation is of critical significance here, especially in product-as-service, bundling, dematerialisation, life extension and similar models that depend on fine-tuning or combinations (Charter and McLanaghan 2018; McCausland 2022). These require transitions from production-driven to customer-centred approaches and changes in collaboration patterns and supply chain structures (Qi et al. 2022; Wang et al. 2022; Xiang et al. 2022). Whether the business model follows an innovation or a resource strategy (Bocken and Ritala 2022), rich information is a prerequisite for reliability and feasibility (Shah et al. 2023). Projected states and indicators must be substan- tiated and monitored, so that lessons learned are fed back to related decisions. The same organisational aspects and their goals are critical for the utilisation of information technologies. Despite the key role of information, the digitalisation of 14 A. Koutamanis A. Koutamanis products and processes is not always included in digital twinning business models, which often retain legacy conditions and practices (Deckert et al. 2022). Digitalisation is still treated as external to core processes: a layer to be superimposed when needed. Consequently, the business case for digitalisation and information is hampered by investment and operation costs that are deemed too high, despite the promise of substantial efficiency improvement. In AECO, digitalisation has yet to develop into a connecting tissue between all stakeholders and actors, as in other economic areas (Floridi 2014). Attachment to analogue practices and their information carriers remains too strong, regardless of changes in the objectives of projects, enterprises or society. This contrasts sharply not only with other industries but even more with daily life. The same AECO practitioners who are reluctant to fully embrace integrated digital information solu- tions in their professional activities make extensive use of social media, e-commerce, e-banking, etc., in their private lives. The result is that AECO computerisation is characterised by isolated islands, not the networks necessary for business value. BIM, digital twinning and all other forms of digital information are treated as the product of integration rather than the integrator that enables better collaboration and performance (Davila Delgado and Oyedele 2021). p g y This does not imply lack of attempts at new business models that build on digitalisation. 1 From Building Information Modelling to Digital Twins. . . 15 Such arguments sound autocratic but nevertheless produce clear solutions in a notoriously fragmented and backward-looking industry like AECO. Judging from the half-hearted commitment and relatively low investment in computerisation, business models involving BIM or digital twinning need to include the technologies in their core and give them the primary role of integrator. Developing add-on business models for digitalisation on top of circularity models is self-defeating because it makes information technologies an option, moreover an expensive one, with tenuous connections to goals and values. So long as stakeholders are under the impression that circularity in the built environment is feasible without a radical digital reform of practically all processes, there is little hope for wide and effective deployment. Digitalisation should be specified according to general principles, rather than specific objectives such as circularity, so as to ensure inclusiveness and complete- ness. This provides the necessary context for explaining how different aspects can support each other in the business model, e.g. how maintenance activities contribute to the fine-tuning of timely deconstruction, thereby alleviating the burden of fact- finding in circularity monitoring and assessment. Conversely, circularity constraints guide maintenance towards not only timely replacement but also higher performance in the building. 1.5 Business Models for BIM and Digital Twinning in a Circular Built Environment On the contrary, there are many proposals from which we can learn. Looking at business models related to digital twinning (as the most demanding case) across application areas, industries and countries (Kumar et al. 2022), certain characteristics emerge: This does not imply lack of attempts at new business models that build on digitalisation. On the contrary, there are many proposals from which we can learn. Looking at business models related to digital twinning (as the most demanding case) across application areas, industries and countries (Kumar et al. 2022), certain characteristics emerge: • The emphasis is on potential (rather than effectiveness), particularly for compet- itiveness, which requires venturing beyond legacy solutions and comfort zones. • Control applications appear to offer easier deployment than production applica- tions, but in both cases the main promise is value co-creation through support for decision-making and management of operations and services (West et al. 2021). • Differences between industries are largely due to legacy practices and industry structures (Morelli et al. 2022). There appears to be no uniform solution for universal transformation. • Importance is attached to platforms, autonomous stakeholders operating on them and networks emerging from the interaction between stakeholders and platforms (Rocca et al. 2020). • Importance is attached to platforms, autonomous stakeholders operating on them and networks emerging from the interaction between stakeholders and platforms (Rocca et al. 2020). In summary, digital twinning seems not easily attainable in practice, especially for subjects like buildings, which undergo many, often invisible changes in their protracted lifespans and require a high level of detail to capture both contexts and user experiences. Some therefore argue that the business case should be motivated by a clear goal such as the reduction of energy consumption. This guides the development of business value towards measurable results while serving wider societal goals like sustainability and improving the lives of users and consumers. They also stress that data strategies should be imposed top-down, as part of business value, rather than left to the willingness or ability of stakeholders and actors (Apte and Spanos 2021). 1 From Building Information Modelling to Digital Twins. . . 1.6 Discussion One thing we no longer need to justify or defend is digitalisation. Everyone is aware of its importance and pervasiveness. The fact that information is key to digitalisation is sometimes less obvious, let alone that information is the integrator of human interactions. Goals like circularity are not only highly demanding in information, they also require radical changes in all related industries. These characteristics make circularity clearly dependent on the digital transformation of the whole of AECO, in the same way that digitalisation has transformed communications, entertainment, social contacts, etc. While such transformation is feasible, the problem with digitalisation in AECO is not lack of potential but low priority. So long as it is seen as a mere means to basic tasks, it cannot deliver its full promise. In turn, this reduces willingness to invest in digitalisation and hence the performance of digital solutions. To break this vicious circle, brave plans are necessary. Circularity has to assume fully integrated digital information for the built environment and include it in the core of its processes as the connecting tissue between aspects, stakeholders and actors. In other words, the first, critical step is that AECO commits to BIM and applies it to all aspects and tasks. This ensures reliable and effective support for circularity, as well as a wide scope for it, for two key reasons. Firstly, being successful with just a few components or materials does not justify the circularity claims and investments – for circularity to be truly effective, it must apply widely to the built environment. Secondly, to achieve that, circularity must be present in all 16 A. Koutamanis A. Koutamanis aspects, become embraced by the corresponding disciplines and made part of their goals and methods. Keeping it separate, as an additional layer, turns it into an afterthought and an option. This information environment cannot be initiated by any single aspect or goal. Circularity may endorse it, but it is the whole of AECO that must sustain it throughout the life cycle. This sounds like a tall order, but thankfully BIM, properly and consistently applied, is a good starting point. Its limitations are not trivial but not such that they preclude effectiveness and efficiency in any discipline or the collab- oration between disciplines. What AECO needs is more experience with working in such an environment – experience that can be invaluable in further transitions, e.g. 1.6 Discussion to the enticing prospect of digital twinning. 1.7 Key Takeaways • BIM has considerable potential to integrate information processing, thus provid- ing comprehensive and situated information that covers most circularity needs. • BIM has considerable potential to integrate information processing, thus provid- ing comprehensive and situated information that covers most circularity needs. g p y • BIM seamlessly links circularity to other activities in design, construction and operation. • BIM seamlessly links circularity to other activities in design, construction and operation. • Digital twinning promises even more: digital replicas in full synchronisation with the physical twin and its past, present and future states. • The successful deployment of powerful technologies such as BIM and digital twinning requires significant investment, commitment and consistency. • The successful deployment of powerful technologies such as BIM and digital twinning requires significant investment, commitment and consistency. 1 From Building Information Modelling to Digital Twins. . . Bejtullahu F, Morishita-Steffen N (2021) From resilient and regenerative materials to a resilient and regenerative built environment. In: Andreucci MB, Marvuglia A, Baltov M, Hansen P (eds) Rethinking sustainability towards a regenerative economy. Springer International Publishing, Cham, pp 263–278 pp Benn M, Stoy C (2022) BIM for CREM: exploring the benefit of building information modelling for facility management in corporate real estate management. Buildings 12:400. https://doi.org/ 10.3390/buildings12040400 Bertin I, Mesnil R, Jaeger J-M, Feraille A, Le Roy R (2020) A BIM-based framework and databank for reusing load-bearing structural elements. Sustainability 12:3147. https://doi.org/10.3390/ su12083147 Bianchini C, Attenni M, Potestà G (2021) Regenerative design tools for the existing city: Hbim potentials. In: Andreucci MB, Marvuglia A, Baltov M, Hansen P (eds) Rethinking sustainability towards a regenerative economy. Springer International Publishing, Cham, pp 23–43 Bocken N, Ritala P (2022) Six ways to build circular business models. J Bus Strategy 43:184–192 https://doi.org/10.1108/JBS-11-2020-0258 Boje C, Guerriero A, Kubicki S, Rezgui Y (2020) Towards a semantic construction digital twin: directions for future research. Autom Constr 114:103179. https://doi.org/10.1016/j.autcon. 2020.103179 Çetin S, De Wolf C, Bocken N (2021) Circular digital built environment: an emerging framework. Sustainability 13:6348 Çetin S, Gruis V, Straub A (2022) Digitalization for a circular economy in the building industry: multiple-case study of Dutch social housing organizations. RCR Adv 15:200110. https://doi. org/10.1016/j.rcradv.2022.200110 g j Chabris CF, Simons DJ (2010) The invisible gorilla : and other ways our intuitions deceive us. Crown, New York Charef R (2022) The use of building information modelling in the circular economy context: several models and a new dimension of BIM (8d). Clean Eng Technol 7:100414. https://doi.org/10. 1016/j.clet.2022.100414 j Charef R, Emmitt S (2021) Uses of building information modelling for overcoming barriers to a circular economy. J Clean Prod 285:124854. https://doi.org/10.1016/j.jclepro.2020.124854 Charter M, McLanaghan S (2018) Business models for a circular economy. In: Charter M (ed) Designing for the circular economy. Routledge, London, pp 89–101 Chen Y (2017) Integrated and intelligent manufacturing: perspectives and enablers. Engineering 3 588–595. https://doi.org/10.1016/J.ENG.2017.04.009 Chen Z, Huang L (2020) Digital twin in circular economy: remanufacturing in construction. IOP Conf Ser Earth Environ Sci 588:032014. https://doi.org/10.1088/1755-1315/588/3/032014 Chen C, Zhao Z, Xiao J, Tiong R (2021) A conceptual framework for estimating building embodied carbon based on digital twin technology and life cycle assessment. Sustainability 13:13875. https://doi.org/10.3390/su132413875 Copeland S, Bilec M (2020) Buildings as material banks using RFID and building information modeling in a circular economy. Procedia CIRP 90:143–147. References Abideen DK, Yunusa-Kaltungo A, Manu P, Cheung C (2022) A systematic review of the extent to which BIM is integrated into operation and maintenance. Sustainability 14:8692. https://doi.org/ 10.3390/su14148692 Akanbi LA, Oyedele LO, Omoteso K, Bilal M, Akinade OO, Ajayi AO, Davila Delgado JM, Owolabi HA (2019) Disassembly and deconstruction analytics system (d-das) for construction in a circular economy. J Clean Prod 223:386–396. https://doi.org/10.1016/j.jclepro.2019.03.172 Akinade OO, Oyedele LO, Omoteso K, Ajayi SO, Bilal M, Owolabi HA, Alaka HA, Ayris L, Henry Looney J (2017) BIM-based deconstruction tool: towards essential functionalities. Int J Sustain Built Environ 6:260–271. https://doi.org/10.1016/j.ijsbe.2017.01.002 Alibrandi U (2022) Risk-informed digital twin of buildings and infrastructures for sustainable and resilient urban communities. ASCE-ASME J Risk U A 8:04022032. https://doi.org/10.1061/ AJRUA6.0001238 Ammar A, Nassereddine H, AbdulBaky N, AbouKansour A, Tannoury J, Urban H, Schranz C (2022) Digital twins in the construction industry: a perspective of practitioners and building authority. Front Built Environ 8. https://doi.org/10.3389/fbuil.2022.834671 Apte PP, Spanos CJ (2021) The digital twin opportunity. MIT Sloan Manag Rev 63:15–17 Apte PP, Spanos CJ (2021) The digital twin opportunity. MIT Sloan Manag Rev 63:15–17 Begić H, Galić M (2021) A systematic review of construction 4.0 in the context of the BIM 4.0 premise. Buildings 11:337. https://doi.org/10.3390/buildings11080337 egić H, Galić M (2021) A systematic review of construction 4.0 in the context of the BIM 4.0 premise. Buildings 11:337. https://doi.org/10.3390/buildings11080337 1 From Building Information Modelling to Digital Twins. . . 17 1 From Building Information Modelling to Digital Twins. . . https://doi.org/10.1016/j.procir. 2020.02.122 Dainty A, Leiringer R, Fernie S, Harty C (2017) BIM and the small construction firm: a critica perspective. Build Res Inf 45:696–709. https://doi.org/10.1080/09613218.2017.1293940 Davies K (2017) Making friends with frankenstein: hybrid practice in BIM. Eng Constr Archi Manag 24:78–93. https://doi.org/10.1108/ECAM-04-2015-0061 Davila Delgado JM, Oyedele L (2021) Digital twins for the built environment: learning from conceptual and process models in manufacturing. Adv Eng Inform 49:101332. https://doi.org/ 10.1016/j.aei.2021.101332 Deckert C, Kalefeld J, Kutz M (2022) Business model innovation for the internet of things. Springer International Publishing, Cham, pp 321–333 18 A. Koutamanis Durdyev S, Ashour M, Connelly S, Mahdiyar A (2022) Barriers to the implementation of building information modelling (BIM) for facility management. J Build Eng 46:103736. https://doi.org/ 10.1016/j.jobe.2021.103736 j j Durmišević E (2018) Reversible building design. In: Charter M (ed) Designing for the circular economy. Routledge, London, pp 344–359 Ernstsen SN, Whyte J, Thuesen C, Maier A (2021) How innovation champions frame the future: three visions for digital transformation of construction. J Constr Eng Manag 147:05020022. https://doi.org/10.1061/(ASCE)CO.1943-7862.0001928 Farsi M, Daneshkhah A, Hosseinian-Far A, Jahankhani H (eds) (2020) Digital twin technologies and smart cities. Springer International Publishing, Cham Floridi L (2014) The 4th revolution: how the infosphere is reshaping human reality. Oxfor University Press, New York/Oxford Fuller A, Fan Z, Day C, Barlow C (2020) Digital twin: enabling technologies, challenges and ope research. IEEE Access 8:108952–108971. https://doi.org/10.1109/ACCESS.2020.2998358 Funari MF, Hajjat AE, Masciotta MG, Oliveira DV, Lourenço PB (2021) A parametric scan-to-fem framework for the digital twin generation of historic masonry structures. Sustainability 13: 11088. https://doi.org/10.3390/su131911088 p g Ganiyu SA, Oyedele LO, Akinade O, Owolabi H, Akanbi L, Gbadamosi A (2020) BIM compe- tencies for delivering waste-efficient building projects in a circular economy. DIBE 4:100036. https://doi.org/10.1016/j.dibe.2020.100036 1 From Building Information Modelling to Digital Twins. . . 1 From Building Information Modelling to Digital Twins. . . 19 Miatto A, Sartori C, Bianchi M, Borin P, Giordano A, Saxe S, Graedel TE (2022) Tracking the material cycle of italian bricks with the aid of building information modeling. J Ind Ecol 26: 609–626. https://doi.org/10.1111/jiec.13208 Miettinen R, Paavola S (2014) Beyond the BIM utopia: approaches to the development and implementation of building information modeling. Autom Constr 43:84–91. https://doi.org/ 10.1016/j.autcon.2014.03.009 Minunno R, O’Grady T, Morrison GM, Gruner RL, Colling M (2018) Strategies for applying the circular economy to prefabricated buildings. Buildings 8:125. https://doi.org/10.3390/ buildings8090125 Morelli G, Musso F, Murmura F, Bravi L (2022) Knowledge analysis on the industry 4.0 diffusion in italian manufacturing: opportunities and threats. Springer International Publishing, Cham, pp 195–214 Murguia D, Vasquez C, Demian P, Soetanto R (2023) BIM adoption among contractors: a longitudinal study in Peru. J Constr Eng Manag 149:04022140. https://doi.org/10.1061/ (ASCE)CO.1943-7862.0002424 O’Grady TM, Brajkovich N, Minunno R, Chong H-Y, Morrison GM (2021) Circular economy and virtual reality in advanced BIM-based prefabricated construction. Energies 14:4065. https://doi. org/10.3390/en14134065 g Oesterreich TD, Teuteberg F (2019) Behind the scenes: understanding the socio-technical barriers to BIM adoption through the theoretical lens of information systems research. Technol Forecast Soc Change 146:413–431. https://doi.org/10.1016/j.techfore.2019.01.003 g Oesterreich TD, Teuteberg F (2019) Behind the scenes: understanding the socio-technical barriers to BIM adoption through the theoretical lens of information systems research. Technol Forecast Pinti L, Codinhoto R, Bonelli S (2022) A review of building information modelling (BIM) for facility management (FM): implementation in public organisations. Appl Sci 12:1540. https:// doi.org/10.3390/app12031540 g pp Qi Q, Tao F, Nee AYC (2022) Chapter 1 – From service to digital twin service. In: Tao F, Qi Q, Nee AYC (eds) Digital twin driven service. Academic Press, pp 1–31 Rita LPS, Silva JR, Junior RRF (2022) Best regional practices for digital transformation in industry: the case of the industry 4.0 program in Portugal. Springer International Publishing, Cham, pp 163–181 Robinson JP, Godbey G (1999) Time for life : the surprising ways americans use their time. Pennsylvania State University Press, University Park Rocca R, Rosa P, Sassanelli C, Fumagalli L, Terzi S (2020) Integrating virtual reality and digital twin in circular economy practices: a laboratory application case. Sustainability 12:2286. https:// doi.org/10.3390/su12062286 g Sacks R, Eastman C, Lee G, Teicholz P (2018) BIM handbook. g https://doi.org/10.1016/j.dibe.2020.100036 Gao X, Pishdad-Bozorgi P (2019) BIM-enabled facilities operation and maintenance: a review. Ad Eng Inform 39:227–247. https://doi.org/10.1016/j.aei.2019.01.005 g p g j Hillebrandt A, Riegler-Floors P, Rosen A, Seggewies J-K (2019) DETAIL. München Honic M, Kovacic I, Rechberger H (2019) Improving the recycling potential of buildings through material passports (MP): an Austrian case study. J Clean Prod 217:787–797. https://doi.org/10. 1016/j.jclepro.2019.01.212 Kebede R, Moscati A, Tan H, Johansson P (2022) Integration of manufacturers’ product data in BIM platforms using semantic web technologies. Autom Constr 144:104630. https://doi.org/10. 1016/j.autcon.2022.104630 Koutamanis A (2022) Building information – representation and management: principles an foundations for the digital era. TU Delft OPEN, Delft Ž Koutamanis A, Dainty A, Kvan T, Turk Ž (2021) The enigma of BIM. Archit Struct Construct 3:1 https://doi.org/10.1007/s44150-021-00017-6 Kumar V, Leng J, Akberdina V, Kuzmin E (eds) (2022) Digital transformation in industry: digita twins and new business models. Springer International Publishing, Cham Liu Z, Meyendorf N, Mrad N (2018) The role of data fusion in predictive maintenance using digita twin. AIP Conf Proc 1949:020023. https://doi.org/10.1063/1.5031520 Lu Q, Xie X, Heaton J, Parlikad AK, Schooling J (2020) From BIM towards digital twin: strategy and future development for smart asset management. Springer International Publishing, Cham, pp 392–404 pp Mahmoodian M, Shahrivar F, Setunge S, Mazaheri S (2022) Development of digital twin for intelligent maintenance of civil infrastructure. Sustainability 14:8664. https://doi.org/10.3390/ su14148664 Marzouk M, Elmaraghy A (2021) Design for deconstruction using integrated lean principles and BIM approach. Sustainability 13:7856. https://doi.org/10.3390/su13147856 Matos R, Rodrigues H, Costa A, Rodrigues F (2022) Building condition indicators analysis for BIM-FM integration. Arch Comput Methods Eng 29:3919–3942. https://doi.org/10.1007/ s11831-022-09719-6 McCausland T (2022) Digital twins. Res Technol Manag 65:69–71. https://doi.org/10.1080/ 08956308.2022.1999637 Mêda P, Calvetti D, Hjelseth E, Sousa H (2021) Incremental digital twin conceptualisations targeting data-driven circular construction. Buildings 11:554. https://doi.org/10.3390/ buildings11110554 1 From Building Information Modelling to Digital Twins. . . Wiley, Hoboken Sacks R, Brilakis I, Pikas E, Xie HS, Girolami M (2020) Construction with digital twin informatio systems. Data-centric Eng 1:e14. https://doi.org/10.1017/dce.2020.16 Sanchez B, Rausch C, Haas C, Hartmann T (2021) A framework for BIM-based disassembly models to support reuse of building components. Resour Conserv Recycl 175:105825. https:// doi org/10 1016/j resconrec 2021 105825 Sepasgozar SME (2021) Differentiating digital twin from digital shadow: elucidating a paradigm shift to expedite a smart, sustainable built environment. Buildings 11:151. https://doi.org/10. 3390/buildings11040151 Shah D, Kathiriya H, Suthar H, Pandya P, Soni J (2023) Enhancing the building’s energy performance through building information modelling—a review. Springer Nature Singapore, Singapore, pp 247–253 Shaharuddin S, Abdul Maulud KN, Syed Abdul Rahman SAF, Che Ani AI (2022) Digital twin for indoor disaster in smart city: a systematic review. Int Arch Photogramm Remote Sens Spat Inf Sci XLVI-4:315–322. https://doi.org/10.5194/isprs-archives-XLVI-4-W3-2021-315-2022 Shahat E, Hyun CT, Yeom C (2021) City digital twin potentials: a review and research agenda. Sustainability 13:3386. https://doi.org/10.3390/su13063386 20 A. Koutamanis A. Koutamanis Tagliabue LC, Cecconi FR, Maltese S, Rinaldi S, Ciribini ALC, Flammini A (2021) Leveraging digital twin for sustainability assessment of an educational building. Sustainability 13:480. https://doi.org/10.3390/su13020480 Tsay GS, Staub-French S, Poirier É (2022) BIM for facilities management: an investigation into the asset information delivery process and the associated challenges. Appl Sci 12:9542. https://doi. org/10.3390/app12199542 g pp Turk Ž (2020) Interoperability in construction – mission impossible? DIBE 4:100018. https://doi. org/10.1016/j.dibe.2020.100018 Turk Ž (2021) Structured analysis of ICT adoption in the european construction industry. Int J Constr Manag 1–7. https://doi.org/10.1080/15623599.2021.1925396 van den Berg M, Voordijk H, Adriaanse A (2021) BIM uses for deconstruction: an activity- theoretical perspective on reorganising end-of-life practices. Constr Manag Econ 39:323–339. https://doi.org/10.1080/01446193.2021.1876894 Wang X, Kumar V, Kumari A, Kuzmin E (2022) Impact of digital technology on supply chain efficiency in manufacturing industry. Springer International Publishing, Cham, pp 347–371 West S, Stoll O, Meierhofer J, Züst S (2021) Digital twin providing new opportunities for value co-creation through supporting decision-making. Appl Sci 11:3750. https://doi.org/10.3390/ app11093750 Wong K, Fan Q (2013) Building information modelling (BIM) for sustainable building design Facilities 31:138–157. https://doi.org/10.1108/02632771311299412 Xiang F, Fan J, Ke S, Zuo Y (2022) Chapter 2 – Digital twin-driven service collaboration. In: Tao F, Qi Q, Nee AYC (eds) Digital twin driven service. Academic Press, pp 33–58 Xing K, Kim KP, Ness D (2020) Cloud-BIM enabled cyber-physical data and service platforms for building component reuse. Sustainability 12:10329. 1 From Building Information Modelling to Digital Twins. . . https://doi.org/10.3390/su122410329 Alexander Koutamanis studied architecture in Greece and received his PhD from Delft University of Technology, where he is associate professor of computational design. He has also worked as a designer and consultant in practice. His research interests include representation, recognition, information, interaction, affordances, briefing and decision support. Recent publications include an open textbook on building information management, an edited volume on construction and demolition waste recycling (including a chapter on BIM) and journal papers on dimensions and potential in BIM. Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0 International License which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and (http://creativecommons.org/licenses/by/4.0/), indicate if changes were made. The images or other third party material in this chapter are included in the chapter’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the chapter’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
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German
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Radikaloperation eines primären Lungenkarzinoms<sup>1</sup>)
Deutsche medizinische Wochenschrift/Deutsche Medizinische Wochenschrift
1,913
public-domain
9,743
Radikaloperation eines primären Lungen- karzinoms.1) Operation am 13. September 1912. Morphium-Skopolamin- Narkose. Chloroform-Aether. Ueberdruck mit Apparat von Tiegel. Lagerung auf die linke Seite. Kissen unter die linke Brustseite. Um- schneidung und wasserdichte Uebernähung der thermokauterisierten Granulationsfläche (in Höhe der siebenten Rippe), die von'der voraus gegangenen Operation von Herrn Dr. Sauer herrührte. E i i Von Prof. J. Rotter in Berlin. Unter den Operationen an der Lunge haben die Pneumo- tomien, die Eröffnungen von Höhlen der Lunge, bereits ein sehr umfangreiches Material in die Literatur geliefert. Die Ent- fernung von Te i 1 e n der Lungensubstanz ist indessen bisher nur in einer recht bescheidenen Anzahl von Fällen ausgeführt worden, insbesondere ist die Amputation von ganzen Lappen der Lunge - soweit ich die Literatur übersehe - bisher so selten mitgeteilt worden, daß es heutzutage noch erwünscht erscheint, derartige Einzelfälle zu publizieren. g g g p Exstirpation des Tumors: Da Fig. 1. die Haut von der zehnten bis zur siebenten Rippe mit der von der Neubildung durch- wachsenen Brust- wand (im Bereiche des Röntgenschat- tens) verwachsen ist, muß sie in dieser Ausdehnung geopfert werden. Es wird der Haut- schnitt oben in dem Interkostal. raum zwischen der sechsten und sie- benten Rippe geführt, aber weil das Messer in der Brustwandnoch in die Neubildung gelangt, muß der nächst höhere Interkostalraum zwischen der sechsten und fünften Rippe zur DurchtrennungderBrustwand be- nutzt werden, und zwar in einer Länge von etwa17cm, medianwärte bis zum Rippenknorpel und hinten bis nahe ai{den Rippenwinkel. E d i d Lä d S h itt di f i Pl höhl Fig. 1. Heruntergeladen von: NYU. Urheberrechtlich geschützt. g p Ich hatte Gelegenheit, im verflossenen Jahre mehr als den ganzen rechten Unterlappen der Lunge zu amputieren, und zwar, was wieder besonders selten bisher vorgekommen ist, wegen eines primären Karzinoms der Lunge. Krankengeschichte. H. G., 51 Jahre alt, Beamter. l i d d f ll d g A n a m n e s e. Als Kind Lungen- und Brustfellentzündung. Vor einem Jahre zwischen dritter bis fünfter Rippe Druckgefühl und später Schmerzen daselbst, besonders bei Bewegungen und beim Husten. Seit Februar 1912 traten heftige Schmerzen auf der rechten Brustseite auf, weshalb er das Hedwig.Krankenhaus aufsuchte. Auf der Inneren Ab. teilung wurde folgendes bei dem mittelgroßen Manne festgestellt: Mittlerer Ernihrungs- und Kräftezustand. Begründet von Dr- Paul Börner Begründet von Dr- Paul Börner VERLAG: GEORG THIEME LEIPZIG Rabensteinplatz 2 HERAUSGEBER: Gek San.-Rat Prof. Dr. Schwalbe Berlin - Charlottenburg, Schlüterstr. 53 Aus dem St. Hedwig-Krankenhaus in Berlin. Aus dem St. Hedwig-Krankenhaus in Berlin. 1) Vorgetragen in der Sitzung der Berliner Gesellschaft für Chirurgie am 23. Juni 1913. Radikaloperation eines primären Lungen- karzinoms.1) Rechts hinten unten neben der Wirbelsäule ist die Pleura und Lunge gesund, weiter nach vorn besteht Dämpfung und aufgehobene Atmung bis hinauf zur sechsten Rippe und nach vorn bis nahe zu den Rippenknorpeln. Status: Mittlerer Ernährungs- und Kräftezustand. Temperatur normal. Rechte Brustseite deutlich eingezogen. Die Atmung bleibt gegen die linke Seite zurück. In der vorderen Axillarlinie in Höhe der sechsten und siebenten Rippe eine kleinfingerlange, 1/2 cm tiefe, querver. laufende Granulationsfläche, die von der Operation des Herrn Dr. Sauer herrührte. Rechts hinten unten neben der Wirbelsäule ist die Pleura und Lunge gesund, weiter nach vorn besteht Dämpfung und aufgehobene Atmung bis hinauf zur sechsten Rippe und nach vorn bis nahe zu den Rippenknorpeln. Oben, median und unten war jetzt der von der Neubildung durchwachsene Teil der Brustwand umschnitten. Nun wurde noch hinten die Brustwand von unten ñach oben - in der Gegend der Anguli costarum -. durchschnitten, und zwar im Bereiche der zehnten, neunten, achten, siebenten und sechsten Rippe. Oben, median und unten war jetzt der von der Neubildung durchwachsene Teil der Brustwand umschnitten. Nun wurde noch hinten die Brustwand von unten ñach oben - in der Gegend der Anguli costarum -. durchschnitten, und zwar im Bereiche der zehnten, neunten, achten, siebenten und sechsten Rippe. Oben, median und unten war jetzt der von der Neubildung durchwachsene Teil der Brustwand umschnitten. Nun wurde noch hinten die Brustwand von unten ñach oben - in der Gegend der Anguli costarum -. durchschnitten, und zwar im Bereiche der zehnten, neunten, achten, siebenten und sechsten Rippe. Dèr rings umschnittene Brustwandlappen konnte mit der an ihn festgewachsenen Lunge noch nicht aus der Thoraxhöhle hervorgezogen werden, weil die Neubildung weitgehend auch in das Zwerchfell hinein- gewachsen und an dieses fixiert war. Es mußte jetzt die Lunge im Gesunden von dem Tumor abgetrennt werden, was sich am bequemsten an der kollabierten Lunge ausführen läßt. Deshalb wurde von jetzt ab der Ueberdruck weggelassen, ohne daß bei dem gut narkotisierten Patienten unbequeme Pneuniothoraxsym- ptome aufgetreten wären. Ich trug dann die kollabierte Lunge oberhalb des Tumors im Gesunden quer herüber ab, in einer Linie, welche in Höhe Das Röntgenbild (Nr. 1 ergab bei der Aufnahme von vorn nach hinten einen Schatten, der das Dreieck zwischen Lebersehatten, seit- licher Rippenwandlinie bis hinauf zur sechsten Rippe (in der Axillar. linie) ausfühlte. Zwischen diesem Schatten und dem Herzschatten ober- halb der Leber besteht eine zweiquerfingerbreite Zone von heller (luf t- haltiger) Lunge. (S. Fig. Radikaloperation eines primären Lungen- karzinoms.1) Zwischen dritter und fünfter rechter Rippeund zwischen der vorderen und mittleren Axillarlinie findet sich eine etwa kleinhandtellergroße geringe Niveaudifferenz - im Vergleich zur korrespondierenden Stelle der linken Seite - und bei der Palpation hat man den Eindruck einer geringen Infiltration. Bei Druck auf diese Gegend äußert der Patient eine ziemlich lebhafte Schmerzempfindung, die sich den Interkostalnerven entlang ausbreitet. Es wurde in der ganzen Länge des Schnittes die freie Pleurahöhle eröffnet, ohne daß (unter Ueberdruck) dabei unangenehme Erscheinungen auftraten. Die eingeführte Hand stellte fest, daß wenig unter der sechsten Rippe der in eine harte Masse verwandelte untere Lungenlappen mit der seitlichen Thoraxwand fest verwachsen war, daß aber median - in der Gegend der Rippenknorpel und des Mediastinums - und hinten in der Gegend der Anguli costarum die Lunge bis hinab zum Zwerchfell frei, ohne Adhäsionen war. Nach oben zu im Bereiche des Mittel- und Ober- lappens bestanden keinerlei Verwachsungen. Die Pleurahöhle wurde pro- visorisch mit Gazetüchern tamponiert. Hierauf wurde die Brustwand median von oben nach unten, vom sechsten Rippenknorpel hinab bis an den Rippenbogen, durchschnitten. Nach unten zu reichte die mit der Brustwand verwachsene Neubildung zwischen der Mamillarlinie und der Axillarlinie bis nahe an den Rippenbogen". Es mußte daher unten die Haut und die Brustwand nahe und parallel dem Rippenbogen durchtrennt werden, wobei der knöcherne Teil der zehnten Rippe mit entfernt wurde. Nachdem der Patient sich für einige Wochen einer Badekur unter- worfen hatte, gelangte er in Wittenberge in die Behandlung des Herrn Dr. Sauer, der am 30. Juli 1912 eine Operation vornahm. Dabei wurden Stücke aus der neunten, achten und siebenten Rippe reseziert und festgestellt, daß nicht, wie vorher angenommen worden war, ein ent- zündlicher Prozeß, sondern eine Neubildung vorlag, welche die Brustwand durchwachsen hatte. Die mikroskopische Untersuchung zeigte ein Karzinom, das von der Lunge seinen Ausgang genommen hatte. Herr Dr. Sauer hat in Ermangelung eines Ueberdruckapparates den Patienten dem St. Hedwigs-Krankenhaus überwiesen, wo er am 10. September 1912 aufgenommen wurde. Status: Mittlerer Ernährungs- und Kräftezustand. Temperatur normal. Rechte Brustseite deutlich eingezogen. Die Atmung bleibt gegen die linke Seite zurück. In der vorderen Axillarlinie in Höhe der sechsten und siebenten Rippe eine kleinfingerlange, 1/2 cm tiefe, querver. laufende Granulationsfläche, die von der Operation des Herrn Dr. Sauer herrührte. Nr. 35 Nr. 35 BERLIN, DEN 28. FtUGUST 1913 39. JFIHROFINO Diagnose. Auf Grund dieses Befundes und des mikroskopischen Präparates von Herrn Dr. Sauer wurde die Diagnose auf ein Karzinom Aus dem St. Hedwig-Krankenhaus in Berlin. des rechten unteren Lungenlappens gestellt, das sich lateral auf die Brust- wand ausgebreitet, dagegen medianwärts, nach dem Hilus zu, die Lunge noch frei gelassen habe und sich für eine Exstirpation vielleicht eignen könne. Deutsche MedizinIsche Wochenschrifi Begründet von Dr- Paul Börner Radikaloperation eines primären Lungen- karzinoms.1) Ende Oktober hatte sich die Granulationsfläche auf der Oberfläche der Leber und im Bereiche des freiliegenden Mediastinums erheblich verkleinert. Letzteres bewegte sich bei ruhiger Atmung ein wenig, indessen machte es beim Husten noch starke Exkursionen. Oberhalb der Leber folgte in der Tiefe der Granu- lationshöhle ein schmaler Streifen von der hinteren Thoraxwand und dar- über die granulierende Resektionsfläche der Lunge in der Höhe des sechsten bis zum dritten Rippenknorpel. Am medianen Ende derseJben war ein großer offener Bronchus zu sehen, der Hauptbronchus des unteren ( resezierten) Lungenlappens, aus dem besonders beim Husten die Luft unter scharfem Geräusch ausströmte. Die übrigen hei der Operation durchschnittenen Bronchi hatten sich geschlossen. pp gg Versorgung der Wundhöhle. Im Bereich der Leberoberfläche wurde hinter die Reste des Zwerchfells seitlich und vorn das Peritoneum mit der Serosa der Leber vernäht und darüber die Haut mit Nähten in der Richtung von vorn nach hinten zusammengezogen, so weit es möglich war. Der größte Teil der Leberoberfläche blieb infolge des großen Haut- defektes unbedeckt. Des weiteren stand die Aufgabe vor uns, die große Höhle des oberen Thoraxraumes einigermaßen zu decken. Infolge des ausgedehnten Verlustes an Haut war es unmöglich, den oberen Haut- rand in Höhe der fünften Rippe mit dem unteren Rand der zurück- gelassenen - kollabierten - Lunge zu vernähen. Um das zu erreichen, blieb nichts anderes übrig, als von der restierenden oberen Rippenwand noch ein großes Stück im Bereich der fünften, vierten und dritten Rippe mit der großen Rippenschere zu exstirpieren. Danach gelang es, den oberen Hautrand an den unteren Rand der zurückgebliebenen kollabierten Lunge ohne Spannung anzunähen. Indessen legte sich die Haut nur auf dem unteren Ende der Lunge auf, während weiter oben zwischen Lunge und Haut und Brustwand bis hinauf zur Kuppel der Thoraxhöhle noch ein großer Hohlraum, gewiß von Kindskopfgröße, übrig blieb. Um das Sekret aus diesem Raume abzuleiteu, wurde ein Drainrohr einge- führt. Zwischen diesem durch die Haut abgedeckten oberen Thoraxraum und der Leberoberfläche blieb ein großer, offener Wundraum übrig, der unten von der Leberoberfläche, oben von der an die Lunge angenähten Haut und der Resektionsfläche der Lunge und nach innen von dem Herz- beutel und dem (bis zum unteren Rand des Hilus freiliegenden) Media- stinum gebildet wurde. Radikaloperation eines primären Lungen- karzinoms.1) Nur die auf- gepackte Gaze wurde gewechselt. des unteren Randes des Lungenhilus horizontal nach außen verlief. In dieser Linie wurde mittels Desehamps das gesunde Lungengewebe in größeren Portionen umstochen und (mit Katgut) fest abgebunden, was ganz ohne Blutung gelang. Die Bronchien und Gefäße wurden nicht be- sonders herauspräpariert. Der Hauptbronchus für den unteren Lungen- lappen wurde, wie später die Sektion zeigte, 4-5 cm von der Bifur- kation entfernt, an der Stelle, wo er vom rechten Hauptbronchus abgeht, abgebunden. In den ersten Wochen post operationem klagte Patient viel über Schlingbeschwerden und Schmerzen den Oesophagus entlang bis hinab zum Magen. Dadurch wurde die Nahrungsaufnahme recht erschwert. Später verloren sieh diese Beschwerden. Der Magen vermochte noch lange Zeit keine größeren Mengen von Nahrung aufzunehmen, weil das Gefühl von Druck und Völle, Neigung zum Erbrechen nach stärkerer Füllung des Magens sich einstellte. g g Nun hing das Präparat noch am Zwerchfell. Es zeigte sich, daß der Tumor in großer Ausdehnung mit dem Zwerchfell verwachsen war und daß die Neubildung das Zwerchfell medianwärts bis dicht an den Herzbeutel in Form einer harten Platte durchwachsen hatte. Es mußte deshalb fast das ganze rechte Zwerchfell ausgeschnitten werden, median bis dicht an den Herzbeutel, vorn und lateral einschließlich des Rippen- ansatzes. Hinten blieb noch ein zweiquerfingerbreiter Streifen übrig. Etwa 14 Tage post operationem stellten sich eigenartige Anfälle von Atemnot ein, die mit Schmerzen im Rücken und in der rechten Schulter verbunden waren und einige Minuten bis eine Viertelstunde dauerten. Sie konnten meist mit Morphium schnell beseitigt werden und traten täglich ein bis mehrere Male auf. Trotzdem erholte sich der Patient zusehends und machte einen gegen alle Erwartungen günstigen Eindruck. Damit war die Exstirpation der Neubildung beendet. Wir standen jetzt vor einer riesigen Wundhöhle : man sah u n t e n die ganze freiliegende Oberfläche des rechten Leberlappen, m e d i a n den Herzbeutel und über diesem das Mediastinum bis zum Ililus der Lunge, und weiter oben den kollabierten oberen und den größten Teil des mittleren Lungenlappens, welche - weil kollabiert - als wenig voluminöse Masse neben der Wirbel- sï.ule lagen. Davor dehnte sich ein gewaltiger Hohlraum bis hinauf zur Lungenspitze aus, der vorn begrenzt wurde durch die Thoraxwand der fünf oberen Rippen. Zu dieser Höhle führte ein kolossaler Defekt der Brustwand im Bereich der sechsten bis zehnten Rippe, wo nicht bloß die Rippen, sondern auch die Haut weggenommen worden waren. Die Wundheilung machte gute Fortschritte. Radikaloperation eines primären Lungen- karzinoms.1) Wir wurden sehr angenehm überrascht davon, daß das Drainrohr gar keinen Eiter ableitete und daß sich in diesem Oberhalb der granulierenden Resektionsfläche der Lunge setzte sieh in Höhe des dritten Rippenknorpels die Thoraxhaut an, die bei der Operation auf den untersten Band der zurückgelassenen Lungen- pleura aufgenäht worden war und die den oberen Thoraxraum abschloß. Ich hatte angenommen daß sich in Fig. 2. Fig. 2. Die eigentliche Wundhöhle im Bereiche des Mediastinums der Leber- oberfläche, der hinteren Thoraxwand und des unteren Randes der Mittel- lappen der Lunge hatte sich allmählich infolge der Vernarbungsschrump- fung wesentlich verkleinert und der gewaltige Tailleneinschnitt bedeutend abgeflacht. Aber trotzdem sahen wir doch noch eine recht große Granu- lationsfläche vor uns. Deshalb, und um den offenen Bronchus zum Ver- schluß zu bringen, wurde am 3. November eine Nachoperation (unter Lokalanästhesie) ausgeführt. In der Gegend des M. pectoralis major wurde ein vierquerfingerbreiter Hautlappen mit medianem Stiel gebildet und so heruntergeklappt, daß die Granulationsfläche der Lunge, des Mediastinums und der hinteren Brustwand bedeckt wurde. Der Lappen heilte an. G E d N b k d P i d B l d g p Postoperativer Verlauf. Als der Patient nach dieser über zwei Stunden andauernden Operation in das Bett gefahren wurde, waren wir der Ueberzeugung, daß er wahrscheinlich noch am selben Tage sterben würde. Zu unserer Freude erholte er sich aber sehr schnell von dem kolossalen Eingriff: der Puls war um 120. Am ersten und zweiten Tage bestand etwas blutiger Auswurf. Beim Husten stellte sich stets infolge Mediastinalflatterns große Atemnot ein. Dieserhalb und weil er über heftige Schmerzen klagte, wurde ihm sehr reichlich Morphium verabfolgt, das ausgezeichnete Dienste leistete, weil der Hustenreiz und damit das Mediastinaiflattern herabgesetzt wurde. So gestaltete sich bereits am zweiten Tage das Befinden ganz zufriedenstellend. Puls zwischen 100 und 120 Schlägen. Temperatur in der ersten Zeit um 38° herum. Am fiiniten Tage post operationem wurde die in die Schürze ge- stopfte Gaze gezogen, wobei ein heftiger Hustenanfall und hochgradiges Mediastinaflattern auftrat. Unter der Schürze stellte sich eine lebhafte Blutung an der Lungenwundfläche ein. Die Situation erschien überaus bedenklich. Es mußte eine leichte (Inhalations.) Narkose ausgeführt Postoperativer Verlauf. Als der Patient nach dieser über zwei Stunden andauernden Operation in das Bett gefahren wurde, waren wir der Ueberzeugung, daß er wahrscheinlich noch am selben Tage sterben würde. Zu unserer Freude erholte er sich aber sehr schnell von dem kolossalen Eingriff: der Puls war um 120. Radikaloperation eines primären Lungen- karzinoms.1) 1.) Das Röntgenbild (Nr. 1 ergab bei der Aufnahme von vorn nach hinten einen Schatten, der das Dreieck zwischen Lebersehatten, seit- licher Rippenwandlinie bis hinauf zur sechsten Rippe (in der Axillar. linie) ausfühlte. Zwischen diesem Schatten und dem Herzschatten ober- halb der Leber besteht eine zweiquerfingerbreite Zone von heller (luf t- haltiger) Lunge. (S. Fig. 1.) pp Dèr rings umschnittene Brustwandlappen konnte mit der an ihn festgewachsenen Lunge noch nicht aus der Thoraxhöhle hervorgezogen werden, weil die Neubildung weitgehend auch in das Zwerchfell hinein- gewachsen und an dieses fixiert war. Dèr rings umschnittene Brustwandlappen konnte mit der an ihn festgewachsenen Lunge noch nicht aus der Thoraxhöhle hervorgezogen werden, weil die Neubildung weitgehend auch in das Zwerchfell hinein- gewachsen und an dieses fixiert war. g Es mußte jetzt die Lunge im Gesunden von dem Tumor abgetrennt werden, was sich am bequemsten an der kollabierten Lunge ausführen läßt. Deshalb wurde von jetzt ab der Ueberdruck weggelassen, ohne daß bei dem gut narkotisierten Patienten unbequeme Pneuniothoraxsym- ptome aufgetreten wären. Ich trug dann die kollabierte Lunge oberhalb des Tumors im Gesunden quer herüber ab, in einer Linie, welche in Höhe g Es mußte jetzt die Lunge im Gesunden von dem Tumor abgetrennt werden, was sich am bequemsten an der kollabierten Lunge ausführen läßt. Deshalb wurde von jetzt ab der Ueberdruck weggelassen, ohne daß bei dem gut narkotisierten Patienten unbequeme Pneuniothoraxsym- ptome aufgetreten wären. Ich trug dann die kollabierte Lunge oberhalb des Tumors im Gesunden quer herüber ab, in einer Linie, welche in Höhe Diagnose. Auf Grund dieses Befundes und des mikroskopischen Präparates von Herrn Dr. Sauer wurde die Diagnose auf ein Karzinom Diagnose. Auf Grund dieses Befundes und des mikroskopischen Präparates von Herrn Dr. Sauer wurde die Diagnose auf ein Karzinom 209 DEUTSCHE MEDIZIMSC11E WOCHENSORRIFT. Nr. 35 Nr. 35 1666 werden, um den Hustenreiz zu beschwichtigen und die blutende Stelle in der Lungenwundfläche mit Kremallierenzangen fassen und ligieren zu können. Auch diesen Eingriff vertrug der Patient gut. Von neum wurde eine Schürzentamponade angelegt, die dann trotz der starken Durchtränkung mit Sekret etwa zehn Tage liegen blieb. Nur die auf- gepackte Gaze wurde gewechselt. werden, um den Hustenreiz zu beschwichtigen und die blutende Stelle in der Lungenwundfläche mit Kremallierenzangen fassen und ligieren zu können. Auch diesen Eingriff vertrug der Patient gut. Von neum wurde eine Schürzentamponade angelegt, die dann trotz der starken Durchtränkung mit Sekret etwa zehn Tage liegen blieb. Radikaloperation eines primären Lungen- karzinoms.1) Es entstand dabei ein ungemein tiefer Einschnitt in das Thoraxprofil, der hinten bis an die Rippenwinkel reichte und unten von der Leberoberfläche und o b e n von der auf die Lunge aufgenähten Haut gebildet wurde. Auf diese gewaltige Wundfläche wurde eine Jodoformgazeschürze gelegt und diese mit einer großen Menge steriler Gaze ausgestopft und mittels Ref tpf lasterstreifen, welche die linke Lunge nicht komprimierten, fixiert. Ueber das Ganze wurde schließlich ein locker angelegter Bindenverband gelegt. Das Verhalten des Media- stinums war, so lange die Narkose tief war, sehr günstig, indem es durch die Atmung der gesunden (linken) Lunge nur wenig hin und her bewegt wurde. Am Schluß der Operation aber, als etwas Husten auftrat, geriet es mit fürchterlichen Exkursionen ins Flattern". Wir mußten mit großen Gazetüchern gegenstützen, um besonders die starke Verschie- bung nach der kranken Seite zu verhüten. Es trat starke Zyanose dabei auf, aber glücklicherweise kein bedrohlicher Kollaps. P t ti V l f Al d P i h di b i Heruntergeladen von: NYU. Urheberrechtlich geschützt. Oberhalb der granulierende sieh in Höhe des dritten Rippenk der Operation auf den untersten pleura aufgenäht worden war und Ich hatte angenommen, daß sich in diesem durch ein Gummirohr drai- nierten Raume ein Empyem eut- wickeln würde. Wir wurden sehr angenehm überrascht davon, daß das Drainrohr gar keinen Eiter ableitete und daß sich in diesem großen Hohlraum infolge Resorp- tion der darin enthaltenen Luft die Lunge wieder ausgedehnt hatte (Fig. 2) und den Hohlraum bis auf eine taubeneigroße Höhle oben an der Lungenspitze voll- kommen ausfüllte. Offenbar hatte sich das Drainrohr verstopft, und so war der große Luftraum von der Außenwelt luftdicht abge- schlossen worden. Das Allge- meinbefinden hatte sich so ge- bessert, daß der Patient Mitte Oktober das Bett verlassen und etwas umhergehen konnte. Oberhalb der granulierenden Resektionsfläche der Lunge setzte sieh in Höhe des dritten Rippenknorpels die Thoraxhaut an, die bei der Operation auf den untersten Band der zurückgelassenen Lungen- pleura aufgenäht worden war und die den oberen Thoraxraum abschloß. Ich hatte angenommen, daß sich in diesem durch ein Gummirohr drai- Fig. 2. nierten Raume ein Empyem eut- wickeln würde. Radikaloperation eines primären Lungen- karzinoms.1) W d M ll (R k) (5) d h Ob l i Von älteren Fällen erwähnt G arr è in seinem Handbuch Lungen- chirurige 1912 sieben tödlich verlaufene Fälle und noch drei erfolgreiche von Tuffier, Lowson und Doyen. W d M ll (R k) (5) d h Ob l i y Wurde von Müller (Rostock) (5) der rechte Oberlappen mit Glück amputiert, die Brusthöhle geschlossen bis auf eine Stelle, wo ein Tampon auf den Hilusstumpf eingeführt wurde. Der Patient starb drei Wochen post operationem an tuberkulöser Meningitis d di li k Wurde von Müller (Rostock) (5) der rechte Oberlappen mit Glück amputiert, die Brusthöhle geschlossen bis auf eine Stelle, wo ein Tampon auf den Hilusstumpf eingeführt wurde. Der Patient starb drei Wochen post operationem an tuberkulöser Meningitis p p g Von Macewen (6) wurde die ganze linke Lunge, in der eine große Kaverne pneumotomiert worden und von der nicht mehr viel Parenchym übrig geblieben war, subtotal aus dem verwachsenen Pleura- raum ausgelöst und entfernt. Die ganze Lungenhöhle wurde tamponiert. Der Patient befand sich 16 Jahre nach der Operation noch gesund. Von Macewen (6) wurde die ganze linke Lunge, in der eine große Kaverne pneumotomiert worden und von der nicht mehr viel Parenchym übrig geblieben war, subtotal aus dem verwachsenen Pleura- raum ausgelöst und entfernt. Die ganze Lungenhöhle wurde tamponiert. Der Patient befand sich 16 Jahre nach der Operation noch gesund. b) W i h R b) Wegen traumatiseher Ruptur hat S au erbru ch neuerdings (persönliche Mitteilung) den linken Unter- lappen aus der freien Pleurahöhle amputiert. Der Hilus ließ sich mit Lungengewebe übernähen. Die Thoraxhöhle wurde geschlossen und eine glatte Heilung erzielt. b) Wegen traumatiseher Ruptur hat S au erbru ch neuerdings (persönliche Mitteilung) den linken Unter- lappen aus der freien Pleurahöhle amputiert. Der Hilus ließ sich mit Lungengewebe übernähen. Die Thoraxhöhle wurde geschlossen und eine glatte Heilung erzielt. Nachdem die Krankengeschichte des Falles mitgeteilt worden ist, will ich Ihnen das von mir gesammelte, in der Literatur niedergelegte Material, das die E n t fern u ng y o n Teilen der Liingensubstanz betrifft, kurz mitteilen. Am häufigsten sind Lungenamputationen wegen ) B hi k i füh d I h k e) Bronchiektasien ausgeführt worden. Ich konnte im ganzen 16 Fälle zusammenstellen. Die meisten dieser Opera- tionen sind bei h Pl höhl d I. Radikaloperation eines primären Lungen- karzinoms.1) Am ersten und zweiten Tage bestand etwas blutiger Auswurf. Beim Husten stellte sich stets infolge Mediastinalflatterns große Atemnot ein. Dieserhalb und weil er über heftige Schmerzen klagte, wurde ihm sehr reichlich Morphium verabfolgt, das ausgezeichnete Dienste leistete, weil der Hustenreiz und damit das Mediastinaiflattern herabgesetzt wurde. So gestaltete sich bereits am zweiten Tage das Befinden ganz zufriedenstellend. Puls zwischen 100 und 120 Schlägen. Temperatur in der ersten Zeit um 38° herum. Am fiiniten Tage post operationem wurde die in die Schürze ge- stopfte Gaze gezogen, wobei ein heftiger Hustenanfall und hochgradiges Mediastinaflattern auftrat. Unter der Schürze stellte sich eine lebhafte Blutung an der Lungenwundfläche ein. Die Situation erschien überaus Gegen Ende November konnte der Patient das Bett verlassen und allmählich auf dem Korridor spazieren gehen. Ende November konnte festgestellt werden, daß aus dem offenen Bronchus doch noch Luft neben den Lappen unter Geräusch hervordrang. Das Mediastinum war durch den aufgewachsenen Hautlappen besser fixiert, infolge Narbenschrumpfung etwas nach rechts disloziert und bewegte sich beim ruhigen Atmen nur ganz wenig, aber beim Husten doch immer noch recht stark. An der gesunden linken Lunge ließ sich sowohl perkutorisch als auch am Röntgenbilde ein bedeutendes vikariierendes Emphysem fest- stellen. Die Lunge reichte bis zur elften Rippe herunter und hatte das Zwerchfell nach abwärts gedrückt. Die linke Thoraxseite arbeitete auch beim ruhigen Atmen mit den Hilf smuskeln am Halse, und das linke Zwerch- Ende November konnte festgestellt werden, daß aus dem offenen Bronchus doch noch Luft neben den Lappen unter Geräusch hervordrang. Das Mediastinum war durch den aufgewachsenen Hautlappen besser fixiert, infolge Narbenschrumpfung etwas nach rechts disloziert und bewegte sich beim ruhigen Atmen nur ganz wenig, aber beim Husten doch immer noch recht stark. A d d li k L li ß i h hl k i h l An der gesunden linken Lunge ließ sich sowohl perkutorisch als auch am Röntgenbilde ein bedeutendes vikariierendes Emphysem fest- stellen. Die Lunge reichte bis zur elften Rippe herunter und hatte das Zwerchfell nach abwärts gedrückt. Die linke Thoraxseite arbeitete auch beim ruhigen Atmen mit den Hilf smuskeln am Halse, und das linke Zwerch- An der gesunden linken Lunge ließ sich sowohl perkutorisch als auch am Röntgenbilde ein bedeutendes vikariierendes Emphysem fest- stellen. Die Lunge reichte bis zur elften Rippe herunter und hatte das Zwerchfell nach abwärts gedrückt. Radikaloperation eines primären Lungen- karzinoms.1) Dezember ein Ende bereitete. Am 2. Dezember 1912 trat eine heftige Angina auf mit Temperaturen bis über 390, die sich in Form eines schweren Katarrhes rasch auf die Luftwege der gesunden Lunge fortsetzte und ihm bei dem dauernden heftigen Hustenreiz die größte Atemnot bereitete und seinem Leben unter den Symptomen der Erstickung am 9. Dezember ein Ende bereitete. g Während bei den bisher besprochenen Fä]len bei ver- wachsener Pleurahöhle operiert wurde, sind b i i ih ll b i f i l h hl Während bei den bisher besprochenen Fä]len bei ver- wachsener Pleurahöhle operiert wurde, sind B. bei einer Reihe von Fällen bei freier Pleurahöhle, wo also die Gefahr des akuten Pneumothorax übernommen werden muß, kleinere Teile der Lunge entfernt worden. B. bei einer Reihe von Fällen bei freier Pleurahöhle, wo also die Gefahr des akuten Pneumothorax übernommen werden muß, kleinere Teile der Lunge entfernt worden. Präparat (Dr. Rheindorf): Im exstirpierten rechten unteren Lungenlappen findet sich eine haselnußgroße Höhle, die in einer derben, grauweißlichen, fast homogenen Tumormasse liegt. Die Oberfläche der Höhlenwand ist hockerig, uneben und ihre Begrenzung gegen das Lungengewebe unscharf. Präparat (Dr. Rheindorf): Im exstirpierten rechten unteren Lungenlappen findet sich eine haselnußgroße Höhle, die in einer derben, grauweißlichen, fast homogenen Tumormasse liegt. Die Oberfläche der Höhlenwand ist hockerig, uneben und ihre Begrenzung gegen das Lungengewebe unscharf. Gerulanos (10) hat in seiner Arbeit vier Fälle (Sedillot, Krön- 1cm (faustgroßer Tumor), Müller (3 : 9 cm großer Tumor) und König) erwähnt, wo bei der Entfernung von Brustwandtumoren kleinere, mit letzterem verwachsene Teile der Lunge exzidiert wurden. Der Lungen- defekt konnte in diesen vier Fällen, da größere Bronchien nicht verletzt waren, übernäht und versenkt und die Pleurahöhle und Thoraxwand wieder geschlossen werden. Alle diese Fälle haben den Eingriff gut überstanden. Mikroskopisch handelt es sich um ein Karzinom mit klar an- gedeuteter Verhornung. Typische Hornperlen fehlen. Das Wachstum erfolgt in großen Zapfen, in denen auch Andeutung von Drilsenbildung vorhanden ist. Einige Zapfen zeigen zentral starke Detritusbildung. Vermutlich ist der Ausgangspunkt eine bronchiektatische oder phthisische Höhle. In der Wand konnten tuberkulöse Veränderungen nicht nach- gewiesen werden. An der linken Lunge hatte der Patient Zeichen einer geheilten Tuberkulose. Mikroskopisch handelt es sich um ein Karzinom mit klar an- gedeuteter Verhornung. Typische Hornperlen fehlen. Das Wachstum erfolgt in großen Zapfen, in denen auch Andeutung von Drilsenbildung vorhanden ist. Einige Zapfen zeigen zentral starke Detritusbildung. Vermutlich ist der Ausgangspunkt eine bronchiektatische oder phthisische Höhle. Radikaloperation eines primären Lungen- karzinoms.1) Die linke Thoraxseite arbeitete auch beim ruhigen Atmen mit den Hilf smuskeln am Halse, und das linke Zwerch- 1667 DEUTSCHE MEDIZINISCHE WOCHENSOHEIFT. 28. August 1913. erzielt worden sein. Man kann kaum Zweifel und die Frage unterdrücken, ob hier nicht vielleicht bei der mikroskopischen Untersuchung, auf welche die Diagnose sich stützt, ein Irrtum vorgekommen sein könnte. erzielt worden sein. Man kann kaum Zweifel und die Frage unterdrücken, ob hier nicht vielleicht bei der mikroskopischen Untersuchung, auf welche die Diagnose sich stützt, ein Irrtum vorgekommen sein könnte. erzielt worden sein. Man kann kaum Zweifel und die Frage unterdrücken, ob hier nicht vielleicht bei der mikroskopischen Untersuchung, auf welche die Diagnose sich stützt, ein Irrtum vorgekommen sein könnte. erzielt worden sein. Man kann kaum Zweifel und die Frage unterdrücken, ob hier nicht vielleicht bei der mikroskopischen Untersuchung, auf welche die Diagnose sich stützt, ein Irrtum vorgekommen sein könnte. fell verschob sich so tief nach abwärts, daß die Bauchwand stark vorge- wölbt wurde und die Leber, welche des Gegenhalters der Rippenwand beraubt war, sich bei jedem Atemzug stark nach rechts vorwölbte. Beim Husten waren diese Phänomene in hohem Grade ausgesprochen. Bedenkt man weiter, daß bei heftigerem Exspirieren auch noch eine gewisse, wenn auch kleine Menge Luft durch die Bronchusfistel entwich, so begreift man, daß der Patient selbst für die ruhige Atmung große Muskelkraft ver- geuden mußte. So kam es, daß er oft über Atemnot klagte und diese schon bei leichten Anstrengungen, wenn er z. B. etwas langer sprach, fühlte. Man hatte den Eindruck, daß er des Lebens nicht recht froh werden konnte. g g e) Fünf Fälle gelangten zur Operation, weil größere Bronchusfisteln im Anschluß an eine Pneumotomie, die wegen Lungenabszeß ausgeführt war, nicht heilen wollten, und zwar ein Fall von F. Krause (7), drei Fälle von Garrè (8) und ein Fall von Perthes (9). Die Autoren haben die Bronchusfistel dadurch zum Verschluß gebracht, daß sie die Wand der Lungenhöhle, auf deren Grund der Bronchus ausmündete, anfrischten, also eine mehr oder weniger dicke Schicht Lungengewebe abtrugen, und die angefrischten Flächen miteinander vernähten, worauf in allen diesen Fällen der gewünschte Er- folg erzielt wurde. Am 2. Dezember 1912 trat eine heftige Angina auf mit Temperaturen bis über 390, die sich in Form eines schweren Katarrhes rasch auf die Luftwege der gesunden Lunge fortsetzte und ihm bei dem dauernden heftigen Hustenreiz die größte Atemnot bereitete und seinem Leben unter den Symptomen der Erstickung am 9. Radikaloperation eines primären Lungen- karzinoms.1) Beginnen wir mit der Entfernung von kleineren Teilen der Lunge und betrachten hier wieder geordnet jene Fälle, bei denen die Operation bei verwachsener oder freier Pleurahöhle ausgeführt worden ist. A B i h Pl höhl h b b i verwachsener Pleurahöhle vorgenommen worden, nämlich bei sechs Fällen, und zwar: Ei F ll G è (11) h il i F ll H id h i (12) verwachsener Pleurahöhle vorgenommen worden, nämlich bei sechs Fällen, und zwar: Ei F ll G è (11) h il i F ll H id h i (12) Ein Fall von Garrè (11) geheilt, ein Fall von Heidenhain (12) geheilt, ein Fall von Körte (13) geheilt, ein Fall von Lenhartz (14) geheilt, ein Fall von Quervain (14) geheilt, ein Fall von Gluck (16) geheilt. B i f i h Pl höhl A. Bei verwachsener Pleurahöhle haben a) bei Lungen- Aktinomykose K ki (1) d J d i ki (2) hd i hö i F A. Bei verwachsener Pleurahöhle haben a) bei Lungen- Aktinomykose K ki (1) d J d i ki (2) hd i h i F Karewski (1) und Jadwinski (2), nachdem ein gehöriges Fenster in der Thoraxwand gebildet worden war, die erkrankten Lungenpartien mittels Thermokauter und Schere und scharfem Löffel entfernt, wobei eine nahezu faustgroße, respektive hühnereigroße Höhle in der Lunge gebildet wurde. In beiden Fällen ist eine Dauerheilung erzielt worden. b) B i i bl L k i i Karewski (1) und Jadwinski (2), nachdem ein gehöriges Fenster in der Thoraxwand gebildet worden war, die erkrankten Lungenpartien mittels Thermokauter und Schere und scharfem Löffel entfernt, wobei eine nahezu faustgroße, respektive hühnereigroße Höhle in der Lunge gebildet wurde. In beiden Fällen ist eine Dauerheilung erzielt worden. b) B i i bl L k i i Bei freier unverwachsener Pleurahöhle wurde operiert: p Ein Fall von Garrè (11) mit glücklichem Ausgang, ein Fall von Friedrich (17) Amputation des linken Unterlappens. Bronehienver- sorgung nach seiner Methode und Uebernähung mit Lungengewebe. Verschluß des Thoraxfensters bis au.f Tamponöffnung. Am fünften Tage post operationem Mediastinalemphysem und Tod. Die Sektion vermochte die Stelle des undichten Bronchus nicht festzustellen. Zwei Fälle von Willy Meyer (18), die beide am Schluß der Operation starben, und zwar, wie er angibt, infolge von Vaguslähmung und Kohlensäure- vergiftung (letztere, weil die Uoberdruekmaske zu selten geliiftet worden war). Am häufigsten sind Lungenamputationen wegen ) B hi kt i füh t d I h k Radikaloperation eines primären Lungen- karzinoms.1) In der Wand konnten tuberkulöse Veränderungen nicht nach- gewiesen werden. An der linken Lunge hatte der Patient Zeichen einer geheilten Tuberkulose. II. Gehen wir nunmehr zu den Fällen über, bei denen ganze Lungenlappen und mehr amputiert worden sind. Ich konnte folgendes Material aus der Literatur sammeln, das zunächst A h d A d k k d Sektionsbefund (Dr. Rheindorf): Defekt der vierten bis neunten Rippe und des rechten Zwerchfells, wie die Krankengeschichte angibt. Rechts Leberkonvexität in Höhe der siebenten, der linken in Höhe der sechsten Rippe. Herz ganz nach rechts hinübergezogen. Der Herzbeutel ohne Verwachsungen. Die rechte Lunge, von welcher der untere Lappen fehlt, ist mit dem Rest der rechten oberei Thoraxwand und der Haut fest verwachsen und emphysematös. An ihrer Spitze zwischen Pleura pulmonalis und costalis eine hiihnerei- große Höhle, die mit einer gelblich - rötlichen Flüssigkeit gefüllt ist. Am Lungenhilus findet man einen strohhalmdicken, blind endenden Bronchus, der 7 cm lang ist und weiter unten einen zweiten, gut bleistiftdicken, 4 cm langen Bronchus, der mit einer strohhalmdicken Oeffnung frei unter dem deckenden Hautlappen endigt. Die Oeff- nung hatte sich durch die Vernrbungsprozesse so weit verengert. Die linke Lunge sehr voiuminös, Alveolen groß und lufthaitig. Die Bronchien sehr weit und mit schleimig-eitriger Flüssigkeit gefüllt. In der Spitze mehrere kleine, schiefrige Indurationen und ein hanfkorn großer Kalkherd. An der Pleura im Oberlappen und Unterlappen je ein hanfkorngroßer, derber, flacher Knoten, der sich mikroskopisch als Krebsmetastase erwies. Herz etwas über faustgroß, braun, schlaff. Klappen intakt. Rechter Ventrikel weit, dilatiert. Muskulatur bis 0,6 cm dick. Milz klein - Leber gestaut. Heruntergeladen von: NYU. Urheberrechtlich geschützt. A. nach der Art der Lungenerkrankung geordnet folgen soll. Die Operation wurde ausgeführt: ) L b k l A. nach der Art der Lungenerkrankung geordnet folgen soll. Die Operation wurde ausgeführt: ) L b k l a) wegen Lungentuberkulose: V äl Fäll äh G è i Von älteren Fällen erwähnt G arr è in seinem Handbuch Lungen- chirurige 1912 sieben tödlich verlaufene Fälle und noch drei erfolgreiche von Tuffier, Lowson und Doyen. W d M ll (R k) (5) d h Ob l i Von älteren Fällen erwähnt G arr è in seinem Handbuch Lungen- chirurige 1912 sieben tödlich verlaufene Fälle und noch drei erfolgreiche von Tuffier, Lowson und Doyen. Radikaloperation eines primären Lungen- karzinoms.1) EinFall von 11m mel 1 (21 ), Exstirpation der ganzen rechten Lunge: die gesamte rechte Lunge des 48 Jahre alten Mannes war zu einem zwei- faustgroßen Tumor, der mit der Umgebung vielfach verklebt war, ver- wandelt und der Pleuraraum mit einem blutig-serosen Exsudat gefüllt. Der Tumor und die gesamte Pleura sind mit Krebsknötchen durchsetzt. Der Hilus wird mit starken Klemmen gefaßt, die nach Abtragung der Lunge liegen bleiben. Die Pleurahöhle wird tamponiert. Die ersten Tage Wohlbefinden. Tod am sechsten Tage post operationem unter Sym- ptomen von Sepsis, die vom nekrotischen Hilusstumpf ausging. jst die Versorgung der durchschnittenen größe- ren Bronchi von großer Wichtigkeit für eine gewisse Gruppe der Lungenlappenamputation. Wenn die Wundhöhle oder der Hilusstumpf nach der Operation tamponiert worden ist, wie es bei den Bronchiektasien die Regel ist, dann zieht das Aufgehen der Bronehusligatum keine Gefahren nach sich, weil die aus dem Bronchus ausströmende Luft frei nach außen entweichen kann. Wenn aber die Pleurahöhle nach der Amputation des Lungen- lappens wieder geschlossen wird, dann folgt dem Aufgehen des ligierten Bronchus der Spannungspneumothorax, der in einem Falle von F r j e d r i e h den unglücklichen Ausgang ver- schuldete. Endlich vermag das Mediastinalemphysem das Leben des Patienten zu bedrohen. Friedrich hat diese Korn- plikation bei einem seiner Fälle erleben müssen Heruntergeladen von: NYU. Urheberrechtlich geschützt. Ein Fall von S au e rbr uch (22) : Unter Druckdifferenz Exstirpation des linken karzinomatösen Unterlappens aus der freien Pleurahöhle. Am Hilus blieben etwa 6 cm von der Lungenwurzel stehen, mit welcher der Hilusstumpf unter Deckung aller Bronchien übernTht werden konnte. Eine besondere Versorgung des Bronchus war deshalb nicht notwendig. Die Neubildung ließ sich radikal entfernen bis auf den Teil, wo sie am Perikard und Zwerchfell adhiLrent war. Dort mußte etwas vom Tumor zurückgelassen werden. Der Hilusstumpf wurde in die Pleura eingenäht, nachdem die Lunge unter Druckdifferenz aufgebläht worden war, darüber wurden die Weichteile der Thoraxwand geschlossen. Es war wegen Bronchektasien der linke Unterlappen nach Ab- klemmung des Hilus mittels einer Zange amputiert, die Hilusgefäße isoliert unterbunden und der Hauptbronchus nach seiner eigenen Methode versorgt und der Stumpf mit Lungengewebe übernäht worden. Das Thoraxfenster wurde dann soweit geschlossen, daß der stumpf noch tam- poniert werden konnte. Nach fünf Tage langem ausgezeichneten Wund- verlauf trat plötzlich Mediastinalemphysem auf und führte zum Tode. Die Sektion zeigte, daß der Verschluß des Hauptbronchus nicht nachgelassen hatte. Radikaloperation eines primären Lungen- karzinoms.1) g g Ich habe nur drei Fälle auffinden können; der meinige ist also der vierte. i ll lf i h l Ein Fall von Helferich - Gerulanos (20): Exstirpation des Mittel- und Unterlappens der rechten Lunge. Es handelte sich um ein Sarkom der Thoraxwand rechterseits, das so weit in die unteren beiden Lungenlappen hineingewachsen war, daß die Entfernung beider nötig wurde. Der Hilus wurde mit Umstechungen abgebundèn und über ihm noch vorhandenes Lungengewebe vernüht. Die Thoraxwand mußte wegen der großen Ausdehnung der G eschwulst von der dritten Rippe bis zum Zwerchfell und von den Rippenknorpeln bis zu den Anguli costarum entfernt werden. Der gewaltige Defekt der Brustwand konnte nicht gedeckt werden, weshalb die große Höhle mit Tamponade versorgt wurde. Der 15 Jahre alte Patient war am Schluß der 1 Stunden dauernden Operation kollabiert, erholte sich in den folgenden Stunden etwas, starb aber etwa 20 Stunden nach der Operation unter den Symptomen von Kurz- atmigkeit und beschleunigtem Puls. Ein Fall von Helferich - Gerulanos (20): Exstirpation des Mittel- und Unterlappens der rechten Lunge. Es handelte sich um ein Sarkom der Thoraxwand rechterseits, das so weit in die unteren beiden Lungenlappen hineingewachsen war, daß die Entfernung beider nötig wurde. Der Hilus wurde mit Umstechungen abgebundèn und über ihm noch vorhandenes Lungengewebe vernüht. Die Thoraxwand mußte wegen der großen Ausdehnung der G eschwulst von der dritten Rippe bis zum Zwerchfell und von den Rippenknorpeln bis zu den Anguli costarum entfernt werden. Der gewaltige Defekt der Brustwand konnte nicht gedeckt werden, weshalb die große Höhle mit Tamponade versorgt wurde. Der 15 Jahre alte Patient war am Schluß der 1 Stunden dauernden Operation kollabiert, erholte sich in den folgenden Stunden etwas, starb aber etwa 20 Stunden nach der Operation unter den Symptomen von Kurz- atmigkeit und beschleunigtem Puls. Die Blutstillung hat bei Abtragung der Lungenlappen in keinem der vorliegenden Fälle Schwierigkeiten bereitet, und Nachblutungen sind während des Wundverlaufs nicht be- obachtet worden. Nur bei meinem Falle entstand beim ersten Wechsel der Tamponade aus mehreren Stellen der Lungen- wundfläche infolge eines sehr heftigen Hustenanfalles eine Blu- tung, die in leichter Narkose durch Ligatur rasch gestilit werden konnte. Einer Wiederholung derselben wurde dann dadurch vorgebeugt, daß die Schürzentamponade sehr lang ( gegen zwölf Tage) liegen gelassen wurde. Radikaloperation eines primären Lungen- karzinoms.1) A ß di hi i t i t h Fäll h b i h h b) Bei inoperablen Lungenkarzinonien hat Lenhartz (3) in drei und Küttner (4) in zwei Fällen Erweichungs- höhlen eröffnet und einen Teil der Geschwulstmasse mit dem scharfen Löffel entfernt. Außerdem wurde von Lenhartz in zwei weiteren Fällen versucht, in das nicht erweichte, inoperable Karainom vorzudringen und Teile desselben zu entfernen. Keiner von diesen Fällen ist im Anschluß an die Operation gestorben, doch sind sie, weil der Tumor nur teilweise entfernt worden war, einige Zeit nach der Operation zugrunde gegangen. Nur; ein Fall von Lenhartz, bei dem eine große Erweichungshöhle eröffnet worden war, deren Wandungen später öfter mit Röntgenstrahlen bestrahlt wurden, ist allmählich geheilt und hat sich zwei Jahre später noch in blühender Gesundheit befunden. Obwohl von der Höhlenwand des erweichten Karzinoms nichts entfernt worden ist, soll durch die Rönt- genbestrahlung eine vollkommene Heilung dieses ausgedehnten Tumors Außer diesen hier registrierten zehn Fällen habe ich noch weitere sechs Fälle erwähnt gefunden, aber so kurz, daß ein genaueres Urteil über diese nicht gewonnen werden konnte: Rovsing (19) verlor zwei Fälle anscheinend am akuten Pneumo- thorax, Friedrich einen Fall (aus der Greifswalder Zeit) an Bronchus- insuffizienz und Spannungpneumothorax, Sauer bruch (nach persön- 209 * DEIJTSCTT1 MEDIZINISCHE WOOHENSOJIRIFT. 1668 Nr. 35 Nr. 35 licher Mitteilung) einen Fall am Schluß der Operation an unklaren TJr- sachen, vielleicht infolge der Narkose. Ueber je einen Fall von Murphy und Kiimmell konnte ich Näheres nicht finden. d) R h l h b N bild d L Dagegen sind einige Fälle, bei denen nach dem Operation die Thoraxhöhle ganz geschlossen wurde (zwei Fälle von S au e r - b ru e h , die traumatische Ruptur und das Karzinom der Lunge, ferner der Fall Müllers) ohne Symptome von Infektion glatt geheilt, obwohl Exsudate ex vacuo resombiert werden mußten. Zu erwähnen ist hier auch mein Fall insofern, als die durch Haut abgeschlossene obere Thoraxhöhle - die mit einem Drainrohr versehen war - so aseptisch geblieben ist, daß sich die darin lagernden beiden oberen Lungenlappen nach Re- sorption der Luft ausdehnten und die ganze Höhle schwand bis auf einen taubeneigroßen Raum, der mit trüb-seröser Flüssig- keit gefüllt war, wie die Sektion zeigte. d) Recht selten haben Neubildungen der Lunge zu Radikaloperationen, zur Entfernung von ganzen Lungenlappen, Anlaß gegeben. d) Recht selten haben Neubildungen der Lunge zu Radikaloperationen, zur Entfernung von ganzen Lungenlappen, Anlaß gegeben. Radikaloperation eines primären Lungen- karzinoms.1) Ein genaues Absuchen der übrigen Bronchi ver- m3chte nicht die Stelle aufzufinden, aus der die Luft ausgeströmt war. Vielleicht hat die quetschende Hilusklemme an einem Bronchus einen kleinen, schwer sichtbaren Defekt gesetzt. i i h d d h h i hi Glatter Verlauf. Der Hohlraum an Steile des amputierten Lungen- lappens füllte sich durch Bildung eines Exsudats ex vacuo und nach dessen Resorption durch kompensatorische Blähung des zurück- gebliebenen Oberlappens und Hinaufrücken des Zwerchfells. i i i k h h h d li ik l Die Patientin konnte nach sechs Wochen aus der Klinik entlassen werden. Ei F ll R b füh li h i il E b i Die Patientin konnte nach sechs Wochen aus der Klinik entlassen werden. Ei F ll R b f h li h i il E b i Ein Fall von Rotter oben ausführlich mitgeteilt. Er besitzt große Aehnlichkeit mit dem Fall Helferich- Gerulanos, weil von der Thoraxwand so viel entfernt werden mußte, daß eine Deckung des De- fektes nicht möglich war. B ü li h d A d h f Bezüglich der Ausdehnung des entfernten Lungenabschnittes ist zu bemerken, daß unter diesen eben mitgeteilten 18 Fällen 14 mal nur ein Lungenlappen, und zwar 13 mal der lJnterlappen und 1 mal (Müller, Rostock) der rechte Oberlappen entfernt worden Ist und daß viermal mehr als ein Lappen fortgenommen wurde, nämlich von Helferich- erulanos der rechte Unter- und Mittellappen, von Macewen und von G luck fast die ganze Lunge (aus der verwachsenen Pleurahöhle wegen Tuberkulose resp. Bronchiektasie) und end- ]ich von Kümmell die ganze, zu einem zweifaustgroßen Tumor geschrumpfte karzinomatöse Lunge. N h ll i di R lt t di b i d Die sichere Versorgung der durchschnittenen Bronchi ge- hört augenblicklich noch zu den schwierigsten Aufgaben bei den vorliegenden Operationen. Experimentell ist die Frage schon eingehend bearbeitet, aber unsere klinischen Erfahrungen sind noch recht gering. b h h i i ll i l d Sauerbruch hat in zwei Fällen (ein Pal] von Ruptur der Lunge und ein Fall von Karzinom der Lunge) mittels der Unterbindung des Bronchus und der Uebemnähung des Stumpfes (also nach der Methode von Garre) glatten Verlauf erzielt. Eine weitere Gefahr droht dem Patieñten bei der L ungen- operation durch die Vagusreflexe, die während der Mani- pulation am Hilus auftreten können. DEUTSCHE MEDIZINISCHE WOCHENSCHTRIFT. Im Falle Helferich- Gerulanos wurde ein Sarkom der Thorax- wand und der untere mittlere Lappen der rechten Lunge entfernt, wobei von den Rippen nur die erste, zweite und dritte und zehnte, elfte und zwölfte zuriickblieben. Der riesige Defekt ließ sich nicht decken, und die ganze unverwachsene Pleurahöhle mußte tamponiert werden. Der 15 Jahre alte Knabe starb nach G e r u 1 a n o s infolge des fortbestehenden Pneumothorax bei normal beweglichem Mediastinum 20 Stunden nach der Operation. Gerulanos huit es für fraglich, ob ein Patient unter den gegebenen anatomischen Verhiiltnissen imstande sei, weiter zu leben, wo der volle atmosphärische Luftdruck auf da unverlinderte, weiche, versehiebliche Mediastinum lind auf die schlaffen Hohlvenen und den rechten Vorhof lastet und die Resfirations- und Zirkulationsverhiiltnisse in einer so tief eingreifenden Weise gestört sind. Wenn aber die Lungenoperationen in der weitgeöffneten, freien, unverwachsenen Pleurahöhle ausgeführt worden sind, wo das Mediastinum seine Weichheit und Beweglichkeit bewahrt hatte, dann können das von Garr è so benannte Mediastinal- flattern und durch dieses schwere Atmungs- und Zirkulations- störungen und Kollapse auftreten. Heruntergeladen von: NYU. Urheberrechtlich geschützt. Seit jener Zeit ist - soweit ich die Literatur übersehe bis auf meinen Fall eine ähnliche Beobachtung nicht mitgeteilt worden. Mein Fall besitzt für die vorliegende Frage noch des- halb eine besondere Bedeutung, weil er die Operation ein Viertel- jahr überlebt hat und die Folgen dieser weitgehenden operativen Verstümmelung längere Zeit beobachtet werden konnten. Der Krankheitsverlauf hat gezeigt, daß der Patient in den ersten Wochen nach der Operation nur wenig unter Atmungsbeschwer- den gelitten hat, daß sich diese vielmehr erst später, nach ein paar Wochen, stärker bemerkbar machten und sich allmäh- lich gesteigert haben. Nach der Statistik von Gerulanos ist diese Komplikation in etwa der Häfte der Fälle aufgetreten, doch hat sie in keinem Falle einen tödlichen Ausgang nach sich gezogen. In unserer Statistik der Lungenlappenamputationen bei freier Pleurahöhle ist während der Operation ein Todesfall infolge von Kollaps. der durch den akuten Pneumothorax bedingt worden wäre, auch nicht vorgekommen, obwohl ganz kolossale Defekte in die Brustwand gesetzt worden sind, z. B. im Fall Helferich- Gerulanos und dem meinigen, und obwohl die Operation öfter eine lange Dauer von 1 1/2_2 Stunden erforderte. Das Druckdifferenzverfahren wird in Zukunft die Gefahr des akuten Pneumothorax wohl ganz beseitigen, wie das bereits jetzt in einer ganzen Reihe unserer Lungenlappenamputationen er- freulicherweise beobachtet werden konnte. DEUTSCHE MEDIZINISCHE WOCHENSCHTRIFT. Der akute Pneumo- thorax wird am Schluß der Operation dadurch beseitigt, daß die Pleurahöhle geschlossen und so das mechanische Gleich- gewicht im Thorax wiederhergestelit wird. Dieser Umstand spricht nicht dafür, daß die Ursache der Atmungsinsuffizienz hauptsächlich in der Verschieblichkeit des Mediastinums gelegen habe. Denn die letztere besaß ihren höch- sten Grad in den ersten Woehen nach der Operation. Nachdem aber das Mediastinum im Verlauf von ein paar Wochen sich mit einer Granulationsschicht bedeckt und durch deren Schrump- fung eine gewisse Fixation erhalten hatte, die so weit ging, daß das Herz nach der rechten Seite hinüber gezogen wurde, hätten die Atmungsbeschwerden geringer werden müssen. Die klinische Erfahrung hat aber gelehrt, daß sie von da ab stärker in die Erscheinung traten und dann allmählich noch weiter zu- genommen haben. In seltenen Fällen ist es aber nicht möglich, am Schluß der Operation den Pneumothorax zu beseitigen, nämlich dann, wenn von der Brustwand ein so großer Teil entfernt werden mußte, daß ein Verschluß der Pleurahöhle nicht hergestellt werden kann. Dann resultiert der Zustand eines dauernden Pneu mothorax. In einem gewissen Grade hat die Atmung und die Zirkulation durch Verschiebung des Mediastinums bei der In- und Ex- spiration zweifellos eine Behinderung erlitten, wie das besonders bei angestrengter Atmung und bei Hustenanfällen deutlich in die Augen sprang. Aber daneben haben zweifellos eine Reihe anderer Momente eine, große Rolle gespielt. In erster Linie ist der komplette Ausfall einer ganzen, zumal der größeren rechten Lunge zu nennen. Um ihre Funktion zu ersetzen, mußte das Zwerchfell die linke Lunge ausgiebiger und häufiger bewegen. Darum ist der hohe Grad des vikariierenden Ein- physems entstanden, das, wie das Röntgenbild zeigt, bis hinab zur elften Rippe reichte. Mit der Zunahme des Emphy- sems mußten die Bewegungen des Zwerchfells an Um- fang verlieren, weil dieses in der Exspirationsstellung nicht mehr zur normalen Höhe heraufsteigen konnte und seine Exkursionen an Ausdehnung verloren. Es mußten deshalb da- neben noch alle Atrnungshilfsmittel in Tätigkeit treteti, und zwar dauernd, wie das in der letzten Zeit stets beobachtet werden konnte. li k hf ll d h d h i i Wir beobachteten ihn unter zwei verschiedenen Bedingun- gen, 1. wenn bei entzündlichen Erkrankungen der Lunge und verwachsener Pleura, also bei den Bronchiektasien, operiert wird. Dann bleibt die Pleurahöhle nach Schluß der Operation offen, weil die infizierte Wundhöhle tamponiert werden muß. DEUTSCHE MEDIZINISCHE WOCHENSCHTRIFT. 28. Augast 1913. 2. Ungünstiger als bei verwachsener Pleura gestalteten sich die Verhältnisse, wenn die Operation im freien Pleuraraum ausgeführt wurde und am Schlu 13 die Pleurahöhle wegen des allzu großen Defektes der Thoraxwand nicht geschlossen werden konnte. und Kollaps und rasch der Tod eingetreten sind. Die Narkose war wenigstens für zwei Fälle für das traurige Ereignis nicht verantwortlich zu machen, denn bei einem Falle war Lokalanästhesie und beim zweiten nur einige Tropfen Chloroform angewandt worden. Auch L e n hartz hat ähnliches erlebt. S au e r b r u e h teilte mir persönlich einen Fall von Lungenlappen- amputation mit, der am Schluß der Operation plötzlich starb. Er Ist der Ansicht, daß der Narkose die Schuld für den traurigen Ausgang zu- zuschreiben ist. In dieser Richtung liegen bisher drei Beobachtungen vor, ein Fall von Weinlechner (s. Gerulanos Fall 10, S. 518), ein zweiter Fall von Helferich-Gerulanos und ein dritter von mir. (Im Fall Kümmell, Carcinoma pulmonis, war das Mediastinuin durch Knötehendissemination in eine feste Schwarte. verwandelt und konnte daher zum Flattern des Mediastinums nicht führen.) In solchen Fällen bestehen nianchmal die größten Schwierig- keiten, die Todesursache genau zu bezeichnen, und es wird unsere Aufgabe sein, bei der Operation in Zukunft die Symptome recht genau zu beobachten und zu registrieren, uni allmählich mehr Klarheit in dieses jetzt noch unklare Gebiet zu bringen. Der Patient Weinlechners, bei dem ein mannskopfgroßes Myxoqhondrom und ein Stück Lunge aus der freien Pleurahöhle entfernt wurde. starb 24 Stunden nach der Operation unter den Symptomen der Dyspnoe und schwachen, beschleunigten Pulses. I)ie Sektion zeigte eine eitrige Pleuritis, die zum raschen Tode neben dem Mediastinalflattern gewiß das ihre noch beigetragen hat. Deshalb ist dieser Fall für die vor- liegende Frage nur hedingungsweise verwertbar. 5. An fliufter Stelle ist unter den Gefahren der Lungen- operationen der akute Pneumothorax zu nennen. Diese Gefahr macht sich so gLit wie garnicht geltend bei jenen Fällen, bei welchen vor der Operation das Mediastinum durch entzündliche Prozesse, z. B. bei den Bronchiektasien, verdickt und verhärtet und durch Verwachsungen fixiert worden war und seine Beweglichkeit verloren hatte. Man hat zwar auch bei solchen Fällen leichte Mediastinalverschicbungen beobachtet .- Macewen und Körte - indessen doch nur in so geringem Grade, daß bedenkliche Zustände nicht aufgetreten sind. Radikaloperation eines primären Lungen- karzinoms.1) g p g Nunmehr wollen wir die Resultate, die bei der Amputation von einzelnen oder mehreren Lungenlappen ge- wonnen wurden, kurz betrachten. Die Hauptgefahren, die diese Operationen belasten, sind folgende: 1 Di I f k i Bei Friedrichs Fall Kostbahn mit Druckdifferenz trat beim Fassen des Hauptbronchus mit der Quetschzange eine Atmungssynkope und Kollaps auf, die rasch wieder vorübergingen. Dagegen verlor Willy Meyer seine beiden Lungenmputationen (wegen Bronchiektasie bei freier Pleurahöhle mit Druckdifferenz) am Vagustod. Während der etwas schwierigen Arbeit bei Abtragung des abgeklemmten Hilus, speziell bei der Ligatur eines Hauptgefäßes, kollabierten die Patienten unter Verlang- samung des Pulses und starben, der eine am Schluß der Operation, der andere eine Stunde nach deren Beendigung. Willy Meyer meint, daß neben dem Vagusreflex auch noch die Kohlensäurevergiftung mit- gewirkt habe, welche dadurch zustande gekommen sei, daß bei der Ueberdrucknarkose die Lunge zu wenig ventiliert worden sei. i i i i d d i h b i kl i 1. Die Infektion. Sie spielt trotz der Größe der Opera- tionen keine nennenswerte Rolle. Es liegt kein Fall, wenigstens in der mir vorliegenden Statistik, vor, der einer während der Operation entstandenen Infektion erlegen wäre. Ein Fall ist an einer postopemativen Infektion zugrunde gegangen, nämlich die Totalexstirpation der karzinomatösen Lunge von K ü mme U, aber unter ganz besonderen Verhältnissen. Es war der ganze Hulus mit einer großen Klemme abgequetscht und in einiger Entfernung von ihm die Lunge abgetragen worden. Die Klemme wurde liegen gelassen, und so mußte der distal von ihr liegende Stumpf nekrotisch werden, der - obwohl tam- poniert - zu Sepsis und am sechsten Tage post operationem zum Tode führte. Dieses traurige Ereignis des Vagustodes ist auch bei kleine- ren Lungenoperationen beobachtet worden. So berichtet Körte über drei Fälle (Lungenfistel, bronchektatische Kaverne), bei denen, ohne daß die freie Pleurahöhle eröffnet worden war, nach sonst gelungener Operation (Pneumotomie) plötzliche Atemstörung 1669 DEUTSCHE MEDIZINISCHE WOCHENSCHTRIFT. Literatur: 1. Karewski, Berliner klinische Wochenschrift 1898, Nr. 15. - 2. Jacowski, Zentraiblatt für Chirurgie 1897, Nr. 28. - 3. Lenh artz, bei Müser, Jahrbücher der Hamburger Staats-Krankenhäuser 1907, Bd. 12. - 4. lÇüttner, Ver. handlungen der Deutechen Gesellschaft für Chirurgie 1908. - 5. Müller, Chirurgen. Kongreß 1912. - 6. Macewen, siehe Lungenchirurgie von Garrè und Quincke, zweite Auflage, 1912, S. 170. - 7. F. Krause, Berliner klinische Wochenschrift, Bd. 16, S. 347. - 8. Garrè, Diese Wochenschrift 1904, S. 533. - 9. Perthes, Chirurgen. Kongreß 1908, Bd. 2, S 222. - 10. Gerulanos, Deutsche Zeitschrift für Chirurgie 1898, Bd. 49. - 11. Garrt, Lungenchirurgie, zweite Auflage 1912 und genauer zitiert von Sauerbruch, Deutsche Zeitschrift für Chirurgie 1909, Bd. 102. - 12. Heidenhain, Chirurgen-Kongreß 1901, Bd. 2, S. 636. - 13. Körte, Langenbecks Archiv für klinische Chirurgie, Bd. 85, S. 29-30. - 14. Len h arta, siehe K is sling, Jahrbücher der Hamburger Staatskrankenhäuser, 5. 75, Fall 27. - 15. Quervain, Chirurgen.Kongreß 1912, 5. 41. - 16. Gluck, ebenda 1907. - 17. Friedrich, ebenda 1908, Bd. 2, S. 573. - 18 Willy Meyer, Annales of surgery 1910, Juli-Dezember, Vol. 52, S. 38. - 19. Mollgard.Rovsing, Zentralblatt für Chirurgie 1910, S. 1276. - 20. Gerulanos, Deutsche Zeitschrift für Chirurgie 1898, Bd. 49. - 21. Kümmell, Chirurgen.Kongreß 1911, Bd. 2, S. 147. - 22. Sauerbruch, ebenda 1908, S. i53. - DEUTSCHE MEDIZINISCHE WOCHENSCHTRIFT. In diesen Fällen ist das Mediastinum durch die entzündlichen Prozesse, Verwachsungen und Schwarten so fixiert, daß nur ausnahms- weise Pneumothoraxsymptome auftreten. In der Kasuistik der Lungerilappenamputationen, wo die Pleura verwachsen war, sind nur bei einem Falle nach der Operation Pneumothoraxsymptorne aufgetreten, niimlic h im Falle Macewen. Er entfernte die hochgradig kavernös zerstörte linke Lunge fast ganz und berichtet, daß hinterher durch lange Wochen der Patient Dyspnoe zeigte, welche verschwand, wenn er sich auf die kranke Seite legte, wobei das Modiastinum sich nach der tamponierten I'leurahöhle senkte und das Flattern desselben aufhörte. Im weiteren Wundverlaufe haben sich aber durch die entzündlichen Schwarten, die sieh durch die Granu- lation auf dem Mediastinum bildeten, diese Symptome ganz verloren, und der Patient lebte nach 1 Jahren post operationem noch in recht guter Verfassung. Dem linken Zwerchfell wurde noch durch ein zweites Moment die Arbeit erschwert. Weil hei der Operation das ganze DEIJPSOIIE MEDIZINISCHE WOOHENSORIll'T. Ñr. 35 Ñr. 35 1670 rechte Zwerchfell und der untere Brustkorb hatten entfernt werden müssen, fehlte der Leber die natürliche Befestigung in ihrer Lage. Sie wurde nun vom linken Zwerchfell, das einseitig arbeiten mußte, bei jeder Inspiration weithin über die rechte Seitenkontur des Rumpfes hinausgeschoben und kehrte bei der Exspiration wieder in die natürliche Lage zurück. Diese ausgedehnten Verschiebungen des schweren Organs stellten an die Arbeitskraft des linken Zwerchfells eine nicht zu unter- schätzende hohe Anforderung. rechte Zwerchfell und der untere Brustkorb hatten entfernt werden müssen, fehlte der Leber die natürliche Befestigung in ihrer Lage. Sie wurde nun vom linken Zwerchfell, das einseitig arbeiten mußte, bei jeder Inspiration weithin über die rechte Seitenkontur des Rumpfes hinausgeschoben und kehrte bei der Exspiration wieder in die natürliche Lage zurück. Diese ausgedehnten Verschiebungen des schweren Organs stellten an die Arbeitskraft des linken Zwerchfells eine nicht zu unter- schätzende hohe Anforderung. Endlich ist noch das Bestehen der Bronchusfistel zu erwähnen, die freilich zuletzt durch Narbenschrumpfung ziemlich eng, kaum strohhalmdick, geworden war und, wenn auch nicht viel, doch immerhin etwas den Erfolg der Atem- bewegungen beeinträchtigte. d F it Ziehe ich das Fazit aus diesen Ueberlegungen, so möchte ich sagen, daß der dauernde Pneumothorax, das Frei- liegen des Mediastinums für sich allein, dem Patienten die Existenzfähigkeit nicht geraubt hätte. DEUTSCHE MEDIZINISCHE WOCHENSCHTRIFT. Wie beim Pyothorax schon zur Zeit der Operation das Mediastinum durch voraus- gegangene Entzündung fixiert ist, so ist in meinem Falle das freiliegende Mediastinum durch die Vernarbung allmählich be- festigt worden und hätte für sich allein die Atmung nicht in einer existenzbedrohenden Weise beeinträchtigt. Aber all die übrigen Momente, die bei meinem Falle durch die ausgedehnte Ope- ration hinzugefügt worden waren, würden dem Patienten kaum ein lebenswertes Dasein für die Dauer gestattet haben und haben in der Tat im Verlaufe von drei Monaten seine Wider- standsfähigkeit in so hohem Grade eingeschränkt, daß eine diffuse Bronchitis seinen Tod herbeiführen konnte. Heruntergeladen von: NYU. Urheberrechtlich geschützt. Schluß. Ueberblicken wir zum Schluß noch einmal die Operationsresultate bei den Lungenlappenamputationen, so ergibt sich folgendes: V d G hl d 22 i ll Schluß. Ueberblicken wir zum Schluß noch einmal die Operationsresultate bei den Lungenlappenamputationen, so ergibt sich folgendes: Von der Gesamtzahl der 22 von mir zusammengestellten Fälle müssen wir 5 Fälle (1 Fall von Murphy, 2 Fälle von Rovsing, 1 Fall von Kümmell und 1 Fall von Friedrich) ausschalten, weil ich keine genauen Angaben erlangen konnte. Es verblieben demnach 17 Fälle von Lungenlappen- amputation Schluß. Ueberblicken wir zum Schluß noch einmal die Operationsresultate bei den Lungenlappenamputationen, so ergibt sich folgendes: V d G hl d 22 i ll Von der Gesamtzahl der 22 von mir zusammengestellten Fälle müssen wir 5 Fälle (1 Fall von Murphy, 2 Fälle von Rovsing, 1 Fall von Kümmell und 1 Fall von Friedrich) ausschalten, weil ich keine genauen Angaben erlangen konnte. E bli b d h 17 F ll L l Von der Gesamtzahl der 22 von mir zusammengestellten Fälle müssen wir 5 Fälle (1 Fall von Murphy, 2 Fälle von Rovsing, 1 Fall von Kümmell und 1 Fall von Friedrich) ausschalten, weil ich keine genauen Angaben erlangen konnte. E bli b d h 17 F ll L l Es verblieben demnach 17 Fälle von Lungenlappen- amputation. p Durchgekommen sind li Fälle, und zwar: 1. wegen Tuberkulose operierte Fälle: 2 Fälle (Macewen und Müller), 2. wegen Bronchiektasie operierte Fälle: 7 Fälle (6 bei ver- wachsener Pleura und 1 bei freier Pleurahöhle), 3. wegen Tumor operierte Fälle: 2 Fälle (Sauerbruch und Rotter). G b i d p Durchgekommen sind li Fälle, und zwar: 1. wegen Tuberkulose operierte Fälle: 2 Fälle (Macewen und Müller), 2. DEUTSCHE MEDIZINISCHE WOCHENSCHTRIFT. wegen Bronchiektasie operierte Fälle: 7 Fälle (6 bei ver- wachsener Pleura und 1 bei freier Pleurahöhle), 3. wegen Tumor operierte Fälle: 2 Fälle (Sauerbruch und Rotter). G b i d p Gestorben sind: I A V d 2 Fäll I. An Vagustod 2 Fälle (W. Meyer), 2. an Kollaps am Schluß der Operation 1 Fall (Sauerbrueh), 3. an akutem Pneumothorax und Kollaps 1 Fall (Gerulanos), 4. an Me- diastinalemphysem 1 Fall (Friedrich), 5. an Sepsis von nekro- tischein Blilusstuinpf 1 Fall (Kümmell). Di Z hl i d kl i d ß i B i d M Die Zahlen sind so klein, daß eine Bestimmung der Mor- tahitätsprozente noch zwecklos erscheint, zumal gewiß mancher unglücklich verlaufene Fall nicht publiziert worden ist. Wir leben noch in einer Zeit, wo jeder Fall für sich ein besonderes Interesse besitzt und gesammelt zu werden verdient, und des- halb wollte ich auch mein Schärflein dem kleinen vorhandenen Material hinzufügen.
https://openalex.org/W2043346183
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English
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Molecular Basis for the Resistance of Human Mitochondrial 2-Cys Peroxiredoxin 3 to Hyperoxidation
Journal of biological chemistry/˜The œJournal of biological chemistry
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Molecular Basis for the Resistance of Human Mitochondrial 2-Cys Peroxiredoxin 3 to Hyperoxidation* y y Received for publication,April 3, 2013, and in revised form, August 20, 2013 Published, JBC Papers in Press,September 3, 2013, DOI 10.1074/jbc.M113.473470 Alexina C. Haynes‡1, Jiang Qian§1,2, Julie A. Reisz§, Cristina M. Furdui§3, and W. Todd Lowther‡4 From the ‡Center for Structural Biology and Department of Biochemistry, §Section on Molecular Medicine, Department of Intern Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157 Received for publication,April 3, 2013, and in revised form, August 20, 2013 Published, JBC Papers in Press,September 3, 2013, DOI 10.1074/jbc.M113.473470 Alexina C. Haynes‡1, Jiang Qian§1,2, Julie A. Reisz§, Cristina M. Furdui§3, and W. Todd Lowther‡4 From the ‡Center for Structural Biology and Department of Biochemistry, §Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157 Background: Human 2-Cys peroxiredoxins (Prxs) are differentially susceptible to inactivation by H2O2. Results: Engineered Prx2 and Prx3 variants demonstrate that C-terminal residues modulate the extent of hyperoxidation. Conclusion: Rapid disulfide bond formation protects Prx3 from inactivation. Significance: The reactivity of Prx3 with H2O2 is important for understanding its protective role in the mitochondria. Background: Human 2-Cys peroxiredoxins (Prxs) are differentially susceptible to inactivation by H2O2. Results: Engineered Prx2 and Prx3 variants demonstrate that C-terminal residues modulate the extent of hyperoxidation. Conclusion: Rapid disulfide bond formation protects Prx3 from inactivation. Results: Engineered Prx2 and Prx3 variants demonstrate that C-terminal residues modulate the extent of hyperoxidation. Conclusion: Rapid disulfide bond formation protects Prx3 from inactivation. Significance: The reactivity of Prx3 with H2O2 is important for understanding its protective role in the mitochondria. p p Significance: The reactivity of Prx3 with H2O2 is important for understanding its protective role in the mitochondria. he reactivity of Prx3 with H2O2 is important for understanding its protective role in the mitochondria. Peroxiredoxins (Prxs) detoxify peroxides and modulate H2O2-mediated cell signaling in normal and numerous patho- physiological contexts. The typical 2-Cys subclass of Prxs (human Prx1–4) utilizes a Cys sulfenic acid (Cys-SOH) interme- diate and disulfide bond formation across two subunits during catalysis. During oxidative stress, however, the Cys-SOH moiety can react with H2O2 to form Cys sulfinic acid (Cys-SO2H), resulting in inactivation. The propensity to hyperoxidize varies greatly among human Prxs. Mitochondrial Prx3 is the most resistant to inactivation, but the molecular basis for this prop- erty is unknown. Molecular Basis for the Resistance of Human Mitochondrial 2-Cys Peroxiredoxin 3 to Hyperoxidation* A panel of chimeras and Cys variants of Prx2 and Prx3 were treated with H2O2 and analyzed by rapid chemi- cal quench and time-resolved electrospray ionization-TOF mass spectrometry. The latter utilized an on-line rapid-mixing setup to collect data on the low seconds time scale. These approaches enabled the first direct observation of the Cys-SOH intermediate and a putative Cys sulfenamide (Cys-SN) for Prx2 and Prx3 during catalysis. The substitution of C-terminal resi- dues in Prx3, residues adjacent to the resolving Cys residue, resulted in a Prx2-like protein with increased sensitivity to hyperoxidation and decreased ability to form the intermolecu- lar disulfide bond between subunits. The corresponding Prx2 chimera became more resistant to hyperoxidation. Taken together, the results of this study support that the kinetics of the Cys-SOH intermediate is key to determine the probability of hyperoxidation or disulfide formation. Given the oxidizing environment of the mitochondrion, it makes sense that Prx3 would favor disulfide bond formation as a protection mecha- nism against hyperoxidation and inactivation. Peroxiredoxins (Prxs)5 are ubiquitous, highly expressed anti- oxidant enzymes that can convert hydrogen peroxide (H2O2), peroxynitrite (ONOO), and lipid peroxides (ROOH) to water. Although this function was originally thought to be primarily protective in nature, Prxs also play a key role in modulating H2O2-mediated cell signaling in normal and pathophysiologi- cal contexts, including cell growth, differentiation, adrenal ste- roidogenesis, neurodegeneration, and cancer (1–5). Human cells contain six Prx isoforms with differences in subcellular localization and the content of Cys residues (6). The typical 2-Cys or Prx1 subclass (human Prx1–4) contains two catalytic Cys residues on each monomer of an obligate homodimer (Fig. 1A). Under normal conditions, the peroxidatic Cys residue (Cys-SPH) attacks a H2O2 molecule to form a sulfenic acid intermediate (Cys-SPOH). Subsequent structural rearrange- ments enable the active site to transition from the fully folded (FF) to a locally unfolded conformation. The Cys-SPH residue can then form a disulfide with the resolving Cys residue (Cys- SRH), located near the C terminus of the adjacent subunit. This disulfide (SP-SR) is reduced by the thioredoxin-thioredoxin reductase system. Additionally, during the catalytic cycle, an interchange between dimeric and higher order oligomeric states occurs, with the reduced decamer typically being the most active form (7, 8). Under conditions of high oxidative stress, a second H2O2 molecule can react with the Cys-SPOH moiety to form a Cys sulfinic acid (Cys-SPO2H) moiety within some Prx isoforms (9). THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 288, NO. 41, pp. 29714–29723, October 11, 2013 © 2013 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 288, NO. 41, pp. 29714–29723, October 11, 2013 © 2013 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 288, NO. 41, pp. 29714–29723, October 11, 2013 © 2013 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. 1 Both authors contributed equally to this work. * Thisworkwassupported,inwholeorinpart,byNationalInstitutesofHealth Grant R01 GM072866 from NIGMS (to W. T. L.) and Grant R01 CA136810 from NCI (to C. M. F.). 5 The abbreviations used are: Prx, peroxiredoxin; FF, fully folded; ESI, electro- spray ionization. * Thisworkwassupported,inwholeorinpart,byNationalInstitutesofHealth Grant R01 GM072866 from NIGMS (to W. T. L.) and Grant R01 CA136810 from NCI (to C. M. F.). 2 Present address: Dept. of Medicine, Duke University Medical Center, Dur- ham, NC 27710. 3 To whom correspondence may be addressed: Section on Molecular Medi- cine, Dept. of Internal Medicine, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, NC 27157. Tel.: 336-716-2697; Fax: 336-716- 1214; E-mail: cfurdui@wakehealth.edu. Molecular Basis for the Resistance of Human Mitochondrial 2-Cys Peroxiredoxin 3 to Hyperoxidation* This hyperoxidation of the Prx molecule results in inactivation and is thought to enable H2O2 to modulate the activity of a variety of other proteins, including phosphatases and the mas- ter redox transcription factor Nrf2 (10–12). Repair of the Prx molecules by sulfiredoxin restores the peroxidase activity, low- ers peroxide levels, and terminates subsequent downstream signaling events (9, 13–15). However, the susceptibility of human 2-Cys Prxs to hyperoxidation varies greatly, with the cytoplasmic Prx1 and Prx2 being more susceptible than the mitochondrial Prx3 (16). The resistance of Prx3 to hyperoxida- tion is consistent with its ability to maintain function within a highly oxidative environment, but the molecular basis for this 4 To whom correspondence may be addressed: Center for Structural Biology andDept.ofBiochemistry,WakeForestSchoolofMedicine,MedicalCenter Blvd., Winston-Salem, NC 27157. Tel.: 336-716-7230; Fax: 336-713-1283; E-mail: tlowther@wakehealth.edu. VOLUME 288•NUMBER 41•OCTOBER 11, 2013 29714 JOURNAL OF BIOLOGICAL CHEMISTRY * Thisworkwassupported,inwholeorinpart,byNationalInstitutesofHealth Grant R01 GM072866 from NIGMS (to W. T. L.) and Grant R01 CA136810 from NCI (to C. M. F.). 1 Both authors contributed equally to this work. 2 Present address: Dept. of Medicine, Duke University Medical Center, Dur- ham, NC 27710. 3 To whom correspondence may be addressed: Section on Molecular Medi- cine, Dept. of Internal Medicine, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, NC 27157. Tel.: 336-716-2697; Fax: 336-716- 1214; E-mail: cfurdui@wakehealth.edu. 4 To whom correspondence may be addressed: Center for Structural Biology andDept.ofBiochemistry,WakeForestSchoolofMedicine,MedicalCenter Blvd., Winston-Salem, NC 27157. Tel.: 336-716-7230; Fax: 336-713-1283; E-mail: tlowther@wakehealth.edu. Molecular Basis for Resistance of hPrx3 to Hyperoxidation The struc- ture of hyperoxidized Prx2 (Fig. 1C) illustrates the proximity of these regions to the Cys-SPH residue (19). In particular, the GGLG motif interacts with the C-terminal helix of the adjacent Prx subunit, which contains the Tyr and Phe residues of the YF motif. This specific interaction is postulated to slow the rate of formation of the intermolecular disulfide intermediate (SP-SR) during catalysis, enabling hyperoxidation to occur (6, 10). The changes in the Prx3 sequence in the proximity of the Cys-SRH residue and the YF motif have been postulated to alter the inter- action with the rest of the Prx molecule, resulting in a decreased susceptibility to hyperoxidation (9, 16). Therefore, changes in both regions in Prx3 may result in its unique biochemical and physiological properties. y g In this study, a panel of Prx2 and Prx3 variants and chimeras was analyzed to investigate the contribution of the observed sequence changes near the GGLG motif and the C terminus to hyperoxidation. Previous reports have used long time scales, nonreducing SDS-PAGE, two-dimensional PAGE, and West- ern blotting to monitor the hyperoxidation of Prx molecules (16, 20, 21). In contrast, the data presented herein was collected using a combination of rapid chemical quench and time-re- solved ESI-TOF mass spectrometry methods to facilitate anal- ysis under both denaturing and native conditions (22, 23). These improvements and the strategic use of Cys variants have enabled the direct observation of the Cys-SPOH intermediate during catalysis. Moreover, the stability of this intermediate in Prx2 is supported by the time-dependent formation of a puta- tive Cys-sulfenamide (SN) intermediate. Changing the C-ter- minal residues of Prx2 and Prx3 had the largest impact on resistance to hyperoxidation. The residues near the GGLG motif appeared to play a minimal role. Although Prx3 could be converted into a Prx2-like molecule and vice versa, the trans- formations were incomplete suggesting that additional resi- dues, regions of the protein, and perhaps the equilibrium of the oligomeric states may also be involved in regulating the ease of hyperoxidation. Altogether, the data support that the unique C-terminal residues of Prx3 facilitate the rapid formation of the SP-SR disulfide, thus protecting the enzyme from inactivation. For the Prx3 variants (WT, HA 3 PP (H155P and A159P), C2S (C127S and C229S), CT (N232G, T234K, D236G, and P238D), HA 3 PP  CT), the E. Molecular Basis for Resistance of hPrx3 to Hyperoxidation Molecular Basis for Resistance of hPrx3 to Hyperoxidation For the Prx2 variants (WT, PP 3 HA (P98H and P102A), C2S (C70S and C172S), CT (G175N, K177T, G179D, and D181P), PP 3 HA  CT), the E. coli cells were grown at 37 °C until an A600 of 0.8 and induced with 0.5 mM isopropyl 1-thio--D-ga- lactopyranoside at 25 °C for 4–5 h. Given the absence of an affinity tag, the purification required four chromatographic steps. The cells were lysed in 100 ml of 20 mM HEPES, pH 7.9, 100 mM NaCl, 1 mM EDTA containing protease inhibitors (PMSF and benzamidine; both at 0.1 mM) using an Emulsiflex C5 homogenizer (Avestin, Inc.). This mixture was then centri- fuged, and the supernatant was treated with 2.5% streptomycin sulfate followed by centrifugation. Ammonium sulfate was added to a final concentration of 20% to the supernatant, and the solution was filtered. This solution was loaded onto a phe- nyl-Sepharose high performance (Low Sub) column (GE Healthcare) and eluted with a 600-ml linear gradient to buffer without ammonium sulfate. The fractions corresponding to the Prx molecule, as determined by SDS-PAGE, were dialyzed into 20 mM Tris, pH 7.9, subsequently loaded onto a Q-Sepharose FF column (GE Healthcare), and eluted with a 600-ml linear gra- dient to 500 mM NaCl. The Prx fractions were pooled and dia- lyzed into 7 mM potassium phosphate, pH 7.0. The dialysate was subsequently loaded onto a CHT ceramic hydroxyapatite col- umn (Bio-Rad) and eluted with a 600-ml linear gradient to 400 mM potassium phosphate, pH 7.0. The Prx2-containing frac- tions were concentrated to 5 ml and loaded onto a Superdex 200 column equilibrated with 20 mM HEPES, pH 7.5, 100 mM NaCl. The Prx fractions were pooled, concentrated, flash-fro- zen with liquid nitrogen, and stored at 80 °C until use. All Prx2 proteins were stored in a buffer without dithiothreitol (DTT) with the exception of Prx2C2S, which was stored in 20 mM HEPES, pH 7.5, 100 mM NaCl, and 10 mM DTT. characteristic is not known. Moreover, a detailed analysis of Prx3 is needed to understand its ability to protect the murine heart from the damage caused by myocardial infarction and cancer cells from apoptosis-inducing drugs (2, 17, 18). An alignment of human Prx1–4 reveals that Prx3 has a unique primary sequence near the GGLG motif within the active site region (Fig. 1B) and near the C terminus. Molecular Basis for Resistance of hPrx3 to Hyperoxidation coli cells were grown at 37 °C until an A600 of 0.8 and induced with 0.5 mM isopropyl 1-thio- -D-galactopyranoside at 18 °C for 16 h. Expression from the pTYB21 vector results in the addition of an N-terminal chitin binding domain contained within an intein sequence, enabling the self-processing and removal of the chitin binding domain- intein tag after incubation with DTT. The cells were lysed in 150 ml of 20 mM Tris, pH 8.5, 500 mM NaCl, and 1 mM EDTA containing protease inhibitors (PMSF and benzamidine; both at 0.1 mM). The supernatant was loaded onto a chitin column (New England Biolabs) and extensively washed. Intein-medi- ated cleavage was initiated by equilibrating the column with 20 mM Tris, pH 8.5, 500 mM NaCl, 1 mM EDTA, and 50 mM DTT followed by a 40-h incubation at room temperature. The mature form of Prx3, residues 62–255, was eluted from the column, dialyzed against 20 mM Mes, pH 6.5, 1 mM DTT and subsequently loaded onto a Q-Sepharose FF column (GE Healthcare) and eluted with a 600-ml (0–50%) linear gradient to 1 M NaCl. The Prx3-containing fractions were concentrated and purified further using the Superdex 200 column, as described for the Prx2 variants. All Prx3 variants were stored in 20 mM HEPES, pH 7.5, 100 mM NaCl with the exception of Prx3 WT, which had 10 mM DTT. Molecular Basis for Resistance of hPrx3 to Hyperoxidation Preparation of Samples for Mass Spectrometry Analysis—Im- mediately prior to analysis, the Prx variants were thawed and reduced with 10 mM DTT at room temperature for 30 min. DTT was removed by passing the protein solution through a Bio-Gel P6 spin column (Bio-Rad) pre-equilibrated with either 50 mM Tris buffer, pH 7.5, or 50 mM ammonium acetate, pH 6.9. Protein concentrations were determined, in duplicate at a min- imum, using the absorbance at 280 nm and the theoretical extinction coefficients for each protein (Prx2 WT, 20,460 M1 cm1; Prx2-C2S, 21,430 M1 cm1; Prx2-CT, 21,555 M1 cm1; Prx2 PP 3 HA, 21,555 M1 cm1; Prx2 PP 3 HA  CT, 21,555 M1 cm1; Prx3 WT, 20,065 M1 cm1; Prx3-C2S, 19,940 M1 cm1; Prx3 CT, 20,065 M1 cm1; Prx3 HA 3 PP, 20,065 M1 cm1; Prx3 HA 3 PP  CT, 20,065 M1 cm1) calculated by the ExPASy ProtParam tool. The protein samples were immediately diluted and analyzed using the chemical quench and time-resolved methods described below. Mass Spectrometry Data Collection and Analysis—For the chemical quench experiments, each DTT-free Prx protein was diluted further in 50 mM Tris, pH 7.5, to a final concentration of 50 M. Oxidation was initiated by the addition of 0.8 eq of standardized H2O2 (240  43.6 M1 cm1) to the protein solu- tion. The solution was incubated at 25 °C in a Thermomixer (Eppendorf) with gentle mixing. In control experiments, all conditions were the same as above except the same volume of H2O instead of H2O2 was used. At 30 s incubation time, the sample was applied to a Bio-Gel P6 spin column pre-equili- brated with 0.03% formic acid in H2O to quench the oxidation reaction. The flow-through was then used directly for ESI-TOF MS analysis. In the comparative time-resolved experiments using the Prx2 and Prx3 variants, protein oxidation was performed using an on-line rapid-mixing setup. The experimental setup con- tained two Hamilton syringes as follows: one containing 100 M DTT-free Prx variant, and the other containing 100 M H2O2, both in 50 mM ammonium acetate, pH 6.9. The syringes were individually connected to separate fused silica capillaries and simultaneously advanced using a syringe pump (KD Scientific). The solutions were combined through a zero dead volume- mixing tee (Upchurch Scientific) into a connecting fused silica capillary (volume, 0.362 l). Molecular Basis for Resistance of hPrx3 to Hyperoxidation The following motifs and residues are high- lighted: GGLG motif, yellow bar; residue differences between the Prxs, pink and purple circles; Cys-SRH residue, black circle. C, active site of hyperoxidized, human Prx2. The same coloring scheme from B is used. The peroxidatic Cys is hyperoxidized and labeled as Csd51. The Cys-SRH residue for Prx2 is Cys-172. PDB code 1QMV (19). All ESI-TOF MS data were recorded in a positive ion mode on an Agilent MSD TOF system with the following settings: capillary voltage (VCap) 3500 V, nebulizer gas (N2) 30 pounds/ inch2, drying gas (N2) 5.0 liter min1; fragmentor 140 V; gas temperature 325 °C. The chemical quench samples were injected for analysis by ESI-TOF MS at a flow rate of 25 l min1 from a 250-l syringe via a syringe pump. For the time- resolved experiments, the samples were injected as described above. The averaged MS spectra were deconvoluted using the Agilent MassHunter workstation software Version B.01.03. Data for the Prx2-C2S variant were fitted using SigmaPlot Ver- sion 11.0 (Systat Software Inc) and KinTek Explorer (KinTek Corp.) based on a simple kinetic model E  S 7 EI; EI  S 7 EP, where E is Prx-C2S; S is H2O2; EI is the Prx-C2S-SPOH, and EP is Prx-C2S-SPO2H. EXPERIMENTAL PROCEDURES Protein Expression and Purification—The human PRDX2 and PRDX3 genes were subcloned into the pET17 (Novagen) and pTYB21 (New England Biolabs), respectively, in a manner that ultimately resulted in the mature form of each protein without any additional N- or C-terminal residues. This was necessary as additional residues at either location could nega- tively impact catalytic activity. All Prx variants were created using the QuikChange site-directed mutagenesis method (Stratagene) with the appropriate primers. All proteins were expressed in BL21-Gold (DE3) Escherichia coli cells (New Eng- land Biolabs). OCTOBER 11, 2013•VOLUME 288•NUMBER 41 JOURNAL OF BIOLOGICAL CHEMISTRY 29715 29715 OCTOBER 11, 2013•VOLUME 288•NUMBER 41 - d n. a r 9. - al 1 1 T, S, P, ) s al e s of of - r ll of e - n F e g - M 2, e d ). - a - a s. s FIGURE 1. Key residues involved in 2-Cys Prx catalysis and hyperoxida- tion. A, 2-Cys Prx catalytic cycle showing oxidation, hyperoxidation, and repair by sulfiredoxin. The monomers of the obligate Prx homodimer are shown in blue and green. Depending on the concentration of peroxide pres- ent, one or both of the peroxidatic Cys residues (Cys-SPH) may be oxidized to the Cys sulfenic acid (Cys-SPOH) or hyperoxidized to the Cys sulfinic acid (Cys- SPO2H). The resolving Cys residue, Cys-SRH, is located near the C terminus and forms an intermolecular disulfide bond with the Cys-SPH residue during nor- mal catalysis. Reduction of this disulfide and the Cys-SPO2H moiety is per- formed by the thioredoxin-thioredoxin reductase-NAPDH (Trx-Trx-NADPH) system and sulfiredoxin (Srx), respectively. The abbreviation used within the main text for each species is indicated in italics. B, sequence alignment of key residues within the active site The following motifs and residues are high xidation Molecular Basis for Resistance of hPrx3 to Hyperoxidation The mixture was then continu- ously flowed into an ESI needle (volume, 1.269 l) inserted in a stainless steel electrospray probe for ESI-TOF MS analysis. Varying flow rates were applied to achieve reaction time points lower than 30 s. FIGURE 1. Key residues involved in 2-Cys Prx catalysis and hyperoxida- tion. A, 2-Cys Prx catalytic cycle showing oxidation, hyperoxidation, and repair by sulfiredoxin. The monomers of the obligate Prx homodimer are shown in blue and green. Depending on the concentration of peroxide pres- ent, one or both of the peroxidatic Cys residues (Cys-SPH) may be oxidized to the Cys sulfenic acid (Cys-SPOH) or hyperoxidized to the Cys sulfinic acid (Cys- SPO2H). The resolving Cys residue, Cys-SRH, is located near the C terminus and forms an intermolecular disulfide bond with the Cys-SPH residue during nor- mal catalysis. Reduction of this disulfide and the Cys-SPO2H moiety is per- formed by the thioredoxin-thioredoxin reductase-NAPDH (Trx-Trx-NADPH) system and sulfiredoxin (Srx), respectively. The abbreviation used within the main text for each species is indicated in italics. B, sequence alignment of key residues within the active site. The following motifs and residues are high- lighted: GGLG motif, yellow bar; residue differences between the Prxs, pink and purple circles; Cys-SRH residue, black circle. C, active site of hyperoxidized, human Prx2. The same coloring scheme from B is used. The peroxidatic Cys is hyperoxidized and labeled as Csd51. The Cys-SRH residue for Prx2 is Cys-172. PDB code 1QMV (19). FIGURE 1. Key residues involved in 2-Cys Prx catalysis and hyperoxida- tion. A, 2-Cys Prx catalytic cycle showing oxidation, hyperoxidation, and repair by sulfiredoxin. The monomers of the obligate Prx homodimer are shown in blue and green. Depending on the concentration of peroxide pres- ent, one or both of the peroxidatic Cys residues (Cys-SPH) may be oxidized to the Cys sulfenic acid (Cys-SPOH) or hyperoxidized to the Cys sulfinic acid (Cys- SPO2H). The resolving Cys residue, Cys-SRH, is located near the C terminus and forms an intermolecular disulfide bond with the Cys-SPH residue during nor- mal catalysis. Reduction of this disulfide and the Cys-SPO2H moiety is per- formed by the thioredoxin-thioredoxin reductase-NAPDH (Trx-Trx-NADPH) system and sulfiredoxin (Srx), respectively. The abbreviation used within the main text for each species is indicated in italics. B, sequence alignment of key residues within the active site. RESULTS AND DISCUSSION Hyperoxidation of Wild-type Prx2 and Prx3—Although human Prx2 and Prx3 exhibit second order rate constants of 107 M1 s1 with H2O2, these enzymes represent divergent 2-Cys Prx molecules with respect to their susceptibility to 29716 JOURNAL OF BIOLOGICAL CHEMISTRY 29716 VOLUME 288•NUMBER 41•OCTOBER 11, 2013 Molecular Basis for Resistance of hPrx3 to Hyperoxidation FIGURE 2. Susceptibility of wild-type Prx2 and Prx3 to hyperoxidation. Chemical quench and ESI-TOF MS were used to assess the oxidation state of each protein (50 M) following treatment with 0.8 eq of H2O2 for 30 s at pH 7.5. The 1st column of panels shows the full spectra for Prx2 and Prx3 with and without H2O2 treatment. The panels to the right show a close-up view of the mass ranges encompassing the monomeric and dimeric species. See Fig. 1A for the abbreviations used for each species. All theoretical and experimental mass values ( S.D.) are given in Table 1; amu, atomic mass units. Molecular Basis for Resistance of hPrx3 to Hyperoxidation FIGURE 2. Susceptibility of wild-type Prx2 and Prx3 to hyperoxidation. Chemical quench and ESI-TOF MS were used to assess the oxidation state of each protein (50 M) following treatment with 0.8 eq of H2O2 for 30 s at pH 7.5. The 1st column of panels shows the full spectra for Prx2 and Prx3 with and without H2O2 treatment. The panels to the right show a close-up view of the mass ranges encompassing the monomeric and dimeric species. See Fig. 1A for the abbreviations used for each species. All theoretical and experimental mass values ( S.D.) are given in Table 1; amu, atomic mass units. hyperoxidation of the catalytic Cys-SPH residue to Cys sulfinic acid (Cys-SPO2H) (24). To evaluate this difference, a panel of human Prx2 and Prx3 variants was expressed and purified from E. coli. Importantly, the expression construct for each protein was designed with the requirement that no affinity tags or addi- tional N- and C-terminal residues remain at the final step of purification, as these can greatly influence the oligomeric state and peroxidase activity (8, 25). Although Prx2 was readily expressed and purified without affinity tags, Prx3 was more problematic requiring the screening of a variety of expression tags and an evaluation of their ease of removal by proteases. RESULTS AND DISCUSSION In the end, only an N-terminal chitin binding domain-intein fusion led to sufficient expression levels for all variants ana- lyzed, resulting in a mature N terminus at residue 62 following DTT treatment. analysis. Moreover, all data presented herein were collected without the presence of DTT or other external reductant like thioredoxin in the reaction mixture. This simplification pre- vents the Prx molecule from cycling and enables partial-turn- over analysis of Prx oxidation. Reduced Prx2 or Prx3 (50 M) was mixed with 0.8 eq of H2O2 at pH 7.5 and incubated for 30 s. The reaction was chemically quenched by passing the sample through a desalting column equilibrated with 0.03% formic acid in H2O and immediately analyzed by ESI-TOF mass spectrometry (Fig. 2). The addition of H2O2 to Prx2 results in the conversion of the reduced mon- omer (SH, M) to the hyperoxidized monomer (SO2H, M  32) and two intermolecular disulfide-linked species, the oxidized (SS  SH, M  M  2) and hyperoxidized (SS  SO2H, M  M  30) dimers (Fig. 1; all theoretical and experimental mass values are given in Table 1). In contrast, the addition of H2O2 to Prx3 results in the same species but with more of the reduced (SH) monomer remaining. Previous in vitro and cellular studies have used gel-based and Western blotting methods to monitor the hyperoxidation of Prx2 and Prx3 (16, 20, 21). Although these low resolution tech- niques do illustrate the differences in reactivity with H2O2, they have missed critical reaction intermediates that may shed light into the molecular mechanism of resistance to hyperoxidation in Prx3. Quantitative ESI-TOF mass spectrometry approaches were used in this study to dissect the appearance and disappear- ance of reaction intermediates (Fig. 1) associated with oxida- tion (Cys-SPOH, M  16) and hyperoxidation (Cys-SPO2H, M  32). A key feature of this approach has been to pre-reduce the samples with DTT and to desalt immediately prior to With the substoichiometric addition of H2O2, the presence of reduced monomer and monomeric and dimeric species con- taining the hyperoxidized Cys-SPO2H moiety for both Prx2 and Prx3 is counterintuitive. The Cys-SPH residue should react quickly with H2O2 to form the Cys-SPOH intermediate and then transition to the SP-SR dimeric species. Based on other biochemical and molecular modeling studies, however, there is evidence for one Cys-SPH residue to be more reactive than the other within the Prx homodimer (26–28). TABLE 1 TABLE 1 Theoretical and experimental mass values for the different oxidation states of Prx2 and Prx3 variants a The removal of the Cys-SRH residue by mutagenesis prevents the possibility of this species forming. See text for details. b Species was not observed. Please see text for experimental details, as some species can only be captured with the time-resolved approach. Not all Prx2 and Prx3 variants were analyzed with the latter approach. c All mass values were determined in triplicate except for Prx3 HA 3 PP  CT, which was performed in duplicate, due to the paucity of material available. order for the Cys-SPOH species to react with a second mol- ecule of H2O2, the active site must be in the FF conformation (6). Thus, it appears that under these nonturnover reaction conditions a small subpopulation of Prx active sites main- tains the Cys-SPOH intermediate in the FF conformation, leading to hyperoxidation. dation, but this species has not been directly observed during Prx turnover before (10, 31). Time-resolved ESI-TOF MS Analysis of Early Reaction Intermediates—The tracking of the formation of the Cys-SPOH species in Prxs was first studied using molecular probes specific for this functional group, including dimedone (32). Advances in the development of chemical probes have revolutionized the isolation and identification of other proteins that form a Cys sulfenic acid within cells exposed to a variety of stress condi- tions (6, 33–35). The reactivity of these probes is, however, not high enough to capture the transient Cys-SPOH intermediate during the Prx reaction cycle. The reported reaction rates vary from 0.003 to 1.65 min1 at a saturating concentration of dime- done (36). Even when using the low pH chemical quench method and ESI-TOF MS at a 30-s time point (Fig. 2), the Cys-SPOH spe- cies was not captured for WT Prx2 and Prx3. Therefore, a more rapid analysis of the reaction intermediates is necessary. In summary, these analyses of the wild-type (WT) proteins are consistent with cell-based and in vitro studies showing that Prx3 is more resistant to hyperoxidation (16, 20, 21). Moreover, the concentrations of Prx and H2O2 used were directly comparable with those found within cells (29, 30). These experiments demonstrate that hyperoxidation of Prx2 and Prx3 can occur on a physiologically relevant time scale without catalytic cycling when the concentration of H2O2 is similar to the amount of Prx protein. RESULTS AND DISCUSSION In addition, in OCTOBER 11, 2013•VOLUME 288•NUMBER 41 OCTOBER 11, 2013•VOLUME 288•NUMBER 41 29717 JOURNAL OF BIOLOGICAL CHEMISTRY 29717 Molecular Basis for Resistance of hPrx3 to Hyperoxidation TABLE 1 Theoretical and experimental mass values for the different oxidation states of Prx2 and Prx3 variants a The removal of the Cys-SRH residue by mutagenesis prevents the possibility of this species forming. See text for details. b Species was not observed. Please see text for experimental details, as some species can only be captured with the time-resolved approach. Not all Prx2 and Prx3 variants were analyzed with the latter approach. c All mass values were determined in triplicate except for Prx3 HA 3 PP  CT, which was performed in duplicate, due to the paucity of material available. TABLE 1 Nonetheless, the ability to capture this putative intermediate, even as a minor product, supports that the Cys-SPOH species is stabilized in Prx2. FIGURE 3. Time-resolved ESI-TOF MS analysis of wild-type Prx2 and Prx3 d i l i h d h l FIGURE 3. Time-resolved ESI-TOF MS analysis of wild-type Prx2 and Prx3 during catalysis. Each variant was treated with an equimolar concentration of H2O2 followed by the continuous analysis of reaction intermediates at pH 6.9. Left panel, representative deconvoluted spectra for Prx2 at different reac- tion time points. The full spectra and a close-up of the region around the monomer are shown. The series of shoulder peaks are consistent with the presence of Na adducts (22 Da). See Table 1 for mass details for the differ- ent species. amu, atomic mass units. Right panel, full spectra for Prx3. In contrast, only the reduced monomer (SH) and the oxi- dized dimer (SS  SH) were observed in the mass spectra for WT Prx3 in the 1.0–5.0-s reaction time range. The absence of the Cys-SPOH and sulfenamide intermediates for Prx3 sup- ports that the lifetime of the Cys-SPOH intermediate is consid- erably shorter than that for Prx2, as a consequence of rapid intermolecular disulfide bond formation (SP-SR). Thus, the presence of the Cys-SRH residue and the ability to form the intermolecular SP-SR species appears to greatly impact the life- time of the Cys-SPOH intermediate. Time-resolved ESI-TOF MS experiments, employing an on-line, rapid-mixing setup, were used to monitor the for- mation of the Cys-SPOH species for Prx2 and Prx3 during catalysis, i.e. under native conditions. In this approach, the Prx proteins were pre-reduced with DTT, desalted into a volatile buffer, and loaded into a Hamilton syringe. The sam- ples were then mixed on-line in an equimolar ratio (100 M each) with H2O2 at varying flow rates (10–80 l/min) to achieve the acquisition of mass spectra at short reaction time points (1–15 s). With this 30-fold reduction of the reaction time scale, the detection of the Cys-SPOH intermediate at pH 7.5 was still not possible. Hyperoxidation of Prx2 and Prx3 Cys Variants—To dissect the contribution of the Cys-SRH residue and SP-SR intermedi- ate formation to the hyperoxidation of Prx2 and Prx3, the Cys- SRH residue and one other noncatalytic Cys residue were mutated to Ser (Prx2-C2S, C70S and C172S; Prx3-C2S, C127S and C229S; numbering scheme based on full-length gene sequence). TABLE 1 These observations also support the notion that the lifetime or stability of the Cys- SPOH intermediate is crucial to enable subsequent hyperoxi- 29718 JOURNAL OF BIOLOGICAL CHEMISTRY VOLUME 288•NUMBER 41•OCTOBER 11, 2013 VOLUME 288•NUMBER 41•OCTOBER 11, 2013 FIGURE4.SusceptibilityofPrx2-C2SandPrx3-C2Stohyperoxidation.Chem- ical quench and ESI-TOF MS were used to assess the oxidation state of each pro- tein (50 M) following treatment with 2 eq of H2O2 for 30 s at pH 7.5. These Prx2 andPrx3variantscontainonlytheCys-SPHresidueandcannotformtheintermo- lecular disulfide reaction intermediate. Therefore, the deconvoluted spectra focus on the monomeric species, as indicated. amu, atomic mass units. cular Basis for Resistance of hPrx3 to Hyperoxidation Molecular Basis for Resistance of hPrx3 to Hyperoxidation FIGURE 3. Time-resolved ESI-TOF MS analysis of wild-type Prx2 and Prx3 during catalysis. Each variant was treated with an equimolar concentration of H2O2 followed by the continuous analysis of reaction intermediates at pH 6.9. Left panel, representative deconvoluted spectra for Prx2 at different reac- tion time points. The full spectra and a close-up of the region around the monomer are shown. The series of shoulder peaks are consistent with the presence of Na adducts (22 Da). See Table 1 for mass details for the differ- ent species. amu, atomic mass units. Right panel, full spectra for Prx3. FIGURE4.SusceptibilityofPrx2-C2SandPrx3-C2Stohyperoxidation.Chem- ical quench and ESI-TOF MS were used to assess the oxidation state of each pro- tein (50 M) following treatment with 2 eq of H2O2 for 30 s at pH 7.5. These Prx2 andPrx3variantscontainonlytheCys-SPHresidueandcannotformtheintermo- lecular disulfide reaction intermediate. Therefore, the deconvoluted spectra focus on the monomeric species, as indicated. amu, atomic mass units. (Cys-SPN, M  2) (Table 1), a novel finding to our knowledge for human Prx proteins. At this point, we cannot determine whether the putative sulfenamide species exists in solution as a minor species or is a result of the dehydration process when the protein ion transitions to the gas phase during MS analysis. Nonetheless, the ability to capture this putative intermediate, even as a minor product, supports that the Cys-SPOH species is stabilized in Prx2. (Cys-SPN, M  2) (Table 1), a novel finding to our knowledge for human Prx proteins. At this point, we cannot determine whether the putative sulfenamide species exists in solution as a minor species or is a result of the dehydration process when the protein ion transitions to the gas phase during MS analysis. Molecular Basis for Resistance of hPrx3 to Hyperoxidation Molecular Basis for Resistance of hPrx3 to Hyperoxidation FIGURE 5. Time-resolved ESI-TOF MS analysis of the Prx2-C2S and Prx3-C2S variants during catalysis. A, representative deconvoluted spectra for Prx2-C2S at the indicated reaction time points. The protein was treated with an equimolar concentration of H2O2 (50 M of each final) at pH 6.9 followed by the analysis of reactionmixturewithESI-TOFmassspectrometry.Thespectraarefocusedonthe following species: Cys-SPH, Cys-SPOH, Cys-SPO2H, and a putative Cys-sulfen- amide (Cys-SPN) intermediate (Table 1). B, global kinetic modeling of the Prx2- C2S kinetic data. The plot shows the determined kinetic profiles for the –SPH and –SPO2H and the combined –SPOH/–SPN species, as the –SPN intermediate logi- cally originates from the –SPOH species. C, deconvoluted spectra for Prx3-C2S treated with H2O2 for 600 s. amu, atomic mass units. Molecular Basis for Resistance of hPrx3 to Hyperoxid constant of 104 Prx2-C2S is consistent with the rate reported for turnover for the WT Prx2 (107 M1 s1), especially given the suboptimal pH conditions and the mutation of the Cys-SRH residue (24, 37–40). One caveat to the Prx2-C2S studies was the unanticipated observation of more oxidization than expected, considering the equimolar proportion of H2O2 added. It is unclear why this occurred for only this Prx2 variant and not others in this study, but it could have been formed during MS analysis. Nonetheless, the data for Prx2-C2S are consistent with the increased lifetime of the Cys-SPOH intermediate and the inability to form the normal SP-SR intermolecular disulfide. In marked contrast, the Cys-SPOH, Cys-SPN, and Cys-SPO2H species were observed at similar levels at 600 s for Prx3-C2S (Fig. 5C), in line with the amount of H2O2 added. Given the significantly lowered reac- tivity of the Prx3-C2S variant, the rates for the formation of the different oxidized and hyperoxidized species were not calculated. An orthogonal analysis of the hyperoxidation of WT Prx2 and Prx3 was recently reported while our studies were in review (41). This analysis focused on determining the rate of hyperoxi- dation, kSOH 3 SO2H (k2 in their scheme), and the rate of disul- fide formation, kSOH 3 SP-SR (k3 in their scheme). Our kSOH 3 SO2H value of 1.1  103 M1 s1, for Prx2-C2S at a sub- optimal pH, is comparable with 1.2  104 M1 s1 for the WT enzyme. Moreover, our chemical quench and time-resolved MS data (Figs. Molecular Basis for Resistance of hPrx3 to Hyperoxidation 2 and 3) directly illustrate the rapid formation of the SP-SR intermediate for Prx3, consistent with the 10-fold higher kSOH 3 SP-SR rate for Prx3 (20 s1 versus 2 s1 for Prx2) and the oxidation of the Cys-SPOH species being the rate-lim- iting step for hyperoxidation. Taken together, the data support the importance of rate of formation of the SP-SR species in con- trolling susceptibility to hyperoxidation, as originally proposed by Wood et al. (10). As described below, a panel of Prx2 and Prx3 chimeras of the active site and C-terminal region, near the Cys-SRH residue, was evaluated in an effort to determine which residues unique to Prx3 may impart the unique resistance to hyperoxidation. FIGURE 5. Time-resolved ESI-TOF MS analysis of the Prx2-C2S and Prx3-C2S variants during catalysis. A, representative deconvoluted spectra for Prx2-C2S at the indicated reaction time points. The protein was treated with an equimolar concentration of H2O2 (50 M of each final) at pH 6.9 followed by the analysis of reactionmixturewithESI-TOFmassspectrometry.Thespectraarefocusedonthe following species: Cys-SPH, Cys-SPOH, Cys-SPO2H, and a putative Cys-sulfen- amide (Cys-SPN) intermediate (Table 1). B, global kinetic modeling of the Prx2- C2S kinetic data. The plot shows the determined kinetic profiles for the –SPH and –SPO2H and the combined –SPOH/–SPN species, as the –SPN intermediate logi- cally originates from the –SPOH species. C, deconvoluted spectra for Prx3-C2S treated with H2O2 for 600 s. amu, atomic mass units. FIGURE 5. Time-resolved ESI-TOF MS analysis of the Prx2-C2S and Prx3-C2S variants during catalysis. A, representative deconvoluted spectra for Prx2-C2S at the indicated reaction time points. The protein was treated with an equimolar concentration of H2O2 (50 M of each final) at pH 6.9 followed by the analysis of reactionmixturewithESI-TOFmassspectrometry.Thespectraarefocusedonthe following species: Cys-SPH, Cys-SPOH, Cys-SPO2H, and a putative Cys-sulfen- amide (Cys-SPN) intermediate (Table 1). B, global kinetic modeling of the Prx2- C2S kinetic data. The plot shows the determined kinetic profiles for the –SPH and –SPO2H and the combined –SPOH/–SPN species, as the –SPN intermediate logi- cally originates from the –SPOH species. C, deconvoluted spectra for Prx3-C2S treated with H2O2 for 600 s. amu, atomic mass units. the intrinsic differences between Prx2 and Prx3. This compar- ison clearly demonstrates that the mutation of the Cys-SRH residue has a significant impact on the reactivity of Prx3 with H2O2. Molecular Basis for Resistance of hPrx3 to Hyperoxidation One likely explanation is that the active site for the Prx3- C2S variant is predominantly in the locally unfolded conforma- tion, thus preventing the reaction with H2O2. These observa- tions are consistent with the decrease in hyperoxidation observed when mutating the Cys-SRH residue to Ser or Ala in other eukaryotic Prxs (37–39). the intrinsic differences between Prx2 and Prx3. This compar- ison clearly demonstrates that the mutation of the Cys-SRH residue has a significant impact on the reactivity of Prx3 with H2O2. One likely explanation is that the active site for the Prx3- C2S variant is predominantly in the locally unfolded conforma- tion, thus preventing the reaction with H2O2. These observa- tions are consistent with the decrease in hyperoxidation observed when mutating the Cys-SRH residue to Ser or Ala in other eukaryotic Prxs (37–39). hyperoxidation. Hyperoxidation of C-terminal and GGLG Motif Chimeras of Prx2 and Prx3—As briefly described earlier, the packing of the C-terminal YF-containing helix against the GGLG motif (Fig. 1C) is a prominent feature of eukaryotic Prxs. This interaction and the resultant stabilization of the active site are thought to slow the rate of formation of the intermolecular SS intermedi- ate during catalysis enabling hyperoxidation (6, 10). In fact, the mutation and truncation of the C terminus results in an increased resistance to hyperoxidation in other Prxs (37, 42–44). The appendage of a C terminus from a Prx molecule sensitive to hyperoxidation to one that is normally resistant can also result in an increase in sensitivity to hyperoxidation (43). Similar studies have not been performed with human Prx2 and Prx3 in an effort to address their differences in hyperoxidation. A sequence alignment (Fig. 1B) of human Prx1–4 reveals that two Pro residues, Pro-98 and Pro-102 of Prx2, are substi- tuted to His and Ala in Prx3, respectively. Their position next to the GGLG motif suggests that these Pro residues may be important for the positioning of this motif to interact with the C terminus of the adjacent Prx subunit. Four additional Hyperoxidation of C-terminal and GGLG Motif Chimeras of Prx2 and Prx3—As briefly described earlier, the packing of the C-terminal YF-containing helix against the GGLG motif (Fig. 1C) is a prominent feature of eukaryotic Prxs. This interaction and the resultant stabilization of the active site are thought to slow the rate of formation of the intermolecular SS intermedi- ate during catalysis enabling hyperoxidation (6, 10). TABLE 1 These mutations leave only the Cys-SPH residue for each protein, and therefore the dimeric SP-SR species cannot form, and the potential for unwanted thiol-disulfide exchange reactions is removed. Decreasing the reaction pH to 6.9, however, enabled the detection of the Cys-SPOH species for wild-type (WT) Prx2 at 1.5 s (Fig. 3), even when the majority of the protein was present as the oxidized dimer (SS  SH), as expected. Importantly, under these reaction conditions and short time scale, the SS  SO2H species was not consistently observed. By 5.8 s the Cys- SPOH intermediate was consumed, and a new peak emerged with a mass consistent with the formation of a Cys sulfenamide An analysis of the variants at pH 7.5, with the addition of 2 eq of H2O2 for 30 s (Fig. 4), was performed using the chemical quench method coupled with ESI-TOF mass spectrometry. The Prx3-C2S variant remained in the reduced state while the Prx2-C2S variant was fully hyperoxidized, further highlighting OCTOBER 11, 2013•VOLUME 288•NUMBER 41 OCTOBER 11, 2013•VOLUME 288•NUMBER 41 29719 JOURNAL OF BIOLOGICAL CHEMISTRY Molecular Basis for Resistance of hPrx3 to Hyperoxidation Importantly, these variants all contain the Cys-SRH residue and can there- fore undergo normal catalytic cycling. species containing the Cys-SPO2H moiety increased (Fig. 6B) over the WT protein. The Prx3 CT chimera was even more sensitive to hyperoxidation, as only the monomeric Cys-SO2H species was observed in addition to a complete loss of SS  SH and SS  SO2H species. The combination of the GGLG and CT variants, Prx3 HA 3 PP  CT, yielded a similar increase in the monomeric SO2H species and a small increase in the SS-con- taining species. It is unclear at this time how the combination of the two sets of mutations could lead to a compensatory effect. The analysis of the Prx2 and Prx3 chimeras supports that the C terminus of Prx3 is the primary determinant to the resistance of the WT enzyme to hyperoxidation and that the residues near the GGLG motif can modulate this resistance to some degree. Moreover, the lack of the dimeric SS  SH and SS  SO2H for the Prx3 CT variant suggests that the active site is stabilized in the FF conformation, causing the Cys-SPOH species to be read- ily hyperoxidized. It is interesting to note that none of the Prx2 and Prx3 chimeras exhibited a full transformation in their sen- sitivity or resistance to hyperoxidation. This finding suggests that other regions of the proteins and their dynamic oligomeric states may also influence the ease of hyperoxidation. species containing the Cys-SPO2H moiety increased (Fig. 6B) over the WT protein. The Prx3 CT chimera was even more sensitive to hyperoxidation, as only the monomeric Cys-SO2H species was observed in addition to a complete loss of SS  SH and SS  SO2H species. The combination of the GGLG and CT variants, Prx3 HA 3 PP  CT, yielded a similar increase in the monomeric SO2H species and a small increase in the SS-con- taining species. It is unclear at this time how the combination of the two sets of mutations could lead to a compensatory effect. The analysis of the Prx2 and Prx3 chimeras supports that the C terminus of Prx3 is the primary determinant to the resistance of the WT enzyme to hyperoxidation and that the residues near the GGLG motif can modulate this resistance to some degree. Molecular Basis for Resistance of hPrx3 to Hyperoxidation In fact, the mutation and truncation of the C terminus results in an increased resistance to hyperoxidation in other Prxs (37, 42–44). The appendage of a C terminus from a Prx molecule sensitive to hyperoxidation to one that is normally resistant can also result in an increase in sensitivity to hyperoxidation (43). Similar studies have not been performed with human Prx2 and Prx3 in an effort to address their differences in hyperoxidation. The Prx2 and Prx3 Cys variants were also analyzed by time- resolved ESI-TOF MS at pH 6.9 to evaluate the formation of reaction intermediates. For Prx2-C2S, the addition of 1 eq of H2O2 resulted in the formation of Cys-SPOH species at 1.2 s (Fig. 5A). By 15 s, three species were present as follows: Cys- SPOH, Cys-SPN, and Cys-SPO2H. At the 600-s time point, the hyperoxidized species predominated. Additional time points were collected, and the relative abundance for each species to the total signal was converted to concentration to generate a plot (Fig. 5B) of the reduced, oxidized, and hyperoxidized spe- cies versus time. The intensities for the Cys-SPOH and Cys-SPN intermediates were combined, as the Cys-SPN intermediate can only form from the Cys-SPOH. A global fit of the data using KinTek Explorer was used to determine the following rate con- stants: kSH 3 SOH, 2.0  104 M1 s1; kSOH 3 SO2H, 1.1  103 M1 s1. A separate exponential fit to the formation of the Cys- SPO2H species yielded the kSH 3 SO2H rate constant of 9.2  102 M1 s1, consistent with the conversion of the Cys-SPOH inter- mediate to the Cys-SPO2H species being the rate-limiting step in Prx2-C2S hyperoxidation. Importantly, the kSH 3 SOH rate A sequence alignment (Fig. 1B) of human Prx1–4 reveals that two Pro residues, Pro-98 and Pro-102 of Prx2, are substi- tuted to His and Ala in Prx3, respectively. Their position next to the GGLG motif suggests that these Pro residues may be important for the positioning of this motif to interact with the C terminus of the adjacent Prx subunit. Four additional VOLUME 288•NUMBER 41•OCTOBER 11, 2013 29720 VOLUME 288•NUMBER 41•OCTOBER 11, 2013 29720 JOURNAL OF BIOLOGICAL CHEMISTRY Molecular Basis for Resistance of hPrx3 to Hyperoxidation Molecular Basis for Resistance of hPrx3 to Hyperoxidation FIGURE 6. Susceptibility of Prx2 and Prx3 GGLG and C-terminal chimeras to hyperoxidation. A, Prx2 variants: WT, PP 3 HA (P98H and P102A); CT (G175N, K177T, G179D, and D181P); PP 3 HA  CT. B, Prx3 variants: WT, HA 3 PP (H155P and A159P); CT (N232G, T234K, D236G, and P238D); HA 3 PP  CT. Chemical quench ESI-TOF analyses were performed with 0.8 eq of H2O2 for 30 s at pH 7.5. A close-up of the mass range for the monomeric (left panel) and dimeric (right panel) species is presented within each panel (Table 1). amu, atomic mass units. Molecular Basis for Resistance of hPrx3 to Hyperoxidation FIGURE 6 Susceptibility of Prx2 and Prx3 GGLG and C terminal chimeras to FIGURE 6. Susceptibility of Prx2 and Prx3 GGLG and C-terminal chimeras to hyperoxidation. A, Prx2 variants: WT, PP 3 HA (P98H and P102A); CT (G175N, K177T, G179D, and D181P); PP 3 HA  CT. B, Prx3 variants: WT, HA 3 PP (H155P and A159P); CT (N232G, T234K, D236G, and P238D); HA 3 PP  CT. Chemical quench ESI-TOF analyses were performed with 0.8 eq of H2O2 for 30 s at pH 7.5. A close-up of the mass range for the monomeric (left panel) and dimeric (right panel) species is presented within each panel (Table 1). amu, atomic mass units. differences between Prx2 and Prx3 were identified adjacent to the Cys-SRH residue (16). In this region, Gly-175, Lys-177, Gly-179, and Asp-181 of Prx2 are substituted with Asn, Thr, Asp, and Pro in Prx3, respectively. A panel of Prx2 and Prx3 variants was generated where these sequence differences were swapped as a group to generate chimeras. The panel was eval- uated using the same experimental conditions as for the WT proteins and using the chemical quench method. Importantly, these variants all contain the Cys-SRH residue and can there- fore undergo normal catalytic cycling. differences between Prx2 and Prx3 were identified adjacent to the Cys-SRH residue (16). In this region, Gly-175, Lys-177, Gly-179, and Asp-181 of Prx2 are substituted with Asn, Thr, Asp, and Pro in Prx3, respectively. A panel of Prx2 and Prx3 variants was generated where these sequence differences were swapped as a group to generate chimeras. The panel was eval- uated using the same experimental conditions as for the WT proteins and using the chemical quench method. REFERENCES (2005) Analysis of the link between enzymatic activity and oligomeric state in AhpC, a bacterial peroxiredoxin. Biochem- istry 44, 10583–10592 Inspection of the Prx2 active site (Fig. 1C) and the residues surrounding the Cys-51-SPH residue reveals that Prx2 would not be able to form a backbone-mediated Cys-SPN intermedi- ate similar to PTP1B. Cys-51 is adjacent to the conserved amino acid Pro-52, which lacks an amide proton and cannot attack the sulfenic acid moiety. Based on studies with synthetic peptides, it is possible that the Cys-SPN formation in Prx2 is mediated through the amine groups of a Lys or Arg side chain (49). Arg- 127, a conserved residue, is the only residue adjacent to Cys-51 that could be involved in Cys-SN formation. Additional solu- tion and structural studies are clearly needed to establish the kinetic competence of the Cys-SN species in Prx2. 9. Lowther, W. T., and Haynes, A. C. (2011) Reduction of cysteine sulfinic acid in eukaryotic, typical 2-Cys peroxiredoxins by sulfiredoxin. Antioxid. Redox. Signal. 15, 99–109 10. Wood, Z. A., Poole, L. B., and Karplus, P. A. (2003) Peroxiredoxin evolu- tion and the regulation of hydrogen peroxide signaling. Science 300, 650–653 11. Rhee, S. G., Woo, H. A., Kil, I. S., and Bae, S. H. (2012) Peroxiredoxin functions as a peroxidase and a regulator and sensor of local peroxides. J. Biol. Chem. 287, 4403–4410 12. Ray, P. D., Huang, B. W., and Tsuji, Y. (2012) Reactive oxygen species (ROS) homeostasis and redox regulation in cellular signaling. Cell Signal. 24, 981–990 13. Jo¨nsson, T. J., Johnson, L. C., and Lowther, W. T. (2008) Structure of the sulphiredoxin-peroxiredoxin complex reveals an essential repair embrace. Nature 451, 98–101 Conclusions—This study supports that human Prx3 is more resistant to hyperoxidation by H2O2 than Prx2, as a conse- quence of rapid intermolecular disulfide formation between the Cys-SPH and Cys-SRH residues. Residues adjacent to Cys-229- SRH of Prx3 (Asn-232, Thr-234, Asp-236, and Pro-238) are unique and influence the lifetime of the Cys-SPOH intermedi- ate and SP-SR formation. These observations attest to the dynamic nature of the C terminus and its ability to modulate catalysis, hyperoxidation, and ultimately repair by sulfiredoxin (9, 10, 13). Given the highly oxidizing environment of the mito- chondria, it makes sense that the Prx3 molecule would favor rapid SP-SR formation to protect the Cys-SPH residue. REFERENCES 1. Rhee, S. G., Chae, H. Z., and Kim, K. (2005) Peroxiredoxins: a historical overview and speculative preview of novel mechanisms and emerging concepts in cell signaling. Free Radic. Biol. Med. 38, 1543–1552 2. Song, I. S., Kim, H. K., Jeong, S. H., Lee, S. R., Kim, N., Rhee, B. D., Ko, K. S., and Han, J. (2011) Mitochondrial peroxiredoxin III is a potential target for cancer therapy. Int. J. Mol. Sci. 12, 7163–7185 3. Ja¨rvela¨, S., Rantala, I., Rodriguez, A., Kallio, H., Parkkila, S., Kinnula, V. L., Soini, Y., and Haapasalo, H. (2010) Specific expression profile and prog- nostic significance of peroxiredoxins in grade II-IV astrocytic brain tu- mors. BMC Cancer 10, 104 4. Lee, K. W., Lee, D. J., Lee, J. Y., Kang, D. H., Kwon, J., and Kang, S. W. (2011) Peroxiredoxin II restrains DNA damage-induced death in cancer cells by positively regulating JNK-dependent DNA repair. J. Biol. Chem. 286, 8394–8404 Although the limited formation of the Prx2 Cys-SN interme- diate does raise some doubts concerning its biological rele- vance, an analysis of its potential likely structure is warranted and informative. For PTP1B, the five-membered Cys-SN inter- mediate occurs between Cys-215 and the backbone amide group of Ser-216. This intermediate is thought to protect Cys- 215 from hyperoxidation and irreversible inactivation and to facilitate glutathionylation (45, 46). Thus, we were surprised to observe the Cys-SPN species for Prx2 because it is more sensi- tive to hyperoxidation than Prx3. It is certainly possible that the Cys-SPN intermediate of Prx2 is readily collapsed back to the Cys-SPOH species by the addition of a water molecule. This scenario would extend the lifetime of the Cys-SPOH species enabling hyperoxidation. 5. Kil, I. S., Lee, S. K., Ryu, K. W., Woo, H. A., Hu, M. C., Bae, S. H., and Rhee, S. G. (2012) Feedback control of adrenal steroidogenesis via H2O2-depen- dent, reversible inactivation of peroxiredoxin III in mitochondria. Mol. Cell 46, 584–594 6. Hall, A., Nelson, K., Poole, L. B., and Karplus, P. A. (2011) Structure-based insights into the catalytic power and conformational dexterity of peroxi- redoxins. Antioxid. Redox. Signal. 15, 795–815 7. Wood, Z. A., Poole, L. B., Hantgan, R. R., and Karplus, P. A. (2002) Dimers to doughnuts: redox-sensitive oligomerization of 2-cysteine peroxiredox- ins. Biochemistry 41, 5493–5504 8. Parsonage, D., Youngblood, D. S., Sarma, G. N., Wood, Z. A., Karplus, P. A., and Poole, L. B. Molecular Basis for Resistance of hPrx3 to Hyperoxidation Moreover, the lack of the dimeric SS  SH and SS  SO2H for the Prx3 CT variant suggests that the active site is stabilized in the FF conformation, causing the Cys-SPOH species to be read- ily hyperoxidized. It is interesting to note that none of the Prx2 and Prx3 chimeras exhibited a full transformation in their sen- sitivity or resistance to hyperoxidation. This finding suggests that other regions of the proteins and their dynamic oligomeric states may also influence the ease of hyperoxidation. Following the addition of 0.8 eq H2O2 for 30 s, the Prx2 GGLG region chimera (Prx2 PP 3 HA) (Fig. 6A) had a compa- rable profile to WT Prx2, with prominent monomeric and dimeric species containing the Cys-SPO2H moiety. In contrast, the Prx2 C-terminal chimera (Prx2 CT) was more resistant to hyperoxidation, as indicated by the lack of formation of the Cys-SPO2H monomeric species and the presence of the SS  SH and SS  SO2H species. The combination of the variants, Prx2 PP 3 HA  CT, did not result in a further increase in protection from hyperoxidation. These observations support that the sequence changes near the GGLG motif of Prx2 do not influence hyperoxidation. The changing of the C-terminal res- idues of Prx2 to those of Prx3, however, resulted in a Prx3-like protein with an increased resistance to hyperoxidation. Potential Implications of Cys-Sulfenamide Formation—The observation of a putative Cys-SPN intermediate for WT Prx2 and Prx2-C2S (Figs. 3 and 5) supports a Cys-SPOH-Cys-SPN equilibrium that prolongs the lifetime of the Cys-SPOH inter- mediate and increases its susceptibility to hyperoxidation. The analysis of the Prx3 HA 3 PP chimera revealed an increase in hyperoxidation, i.e. the monomeric and dimeric OCTOBER 11, 2013•VOLUME 288•NUMBER 41 JOURNAL OF BIOLOGICAL CHEMISTRY 29721 OCTOBER 11, 2013•VOLUME 288•NUMBER 41 29721 Molecular Basis for Resistance of hPrx3 to Hyperoxidation However, the inability to observe the Cys-SPOH and Cys-SPN intermediates for WT Prx3 also supports the rapid formation of the SP-SR disulfide and the resistance of this protein to hyperoxidation. Acknowledgments—We thank Jill Clodfelter, Lauren Filipponi, and Lynnette Johnson for their technical expertise; Candice Summitt for work on the Prx2 CT variant; and Leslie Poole for critical reading of the manuscript. The low abundance of the Prx2 Cys-SPN species, under the current reaction conditions, contrasts sharply with other pro- teins that utilize the Cys-SN intermediate, chiefly protein phos- phatase PTP1B, the distal domain of receptor PTP, and OhrR (45–48). For example, unequivocal electron density was observed for this intermediate in PTP1B and PTP crystals treated with H2O2. For OhrR, treatment of the protein with cumene hydroperoxide in solution resulted in complete con- version to the sulfenamide, which was subsequently verified by a 2-Da shift in the intact protein and tryptic fragment masses, although the latter was still technically challenging given the reversibility of the adduct. Molecular Basis for Resistance of hPrx3 to Hyperoxidation cer cells against hypoxia and drug-induced hydrogen peroxide-dependent apoptosis. Mol. Cancer Res. 1, 682–689 Tsang, A. W., and Furdui, C. M. (2011) Isoform-specific regulation of Akt by PDGF-induced reactive oxygen species. Proc. Natl. Acad. Sci. U.S.A. 108, 10550–10555 Tsang, A. W., and Furdui, C. M. (2011) Isoform-specific regulation of Akt by PDGF-induced reactive oxygen species. Proc. Natl. Acad. Sci. U.S.A. 108, 10550–10555 19. Schro¨der, E., Littlechild, J. A., Lebedev, A. A., Errington, N., Vagin, A. A., and Isupov, M. N. (2000) Crystal structure of decameric 2-Cys peroxire- doxin from human erythrocytes at 1.7 Å resolution. Structure 8, 605–615 35. Paulsen, C. E., Truong, T. H., Garcia, F. J., Homann, A., Gupta, V., Leon- ard, S. E., and Carroll, K. S. (2012) Peroxide-dependent sulfenylation of the EGFR catalytic site enhances kinase activity. Nat. Chem. Biol. 8, 57–64 20. Chevallet, M., Wagner, E., Luche, S., van Dorsselaer, A., Leize-Wagner, E., and Rabilloud, T. (2003) Regeneration of peroxiredoxins during recovery after oxidative stress: only some overoxidized peroxiredoxins can be re- duced during recovery after oxidative stress. J. Biol. Chem. 278, 37146–37153 36. Klomsiri, C., Nelson, K. J., Bechtold, E., Soito, L., Johnson, L. C., Lowther, W. T., Ryu, S. E., King, S. B., Furdui, C. M., and Poole, L. B. (2010) Use of dimedone-based chemical probes for sulfenic acid detection evaluation of conditions affecting probe incorporation into redox-sensitive proteins. Methods Enzymol. 473, 77–94 21. Woo, H. A., Chae, H. Z., Hwang, S. C., Yang, K. S., Kang, S. W., Kim, K., and Rhee, S. G. (2003) Reversing the inactivation of peroxiredoxins caused by cysteine sulfinic acid formation. Science 300, 653–656 37. Cao, Z., Tavender, T. J., Roszak, A. W., Cogdell, R. J., and Bulleid, N. J. (2011) Crystal structure of reduced and of oxidized peroxiredoxin IV en- zyme reveals a stable oxidized decamer and a nondisulfide-bonded inter- mediate in the catalytic cycle. J. Biol. Chem. 286, 42257–42266 22. Li, Z., Sau, A. K., Furdui, C. M., and Anderson, K. S. (2005) Probing the role of tightly bound phosphoenolpyruvate in Escherichia coli 3-deoxy-D- manno-octulosonate 8-phosphate synthase catalysis using quantitative time-resolved electrospray ionization mass spectrometry in the millisec- ond time range. Anal. Biochem. 343, 35–47 38. Yang, K. S., Kang, S. W., Woo, H. A., Hwang, S. C., Chae, H. Z., Kim, K., and Rhee, S. G. Molecular Basis for Resistance of hPrx3 to Hyperoxidation (2002) Inactivation of human peroxiredoxin I during ca- talysis as the result of the oxidation of the catalytic site cysteine to cys- teine-sulfinic acid. J. Biol. Chem. 277, 38029–38036 23. Li, Z., Sau, A. K., Shen, S., Whitehouse, C., Baasov, T., and Anderson, K. S. (2003) A snapshot of enzyme catalysis using electrospray ionization mass spectrometry. J. Am. Chem. Soc. 125, 9938–9939 39. Jara, M., Vivancos, A. P., Calvo, I. A., Moldo´n, A., Sanso, M., and Hidalgo, E. (2007) The peroxiredoxin Tpx1 is essential as a H2O2 scavenger during aerobic growth in fission yeast. Mol. Biol. Cell 18, 2288–2295 24. Nagy, P., Karton, A., Betz, A., Peskin, A. V., Pace, P., O’Reilly, R. J., Hamp- ton, M. B., Radom, L., and Winterbourn, C. C. (2011) Model for the ex- ceptional reactivity of peroxiredoxins 2 and 3 with hydrogen peroxide: a kinetic and computational study. J. Biol. Chem. 286, 18048–18055 40. Winterbourn, C. C. (2008) Reconciling the chemistry and biology of reac- tive oxygen species. Nat. Chem. Biol. 4, 278–286 41. Peskin, A. V., Dickerhof, N., Poynton, R. A., Paton, L. N., Pace, P. E., Hampton, M. B., and Winterbourn, C. C. (2013) Hyperoxidation of per- oxiredoxins 2 and 3: rate constants for the reactions of the sulfenic acid of the peroxidatic cysteine. J. Biol. Chem. 288, 14170–14177 25. Cao, Z., Bhella, D., and Lindsay, J. G. (2007) Reconstitution of the mito- chondrial PrxIII antioxidant defence pathway: general properties and fac- tors affecting PrxIII activity and oligomeric state. J. Mol. Biol. 372, 1022–1033 42. Koo, K. H., Lee, S., Jeong, S. Y., Kim, E. T., Kim, H. J., Kim, K., Song, K., and Chae, H. Z. (2002) Regulation of thioredoxin peroxidase activity by C-ter- minal truncation. Arch. Biochem. Biophys. 397, 312–318 26. Salsbury, F. R., Jr., Yuan, Y., Knaggs, M. H., Poole, L. B., and Fetrow, J. S. (2012) Structural and electrostatic asymmetry at the active site in typical and atypical peroxiredoxin dimers. J. Phys. Chem. B 116, 6832–6843 43. Sayed, A. A., and Williams, D. L. (2004) Biochemical characterization of 2-Cys peroxiredoxins from Schistosoma mansoni. J. Biol. Chem. 279, 26159–26166 27. Yuan, Y., Knaggs, M., Poole, L., Fetrow, J., and Salsbury, F., Jr. (2010) Conformational and oligomeric effects on the cysteine pKa of trypare- doxin peroxidase. J. Biomol. Struct. Dyn. 28, 51–70 44. Wang, X., Wang, L., Wang, X., Sun, F., and Wang, C. C. REFERENCES None- theless, hyperoxidation of Prx3 and its subsequent repair by sulfiredoxin does occur within the mitochondrion and plays a crucial role in adrenal steroidogenesis (5). 14. Woo, H. A., Jeong, W., Chang, T. S., Park, K. J., Park, S. J., Yang, J. S., and Rhee, S. G. (2005) Reduction of cysteine sulfinic acid by sulfiredoxin is specific to 2-Cys peroxiredoxins. J. Biol. Chem. 280, 3125–3128 15. Jeong, W., Bae, S. H., Toledano, M. B., and Rhee, S. G. (2012) Role of sulfiredoxin as a regulator of peroxiredoxin function and regulation of its expression. Free Radic. Biol. Med. 53, 447–456 16. Cox, A. G., Pearson, A. G., Pullar, J. M., Jo¨nsson, T. J., Lowther, W. T., Winterbourn, C. C., and Hampton, M. B. (2009) Mitochondrial peroxire- doxin 3 is more resilient to hyperoxidation than cytoplasmic peroxiredox- ins. Biochem. J. 421, 51–58 17. Matsushima, S., Ide, T., Yamato, M., Matsusaka, H., Hattori, F., Ikeuchi, M., Kubota, T., Sunagawa, K., Hasegawa, Y., Kurihara, T., Oikawa, S., Kinugawa, S., and Tsutsui, H. (2006) Overexpression of mitochondrial peroxiredoxin-3 prevents left ventricular remodeling and failure after myocardial infarction in mice. Circulation 113, 1779–1786 18. Nonn, L., Berggren, M., and Powis, G. (2003) Increased expression of mitochondrial peroxiredoxin-3 (thioredoxin peroxidase-2) protects can- 29722 JOURNAL OF BIOLOGICAL CHEMISTRY VOLUME 288•NUMBER 41•OCTOBER 11, 2013 Molecular Basis for Resistance of hPrx3 to Hyperoxidation (2012) Structural insights into the peroxidase activity and inactivation of human peroxire- doxin 4. Biochem. J. 441, 113–118 28. Budde, H., Flohe, L., Hecht, H. J., Hofmann, B., Stehr, M., Wissing, J., and Lunsdorf, H. (2003) Kinetics and redox-sensitive oligomerisation reveal negative subunit cooperativity in tryparedoxin peroxidase of Trypano- soma brucei. Biol. Chem. 384, 619–633 45. Salmeen, A., Andersen, J. N., Myers, M. P., Meng, T. C., Hinks, J. A., Tonks, N. K., and Barford, D. (2003) Redox regulation of protein tyrosine phos- phatase 1B involves a sulphenyl-amide intermediate. Nature 423, 769–773 29. Halliwell, B., Clement, M. V., and Long, L. H. (2000) Hydrogen peroxide in the human body. FEBS Lett. 486, 10–13 30. Winterbourn, C. C., and Hampton, M. B. (2008) Thiol chemistry and specificity in redox signaling. Free Radic. Biol. Med. 45, 549–561 46. van Montfort, R. L., Congreve, M., Tisi, D., Carr, R., and Jhoti, H. (2003) Oxidation state of the active-site cysteine in protein tyrosine phosphatase 1B. Nature 423, 773–777 31. Claiborne, A., Yeh, J. I., Mallett, T. C., Luba, J., Crane, E. J., 3rd, Charrier, V., and Parsonage, D. (1999) Protein-sulfenic acids: diverse roles for an unlikely player in enzyme catalysis and redox regulation. Biochemistry 38, 15407–15416 47. Lee, J. W., Soonsanga, S., and Helmann, J. D. (2007) A complex thiolate switch regulates the Bacillus subtilis organic peroxide sensor OhrR. Proc. Natl. Acad. Sci. U.S.A. 104, 8743–8748 32. Ellis, H. R., and Poole, L. B. (1997) Novel application of 7-chloro-4-nitro- benzo-2-oxa-1,3-diazole to identify cysteine sulfenic acid in the AhpC component of alkyl hydroperoxide reductase. Biochemistry 36, 15013– 15018 48. Yang, J., Groen, A., Lemeer, S., Jans, A., Slijper, M., Roe, S. M., den Hertog, J., and Barford, D. (2007) Reversible oxidation of the membrane distal domain of receptor PTP is mediated by a cyclic sulfenamide. Biochemis- try 46, 709–719 33. Qian, J., Wani, R., Klomsiri, C., Poole, L. B., Tsang, A. W., and Furdui, C. M. (2012) A simple and effective strategy for labeling cysteine sulfenic acid in proteins by utilization of -ketoesters as cleavable probes. Chem. Commun. 48, 4091–4093 49. Fu, X., Mueller, D. M., and Heinecke, J. W. (2002) Generation of intramo- lecular and intermolecular sulfenamides, sulfinamides, and sulfonamides by hypochlorous acid: a potential pathway for oxidative cross-linking of low-density lipoprotein by myeloperoxidase. Biochemistry 41, 1293–1301 34. Wani, R., Qian, J., Yin, L., Bechtold, E., King, S. B., Poole, L. 34. Wani, R., Qian, J., Yin, L., Bechtold, E., King, S. B., Poole, L. B., Paek, E., Molecular Basis for Resistance of hPrx3 to Hyperoxidation B., Paek, E., OCTOBER 11, 2013•VOLUME 288•NUMBER 41 JOURNAL OF BIOLOGICAL CHEMISTRY 29723 OCTOBER 11, 2013•VOLUME 288•NUMBER 41
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The gaugino condensate from asymmetric four-torus with twists
˜The œJournal of high energy physics/˜The œjournal of high energy physics
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Published for SISSA by Springer Received: November 15, 2022 Accepted: December 19, 2022 Published: January 23, 2023 Received: November 15, 2022 Accepted: December 19, 2022 Published: January 23, 2023 Keywords: Anomalies in Field and String Theories, Nonperturbative Effects, Supersym- metric Gauge Theory Open Access, c⃝The Authors. Article funded by SCOAP3. The gaugino condensate from asymmetric four-torus with twists JHEP01(2023)118 Mohamed M. Anbera and Erich Poppitzb aCentre for Particle Theory, Department of Mathematical Sciences, Durham University, South Road, Durham DH1 3LE, U.K. bDepartment of Physics, University of Toronto, 60 St George St., Toronto, ON M5S 1A7, Canada Mohamed M. Anbera and Erich Poppitzb aCentre for Particle Theory, Department of Mathematical Sciences, Durham University, South Road, Durham DH1 3LE, U.K. bDepartment of Physics, University of Toronto, 60 St George St., Toronto, ON M5S 1A7, Canada E-mail: mohamed.anber@durham.ac.uk, poppitz@physics.utoronto.ca Abstract: We calculate the gaugino condensate in SU(2) super Yang-Mills theory on an asymmetric four-torus T4 with ’t Hooft’s twisted boundary conditions. The T4 asymmetry is controlled by a dimensionless detuning parameter ∆, proportional to L3L4 −L1L2, with Li denoting the T4 periods. We perform our calculations via a path integral on a T4. Its size is taken much smaller than the inverse strong scale Λ and the theory is well inside the semi-classical weak-coupling regime. The instanton background, constructed for ∆≪1 in [1], has fractional topological charge Q = 1 2 and supports two gaugino zero modes, yielding a non-vanishing bilinear condensate, which we find to be ∆-independent. Further, the theory has a mixed discrete chiral/1-form center anomaly leading to double degeneracy of the energy eigenstates on any size torus with ’t Hooft twists. In particular, there are two vacua, |0⟩and |1⟩, that are exchanged under chiral transformation. Using this information, the ∆-independence of the condensate, and assuming further that the semi-classical theory is continuously connected to the strongly-coupled large-T4 regime, we determine the numerical coefficient of the gaugino condensate: ⟨0|trλλ|0⟩= |⟨1|trλλ|1⟩| = 32π2Λ3, a result equal to twice the known R4 value. We discuss possible loopholes in the continuity approach that may lead to this discrepancy. Keywords: Anomalies in Field and String Theories, Nonperturbative Effects, Supersym- metric Gauge Theory Keywords: Anomalies in Field and String Theories, Nonperturbative Effects, Supersym- metric Gauge Theory ArXiv ePrint: 2210.13568 Open Access, c⃝The Authors. Article funded by SCOAP3. Open Access, c⃝The Authors. Article funded by SCOAP3. https://doi.org/10.1007/JHEP01(2023)118 Contents 1 Introduction 1 1.1 Gaugino condensate: a historical prelude 2 1.2 Gaugino condensate on asymmetric T4: a summary of the procedure and results 4 1.3 Future directions 7 1.4 Outline 8 2 Fractional instantons on the symmetric torus 9 3 Fractional instantons and gaugino zero modes on the asymmetric torus 13 3.1 Fermion zero modes 15 3.2 Bosonic zero modes 15 4 The path integral: bosonic and fermionic measures 17 4.1 Fermionic measure 17 4.2 Bosonic measure 18 5 The Hamiltonian formalism, Wilson loops, and the moduli space 19 5.1 Pure Yang-Mills theory 19 5.2 SYM theory 22 6 The gaugino condensate 24 A Constructing instantons on the asymmetric T4 with twists 25 A.1 Constructing the self-dual fractional instanton for small ∆ 28 A.2 The field strength tensor of the fractional instanton to order ∆ 34 A.3 The gauge invariants of the fractional instanton background 36 B Zero modes of the fractional instanton 38 B.1 Leading-order bosonic zero-modes and measure 38 B.2 Fermions and their zero-mode measure 40 B.2.1 No zero modes of D2 = D ¯D on the asymmetric T4 42 B.2.2 The zero modes of D on the asymmetric T4 via the Dirac equation 42 B.2.3 Zero modes of D and ¯D on the symmetric T4 44 B.2.4 The zero modes of D on the asymmetric T4 via supersymmetry 45 B.3 The moduli space metric, to any order in ∆ 46 B.3.1 Fermion zero-mode measure to arbitrary order in ∆ 46 B.3.2 Bosonic zero-modes and moduli-space metric to any order in ∆ 47 B.3.3 The derivatives of the O( √ ∆) solution and the gauge condition 50 B.3.4 The Jacobian and the all-order bosonic measure 54 1 Introduction In practice, the PSU(N) flux is turned on by imposing twisted boundary conditions on the fields that live on T4. Next, we examine the partition function Z[PSU(N)] of SYM in this background by performing a Zdχ 2N rotation. We find Z[PSU(N)] →ei 2π N Z[PSU(N)], and thus, the theory stops being invariant under the action of Zdχ 2N once we gauge the 1-form symmetry. This is the sought generalized ’t Hooft anomaly — a mixed anomaly between the Z(1) N 1-form symmetry and the Zdχ 2N 0-form discrete chiral symmetry. The anomaly indicates that the IR theory cannot be trivially gapped. Assuming JHEP01(2023)118 Assuming a gauge theory generates a mass gap in the infrared (IR), one way to match its ’t Hooft anomalies is via the formation of condensates. A famous example, and the subject of this paper, is the formation of gaugino condensates in N = 1 SU(N) super Yang-Mills theory (SYM), which are needed to match a generalized ’t Hooft anomaly. This anomaly can be understood as follows. In addition to the Z(1) N 1-form symmetry that acts on the Wilson lines, SYM enjoys a Zdχ 2N 0-form global discrete chiral, or R, symmetry. We may gauge the 1-form symmetry by turning on a background gauge field of Z(1) N , which is done either by coupling SYM to a ZN TQFT [13] or by activating a ’t Hooft flux [14, 15]. The latter is a field configuration on T4 that carries a fractional flux B ∈H2(T4, ZN) (i.e. the flux piercing 2-cycles obeys the quantization rule R T2⊂T4 B ∈2πZ N ) and fractional topological charge Q = 1 8π2 R T4 B ∧B ∈Z N . In mathematical language, we consider the PSU(N) ≡SU(N)/ZN bundle instead of the SU(N) bundle. The former has a non-trivial Brauer class w ∈H2(BPSU(N), ZN) that obstructs the lifting of PSU(N) to SU(N), and we set B = w. In practice, the PSU(N) flux is turned on by imposing twisted boundary conditions on the fields that live on T4. Next, we examine the partition function Z[PSU(N)] of SYM in this background by performing a Zdχ 2N rotation. We find Z[PSU(N)] →ei 2π N Z[PSU(N)], and thus, the theory stops being invariant under the action of Zdχ 2N once we gauge the 1-form symmetry. Contents JHEP01(2023)118 – i – 1 Introduction Strongly coupled gauge theories have been under intense study over the past few years, thanks to the recent developments of generalized global symmetries [2]. These are operations that implement the group multiplication laws via topological constructions such that the symmetry operations are supported on topological surfaces that are robust under small deformations. An ordinary 0-form symmetry G, which acts on point-like particles, is implemented by operators supported on co-dimension 1 surfaces. These surfaces obey the group-multiplication laws via fusion rules and give rise to phases valued in G when they cross the charged objects. Likewise, a 1-form symmetry acts on 1-dimensional objects and is implemented via co-dimension 2 surfaces. For example, Wilson lines in 4-D SU(N) pure or super Yang-Mills theories are charged under Z(1) N 1-form symmetry. The 1-form symmetry is implemented via topological 2-dimensional surfaces that obey the ZN group multiplication laws and give rise to ZN phases when they link with Wilson lines. Like ordinary 0-form symmetries, 1-form symmetries organize the spectrum of a theory into representations, satisfy Ward identities, and may become anomalous if one tries to gauge them. In particular, ’t Hooft anomaly matching conditions (or ’t Hooft anomalies for short), which impose stringent constraints on quantum field theory (QFT), can be generalized to include anomalies of 1-form symmetries. Detecting the anomaly in 4-D requires defining a given QFT on manifolds with nontrivial 2-cycles, the typical example being the 4-torus T4. Generalized ’t Hooft anomalies provide a framework for classifying QFT and its phases. Many recent works entertained this generalized framework to shed light on a plethora of asymptotically free gauge theories, including vector-like [3–10] and chiral theories [11, 12]. Strongly coupled gauge theories have been under intense study over the past few years, thanks to the recent developments of generalized global symmetries [2]. These are operations that implement the group multiplication laws via topological constructions such that the symmetry operations are supported on topological surfaces that are robust under small deformations. An ordinary 0-form symmetry G, which acts on point-like particles, is implemented by operators supported on co-dimension 1 surfaces. These surfaces obey the group-multiplication laws via fusion rules and give rise to phases valued in G when they cross the charged objects. Likewise, a 1-form symmetry acts on 1-dimensional objects and is implemented via co-dimension 2 surfaces. 1 Introduction For example, Wilson lines in 4-D SU(N) pure or super Yang-Mills theories are charged under Z(1) N 1-form symmetry. The 1-form symmetry is implemented via topological 2-dimensional surfaces that obey the ZN group multiplication laws and give rise to ZN phases when they link with Wilson lines. Like ordinary 0-form symmetries, 1-form symmetries organize the spectrum of a theory into representations, satisfy Ward identities, and may become anomalous if one tries to gauge them. In particular, ’t Hooft anomaly matching conditions (or ’t Hooft anomalies for short), which impose stringent constraints on quantum field theory (QFT), can be generalized to include anomalies of 1-form symmetries. Detecting the anomaly in 4-D requires defining a given QFT on manifolds with nontrivial 2-cycles, the typical example being the 4-torus T4. Generalized ’t Hooft anomalies provide a framework for classifying QFT and its phases. Many recent works entertained this generalized framework to shed light on a plethora of asymptotically free gauge theories, including vector-like [3–10] and chiral theories [11, 12]. Assuming a gauge theory generates a mass gap in the infrared (IR), one way to match its ’t Hooft anomalies is via the formation of condensates. A famous example, and the subject of this paper, is the formation of gaugino condensates in N = 1 SU(N) super Yang-Mills theory (SYM), which are needed to match a generalized ’t Hooft anomaly. This anomaly can be understood as follows. In addition to the Z(1) N 1-form symmetry that acts on the Wilson lines, SYM enjoys a Zdχ 2N 0-form global discrete chiral, or R, symmetry. We may gauge the 1-form symmetry by turning on a background gauge field of Z(1) N , which is done either by coupling SYM to a ZN TQFT [13] or by activating a ’t Hooft flux [14, 15]. The latter is a field configuration on T4 that carries a fractional flux B ∈H2(T4, ZN) (i.e. the flux piercing 2-cycles obeys the quantization rule R T2⊂T4 B ∈2πZ N ) and fractional topological charge Q = 1 8π2 R T4 B ∧B ∈Z N . In mathematical language, we consider the PSU(N) ≡SU(N)/ZN bundle instead of the SU(N) bundle. The former has a non-trivial Brauer class w ∈H2(BPSU(N), ZN) that obstructs the lifting of PSU(N) to SU(N), and we set B = w. 1.1 Gaugino condensate: a historical prelude Generally speaking, the matching conditions can only provide kinematical constraints and do not, by themselves yield insights into the details of the IR dynamics of a gauge theory. One needs an extra guide if, at all, there is a hope to understand the dynamics, e.g., the condensates. Thanks to supersymmetry, such studies are possible in SYM. These date back to the early eighties [17–21] (see [22–27] for reviews). The condensate calculations are based on the Belavin-Polyakov-Schwartz-Tyupkin (BPST) instanton calculus [28]: BPST instantons are (anti) self-dual Yang-Mills configurations that violate the non-renormalization theorems of SYM and hence, give a non-zero vacuum expectation value to the condensates. On dimensional-analysis grounds one can write ⟨trλ2 16π2 ⟩= cΛ3, where Λ is the strong-coupling scale and c is a numerical factor. The exact value of c was a controversial issue that caused many debates in the past. Generally, there are two methods to compute the bilinear gaugino condensate in 4-D SYM: the strong-coupling and the weak-coupling instanton methods. JHEP01(2023)118 In the first method, we start directly from the 4-D SYM in its strong-coupling regime and do instanton calculus, as in [17, 18]. A single SU(N) BPST instanton carries integer topological charge Q ∈Z, and the configuration with the lowest topological charge Q = 1 admits 2N gaugino zero modes. The saturation of the zero modes in the Q = 1 instanton background gives a nonzero value to the 2N-point function ⟨(trλ2)N⟩, from which one can naively extract the value of the 2-point function ⟨(trλ2)⟩= h ⟨(trλ2)N⟩ i1/N. A detailed calculation, keeping track of all numerical coefficients, gives ⟨(trλ2)⟩= 2((N −1)!(3N − 1))−1/N(16π2Λ3)ei 2πk N , with k = 0, 1, . . . , N −1. The complex phase results from taking the Nth root of unity, in accordance with the expectation that the theory admits N distinct vacua needed to match the generalized ’t Hooft anomaly. In the weak-coupling instanton method, we consider super QCD with N −1 fundamental flavors Φi, i = 1, . . . , N −1, where Φi is a chiral superfield, and give all the flavors small masses m. We work in the limit |Φi| ≫ΛQ, where ΛQ is the strong scale in the presence of quarks. Since there are N −1 flavors, the gauge group fully abelianizes and we are well inside the weak-coupling regime. 1 Introduction This is the sought generalized ’t Hooft anomaly — a mixed anomaly between the Z(1) N 1-form symmetry and the Zdχ 2N 0-form discrete chiral symmetry. The anomaly indicates that the IR theory cannot be trivially gapped. Assuming – 1 – confinement, the theory breaks its Zdχ 2N symmetry and forms N vacua separated by domain walls. The order parameter of Zdχ 2N symmetry is the bilinear gaugino condensate ⟨trλ2⟩or higher-order condensates ⟨(trλ2)n⟩, n > 1 and n mod N ̸= 0. The existence of N vacua is also in accordance with the Witten index [16]. 1The comparison between the weak-coupling and strong-coupling instanton methods in SU(2) was first performed in [21], where the correct ratio between the two methods was given. 1.1 Gaugino condensate: a historical prelude The total superpotential of this theory takes the from W = mi j ¯ΦjΦi + Λ2N+1 Q Det(¯ΦΦ), where the second term is the Affleck-Dine-Seiberg (ADS) superpotential [20]. The ADS term is nonperturbative in nature and is based on holomorphy and the symmetry structure of super QCD. It also results from saturating the quarks’ zero modes in the BPST instanton background(the numerical coefficient was obtained1 in [29], and corrected in [30]). Since we are in a weak-coupling limit, the instanton calculations are reliable. Minimizing the energy, we obtain the supersymmetric vacuum ¯ΦjΦi = m−1j i h Λ(2N+1) Q Detm i1/N. Finally, we substitute this result back into W to find – 2 – W = N h Λ2N+1 Q Detm i1/N. We then decouple the quarks by taking m ≫ΛQ, thus, leaving the weak-coupling regime. Using holomorphy, we can write Weff= NΛ3, where Λ is the strong scale at the mass threshold, and it exactly coincides with SYM strong scale at the decoupling limit. Recalling that one can write the holomorphic strong scale as Λ = µeiτ/3N, with τ = 4πi g2(µ) and µ is some arbitrary energy scale, and that ⟨trλ2⟩= −16πi∂Weff ∂τ , one obtains ⟨trλ2⟩= 16π2Λ3ei 2πk N in the k-th vacuum.2 Having two different methods that yield two different answers resulted in many debates in the literature about the validity of both methods. It was earlier understood that the strong-coupling instanton method is in tension with the cluster decomposition principle (CDP). Consider the correlator ⟨trλ2(x)trλ2(x′)⟩. In the limit |x −x′| →∞we expect ⟨trλ2(x)trλ2(x′)⟩= ⟨trλ2⟩2. However, since a BPST instanton cannot saturate 2 gaugino zero modes, one finds ⟨trλ2⟩= 0, contradicting CDP. A possible resolution of this puzzle was proposed in [32]. It was hypothesized that SYM admits an extra phase with vanishing bilinear condensate ⟨trλ2⟩= 0 and that averaging over the chirally symmetric and non- symmetric phases gives the result of the strong-coupling instanton method. This hypothesis was carefully examined in [33] by considering a softly broken N = 2 Seiberg-Witten theory down to SYM. It was shown that the chirally-symmetric phase is absent, casting doubt on the averaging hypothesis. Further considerations in [34] excluded the symmetric vacuum. We also note that the anomaly-matching argument of [35] also precludes such a phase. It was further shown in [36] that strong-coupling multi-instanton calculations are inconsistent with CDP. 2The definition of the strong coupling scale we follow in this paper is given by Λ3 = µ3 e−8π2/Ng2 g2 , the one used in [25, 26, 31]. 3The 4-D coupling constant on R3 × S1 L ceases to run at scale ∼1/NL, roughly the W-boson mass. Taking L ≪(NΛ)−1, we stay in the weakly-coupled regime. 4A SU(N) caloron with a unit topological charge is composed of N monopole instantons. Calorons are Yang-Mills (anti) self-dual configurations defined on R3 × S1 with integral topological charges and non-trivial holonomy (the expectation value of the Polyakov’s loop) along S1. A BPST instanton, in contrast, (or more precisely, the Harrington-Shepard solution [38] defined on R3 × S1) has a trivial holonomy. Calorons were discovered by Kraan and van Baal [39] using the Atiyah-Drinfeld-Hitchin-Manin (ADHM) construction [40] and independently by Lee and Yi [41] and Lee and Lu [42] in the context of D-branes. Let L and P be the size of S1 and the holonomy (in units of 1/L). If LP ≳1, then the monopole constituents are well-separated in space, and one can make sense of them in a semi-classical treatment, as in the case of SYM on R3 × S1 L. In particular, in the supersymmetric vacuum, which preserves the 0-form ZN center symmetry of the theory, the constituent monopoles are of equal action S = 8π2 Ng2 . In the opposite limit, LP ≪1, the monopoles hide inside the caloron core. 2The definition of the strong coupling scale we follow in this paper is given by Λ3 = µ3 e−8π2/Ng2 g2 , the one used in [25, 26, 31]. 3 3 1 1.1 Gaugino condensate: a historical prelude JHEP01(2023)118 Extra support to the weak-coupling calculations came from studying SYM on R3 × S1 L, where S1 L is a small spatial circle with circumference L ≪(NΛ)−1, and both gauge fields and gauginos are given periodic boundary conditions on S1 L [31, 37]. Compactification over a small circle causes this theory to fully abelianize and enter its weakly-coupled regime.3 The theory on R3 × S1 L admits monopole-instantons, the microscopic constituents of calorons.4 At the supersymmetric vacuum, the monopoles have topological charges of 1/N. Using the index theorem, we deduce that a single monopole can saturate 2 gaugino zero modes giving rise to the bilinear condensate. Detailed calculations give ⟨trλ2 16π2 ⟩= Λ3, the exact same – 3 – result from 4-D weak-coupling instanton calculations. The advantage of the compactified theory over the 4-D theory at weak coupling is that in the former, one can understand the dynamics responsible for the condensate formation without relying on the miracle of holomorphy. As a bonus, the proliferation of the monopoles causes the compactified theory to generate a mass gap and confine, a result that is prohibitively difficult to understand in 4-D. The continuity of confinement and condensate between the small and large L limits may imply that the fractional instantons are responsible for the dynamics on R4, even though one may not make analytical sense of them in a strongly-coupled setup. The continuity conjecture was taken seriously over the past decade in supersymmetric and nonsupersymmetric theories; see [43, 44] for reviews. The conjecture withstood many tests, but we are still far from a firm conclusion about the role of fractional microscopic objects in strongly-coupled phenomena. This continuity was mainly tested on R3 × S1 L, and one wishes to examine whether it holds in other geometries. JHEP01(2023)118 One such geometry is T4, very natural from the point of view of lattice practicalities. Right after ’t Hooft presented his twisted solutions (solutions with twisted boundary conditions, i.e. PSU(N) bundle solutions, with fractional topological charges) [15], van Baal studied their mathematical properties [45, 46]. 1.1 Gaugino condensate: a historical prelude Later, it was argued in a series of works [47–49], see also the review [50], that (anti) self-dual ’t Hooft fractional instantons can be seen in realistic simulations of 4-D pure Yang-Mills theory and that such configurations could be utilized to explain confinement.5 Further, it was argued in [53], via extended lattice simulations, that ’t Hooft fractional instantons on T4 are ultimately connected to monopole instantons in the infinite 3-volume limit and finite time6 direction. In particular, it was shown that an exact SU(2) caloron solution with a unit topological charge and equal-action constituent monopoles (see Footnote 4) can be constructed on the twisted T4 by gluing two twisted solutions, each carrying Q = 1 2 charge, along the space directions.7 1.2 Gaugino condensate on asymmetric T4: a summary of the procedure and results 5Even before these studies, a program known as the “femtouniverse” utilized the Hamiltonian formalism on R × T3, to study Yang-Mills theories at small volumes [51]; see [52] for a review. 6Notice that these are simulations in pure Yang-Mills theory, and thus, unlike SYM, there is no distinction between thermal and spatial circles. 7In fact, there is an obstruction to the existence of Q = 1 (anti) self-dual caloron on T4 with untwisted boundary conditions [54]. Yet, in practice, one can find a very good approximate self-dual solution even in the absence of twists. 8We interchangeably use the term “’t Hooft flux background” and “’t Hooft twists.” The latter is more precise, since it refers to the twist of the boundary conditions, which does not always lead to nonzero “flux,” i.e. nonzero gauge field strength. Whether such field strength is present or not is a dynamical issue, see e.g. [16]. We hope that our abuse of terminology does not lead to confusion. 8We interchangeably use the term “’t Hooft flux background” and “’t Hooft twists.” The latter is more precise, since it refers to the twist of the boundary conditions, which does not always lead to nonzero “flux,” i.e. nonzero gauge field strength. Whether such field strength is present or not is a dynamical issue, see e.g. [16]. We hope that our abuse of terminology does not lead to confusion. 5Even before these studies, a program known as the “femtouniverse” utilized the Hamiltonian formalis on R × T3, to study Yang-Mills theories at small volumes [51]; see [52] for a review. 6Notice that these are simulations in pure Yang-Mills theory, and thus, unlike SYM, there is no distincti between thermal and spatial circles. 7 4 7In fact, there is an obstruction to the existence of Q = 1 (anti) self-dual caloron on T4 with untwisted undary conditions [54]. Yet, in practice, one can find a very good approximate self-dual solution even in e absence of twists. 1.2 Gaugino condensate on asymmetric T4: a summary of the procedure and results The possible connection between ’t Hooft’s solutions and monopole-instantons [53] calls for a serious examination of this finding. Since both the R3 × S1 L monopole-instanton and 4-D weak-coupling instanton methods give the same gaugino condensate, one wonders whether the same result can be obtained in the ’t Hooft flux background.8 This is especially timely after the advent of the new generalized anomalies, which can be easily detected when – 4 – a QFT is put on T4 with a PSU(N) bundle (or ’t Hooft twisted boundary conditions). Recently, Ünsal advocated that a refinement of the instanton sum in the partition functions of SU(N) theories has to be considered: while fractional instantons of PSU(N) bundles contribute to observables like the gaugino condensate and vacuum energy, the sum over the fractional objects has to be constrained to yield the integer topological charges of the SU(N) bundle [55] (see also [52] for an earlier assertion). In this paper, we put this proposal under scrutiny and perform detailed calculations of the gaugino condensate on T4 and a PSU(2) bundle.9 Our conclusion is that the condensate in any of the two vacua is given by ⟨0|trλ2|0⟩= |⟨1|trλ2|1⟩| = 32π2Λ3, with a coefficient that is twice that obtained via the weak-coupling instanton method on R4 and the semi- classical calculations on R3 × S1 L. The extra factor of 2 is unexpected and calls for further serious examinations of the role of the PSU(N) bundles in SU(N) gauge theories and of the continuity conjecture. JHEP01(2023)118 The calculations that lead to this puzzling result are surprisingly rich. The simplest SU(2) pure Yang-Mills (i.e. Yang-Mills equations with zero source) fractional instanton with topological charge Q = 1 2 and action S0 = 4π2 g2 was constructed by ’t Hooft in his seminal work [15]. This solution is abelian in nature, i.e. the gauge field components are along the Cartan direction. The solution must be (anti) self-dual, otherwise, the fluctuations in this background will have negative modes signaling instability. Let L1, L2, L3, L4 be the lengths of the periods in T4. Then, the self-duality of the abelian solution is guaranteed if and only if L1L2 = L3L4. We dub the T4 that obeys this relation as the self-dual torus, the simplest one being the symmetric T4 with L1=L2=L3=L4. 9The gaugino condensate on a symmetric T4 in the background of ’t Hooft flux was first considered long ago in [56]. These calculations were solely based on supersymmetry transformations along with dimensional analysis, and no attempt to determine the numerical coefficient was made. 1.2 Gaugino condensate on asymmetric T4: a summary of the procedure and results Given the simplicity of the abelian solution on the symmetric T4, one is tempted to use it as a source for the gaugino condensate. According to the index theorem, this background must saturate 2 gaugino zero modes. Nevertheless, the direct solution of the Dirac equation yields 6 zero modes (four “undotted” and two “dotted” ones). To make things worse, the extra zero modes source the super Yang-Mills equations of motion, hinting that such an abelian solution might not be a consistent background. The resolution of both puzzles could have been achieved had we been able to show that higher-order corrections (including loops) lift the extra gaugino zero modes. Although we believe that this should be the case, we were not able to show it in a satisfactory way. In order to circumvent this difficulty, we chose to depart from the symmetric self-dual to the non-self-dual torus. This is both a blessing and a curse. The curse is the technical difficulty of the problem, while the blessing is that the asymmetric torus enables us to take various interesting limits, e.g. R × T3 and R2 × T2. If the relation L1L2 = L3L4 is violated, the abelian solution must be modified to include non-abelian pieces, ensuring that the solution persists to be (anti) self-dual. To date, there exists no analytical solution with Q = 1 2 on T4 with arbitrary shape. However, a systematic procedure to deal with non-self-dual tori was developed in [1]. This method gives an approximate analytical – 5 – self-dual solution, with charge |Q| = 1 2 and action S0 = 4π2 g2 , as an expansion in a “detuning” parameter ∆≡(L3L4 −L1L2)/√L1L2L3L4 measuring the deviation from a self-dual T4. Solving the Dirac equation on a small asymmetric T4 with ∆≪1 and limiting our explicit treatment to the lowest order in ∆, we find exactly 2 gaugino zero modes as per the index theorem. We also verified that the explicit solutions of the fermion zero modes are consistent with supersymmetry transformations. These modes do not source the Yang-Mills equations of motion, implying that our approximate solution is a consistent background. The gauge field fluctuations admit 4 bosonic zero modes (also in accordance with the index theorem), interpreted as translational moduli. Supersymmetry guarantees the cancelation between the bosonic and fermionic excited states, leaving only the bosonic and fermion zero mode integrals to deal with. 10Effectively, a Wilson loop measures the Z2 flux of the twisted solution. 1.2 Gaugino condensate on asymmetric T4: a summary of the procedure and results JHEP01(2023)118 The contributions of zero modes to the path integral are taken into account using the method of collective coordinates, and therefore, we need to integrate over the moduli space M. To correctly identify the shape and size of M, we carefully examine all gauge invariant observables in the background of the fractional instanton on T4. This includes both local gauge-invariant densities and Wilson loops. While gauge-invariant densities are invariant under translations over a period on T4, a Wilson loop acquires a Z2 phase.10 Therefore, we find M ∼T4 with double the periods of the physical torus to account for the gauge inequivalent classes. This result is further supported by investigating the Hamiltonian formalism of the theory. Interestingly, the metric on M is found to be proportional to the background action and is, hence, independent of ∆. Putting the pieces together, we finally obtain ⟨trλ2⟩= 64π2Λ3, with a coefficient four times the expected number on R4. To understand the significance of this result, we need to interpret the expectation value ⟨trλ2⟩using the Hamiltonian formalism. Due to the mixed discrete chiral/one-form center anomaly, the energy eigenstates are doubly degenerate in the background of a ’t Hooft flux on any torus size: there are 2 vacua that are exchanged under the operation of chiral transformation, which explains the extra factor of 2, while the relative phase in the condensate in the two vacua is compensated by the ’t Hooft twist in the Euclidean time direction [57]. Thus, restricting the condensate to one vacuum, upon taking the limit of large T4, we obtain ⟨0|trλ2|0⟩= |⟨1|trλ2|1⟩| = 32π2Λ3. This coefficient is twice the known value on R4 (using the weak-coupling instanton method) or on R3 × S1 L. We emphasize that our calculations are performed on a small T4, compared to the strong scale of the theory, and thus, we are well inside the semi-classical regime. The calculations in this regime are under analytic control, thanks to the smallness of the coupling constant. However, to make a connection to the result on R4, we made a few assumptions. The invalidation of any of these assumptions can explain the discrepancy between our result and the expected one. We now list the assumptions that led to our result: 1. We assume that there is a unique fractional instanton on the asymmetric T4 with topological charge Q = 1 2. 1.2 Gaugino condensate on asymmetric T4: a summary of the procedure and results This solution is nonabelian in nature and is obtained from ’t Hooft’s abelian solution on a symmetric T4 as an expansion in the detuning 1. We assume that there is a unique fractional instanton on the asymmetric T4 with topological charge Q = 1 2. This solution is nonabelian in nature and is obtained from ’t Hooft’s abelian solution on a symmetric T4 as an expansion in the detuning – 6 – parameter ∆[1]. However, we were not able to prove the uniqueness11 of the solution. Instead, we rely on the numerical evidence in [1]. parameter ∆[1]. However, we were not able to prove the uniqueness11 of the solution. Instead, we rely on the numerical evidence in [1]. 2. Another lingering issue is the radius of convergence of the expansion, which is yet to be understood. Although our final result does not depend on ∆, one needs to be cautious when interpreting the result. In order to interpret the result and compare with the condensate on R4, we had to make use of the Hamiltonian formalism. Here, first, one puts the theory on a small spatial torus T3, with a ’t Hooft twist, and with periods of length L ≪Λ−1, and then takes the limit of a large Euclidean time direction, L4 ≫Λ−1. This is the limit ∆∼ q L4 L ≫1, well outside the small-∆regime used to compute the condensate. 2. Another lingering issue is the radius of convergence of the expansion, which is yet to be understood. Although our final result does not depend on ∆, one needs to be cautious when interpreting the result. In order to interpret the result and compare with the condensate on R4, we had to make use of the Hamiltonian formalism. Here, first, one puts the theory on a small spatial torus T3, with a ’t Hooft twist, and with periods of length L ≪Λ−1, and then takes the limit of a large Euclidean time direction, L4 ≫Λ−1. This is the limit ∆∼ q L4 L ≫1, well outside the small-∆regime used to compute the condensate. JHEP01(2023)118 3. After taking ∆large, one needs to take the size of the remaining T3 periods beyond the inverse strong-coupling scale. Thus, we necessarily leave the semi-classical regime, yet we assume no extra instantons contribute to the condensate in this limit. p 12The definition of a self-dual torus in SU(N) is different from the SU(2) case [15]. 11To avoid possible confusion, we note that the series in ∆determines a unique self-dual configuration for fixed values of the moduli (see the proof in appendix A.1, near eq. (A.31)). The possibility of non-uniqueness mentioned here refers to existence of a genuinely nonabelian Q = 1 2 solution not connected to ’t Hooft’s abelian solution. The numerical study of [1] appears to support uniqueness in this sense, but does not constitute a proof. 1.2 Gaugino condensate on asymmetric T4: a summary of the procedure and results (However, we can not help but note that this is similar, at least in spirit, to the extrapolation of the R3 × S1 L semiclassical calculation of the gaugino condensate to R4.) 4. In carrying out our calculations, we assume that quantum corrections due to bosonic, fermionic, and ghost fluctuations cancel exactly in our supersymmetric background, to all loop orders, and for arbitrary T4 size. Although the cancellation of the determinants to any loop order is well-established in R4, one may need to examine this assumption more carefully in the fractional instanton background of T4. In view of the above discussion, in the bulk of the paper, we present our calculations in sufficient detail to help the interested readers follow all numerical factors and enable them to dwell on the procedures used — and on improving the interpretation of our result. 1.3 Future directions This situation is different from the calculations on R3 × S1 L, where a monopole-instanton always supports 2 zero modes for all gauge groups, even those with no center symmetry. Therefore, at first, it is not clear how the twists and monopoles are connected. Investigating this problem is important for the continuity program. Spin(2N) has a Z4 or a Z2 × Z2 center group depending on whether N is odd or even. Owing to the small centers, ’t Hooft fluxes (or fractional instantons) of these groups will, in general, support more than 2 gaugino zero modes. This situation is different from the calculations on R3 × S1 L, where a monopole-instanton always supports 2 zero modes for all gauge groups, even those with no center symmetry. Therefore, at first, it is not clear how the twists and monopoles are connected. Investigating this problem is important for the continuity program. 3. It is also interesting to carry out our procedure to higher orders in ∆. The convergence of the series in ∆may shed more light on the problem of continuity. In this regard, we note that the closely related work [59] in the two-dimensional abelian Higgs model was able to carry the ∆-expansion to 51-st order, with the results indicating convergence to the infinite volume limit. JHEP01(2023)118 4. Another interesting geometry is to consider SYM on T2×R2 with a ’t Hooft flux turned on T2. This setup was considered previously in [60]. It was shown via dimensional reduction from T2 ×R2 to R2 that the theory admits ZN vortices and that the gaugino condensate forms in the 2-D effective theory ⟨trλ2⟩∼Λ3, as expected. However, the authors did not attempt to compute the numerical coefficient of the condensate. Such a calculation would mandate a more careful treatment of the dimensionally reduced 2-D theory, presumably using the power of supersymmetry. We also note that T2 × R2 is the limiting geometry of our asymmetric T4 after taking ∆to infinity. 1.3 Future directions Here, in lieu of a conclusion, we point out that our study warrants a few expansion direction 1. An immediate step would be generalizing the SU(2) result to SU(N ≥3). Self-dual instantons with topological charge 1 N , N ≥3, are necessarily non-abelian solutions of Yang-Mills equations [15]. This makes the treatment more involved, especially as we deviate from the self-dual torus.12 Fortunately, a systematic analysis to deal with this problem, a generalization of the method in [1], appeared in [58]. One can follow the same line of thought in our work to compute the condensate in SU(N). 2. It is tempting to study the condensates in other gauge groups, e.g., Sp(N) and Spin(2N) groups. These groups have small center groups: Sp(N) has a Z2 and 2. It is tempting to study the condensates in other gauge groups, e.g., Sp(N) and Spin(2N) groups. These groups have small center groups: Sp(N) has a Z2 and – 7 – Spin(2N) has a Z4 or a Z2 × Z2 center group depending on whether N is odd or even. Owing to the small centers, ’t Hooft fluxes (or fractional instantons) of these groups will, in general, support more than 2 gaugino zero modes. This situation is different from the calculations on R3 × S1 L, where a monopole-instanton always supports 2 zero modes for all gauge groups, even those with no center symmetry. Therefore, at first, it is not clear how the twists and monopoles are connected. Investigating this problem is important for the continuity program. Spin(2N) has a Z4 or a Z2 × Z2 center group depending on whether N is odd or even. Owing to the small centers, ’t Hooft fluxes (or fractional instantons) of these groups will, in general, support more than 2 gaugino zero modes. This situation is different from the calculations on R3 × S1 L, where a monopole-instanton always supports 2 zero modes for all gauge groups, even those with no center symmetry. Therefore, at first, it is not clear how the twists and monopoles are connected. Investigating this problem is important for the continuity program. Spin(2N) has a Z4 or a Z2 × Z2 center group depending on whether N is odd or even. Owing to the small centers, ’t Hooft fluxes (or fractional instantons) of these groups will, in general, support more than 2 gaugino zero modes. 1.4 Outline Our paper is organized as follows: In section 2, we formulate the theory and spell out all the necessary ingredients to define the partition function and the condensate on T4 with twisted boundary conditions. Further, we explain that a self-dual torus gives rise to extra, unexpected, zero modes. Then, we present the solution on the asymmetric T4 in section 3 and discuss both the fermion and bosonic zero modes. In section 4, we calculate the measures of the bosonic and fermion zero modes. In section 5, we deviate to the Hamiltonian formalism to discuss two important aspects. First, we argue that the moduli space of the bosonic zero modes is isomorphic to T4 with a period size twice the size of the physical period. Next, we recall that the 0-form/1-form mixed anomaly implies that the energy eigenstates on T3 are doubly degenerate and the theory admits 2 degenerate vacua. These features are important for the interpretation of our calculation of the gaugino bilinear. Finally, in section 6, we put all the pieces together to obtain our result of the gaugino condensate. Owing to the mismatch between our and both R4 and R3 × S1 L results for the gaugino condensate, and in order to offer the reader the opportunity to catch mistakes, if any, we present our rather detailed calculations of various quantities in two appendices. In appendix A, we review in great detail the construction of [1] of the fractional instanton to order ∆, with emphasis on the dependence on the collective coordinates. We also provide expressions of the field strengths and Wilson loops in the background of the leading-order solution. – 8 – In appendix B, we construct the fermion zero modes by directly solving the Weyl equation as well as by using supersymmetry transformation, and we prove that both methods yield the same result. Then, we construct the bosonic zero modes to any order in ∆, first by employing the fermionic zero modes and then by taking derivatives of the classical background solution w.r.t. the collective coordinates modulo gauge transformation (we also determine these gauge transformations). Finally, we determine the Jacobian of the bosonic zero modes moduli space needed to complete the calculations. 13The Euclidean action, supersymmetry transformations, and the matrices σn, ¯σn, σmn, ¯σmn, are as in [25], except that we use hermitean gauge fields, necessitating the replacement Athat ref. = iAthis paper. See also appendices A.1 and B.2. 2 Fractional instantons on the symmetric torus The periodicity condition on the gauge fields and gaugino in R4 defines the – 9 – T4 fields: A(x + ˆenLn) = Ωn(x)(A(x) −id)Ω−1 n (x), n = 1, 2, 3, 4, ∀x ∈R4, λ( + ˆ L ) Ω( )λ( )Ω−1( ) A(x + ˆenLn) = Ωn(x)(A(x) −id)Ω−1 n (x), n = 1, 2, 3, 4, ∀x ∈R4, λ(x + ˆenLn) = Ωn(x)λ(x)Ω−1 n (x) , (2.6) where we denoted A(x) = 4P n=1 An(x)dxn. Let the SU(2) non-abelian field Φ denote either the gauge field or the gaugino and expand Φ using the Cartan-Weyl basis: Φ(x) = Φ3 τ 3 2 + Φ+τ + + Φ−τ −. (2.7) (2.7) JHEP01(2023)118 The Pauli matrices τ 3, τ ± are the generators of SU(2) in this basis. Using the commutation relations [τ 3, τ ±] = ±τ 3, [τ +, τ −] = τ 3 along with the Baker-Campbell-Hausdorffformula, one finds that the boundary conditions on Φ are satisfied if and only if: The Pauli matrices τ 3, τ ± are the generators of SU(2) in this basis. Using the commutation relations [τ 3, τ ±] = ±τ 3, [τ +, τ −] = τ 3 along with the Baker-Campbell-Hausdorffformula, one finds that the boundary conditions on Φ are satisfied if and only if: Φ3(xi + Li) = Φ3(x) + I , Φ±(x1 + L1, x2, x3, x4) = Φ±(x1, x2, x3, x4) , Φ±(x1, x2 + L2, x3, x4) = e∓i 2πx1 L1 Φ±(x1, x2, x3, x4) , (2.8) (2.8) where I is a nonhomogeneous term that contributes to the gauge field and appears upon shifting the x2 coordinate: A3 n(x + ˆe2L2) = A3 n(x) + 2π L1 δn,1. Similar boundary condi- tions hold in the 3–4 plane. As we shall show, there is a classical solution to the equa- tions of motion (2.3), which satisfies the boundary conditions (2.8) and has a topological charge Q = 1 2. 2 The Euclidean partition function of our system is given by the path integral: ZSYM[n12 = 1, n34 = 1] = X ν∈Z Z [DAµ][Dλ][D¯λ]e−SSYM−i(ν+ 1 2 )θ|n12=1,n34=1 , (2.9) (2.9) where we have emphasized that this path integral is to be computed with the twists in the 1–2 and 3–4 plane, as per the transition functions (2.4), and thus, all the fields need to satisfy the boundary conditions (2.8). 14If ν ̸= 0, the transition functions (2.4) (but not the cocycle conditions (2.5)) have to be appropri- ately modified. 2 Fractional instantons on the symmetric torus JHEP01(2023)118 We consider the SU(2) SYM theory on T4 with periods of lengths L1, L2, L3, L4. The Euclidean action of the theory is given by13 SSYM = 1 g2 Z T4 tr 1 2FmnFmn + 2  ∂n¯λ ˙α + i[An, ¯λ ˙α]  ¯σ ˙αα n λα  , (2.1) (2.1) and λ is a left-handed adjoint Weyl fermion, the gaugino. Dn = ∂n + i[An, ] is the covariant derivative, σn ≡(i⃗σ, 1), ¯σn ≡(−i⃗σ, 1), ⃗σ are the Pauli matrices, and the Latin letters n, m run over 1, 2, 3, 4. The field strength is given by Fmn = ∂mAn −∂nAm + i[Am, An]. This action is invariant under the supersymmetry transformations δAn = ζα σn α ˙α ¯λ ˙α+¯ζ ˙α ¯σ ˙αα n λα , δλα = −σ β mn α ζβ Fmn , δ¯λ ˙α = −¯σ ˙α mn ˙β ¯ζ ˙β Fmn , (2.2) δAn = ζα σn α ˙α ¯λ ˙α+¯ζ ˙α ¯σ ˙αα n λα , δλα = −σ β mn α ζβ Fmn , δ¯λ ˙α = −¯σ ˙α mn ˙β ¯ζ ˙β Fmn , (2.2) where the spinors obey ξ1 = ξ2, ξ2 = −ξ1 and likewise for the dotted ones. The equations of motion that result from the variation of SSYM are (DmFmn)A = −i tr ¯λ¯σn[T A, λ] , ¯σ ˙αα n DnλA α = 0 , σn α ˙αDn¯λA ˙α = 0, (2.3) (2.3) where A = 1, 2, 3 labels the color group generators T A = τ A/2 with τ A the Pauli matrices. We shall consider SYM with twisted boundary conditions on T4. Without loss of generality, we can use the following transition functions: Ω2(x) = e−i2π x1 L1 τ3 2 , Ω4(x) = e−i2π x3 L3 τ3 2 , while Ω1 = Ω3 = 1. (2.4) (2.4) Ω2 and Ω4 implement the twists along the x2 and x4 directions, while the transition functions along the x1 and x3 directions are trivial. The transition functions obey the cocycle conditions Ωi(x + Ljˆej) Ωj(x) = eiπnijτ3 Ωj(x + Liˆei) Ωi(x), i, j = 1, 2, 3, 4, ∀x ∈R4, (2.5) (2.5) where ˆen is a unit vector in the xn direction, n12 = n34 = −n21 = −n43 = 1, and the rest of nij are zeros. 2 Fractional instantons on the symmetric torus Notice that one also needs to sum over the integer topological sectors ν ∈Z in order for ZSYM to respect locality and unitarity.14 The vacuum angle θ can be transformed away by applying an axial rotation on the gauginos. Our main aim is to find the bilinear gaugino condensate starting from (2.9). The solution of ZSYM, as well as the condensate, will proceed by using the semi-classical techniques, which amount to computing the path integral as the sum of paths of small fluctuations in the background of instantons. The semiclassical approach is justified in the limit of small volume. Notice, however, that this partition function vanishes identically, which can be under- stood in two different ways. First, as we shall show, the theory exhibits 2 fermion zero modes. These are the zero modes that are saturated in the twisted background and give – 10 – rise to the fermion condensate. We can also argue that ZSYM = 0 because of the mixed anomaly between the 0-form discrete chiral and 1-form center symmetries, as was previously shown in [57]. The gaugino condensate calculations can proceed by inserting the gaugino bilinear tr λλ in the path integral (2.9), where the trace is taken in the color space. We define the expectation value of the gaugino condensate as: ⟨tr λλ⟩= N −1 X ν∈Z Z [DAµ][Dλ][D¯λ] tr λλ e−SSYM−i(ν+ 1 2 )θ|n12=1,n34=1 , (2.10) (2.10) with normalization constant N. Only the ν = 0 sector (in the presence of the twists) can contribute to the bilinear condensate, and thus, we restrict our calculations to this sector. The standard way of normalizing the expectation value of an operator is to divide by the partition function. Since ZSYM = 0, we need to search for another appropriate way to normalize our physical observables. We choose to divide by the partition function with twists only in the 1–2 plane. Explicitly, JHEP01(2023)118 N = X ν∈Z Z [DAµ][Dλ][D¯λ] e−SSYM−iνθ|n12=1 . (2.11) (2.11) This partition function is saturated by the ν = 0 term. In the small-T4 limit, it can be evaluated using a semiclassical expansion around two zero-action classical saddle point configurations, related by the Z2 center symmetry in the x3 direction, generated by the “improper gauge transformation” T3. In a gauge with constant transition functions15 in the x1-x2 plane, these saddle points are A = 0 and A = −iT3dT −1 3 [16]. 15These zero-action configurations can also be exhibited in a gauge where Ω2 is as in (2.4), with Ω1,3,4 = 1, but details are to be given elsewhere. 2 Fractional instantons on the symmetric torus Each of these saddle points gives an identical contribution to N. There are no zero modes (see [61] for calculations of the spectrum) and all determinants, fermionic and bosonic, are the ones computed in the A = 0 background (we note that this is the normalization of instanton transition amplitudes already taken in [62]). The partition function (2.11), up to a normalization factor that is expected to cancel the numerical factor in the numerator of (2.10), is equal to the Witten index Tr[(−1)F ], which counts the number of the ground states. Thus, we take N = 2. See section 5 for a Hamiltonian treatment. As a first trial, let us find a self-consistent Q = 1/2 fractional-instanton solution to the equations of motion (2.3) with the boundary conditions (2.8). It is easy to see that the abelian gauge configuration: ¯A3 1 = 2πx2 L1L2 + z1 L1 , ¯A3 2 = z2 L2 , ¯A3 3 = 2πx4 L3L4 + z3 L3 , ¯A3 4 = z4 L4 , (2.12) (2.12) obeys (2.8). The bar is introduced here to serve a later convenience, and the constants zm are the collective coordinates, which will be set to zero in this section without loss of generality. This field configuration was first found by ’t Hooft, and it solves the Pure Yang-Mills equations DmFmn = 0, owing to its abelian nature and constant field strength. 15These zero-action configurations can also be exhibited in a gauge where Ω2 is as in (2.4), with Ω1,3,4 = 1, but details are to be given elsewhere. – 11 – It carries a topological charge Q = 1 2 and its action is half the action of a BPST instanton: S = S0 ≡4π2 g2 . This solution must be self-dual or anti-self-dual, Fmn = ±1 2ϵmnpqFpq, which guarantees that the bosonic and fermionic determinants in this background do not yield negative zero modes, a sign of instability of the solution on T4. Self-duality of the Q = 1/2 solution (2.12) implies the condition L1L2 = L3L4 . (2.13) (2.13) A torus that satisfies the relation (2.13) is said to be self-dual, and a simple choice that satisfies the condition (2.13) is the symmetric torus with L1 = L2 = L3 = L4. The classical solution (2.12) will also hold in SYM provided that the right-hand side of the first equation in (2.3) vanishes. 16For completeness, we note that an analogous problem occurs with the bosonic zero modes around the solution (2.12) on the self-dual torus: there are 8 (four real and two complex), rather than 4, bosonic zero modes, as was shown long ago by van Baal [46]. We also stress that the existence of the four undotted and two dotted fermionic zero modes (2.14) is consistent with the index theorem, which only determines their difference. 2 Fractional instantons on the symmetric torus To check that, we first need to solve the Weyl equations (second and third equations in (2.3)) in the background (2.12), along with the boundary conditions (2.8). We find 6-independent zero modes: 4 modes for λ and 2 modes for ¯λ: JHEP01(2023)118 λ = τ 3 2 " ξ1 ξ2 # + ∞ X n1,n3=−∞ e−i2π(n1 x1 L1 +n3 x3 L3 )h12 0 (x2 −n1L2) h34 0 (x4 −n3L4)τ + " 0 ξ3 # + ∞ X n1,n3=−∞ ei2π(n1 x1 L1 +n3 x3 L3 )h12 0 (x2 −n1L2) h34 0 (x4 −n3L4)τ − " ξ4 0 # , ¯λ = τ 3 2 " ξ5 ξ6 # , (2.14) ¯λ = τ 3 2 " ξ5 ξ6 # , ξ5 ξ6 # , (2.14) (2.14) where ξi are Grassmann numbers. The functions h12 0 and h34 0 are the ground eigenstates of the simple harmonic oscillator, of frequencies ω12 = 2π L1L2 and ω34 = 2π L3L4 , respectively; see appendices A.1 and B.2.3. Owing to the abelian nature of the classical background, the Weyl equation yields the solutions in the τ 3 directions. Substituting the fermion zero mode solutions into the right-hand side of the bosonic equation of motion in (2.3), one easily finds that the source term is nonzero. This simple exercise shows that the abelian background (2.12) is either inconsistent or that some gaugino zero modes must be lifted by higher-order corrections in order to have tr¯λ¯σn[T A, λ] = 0. Presumably, higher-order corrections will gap 4 of the fermion zero modes, and in the end, we will have a consistent story. We were not able to show that this is the case in a satisfactory way.16 Instead, we chose to detune the self-dual torus, i.e., to relax the condition L1L2 = L3L4, and modify the abelian background to include non-abelian pieces that are needed to guarantee the self-duality of the fractional instanton on an asymmetric T4. The detuned solution does not suffer from any of the above-mentioned problems. A further motivation for considering the asymmetric T4 connects to interesting semiclassical limits that have been considered. – 12 – 3 Fractional instantons and gaugino zero modes on the asymmetric torus Fractional instantons and gaugino zero modes on the asymmetric torus In order to circumvent the problems of the self-dual T4, we instead search for a self-dual instanton on an asymmetric torus using a perturbation technique introduced in [1]. The gauge field An can be written in the general form Acl n (x, z) =  ¯A3 n(x, z) + Sn(x, z)  τ 3 2 + Wn(x, z)τ + + W ∗ n(x, z)τ −, (3.1) (3.1) where we have split the τ 3 component into two parts. The first part ¯A3 n(x, z) is the abelian background (2.12) that solves the sourceless Yang-Mills equations on the symmetric T4. The functions Sn(x, z) and Wn(x, z) will be determined perturbatively. We also introduce the dimensionless detuning parameter ∆≡(L3L4 −L1L2) /√L1L2L3L4, which measures the deviation from the self-dual torus, and take ∆> 0. The solution of the sourceless Yang- Mills equations on the asymmetric T4 is obtained by imposing the self-duality condition Fmn = 1 2ϵmnpqFpq, where ϵ1234 = 1, etc. In order to reduce the gauge redundancy, one also imposes the background gauge condition ∂nAcl n + i[ ¯An, Acl n ] = 0. JHEP01(2023)118 The details of the construction of the self-dual solution in an expansion in powers of ∆ is given in appendix A.1. The presentation there follows [1] but for completeness we present it in detail using our notation, with an emphasis on the dependence of the solution of the zn variables. Here, we only give an idea of the construction of the fractional instanton and present its main features. To simplify the equations, it is convenient to use a quaternion notation. Thus, we introduce the matrices: w = σnWn , wc = Cw∗C , s = σnSn , (3.2) 2) ¯σn = (σn)† and C = 0 −i ! Self-duality and the background w = σnWn , wc = Cw∗C , s = σnSn , (3.2) where σn = (i⃗σ, 12×2), ¯σn = (σn)† and C = 0 −i i 0 ! . Self-duality and the background gauge conditions (see (A.12)) then yield the following equations: w = σnWn , wc = Cw∗C , s = σnSn , (3.2) (3.2) where σn = (i⃗σ, 12×2), ¯σn = (σn)† and C = 0 −i i 0 ! . 3 Fractional instantons and gaugino zero modes on the asymmetric torus Self-duality and the backgroun gauge conditions (see (A.12)) then yield the following equations: where σn = (iσ, 12×2), σn = (σn)† and C = i 0 ! . Self-duality and the background gauge conditions (see (A.12)) then yield the following equations: ¯σn∂ns = 2π∆ √ V iτ 3 −i w† cwc −w†w  , ¯σn  ∂n + i ¯A3 n  w = −i 2 s†w −w† cs  . (3.3) (3.3) These equations are subject to the boundary conditions (2.8). The solutions to (3.3) is found as series expansions in √ ∆: w = ∆1/2 ∞ X j=0 wj∆j , s = ∞ X j=1 sj∆j . (3.4) (3.4) The symmetry structure of the self-duality equations (3.3), as well as their solution to the leading order in ∆, is discussed in appendix A.1. The final answer for the fractional instanton solution, giving the order √ ∆terms in (3.1), reads: The symmetry structure of the self-duality equations (3.3), as well as their solution to the leading order in ∆, is discussed in appendix A.1. The final answer for the fractional instanton solution, giving the order √ ∆terms in (3.1), reads: W1(x, z, α) = −i 2 √ ∆F(x, z)eiα √ 2π V 1/4 + O(∆3/2) W2(x, z, α) = 1 2 √ ∆F(x, z)eiα √ 2π V 1/4 + O(∆3/2) = iW1 + O(∆3/2), W3 = O(∆3/2) , W4 = O(∆3/2) , Sn = O(∆) . (3.5) (3.5) – 13 – – 13 – We stress that the O(∆) contribution to Sn is determined by the O( √ ∆) terms shown above, in a manner described in appendix A.1, but explicit expressions will not be needed. The arbitrary phase α is due to the gauge freedom to rotate around the τ 3 isospin direction, and the function F(x, z) is given by the expression: We stress that the O(∆) contribution to Sn is determined by the O( √ ∆) terms shown above, in a manner described in appendix A.1, but explicit expressions will not be needed. 3 Fractional instantons and gaugino zero modes on the asymmetric torus The arbitrary phase α is due to the gauge freedom to rotate around the τ 3 isospin direction, and the function F(x, z) is given by the expression: F (x, z) = p L2L4 ∞ X n1,n3=−∞ e −i2π  n1 x1 L1 +n3 x3 L3  e−i z2 L2 (x2−n1L2)−i z4 L4 (x4−n3L4) × h12 0  x2 −  n1 −z1 2π  L2  h34 0  x4 −  n3 −z3 2π  L4  , (3.6) (3.6) JHEP01(2023)118 with the normalization R T4 |F|2 = Q4 i=1 Li = V . The functions h12,34 0 are the same harmonic oscillator ground state wave functions appearing in eq. (2.14) and described there. It remains to check that this solution obeys the equations of motion (2.3), and in particular, that the fermionic source in the bosonic equation of motion vanishes identically. To this end, we need to find the fermion zero modes, which we do in section 3.1. For this purpose, we will need to use the field strength, a computation carried out in detail in appendix A.2. We find that to order O( √ ∆): F12 = 2π L1L2 , F34 = 2π L3L4 , F13 = −iγ∗eiα s 2π 2L3L4 G(x, z)τ + + iγe−iα s 2π 2L3L4 G∗(x, z)τ −, F14 = γ∗eiα s 2π 2L3L4 G(x, z)τ + + γe−iα s 2π 2L3L4 G∗(x, z)τ −, (3.7) F13 = −iγ∗eiα s 2π 2L3L4 G(x, z)τ + + iγe−iα s 2π 2L3L4 G∗(x, z)τ −, F14 = γ∗eiα s 2π 2L3L4 G(x, z)τ + + γe−iα s 2π 2L3L4 G∗(x, z)τ −, (3.7) (3.7) where γ = i 2 q 2π∆ √ V and the function G(x, z) is where γ = i 2 q 2π∆ √ V and the function G(x, z) is G (x, z) = p L2L4 ∞ X n1,n3=−∞ e −i2π  n1 x1 L1 +n3 x3 L3  e−i z2 L2 (x2−n1L2)−i z4 L4 (x4−n3L4) × h12 0  x2 −  n1 −z1 2π  L2  h34 1  x4 −  n3 −z3 2π  L4  . 3.1 Fermion zero modes The fermion zero modes can be found by solving the Weyl equations from (2.3), Dn¯σnλ = 0 , Dnσn¯λ = 0 in the background (3.1). We perform these explicit computations in appendix B.2.2. The fermion zero modes can also be obtained via the supersymmetry transforma- tions (2.2), with the result agreeing with the direct solution of the Weyl equations. Consider the effect of the supersymmetry transformation (2.2) in the background of the bosonic solution (3.1), with fermions set to zero, ¯λ = λ = 0. Since our solution is self-dual, i.e. obeys ¯σmnFmn = 0, the SUSY transformation only produces λα variations: δλ = −σmnFmnζ , δ¯λ = 0 , (3.9) (3.9) which is true to all orders in ∆. Computing δλ we obtain, see appendix B.2.4, to O( √ ∆): δλ1 δλ2 ! = −2iF (0) 12 ζ1 −ζ2 ! + 2F (1) 13 ζ2 −ζ1 ! −i2F (1) 14 ζ2 ζ1 ! = " η1 η2 ! τ 3 2 + V 1 4 π 1 2 γ∗eiαG(x, z) η2 0 ! τ + + V 1 4 π 1 2 γe−iαG∗(x, z) 0 η1 ! τ − # , (3.10) # (3.10) where in going from the first to second line we used the definitions η1 ≡4πV −1/2ζ1, η2 ≡−4πV −1/2ζ2. Thus, as expected, we find 2 fermion zero modes in accordance with the index theorem. One can easily see that tr¯λ¯σn[T A, λ] = 0, and hence, the self-dual instanton (3.1) on the asymmetric T4 solves the sourceless equations of motion DmFmn = 0 and is a consistent background for SYM. 3 Fractional instantons and gaugino zero modes on the asymmetric torus (3.8 G (x, z) = p L2L4 ∞ X n1 n3= ∞ e −i2π  n1 x1 L1 +n3 x3 L3  e−i z2 L2 (x2−n1L2)−i z4 L4 (x4−n3L4) × h12 0  x2 −  n1 −z1 2π  L2  h34 1  x4 −  n3 −z3 2π  L4  . (3.8) (3.8) The function h1 is the first excited state of the simple harmonic oscillator, and just like F(x, z), G is dimensionless and similarly normalized R T4 |G|2 = Q4 i=1 Li = V . To find the field strength to order O(∆) and establish the self-duality of the solution, one needs to solve for the functions Sn, see (A.43). In appendix A.1, we discuss the relations obeyed by the field strength of Sn (explicit expressions will not be needed in our work). These are important for establishing the self-duality of the solution, and thus of the fact that its action S0 saturates the BPS bound, S0 = 4π2 g2 . g Finally, we stress that the solutions, whose construction via a small-∆expansion was described above, have been subjected to comparison with “exact” solutions obtained by numerically minimizing the lattice Yang-Mills theory action with an n12 = n34 = 1 twist. A good qualitative (and in some cases quantitative) agreement of the gauge – 14 – invariants charactering the solution, computed analytically17 to O(∆), with the numerical approximation of the exact solution was found, for ∆in the range 0.02 −0.09 for various lattice sizes, see [1] for a detailed discussion. The existence of a consistent solution in the form (3.4) to all orders in ∆has been shown in [1], but explicit calculations beyond the leading order have not yet been performed. The radius of convergence in ∆is also not known. In what follows, we assume that the all-order ∆-expansion gives rise to a unique self-dual solution of action S0 = 4π2 g2 , at least for sufficiently small ∆. This is supported by the consistency of (3.4) and the agreement with numerical tests [1]. JHEP01(2023)118 17This is also done in our appendix A.3, where the zn dependence of the local and non-local gau invariants characterizing the solution is discussed in detail. 3.2 Bosonic zero modes For every fermionic zero mode φ (β) A α = −(σmn)(β) α F A mn, β = 1, 2, A = 1, 2, 3, (3.11) φ (β) A α = −(σmn)(β) α F A mn, β = 1, 2, A = 1, 2, 3, (3.11) (3.11) there are two bosonic zero modes. Thus, in total, there are four independent bosonic zero modes. The advantage of the discussion that follows is that the bosonic zero modes 17This is also done in our appendix A.3, where the zn dependence of the local and non-local gauge invariants characterizing the solution is discussed in detail. – 15 – automatically obey the background gauge condition and, furthermore, their construction holds to arbitrary orders in ∆. (β) A The four-vector expressions for the bosonic zero modes are denoted by Z(β) A n and Z(β ′) A n , where β, β′ = 1, 2. These modes are determined as described in e.g. [25, 26]: from each zero mode φ(β) α of the undotted Dirac equation one builds two four-vector bosonic zero modes, denoted by Z(β) n and Z(β ′) n (from here on, we suppress the Lie-algebra index A to reduce clutter). Their four-vector components are then (see appendix B.3.2, eq. (B.37)): Z(β) n = n ℑφ(β) 2 , −ℜφ(β) 2 , ℑφ(β) 1 , ℜφ(β) 1 o , Z(γ ′) n = n ℜφ(γ) 2 , ℑφ(γ) 2 , ℜφ(γ) 1 , −ℑφ(γ) 1 o . JHEP01(2023)118 Using the expression of φ(β) α in terms of Fmn, we can also express Z(β) n and Z(γ ′) n in terms of Fmn: Z(1) n = n ℑφ(1) 2 , −ℜφ(1) 2 , ℑφ(1) 1 , ℜφ(1) 1 o = {−2F14, 2F13, −2F12, 0} , Z(2) n = n ℑφ(2) 2 , −ℜφ(2) 2 , ℑφ(2) 1 , ℜφ(2) 1 o = {2F12, 0, −2F14, 2F13} , Z(1 ′) n = n ℜφ(1) 2 , ℑφ(1) 2 , ℜφ(1) 1 , −ℑφ(1) 1 o = {−2F13, −2F14, 0, 2F12} , Z(2 ′) n = n ℜφ(2) 2 , ℑφ(2) 2 , ℜφ(2) 1 , ℑφ(2) 1 o = {0, 2F12, 2F13, 2F14} . (3.12) (3.12) It is a simple exercise to check DnZ(β) n = 0 and DnZ(γ ′) n = 0, and thus, these zero modes solve the classical equations of motion as expected. 4.1 Fermionic measure The fermion zero modes measure will be inferred from the one for the non-zero modes. We expand the fermions as eigenfunctions of the second order Hermitian operators JHEP01(2023)118 D ¯D = D2 + iFmnσmn , −(D ¯D) β α λβ = ω2λβ (4.1) ¯DD = D2 + iFmn¯σmn = D2, D2¯λ ˙β = ω2¯λ ˙β , JHEP01(2023)118 (4.1) where, in the second line, we used the self-duality of the background. To discuss the measure, we begin by considering the contribution of a single nonzero eigenvalue ω to the fermion path integral. Let −(D ¯D) β α φi β = ω2φi α, where i labels the different eigenfunctions, the commuting functions φi α, with the same eigenvalue ω (we note that there are at least two of them). We expand the nonzero-mode part of the fermion field (for brevity, denoting it with the same letter λ, ¯λ) λα = X i χi φi α (4.2) ¯λ ˙α = X i ¯χi 1 ω ¯D ˙ααφi α, (4.2) where we used the fact that the nonzero eigenfunctions of D ¯D and ¯DD are related as shown and we attach the spinor index to the bosonic solution of the 2nd order equation and not to the Grassmann variable, χi or ¯χi (the fact that there is more than a single solution for every ω is accounted by the index i). We also indicate that the λ and ¯λ expansions have each their separate Grassmann variables χi, ¯χi. where we used the fact that the nonzero eigenfunctions of D ¯D and ¯DD are related as shown and we attach the spinor index to the bosonic solution of the 2nd order equation and not to the Grassmann variable, χi or ¯χi (the fact that there is more than a single solution for every ω is accounted by the index i). We also indicate that the λ and ¯λ expansions have each their separate Grassmann variables χi, ¯χi. 3.2 Bosonic zero modes ( ) ( ′) Further, one can write down Z(β) n and Z(γ′) n as the derivatives with respect to the collective coordinates {zi} modulo gauge transformations. To this end, we define new zero modes Y (i) n , i = 1, 2, 3, 4, by relabeling (3.12) as follows Y (3) n ≡Z(1) n , Y (1) n ≡−Z(2) n , Y (4) n ≡−Z(1 ′) n , Y (2) n ≡−Z(2 ′) n , (3.13) (3.13) and show in appendix B.3.3 that Y (k) n = 4πLk √ V ∂An ∂zk + Dn(Acl)Λ(k) . (3.14) (3.14) There, we also explicitly find the expressions for the background-gauge restoring gauge transformations Λ(k) to order √ ∆and show that they obey boundary conditions preserving the transition functions. For later convenience, we also define the inner product of the zero-mode wave functions (or moduli space metric) Ukl = 2 g2 Z T4 tr Y (k) n Y (l) n (3.15) (3.15) which in diagonal basis is simply Ukl = δlkul. Using (3.12), see appendix B.3.2 for details, we readily obtain Ukl = 4δkl g2 Z T4 tr Fmn ˜Fmn = 4δklS0 = δkl 16π2 g2 . (3.16) (3.16) This result is valid to all orders in ∆, since the action of a fractional instanton does not depend on the size or shape of T4. This result is valid to all orders in ∆, since the action of a fractional instanton does not depend on the size or shape of T4. – 16 – – 16 – 4 The path integral: bosonic and fermionic measures The contributions from the non-zero modes of fermions, bosons, and ghosts cancel in the path integral, thanks to supersymmetry. Thus, in our subsequent discussion, we only discuss the contribution from zero modes to the bosonic and fermionic measures. 4.1 Fermionic measure Plugging (4.2) into the fermionic action (2.1), we obtain after integration by parts and using the fact that φ is an eigenvector of D ¯D: SF = 2 g2 tr (Dn¯λ ˙α¯σ ˙αα n λα) = X ij ¯χjχiω  2 g2 Z T4 tr φiαφj α  (4.3) = ω X ij ¯χjχi Uij F , (4.3) where the fermion mode inner product matrix is where the fermion mode inner product matrix is Uij F = 2 g2 Z T4 tr φi 2φj 1 −φi 1φj 2 , Uij F = −Uji F . (4.4) (4.4) Then we define the fermion nonzero mode path integral so that it produces ω (the minimal number of eigenfunctions with the same eigenvalue is two, i.e. i, j = 1, 2, with UF generically a 2 × 2 matrix) Y dχid¯χi (det UF )−1e−SF = ω . (4.5) Z Y i dχid¯χi (det UF )−1e−SF = ω . (4.5) (4.5) – 17 – When all nonzero eigenvalues are taken into account, we obtain the square root of the product over all nonzero eigenvalues of ¯DD (or D ¯D). When all nonzero eigenvalues are taken into account, we obtain the square root of the product over all nonzero eigenvalues of ¯DD (or D ¯D). The integrals over the fermion zero modes are defined in the same manner via the same mode normalization matrix, Uij F , defined in (4.4). Recalling that only the undotted spinors λα have zero modes, we expand18 λα = X i ηiφi α + nonzero modes, (4.6) (4.6) where we use ηi to denote the zero-mode Grassmann variable. The fermion zero-mode measure is then taken to be the “square root” of (4.5):19 JHEP01(2023)118 dµF = Y i dηi (det UF )−1/2 = Y i dηi (PfUF )−1 . (4.7) (4.7) In appendix B.3.1, we calculate the Pfaffian, using the zero-mode wave functions (3.11), and show that PfUF = −U12 F = 4 × 4π2 g2 , see eq. (B.34). Notice that this result is valid to all orders in ∆(thus including the nonabelian part of the zero modes), since PfUF involves integrating the square of the field strength Fmn over T4, which is proportional to the action, a ∆-independent quantity. (3.11), Furthermore, it follows from (4.6) that tr λαλα = 1 2ηαηβφ(α)A γ φ(β)A δ ϵδγ+(nonzero modes). 4.1 Fermionic measure Thus, combining with (4.7), one finally finds: Z dµF tr λλ(x) = g2 16π2 Z dη1dη2 tr [λαλα(x)] = g2 16π2 1 2  φ(2)A γ φ(1)A δ −φ(1)A γ φ(2)A δ  [x]ϵδγ . (4.8) (4.8) We next note that all gauge invariant quantities in the fractional instanton background depend on the combinations of xi with the dimensionless collective coordinates zl, see eq. (A.9) in appendix A.1. Thus, to calculate the condensate, in eq. (4.8) one should replace We next note that all gauge invariant quantities in the fractional instanton background depend on the combinations of xi with the dimensionless collective coordinates zl, see eq. (A.9) in appendix A.1. Thus, to calculate the condensate, in eq. (4.8) one should replace x1 →x1 −L1z2 2π , x2 →x2 + L2z1 2π , x3 →x3 −L3z4 2π , x4 →x4 + L4z3 2π . (4. (4.9) That all gauge invariant quantities depend on (4.9) follows from the actions of translations in our background and is explained in appendix A.1 (see Footnote 30 there). 19This definition ensures that, upon perturbing with a zero-mode lifting mass term, δSm = m g2 tr λαλα, e obtains m for the zero-mode contribution to the path integral. 18Here and below, we use φi α to denote the zero-mode solutions of D ¯D, obeying (D ¯D) β α φi β = 0. The reader should forgive us for using the same letter as in the non-zero mode discussion near (B.9). 5 The Hamiltonian formalism, Wilson loops, and the moduli space Up to this point, we have all pieces to compute the gaugino condensate except for the shape and size of the moduli space M, or in other words, the range of integration over the collective coordinates {zm}. Determining M will force us to deviate, for now, from the path integral to the Hamiltonian formalism. We refer the reader to [57] for a detailed description of the Hilbert space, while here, we only provide a synopsis needed to study the Wilson loops and moduli space. 4.2 Bosonic measure We express the bosonic field An(x), to be integrated over in the path integral, as a sum of the classical solution Acl n (x, z) (3.1), the zero mode fluctuations normalized as in (B.67) of appendix B.3.3, and the nonzero modes of the fluctuation operator denoted by Zq n (of eigenvalues ωq) using the same notation as in appendix B.1, see the discussion after eq. (B.2): An(x) = Acl n (x, z) + 4 X k=1 ζ(0) k √ V 4πLk Y (k) n (x, z) + X q ζqZ(q) n . (4.10) (4.10) 18Here and below, we use φi α to denote the zero-mode solutions of D ¯D, obeying (D ¯D) β α φi β = 0. The reader should forgive us for using the same letter as in the non-zero mode discussion near (B.9). 18Here and below, we use φi α to denote the zero-mode solutions of D ¯D, obeying (D ¯D) β α φi β = 0. The reader should forgive us for using the same letter as in the non-zero mode discussion near (B.9). 19 19This definition ensures that, upon perturbing with a zero-mode lifting mass term, δSm = m g2 tr λαλα, one obtains m for the zero-mode contribution to the path integral. – 18 – Using the inner product defined in (3.16), the measure of the bosonic zero modes takes the form 1 4 " (0) # 4 (0) Using the inner product defined in (3.16), the measure of the bosonic zero modes takes the form dµB =  det V 16π2LkLl Ukl  1 2 4 Y k=1 " dζ(0) k √ 2π # = V g4 4 Y k=1 dζ(0) k √ 2π . (4.11) (4.11) In appendix B.3.4, we show how we change the variables ζ(0) k to the collective coordi- nates {zm} by inserting a unity, á la Faddeev-Popov gauge-fixing method. The resulting expression is In appendix B.3.4, we show how we change the variables ζ(0) k to the collective coordi- nates {zm} by inserting a unity, á la Faddeev-Popov gauge-fixing method. The resulting expression is dµB = V g4 4 Y k=1 dzk √ 2π . (4.12) (4.12) JHEP01(2023)118 5.1 Pure Yang-Mills theory They also commute with the Hamiltonian and thus all eigenstates of ˆH are also labeled by e1 ∈{0, 1} and e2 ∈{0, 1}.20 The twisted partition function of pure Yang-Mills theory, the one we have been studying in the absence of fermions, is the one with an insertion of a ˆT3 twist: ZY M[n12 = 1, n34 = 1] = trHm3=1 h e−L4 ˆH ˆT3 i = X E(e3), e3={0,1} ⟨E(e3), e3|e−L4E(e3) ˆT3|E(e3), e3⟩ = X E(e3), e3={0,1} ⟨E(e3), e3|e−L4E(e3)|E(e3), e3⟩eiπe3−i θ 2 , (5.1) JHEP01(2023)118 (5.1) where in going from the first to the second line, we summed over a complete set of eigenstates in the physical Hilbert space Hm3=1 that diagonalize ˆH and ˆT3 simultaneously (for brevity, omitting the summation over e1,2). The expectation value of the Wilson loop operator ˆW3 is21 ⟨W3⟩= trHm3=1 h e−L4 ˆH ˆW3 ˆT3 i . Using the relation ˆT3 ˆW3 = −ˆW3 ˆT3 and the fact that ˆT3 (but not ˆW3) commutes with ˆH, we immediately find ⟨ˆW3⟩= −⟨ˆW3⟩, and hence, ⟨ˆW3⟩= 0. One can also show that the expectation value of the Wilson loop winding in any other direction vanishes identically. Since ˆTℓ, ℓ= 1, 2, 3 and ˆH form a set of commuting operators, they can be diagonalized simultaneously. Let {|E(e1, e2, e3), e1, e2, e3⟩} be a set of orthonormal eigenstates of the set of the 4 operators ˆH, { ˆTℓ, ℓ= 1, 2, 3}, where eℓ∈{0, 1} is the Z2 electric flux in the Lℓdirection, and we emphasized that, in general, the energy of the state depends on these fluxes. The expectation value of a general Wilson loop ˆWp wrapping the Lp direction and computed using the ˆT3-twisted partition function (5.1) reads where in going from the first to the second line, we summed over a complete set of eigenstates in the physical Hilbert space Hm3=1 that diagonalize ˆH and ˆT3 simultaneously (for brevity, omitting the summation over e1,2). The expectation value of the Wilson loop operator ˆW3 is21 ⟨W3⟩= trHm3=1 h e−L4 ˆH ˆW3 ˆT3 i . Using the relation ˆT3 ˆW3 = −ˆW3 ˆT3 and the fact that ˆT3 (but not ˆW3) commutes with ˆH, we immediately find ⟨ˆW3⟩= −⟨ˆW3⟩, and hence, ⟨ˆW3⟩= 0. One can also show that the expectation value of the Wilson loop winding in any other direction vanishes identically. 5.1 Pure Yang-Mills theory The moduli space is determined in the absence of fermions, and thus, we start by studying the Hamiltonian formalism of pure Yang-Mills theory with vacuum angle θ on T3 with a unit ’t Hooft magnetic flux. Consider L1,2,3 of T3 as space of volume V3 and L4 as Euclidean time, where V3 is to be taken much smaller than the inverse of Λ3, the strong-coupling scale, while L4 can be varied from small to large w.r.t. Λ−1. Recall that we apply the twists m3 ≡n12 = 1, this is a “magnetic flux” piercing the 1–2 plane, and k3 ≡n34 = 1. The latter is related to a twist of the partition function by a centre symmetry transformation, to be described below. The physical Hilbert space lives along the constant time slices and, thus, is in the m3 = 1 “magnetic flux” background. Let |ψ⟩denote a state in the physical Hilbert space on T3 with twisted boundary conditions, Hm3=1. ( ) We introduce the operator ˆT3 as the generator of the Z(1) 2 1-form center symmetry in the L3 direction. The generator ˆT3 commutes with the Hamiltonian, [ ˆT3, ˆH] = 0, and thus, they can be diagonalized in the same basis. It can be shown that the action of ˆT3 on its eigenstates, |ψ⟩= |e3⟩, in the physical Hilbert space is ˆT3|e3⟩= eiπe3−i θ 2 |e3⟩, where e3 ∈{0, 1} is the Z2 “electric flux” of the state. This terminology can be explained as follows. Since ˆT3 is a center-symmetry generator, it acts on Wilson loops winding around the L3 direction as ˆT3 ˆW3 = −ˆW3 ˆT3. Then, one readily finds ˆT3( ˆW3|e3⟩) = eiπ(e3+1)−i θ 2 ( ˆW3|e3⟩), i.e., the action of ˆW3 on a state increases the Z2 flux of this state by one unit. The fact that ˆW3 can be thought of as creating a winding electric flux tube explains the terminology. We conclude that ˆT3 measures the center flux of a given state in Hilbert space. The generators of the center symmetries in the other two spatial directions, x1 and x2, ˆTℓ, – 19 – ℓ= 1, 2, act similarly on Wilson loops winding in the corresponding directions. 20The action of ˆT1 on states of electric flux e1 is ˆT1|e1⟩= eiπe1|e1⟩(and similar for ˆT2), without the θ/2 factor in the action of ˆT3 (which is due to the m3 = 1 twist). 21We ignore the normalization of Wilson loops. We will come back to normalization in calculating the gaugino condensate. 20The action of ˆT1 on states of electric flux e1 is ˆT1|e1⟩= eiπe1|e1⟩(and similar for ˆT2), without the θ factor in the action of ˆT3 (which is due to the m3 = 1 twist). 5.1 Pure Yang-Mills theory – 20 – We spent so much time explaining the expected result (5.3) because its consistency with semiclassics is one of our main criteria used to determine the moduli space of the frac- tional instanton. We spent so much time explaining the expected result (5.3) because its consistency with semiclassics is one of our main criteria used to determine the moduli space of the frac- tional instanton. Thus, we now contrast the general result (5.3) with the computation of the expectation value of a Wilson loop in the path integral formalism, in the semiclassical approximation. Consider a Wilson loop W(Cn1,n2,n3,n4), with C beginning at an arbitrary point x in T4 and winding nℓtimes around each direction Lℓ: W(x, Cn1,n2,n3,n4) = tr  Pe iR Cn1,n2,n3,n4 Ak(x′)dx′ k Ωn2 2 (x) Ωn4 4 (x)  , (5.4) (5.4) JHEP01(2023)118 where we inserted Ωn2 2 (x) Ωn4 4 (x) to enforce the gauge invariance of W(x, Cn1,n2,n3,n4). Using the classical self-dual background (3.1), (3.5), we show in eq. (A.58) in the appendix, that W to order ∆is: W(x, Cn1,n2,n3,n4) = 2 cos 1 2  n1  z1 + 2πx2 L2  + n2  z2 −2πx1 L1  + n3  z3 + 2πx4 L4  + n4  z4 −2πx4 L2  . × [1 + ∆F(x, z)] . (5.5) (5.5) The O(1) and O(∆) contributions come from the abelian and nonabelian components of (3.1). The cosine function has 4π periodicity in {zi}, while the O(∆) piece F(x, z) is a periodic and even function of {z1 + 2πx2 L2 , z2 −2πx1 L1 , z3 + 2πx4 L4 , z4 −2πx4 L2 } with periodicity 2π for {zi}. 5.1 Pure Yang-Mills theory Since ˆTℓ, ℓ= 1, 2, 3 and ˆH form a set of commuting operators, they can be diagonalized simultaneously. Let {|E(e1, e2, e3), e1, e2, e3⟩} be a set of orthonormal eigenstates of the set of the 4 operators ˆH, { ˆTℓ, ℓ= 1, 2, 3}, where eℓ∈{0, 1} is the Z2 electric flux in the Lℓdirection, and we emphasized that, in general, the energy of the state depends on these fluxes. The expectation value of a general Wilson loop ˆWp wrapping the Lp direction and computed using the ˆT3-twisted partition function (5.1) reads ⟨ˆWp⟩= X E(e1,e2,e3), ei={0,1} e−L4E⟨E(e1, e2, e3), e1, e2, e3| ˆWp ˆT3|E(e1, e2, e3), e1, e2, e3⟩(5.2) = X E(e1,e2,e3), ei={0,1} e−L4E⟨E(e1, e2, e3), e1, e2, e3| ˆWp|E(e1, e2, e3), e1, e2, e3⟩eiπe3−i θ 2 . (5.2) However, the insertion of ˆWp increases the electric flux by one unit in the Lp direction and produces a sum over different energy eigenstates. Thus, its diagonal matrix element in the |E(e1, e2, e3), e1, e2, e3⟩state vanishes. We immediately conclude that a Wilson loop that wraps L1, L2, or L3 must vanish on T4 with twisted boundary conditions. The vanishing of ⟨ˆW4⟩follows by applying a 90-degree rotation to any spatial Wilson loop, i.e. upon considering a different T4 direction as time. Thus, we conclude that for any winding Wilson loop ˆWp, However, the insertion of ˆWp increases the electric flux by one unit in the Lp direction and produces a sum over different energy eigenstates. Thus, its diagonal matrix element in the |E(e1, e2, e3), e1, e2, e3⟩state vanishes. We immediately conclude that a Wilson loop that wraps L1, L2, or L3 must vanish on T4 with twisted boundary conditions. The vanishing of ⟨ˆW4⟩follows by applying a 90-degree rotation to any spatial Wilson loop, i.e. upon considering a different T4 direction as time. Thus, we conclude that for any winding Wilson loop ˆWp, ⟨ˆWp⟩= trHm3=1 h e−L4 ˆH ˆWp ˆT3 i = 0. (5.3) (5.3) 20The action of ˆT1 on states of electric flux e1 is ˆT1|e1⟩= eiπe1|e1⟩(and similar for ˆT2), without the θ/2 factor in the action of ˆT3 (which is due to the m3 = 1 twist). 21 21We ignore the normalization of Wilson loops. We will come back to normalization in calculating the gaugino condensate. 22 ˜ W in the second term is the Wilson loop (5.4), but evaluated in the anti-instanton background, whose explicit form is similar to (5.5) and shall not be needed. 5.1 Pure Yang-Mills theory Now, using the results from the previous section and limiting our discussion to pure Yang-Mills theory and ignoring issues of normalization, the expectation value of a general Wilson loop is W(x,Cn1,n2,n3,n4)⟩ (5.6) ⟨W(x,Cn1,n2,n3,n4)⟩ (5.6) = X ν Z [DAµ]W(x,Cn1,n2,n3,n4)e−SY M−iθ(ν+ 1 2 )|n12=1,n34=1 ∼e−S0−i θ 2 V g4 Z M 4 Y k=1 dzk √ 2π W(x,Cn1,n2,n3,n4)+e−S0+i θ 2 V g4 Z M 4 Y k=1 dzk √ 2π ˜W(x,Cn1,n2,n3,n4), (5.6) = X ν Z [DAµ]W(x,Cn1,n2,n3,n4)e SY M iθ(ν+ 2 )|n12=1,n34=1 ∼e−S0−i θ 2 V g4 Z M 4 Y k=1 dzk √ 2π W(x,Cn1,n2,n3,n4)+e−S0+i θ 2 V g4 Z M 4 Y k=1 dzk √ 2π ˜W(x,Cn1,n2,n3,n4 where in going from the first to the second line, we ignored the quantum loops and used the bosonic zero-mode measure (4.12). We limited the r.h.s. to the contributions of the ν = 0 sector, with total topological charge Q = 1 2, and the ν = −1 sector, with total topological charge Q = −1 2. Ignoring higher-Q contributions is justified in the limit when semiclassics holds, i.e. for a small T4. Furthermore, in writing the above expression, we assumed that the fractional instantons (and antinstantons22) we obtained are the only |Q| = 1 2 saddle points in the path integral, contributing to the first and second terms above, respectively. While we have no proof of – 21 – uniqueness, the favourable comparison of “exact” (i.e. obtained by numerically minimizing the action) fractional instantons on an asymmetric T4 with the solutions obtained by small-∆expansion gives support in favor of this assumption, at least for small enough ∆. In this regard, we note that ref. [1] found good agreement for ∆as large as 0.08. Our point now is that the d4z integral in (5.6) vanishes, and is thus consistent with (5.3), for all values of θ and for all x, if and only if the limits of integration are taken zi ∈[0, 4π). This leads us to conclude that the moduli space M ∼T4 with period 4π in every direction.23 A further argument in favour of this identification of the moduli space is that the classical fractional instanton field configurations with zn differing by 2π are distinguished by the gauge invariant winding Wilson loop operators, while those differing by 2π are not distinguished. Thus one expects that zn and zn + 2π are not to be identified. 5.1 Pure Yang-Mills theory In contrast, no local gauge invariant operators can distinguish between zn and zn + 2π, see section A.3 in the appendix for detail.24 JHEP01(2023)118 23Moreover, it is easy to check that changing the limits of integration to any other values yields a position-dependent Wilson loop. For example, consider ⟨W(x, Cn1=1,n2=0,n3=0,n4=0)⟩and take the range of zi ∈[0, 2π), which yields ⟨W(x, Cn1=1,n2=0,n3=0,n4=0)⟩∼−sin  π x2 L  + O(∆). This result should not be expected on physical grounds since our background has constant field strength on T4 (to leading order in ∆); the expectation value of the Wilson loop should, at most, be a constant (to leading order in ∆). ) ( ) 24We note, without discussing the details, that a virtually identical argument for extending the lim of zn integration holds also in the SU(N) case in the background of the Q = 1/N solutions found by Hooft [15], recently extended in the framework of the small-∆expansion [58]. 5.2 SYM theory Before turning to the calculations of the gaugino condensate using the path integral method, we pause here to discuss SYM theory using the Hamiltonian formalism, akin to our discussion of pure Yang-Mills of section 5.1. The partition function of SYM with twisted boundary conditions in the 1–2 and 3–4 planes, identical for bosons and fermions, is given by ZSYM[n12 = 1, n34 = 1] = trHm3=1 h (−1)F e−L4 ˆH ˆT3 i . (5.7) (5.7) The insertion of the fermion number (−1)F guarantees that both fermions and bosons obey periodic boundary conditions in the time direction. Let ˆX be the Zdχ 4 discrete chiral symmetry generator. Then, it can be shown that the symmetry operators ˆT3 and ˆX obey the algebra: The insertion of the fermion number (−1)F guarantees that both fermions and bosons obey periodic boundary conditions in the time direction. Let ˆX be the Zdχ 4 discrete chiral symmetry generator. Then, it can be shown that the symmetry operators ˆT3 and ˆX obey the algebra: h ˆH, ˆT3 i = 0 , h ˆH, ˆX i = 0 , ˆT3 ˆX = eiπ ˆX ˆT3 , (5.8) (5.8) where the last relation is the result of the mixed anomaly between the 0-form discrete chiral and 1-form center symmetries [57].25 Since ˆH commutes with ˆT3, we can as before, label the physical states in Hm3=1 by |E(e3), e3⟩. The algebra (5.8) requires that ˆX|E(e3), e3⟩= |E(e3), e3 −1⟩, and thus, it is easily seen the states |E(e3), e3 = 1⟩and |E(e3), e3 = 0⟩are degenerate: ˆH|E, e3 = 0⟩= E(e3 = 0)|E, e3 = 0⟩, ˆH|E, e3 = 1⟩= E(e3 = 0)|E, e3 = 1⟩, at any size of the spatial T3, as a consequence of the anomaly. 23Moreover, it is easy to check that changing the limits of integration to any other values yields a position-dependent Wilson loop. For example, consider ⟨W(x, Cn1=1,n2=0,n3=0,n4=0)⟩and take the range of zi ∈[0, 2π), which yields ⟨W(x, Cn1=1,n2=0,n3=0,n4=0)⟩∼−sin  π x2 L  + O(∆). This result should not be expected on physical grounds since our background has constant field strength on T4 (to leading order in ∆); the expectation value of the Wilson loop should, at most, be a constant (to leading order in ∆). [ ] [ ] 25The same algebra arises in the 2-D massless charge-2 Schwinger model [63], due to a similar anomal 5.2 SYM theory 24We note, without discussing the details, that a virtually identical argument for extending the limits of zn integration holds also in the SU(N) case in the background of the Q = 1/N solutions found by ’t Hooft [15], recently extended in the framework of the small-∆expansion [58]. 25The same algebra arises in the 2-D massless charge-2 Schwinger model [63], due to a similar anomaly. – 22 – Now, we can readily calculate the partition function (5.7) to find ZSYM[n12 = 1, n34 = 1] = trHm3=1 h (−1)F e−L4 ˆH ˆT3 i = X E, e3={0,1} (−1)F (−1)e3⟨E, e3|e−EL4|E, e3⟩ = X E, e3={0,1} (−1)F (−1)e3e−EL4 = 0 . (5.9) (5.9) This equation provides one way to see that the twisted partition function of SYM vanishes, by noting that all states in Hilbert space are doubly degenerate and their contributions cancel each other in the twisted partition function (5.9). This equation provides one way to see that the twisted partition function of SYM vanishes, by noting that all states in Hilbert space are doubly degenerate and their contributions cancel each other in the twisted partition function (5.9). JHEP01(2023)118 Now we insert the gaugino condensate, the tr λ2 operator, where the trace is taken in the color space. The operator is inserted at x4 = 0 and some position on T3: ⟨tr λλ⟩= trHm3=1 h (−1)F e−L4 ˆH tr λ2 ˆT3 i trHm3=1 h (−1)F e−L4 ˆH i = N −1 X E, e3={0,1} (−1)F (−1)e3e−EL4⟨E, e3| tr λ2|E, e3⟩. (5.10) (5.10) Here, we took the normalization constant N to be the Witten index: N = trHm3=1 h (−1)F i = 2, given by the partition function on T3 with an n12 twist, but without a ˆT3 twist in the time direction (recall (2.11) in the path integral framework). Next, we know that ˆX|E, e3⟩= |E, e3 + 1⟩from the anomaly (5.8) and that ˆX acts on the condensate as ˆX tr λ2 = −tr λ2 ˆX. Thus, because ⟨E, 0| ˆX† ˆX tr λ2|E, 0⟩= −⟨E, 1| tr λ2|E, 1⟩, (5.11) (5.11) tr λ2 has opposite expectation values in the two degenerate states e3 = 0 and e3 = 1. Thus, we find tr λ2 has opposite expectation values in the two degenerate states e3 = 0 and e3 = 1. 26Equating the result of our calculation, eq. (6.3) below, to the r.h.s. of (5.13) is only possible if we assume that the semi-classical treatment holds as L4 is varied between small and large, and, in particular, there are no new contributions that contribute to the l.h.s. This can be only justified by understanding the convergence radius of the ∆expansion. 27We note that a similar equation holds in SU(N) theories for one of the N vacua of the twisted, small-V3 theory. There N = N and there is N-fold degeneracy of all energy states on T3 with n12 = 1. 5.2 SYM theory Thus, we find ⟨tr λλ⟩= N −1 X E, e3={0,1} (−1)F e−EL4⟨E, 0| tr λ2|E, 0⟩V3,n12 ⟨tr λλ⟩= N −1 X E, e3={0,1} (−1)F e−EL4⟨E, 0| tr λ2|E, 0⟩V3,n12 = X E (−1)F e−EL4⟨E, 0| tr λ2|E, 0⟩V3,n12 , (5.12) = X E (−1)F e−EL4⟨E, 0| tr λ2|E, 0⟩V3,n12 , (5.12) (5.12) where the sum is over only the half of the Hilbert space with e3 = 0 and we are reminded that the condensate is being computed in a small V3 theory Hilbert space with boundary conditions twisted by n12. where the sum is over only the half of the Hilbert space with e3 = 0 and we are reminded that the condensate is being computed in a small V3 theory Hilbert space with boundary conditions twisted by n12. If L4 is small compared to the energy scales in the problem, there is no reason to assume that any particular values of E dominate. Thus, eq. (5.12) is the Hamiltonian expression of the expectation value we have computed for general L4. However, we can try take the L4 →∞limit to obtain26 ⟨tr λλ⟩= ⟨0, 0| tr λ2|0, 0⟩V3,n12 , (5.13) (5.13) 26Equating the result of our calculation, eq. (6.3) below, to the r.h.s. of (5.13) is only possible if we assume that the semi-classical treatment holds as L4 is varied between small and large, and, in particular, there are no new contributions that contribute to the l.h.s. This can be only justified by understanding the convergence radius of the ∆expansion. – 23 – – 23 – where we used that supersymmetry is unbroken and the small-V3 ground state is bosonic, (−1)F = 1.27 In conclusion, eq. (5.13) shows that in the large-L4 limit, the calculation of ⟨tr λ2⟩ using the ˆT3-twisted parition function and normalized by the Witten index, as in (5.10), yields the gaugino condensate in one of the two degenerate ground states of the small-V3 theory with a unit ’t Hooft flux n12. The state |0, 0⟩V3,n12 is further expected, as V3 →∞, to become one of the two degenerate ground states of the SU(2) SYM theory on R4. JHEP01(2023)118 JHEP01(2023)118 6 The gaugino condensate Finally, we put pieces together to read out the condensate. We use the fact that non-zero modes in (2.10) cancel between the bosons, fermions, and ghosts. Then, we combine the integral of tr λ2 over the zero mode measure for the fermions from eq. (4.8) with the boson zero mode measure (4.12). We also recall that we normalize by the Witten index N = 2 to obtain: ⟨trλλ⟩= M3 PV e −4π2 g2 N V g4 (6.1) × Z zi∈[0,4π] 4 Y k=1 dzk √ 2π g2 16π2 1 2 ϵδγ(φ(2)A γ φ(1)A δ −φ(1)A γ φ(2)A δ )[{x}] x1→x1−z2L1 2π , see eq. (4.9) = Λ3 2 V 4π2 1 16π2 2π Z −2π d4z  φ(2)A 2 φ(1)A 1 −φ(1)A 2 φ(2)A 1  −z2L1 2π , z1L2 2π ,−z4L3 2π , z3L4 2π  . (6.1) To obtain the last line, we recalled the substitution of (4.9), the fact that all local gauge invariants are periodic functions of ˆzk (defined in (4.9)) of period 2π, and used shifts of the zn variables to set the xk-coordinates (of period Lk) to zero. Further, Pauli-Villars regularization has been utilized to renormalize the theory, and the scale MPV is the Pauli- Villars mass. The factor M3 PV comes from regularizing the boson and fermion determinants, with each zero-mode contributing an appropriate factor of MPV : the bosonic determinant gives M4 PV and the fermionic determinant gives M−1 PV (we do not describe this in detail, as it is a standard procedure in supersymmetric instanton calculations [25, 26, 31, 37]). In going from the first to the second line of (6.1), we used the fact that Λ3 = M3 P V g2 e −4π2 g2 in the scheme often used for gaugino condensate calculations [25, 26], notably, in the weakly-coupled R3 × S1 set up and its comparison with the weak-coupling calculation on R4 [31]. Next, we rescale the zk variables in (6.1) by appropriate factors of 2π Lp , contributing an overall Jacobian (2π)4 V . Acknowledgments E.P. is grateful to Antonio Gonzalez-Arroyo for many conversations on fractional instantons and the ∆-expansion during the “Fluxtube-22” Workshop at KITP during the Winter of 2022, supported in part by the National Science Foundation under Grant No. NSF PHY-1748958. We also thank F. David Wandler for comments on the manuscript. Both authors would like to thank the Simons Centre for Geometry and Physics, where this work started. E.P. acknowledges the hospitality of Durham University during work on this project and M.A. acknowledges the hospitality of the University of Toronto, where this work was completed. M.A. is supported by STFC through grant ST/T000708/1. E.P. is supported by a Discovery Grant from NSERC. 6 The gaugino condensate Taking the liberty to again call the rescaled variables xk, we obtain – 24 – for the condensate for the condensate ⟨tr λλ⟩= Λ3 2 1 4 Y k Lk Z −Lk dxk  φ(2)A 2 φ(1)A 1 −φ(1)A 2 φ(2)A 1  [−x1, x2, −x3, x4] = Λ3 2 24 4 Z T4 d4x  φ(2)A 2 φ(1)A 1 −φ(1)A 2 φ(2)A 1  [x] = Λ3 2 24 4 g2U21 F . (6.2) (6.2) As indicated, the integrand on the second line is the same as the one appearing in U21 F from (4.4), safe for the absence of a factor of 1/g2. Thus, recalling that U21 F = 16π2 g2 , as per the discussion after (4.7) (see also (B.34)), we finally obtain for (5.12): As indicated, the integrand on the second line is the same as the one appearing in U21 F from (4.4), safe for the absence of a factor of 1/g2. Thus, recalling that U21 F = 16π2 g2 , as per the discussion after (4.7) (see also (B.34)), we finally obtain for (5.12): JHEP01(2023)118 ⟨tr λλ⟩= 32π2Λ3. (6.3) (6.3) Further, assuming that the result extends to L4 →∞, as described in the previous section, we use (5.13) and (6.3) to conclude ⟨0, 0| tr λ2|0, 0⟩V3,n12 = 2 × 16π2Λ3 . (6.4) (6.4) Thus, the condensate in one of the two degenerate vacua of the small-V3, n12 = 1 theory has twice the value calculated on R4 as described in the Introduction.28 Thus, the condensate in one of the two degenerate vacua of the small-V3, n12 = 1 theory has twice the value calculated on R4 as described in the Introduction.28 A Constructing instantons on the asymmetric T4 with twists Our SU(2) Lie algebra convention is as follows. We denote the generators in the Cartan as τ 3 2 and the non-Cartan as τ ±, where τ + = 0 1 0 0 ! = (τ −)†. We expand the Hermitean gauge field as An = A3 n τ 3 2 + A+ n τ + + A− n τ −, A−= (A+)†, n = 1, 2, 3, 4. (A.1) (A.1) 28In the spirit of Footnote 24, without discussing the details, we remark that a similar result is obtained, upon taking the large-L4 limit of ’t Hooft’s SU(N) solutions with Q = 1 N , constructed via the ∆expansion in [58]. One finds, instead of (6.4), that the condensate in one of the N degenerate vacua on T3 with an n12 = 1 twist, ⟨0, 0| tr λ2|0, 0⟩V3,n12 = N × 16π2Λ3, i.e. equals N times the R4 result. – 25 – An identical expression (but without the reality condition) also holds for the adjoint representation fermions λα, ¯λ ˙α (α, ˙α = 1, 2), which are independent variables in Euclidean space, to be discussed in more detail later. The fields are smooth and defined on R4, with coordinates xn, n = 1, 2, 3, 4. The restriction to a T4 with periods Ln, and with ’t Hooft twists is accomplished by imposing periodicities defined by transition functions Ωn(x), x ∈R4. As explained in the main text, we choose a gauge where the T4 transition functions are trivial in the x1 and x3 directions and nontrivial in the x2 and x4 directions Ω2(x) = e−i2π x1 L1 τ3 2 , Ω4(x) = e−i2π x3 L3 τ3 2 , while Ω1 = Ω3 = 12×2, ∀x ∈R4. (A 2) JHEP01(2023)118 (A.2) ( ) Thus, there are two nontrivial twists, n12 = n34 = 1, since (A.2) obey the cocycle conditions ( ) hus, there are two nontrivial twists, n12 = n34 = 1, since (A.2) obey the cocycle conditions Thus, there are two nontrivial twists, n12 = n34 = 1, since (A.2) obey the cocycle conditions Ωi(x + Ljˆej) Ωj(x) = eiπnij Ωj(x + Liˆei) Ωi(x), i, j = 1, 2, 3, 4, ∀x ∈R4, (A.3) (A.3) where ˆen is a unit vector in the xn direction. 29Our convention for gauge transformations, A(x) →g(x)(A(x) −id)g−1(x), implies Fmn = ∂mAn − ∂nAm + i[Am, An] and Dmφ = ∂mφ + i[Am, φ] for any adjoint φ. Adjoint fermions obey the same periodicity conditions as (A.4), but without the inhomogeneous term. 30For example, a translation x1 →x1 +ϵ1 is accompanied by g1(ϵ1, x2) = e i2π ϵ1x2 L1L2 τ3 2 ensuring that Ω2(x1) is invariant: as per (A.5), Ω2(x1) transforms into g1(x2 = L2)Ω2(x1 + ϵ1)g−1 1 (x2 = 0) = Ω2(x1). At the same time, the g1 action on ¯A shifts z2 →z2 −2πϵ1 L1 , showing that the variable ˆz2 = z2 −2πx1 L1 is invariant under the combined action of g1 and translation eϵ1∂1. Our nonabelian solution also exhibits this property: considering, for example, its W1 component of eq. (A.40), we observe that it is invariant under the combined action of translation of x1, the shift of z2 given above, and a gauge transformation by g1, which multiplies W1 by a phase. Gauge invariants built from the solution will then only depend on the ˆzn combinations. A Constructing instantons on the asymmetric T4 with twists (A.8) (A.8) The abelian background (A.7), (A.8) has the following properties: The abelian background (A.7), (A.8) has the following properties: The abelian background (A.7), (A.8) has the following properties: 1. The field strength F (0) mn from (A.8) can be used to explicitly verify that the abelian background (A.7) has topological charge 1/2. This can be seen by recalling that the topological charge only depends on the transition functions. Its fractional nature is owing to the nonzero twists n12 = n34 = 1. 2. In addition, it also follows from (A.8), that for a “symmetric” T4 — one where L1L2 = L3L4 — the background (A.7) is self-dual and hence stable, i.e. it has minimal action for the given topological charge. The action of the self-dual abelian solution is S0 = 4π2 g2 , half that of the BPST instanton. 3. For use below, it is convenient to introduce the variables 3. For use below, it is convenient to introduce the variables 3. For use below, it is convenient to introduce the variables (ˆz1, ˆz2, ˆz3, ˆz4) ≡  z1 + 2πx2 L2 , z2 −2πx1 L1 , z3 + 2πx4 L4 , z4 −2πx3 L3  (A.9) (A.9) The ˆz-variables are important since all gauge invariants characterizing the nonabelian instanton background depend on ˆzn only. In the gauge we are using, the fact that the background depends on ˆz1, ˆz3 is already evident in (A.7). The appearance of the combinations ˆz2, ˆz4 follows from the action of translations in x1 and x3: in order to preserve the transition functions, an x1, x3 translation is accompanied by a non-Ω- periodic gauge transformation which shifts z2 and z4. This ensures that all gauge invariant quantities only depend on ˆzn.30 The ˆz-variables are important since all gauge invariants characterizing the nonabelian instanton background depend on ˆzn only. In the gauge we are using, the fact that the background depends on ˆz1, ˆz3 is already evident in (A.7). The appearance of the combinations ˆz2, ˆz4 follows from the action of translations in x1 and x3: in order to preserve the transition functions, an x1, x3 translation is accompanied by a non-Ω- periodic gauge transformation which shifts z2 and z4. A Constructing instantons on the asymmetric T4 with twists The periodicity condition on the gauge fields in R4 define the T4 fields: A(x + ˆenLn) = Ωn(x)(A(x) −id)Ω−1 n (x), n = 1, 2, 3, 4, ∀x ∈R4, (A.4) (A.4) where we denoted A(x) = 4P n=1 An(x)dxn. The Euclidean path integral is performed over fields obeying (A.4), with fixed transition functions Ωn(x). Gauge transformations g(x) ∈ SU(2), x ∈R4 act on the gauge field the usual way29 while their action on transition functions is Ωn(x) →g(x + ˆenLn)Ωn(x)g−1(x) , n = 1, 2, 3, 4, ∀x ∈R4. (A.5) (A.5) Gauge transformations g(x) which leave the transition functions invariant will be called “Ω-periodic.” With our choice of gauge for the transition functions, Ω-periodic gauge transformations g(x) are periodic in x1 and x3 but not in x2 and x4. The only constant Ω-periodic transformations are the abelian ones, g = eiατ 3. For future use, we note that a fundamental-representation Wilson loop along a unit- winding loop C1 (winding once along xn) is W(C1, x) = tr    Pe i x+ˆenLn R x Ak(x′)dx′ k Ωn(x)    . (A.6) (A.6) Here, the insertion of Ωn(x) ensures invariance under (A.5). Here, the insertion of Ωn(x) ensures invariance under (A.5). 29Our convention for gauge transformations, A(x) →g(x)(A(x) −id)g−1(x), implies Fmn = ∂mAn − ∂nAm + i[Am, An] and Dmφ = ∂mφ + i[Am, φ] for any adjoint φ. Adjoint fermions obey the same periodicity conditions as (A.4), but without the inhomogeneous term. – 26 – A particular field configuration obeying (A.4) is the constant field strength Abelian background, the “fractional instanton” introduced by ’t Hooft, see [15, 46, 64]: ¯An(x, z) = ¯A3 n(x, z)τ 3 2 : ¯A3 1 = 2πx2 L1L2 + z1 L1 , (A.7) ¯A3 2 = z2 L2 , ¯A3 3 = 2πx4 L3L4 + z3 L3 , ¯A3 4 = z4 L4 . (A.7) JHEP01(2023)118 4 Here, zn are constants whose significance as collective coordinates associated with the instan- ton will be discussed at length later. The field strength of the abelian background (A.7) is: F (0) mn = τ 3 2       0 − 2π L1L2 0 0 2π L1L2 0 0 0 0 0 0 − 2π L3L4 0 0 2π L3L4 0       . A.1 Constructing the self-dual fractional instanton for small ∆ As explained in the main text, there are issues regarding the abelian solution in the tuned T4 that have not yet been addressed in full. Notably, they concern the lifting of the extra bosonic zero modes (found in [46]) present in the L1L2 = L3L4 limit. These issues, as well as our desire to probe the more interesting asymmetric T4 limit31 prompt us to introduce a “detuning” parameter ∆, which we define as follows ∆= L3L4 −L1L2 √L1L2L3L4 = L3L4 −L1L2 √ V . (A.10) (A.10) We always take L3L4 > L1L2, i.e. ∆> 0. For small positive ∆, a nonabelian solution of the self-duality equations has been constructed as a series expansion in powers of √ ∆[1], with the leading contribution being the abelian background (A.7). We always take L3L4 > L1L2, i.e. ∆> 0. For small positive ∆, a nonabelian solution of the self-duality equations has been constructed as a series expansion in powers of √ ∆[1], with the leading contribution being the abelian background (A.7). JHEP01(2023)118 In this section, we exhibit this solution, to the leading nontrivial order in ∆, us- ing our notation and carefully including the dependence on zn. To begin, consider the classical background An(x, z) =  ¯A3 n(x, z) + Sn(x, z)  τ 3 2 + Wn(x, z)τ + + W ∗ n(x, z)τ −, (A.11) (A.11) where S, W are the deviations from the abelian background, to be determined in terms of an expansion in √ ∆. Let us momentarily denote them by an ≡Sn τ 3 2 +Wnτ + +W ∗ nτ −. The construction of the self-dual solution on the asymmetric torus by means of an expansion in ∆proceeds by imposing a self-duality condition on the field strength of (A.11) and solving the resulting equations in a series expansion in √ ∆[1]. In order to solve for an, it is subjected to the background-Lorentz gauge condition: Dn( ¯A)an = ∂nan + i[ ¯An, an] = 0, or in components: (A.12) ∂Sn 0 Dn( ¯A)an = ∂nan + i[ ¯An, an] = 0, or in components: (A.12) ∂nSn = 0, 3[pt]  ∂n + i ¯A3 n  W n = 0. (A.12) Further, the boundary conditions (A.4) imply that Sn is periodic in all xn, while Wn is periodic in x1 and x3, but not in x2 and x4. A Constructing instantons on the asymmetric T4 with twists This ensures that all gauge invariant quantities only depend on ˆzn.30 30For example, a translation x1 →x1 +ϵ1 is accompanied by g1(ϵ1, x2) = e i2π ϵ1x2 L1L2 τ3 2 ensuring that Ω2(x1) is invariant: as per (A.5), Ω2(x1) transforms into g1(x2 = L2)Ω2(x1 + ϵ1)g−1 1 (x2 = 0) = Ω2(x1). At the same time, the g1 action on ¯A shifts z2 →z2 −2πϵ1 L1 , showing that the variable ˆz2 = z2 −2πx1 L1 is invariant under the combined action of g1 and translation eϵ1∂1. Our nonabelian solution also exhibits this property: considering, for example, its W1 component of eq. (A.40), we observe that it is invariant under the combined action of translation of x1, the shift of z2 given above, and a gauge transformation by g1, which multiplies W1 by a phase. Gauge invariants built from the solution will then only depend on the ˆzn combinations. – 27 – A.1 Constructing the self-dual fractional instanton for small ∆ 31This is because the asymmetric T4 connects to various semiclassical limits that have been discussed in the literature, see the main text. A.1 Constructing the self-dual fractional instanton for small ∆ Explicitly the boundary conditions are Further, the boundary conditions (A.4) imply that Sn is periodic in all xn, while Wn is periodic in x1 and x3, but not in x2 and x4. Explicitly the boundary conditions are Sn(x + ˆekLk) = Sn(x), ∀k, (A.13) Wn(x + ˆe1L1) = Wn(x), Wn(x + ˆe2L2) = e−i 2πx1 L1 Wn(x), Wn(x + ˆe3L3) = Wn(x), Wn(x + ˆe4L4) = e−i 2πx3 L1 Wn(x). (A.13) To proceed with the construction of the instanton on the twisted asymmetric T4, following [1], we calculate the field strength of (A.11), set its antiselfdual part to zero, and 31This is because the asymmetric T4 connects to various semiclassical limits that have been discussed in the literature, see the main text. – 28 – solve the equations imposing self-duality in a series expansion in powers of √ ∆. To write the subsequent equations, it is convenient to use a quaternion notation. Thus, we introduce the matrices32 solve the equations imposing self-duality in a series expansion in powers of √ ∆. To write the subsequent equations, it is convenient to use a quaternion notation. Thus, we introduce the matrices32 w = σnWn , where σn = (i⃗σ, 12×2), ¯σn = (σn)† , (A.14) (A.14) s = σnSn , wc = Cw∗C , where C = 0 −i i 0 ! . Here ⃗σ are the usual Pauli matrices, acting in spinor space, not to be confused with the τ 3, τ ± group generators from earlier. In terms of the matrices (A.14), the condition that the field strength of (A.11) be self dual is Fmn¯σmσn = 0. This, using (A.12), becomes Here ⃗σ are the usual Pauli matrices, acting in spinor space, not to be confused with the τ 3, τ ± group generators from earlier. In terms of the matrices (A.14), the condition that the field strength of (A.11) be self dual is Fmn¯σmσn = 0. This, using (A.12), becomes JHEP01(2023)118 Fmn¯σmσn = 0 =⇒¯σn∂ns = 2π∆ √ V iτ 3 −i(w† cwc −w†w), (A.15) and ¯σn(∂n + i ¯A3 n)w = −i 2(s†w −w† cs). (A.15) The self-duality equations (A.15) admit a solution as a series expansion in the T4 detuning parameter ∆(A.10), The self-duality equations (A.15) admit a solution as a series expansion in the T4 detuning parameter ∆(A.10), w = ∆1/2 w1 + ∆3/2 w2 + ∆5/2 w3 + . . . 32The n = 1, 2, 3 components of the four-vector matrix σn defined here should not be confused with ⃗σ = {σa, a = 1, 2, 3} = (σ1, σ2, σ3), the usual Pauli matrices. We use lower-case indices a = 1, 2, 3 to denote the usual Pauli matrices σa and reserve τ a for the SU(2) generators. A.1 Constructing the self-dual fractional instanton for small ∆ (A.20) (A.20) Before we continue, we note that (A.20) together with (A.18) implies that the norm of w1 on T4 can be expressed as an R2-integral Before we continue, we note that (A.20) together with (A.18) implies that the norm of w1 on T4 can be expressed as an R2-integral ||w1|| ≡ Z T 4 d4x tr w† 1w1 = X n1,n3 L2 Z 0 dx2 L4 Z 0 dx4 tr wn1,n3 1 †wn1,n3 1 = ∞ Z −∞ dx2 ∞ Z −∞ dx4 tr u† 1(x2, x4)u1(x2, x4) . (A.21) JHEP01(2023)118 (A.21) Thus, finiteness of ||w1|| implies that the elements of the quaternion u1(x2, x4) should be square-normalizable functions on the R2-plane spanned by x2, x4. Any complete basis of such functions on R2 can be used, but below, we shall argue that an especially convenient basis is given by appropriately chosen simple harmonic oscillator eigenfunctions. Continuing with our self-duality equations (A.17), now the second equation in (A.17) together with (A.20) implies that     ∂4 + i z4 L4  + 2π L3L4 x4 − n3 −z3 2π  L4  −  ∂2 + i z2 L2  + 2π L1L2 x2 − n1 −z1 2π  L2   ∂2 + i z2 L2  + 2π L1L2 x2 − n1 −z1 2π  L2   ∂4 + i z4 L4  − 2π L3L4 x4 − n3 −z3 2π  L4     × u1(x2 −n1L2, x4 −n3L4) = 0 . (A.22) The holonomies in the partial derivatives can be absorbed by defining a new quaternion ˜u1(x2 −n1L2, x4 −n3L4) by means of the redefinition he holonomies in the partial derivatives can be absorbed by defining a new quaternion (x2 −n1L2, x4 −n3L4) by means of the redefinition u1(x2 −n1L2, x4 −n3L4) = e−i z2 L2 (x2−n1L2)−i z4 L4 (x4−n3L4)˜u1(x2 −n1L2, x4 −n3L4). ( u1(x2 −n1L2, x4 −n3L4) = e−i z2 L2 (x2−n1L2)−i z4 L4 (x4−n3L4)˜u1(x2 −n1L2, x4 −n3L4). A.1 Constructing the self-dual fractional instanton for small ∆ , (A.16) s = ∆s1 + ∆2 s2 + ∆3 s3 + . . . . (A.16) The difference in powers of √ ∆in the series for w and s follows by the structure of the self-duality equations (A.15). Here, we shall study only the leading-order solution. To exhibit it explicitly, we substitute the expansions in (A.16) in (A.15) and keeping the leading term in each equation, we find that s1, w1 obey ¯σn∂ns1 = 2π √ V iτ 3 −i  w† 1cw1c −w† 1w1  , (A.17) i ¯A3 0 ¯σn∂ns1 = 2π √ V iτ 3 −i  w† 1cw1c −w† 1w1  , (A.17) ¯σn  ∂n + i ¯A3 n  w1 = 0 . (A.17) ¯σn  ∂n + i ¯A3 n  w1 = 0 . We begin with the equation for w1 — the complex quaternion σmWm, obeying the boundary conditions (A.13). Periodicity in x1, x3 is obeyed by writing a Fourier series We begin with the equation for w1 — the complex quaternion σmWm, obeying the boundary conditions (A.13). Periodicity in x1, x3 is obeyed by writing a Fourier series w1 = ∞ X n1,n3=−∞ e −i2π  n1 x1 L1 +n3 x3 L3  wn1,n3 1 (x2, x4), (A.18) (A.18) while the conditions wn1,n3 1 (x2 + L2, x4) = wn1+1,n3 1 (x2, x4) , (A.19) wn1,n3 1 (x2, x4 + L4) = wn1,n3+1 1 (x2, x4) , (A.19) 32The n = 1, 2, 3 components of the four-vector matrix σn defined here should not be confused with ⃗σ = {σa, a = 1, 2, 3} = (σ1, σ2, σ3), the usual Pauli matrices. We use lower-case indices a = 1, 2, 3 to denote the usual Pauli matrices σa and reserve τ a for the SU(2) generators. – 29 – – 29 – ensure the rest of (A.13) and, by induction, imply that all wn1,n3 can be expressed via a single function, ensure the rest of (A.13) and, by induction, imply that all wn1,n3 can be expressed via a single function, wn1,n3 1 (x2, x4) = u1(x2 −n1L2, x4 −n3L4). 33With appropriately shifted center, as in the argument of ˜u1 below, a fact which we do not make explicit for brevity. A.1 Constructing the self-dual fractional instanton for small ∆ (A.28) It is then clear that this equation is satisfied by ˜u1 given by the product of ground state wave functions of the ω12 and ω34 SHOs times a constant 2 × 2 matrix C1: It is then clear that this equation is satisfied by ˜u1 given by the product of ground state wave functions of the ω12 and ω34 SHOs times a constant 2 × 2 matrix C1: ˜u1 = h12 0  x2 −  n1 −z1 2π  L2  h34 0  x4 −  n3 −z3 2π  L4  C1, (A.29) (A.29) where C1 obeys, as a consequence of (A.28) where C1 obeys, as a consequence of (A.28) 0 √2ω12 0 −√2ω34 ! C1 = 0 =⇒C1 = a b 0 0 ! , (A.30) (A.30) with arbitrary complex numbers a, b. Before continuing, let us make the following important remark: Before continuing, let us make the following important remark: • We stress that (A.29), (A.30) is the unique solution and not simply a consistent one. Because of the R2-normalizability (A.21), any solution can be expressed in terms of ω12 and ω34 SHO eigenfunctions. Explicitly, for the ab-th element of the quaternion ˜u1, we have ˜u1 ab(x2, x4) = ∞ P n,m=0 cnm ab h12 n (x2)h34 m(x4). Plugging into (A.28) and using (A.26), (A.27) one finds a set of linear equations for the constants cnm ab : • We stress that (A.29), (A.30) is the unique solution and not simply a consistent one. Because of the R2-normalizability (A.21), any solution can be expressed in terms of ω12 and ω34 SHO eigenfunctions. Explicitly, for the ab-th element of the quaternion ˜u1, we have ˜u1 ab(x2, x4) = ∞ P n,m=0 cnm ab h12 n (x2)h34 m(x4). Plugging into (A.28) and using (A.26), (A.27) one finds a set of linear equations for the constants cnm ab : √ω34 cp,q+1 11 p q + 1 + √ω12 cp−1,q 21 √p = 0, for p, q = 0, 1, 2, 3 . . . , √ω34 cp,q+1 12 p q + 1 + √ω12 cp−1,q 22 √p = 0, √ω12 cp+1,q 11 p p + 1 −√ω34 cp,q−1 21 √q = 0, √ω12 cp+1,q 12 p q + 1 −√ω34 cp,q−1 22 √q = 0. A.1 Constructing the self-dual fractional instanton for small ∆ (A.23) Using this, equation (A.22) becomes (A.23) Using this, equation (A.22) becomes Using this, equation (A.22) becomes    ∂4 + 2π L3L4 x4 − n3 −z3 2π  L4  −∂2 + 2π L1L2 x2 − n1 −z1 2π  L2  ∂2 + 2π L1L2 x2 − n1 −z1 2π  L2  ∂4 − 2π L3L4 x4 − n3 −z3 2π  L4     × ˜u1 (x2 −n1L2, x4 −n3L4) = 0 .    ∂4 + 2π L3L4 x4 − n3 −z3 2π  L4  −∂2 + 2π L1L2 x2 − n1 −z1 2π  L2  ∂2 + 2π L1L2 x2 − n1 −z1 2π  L2  ∂4 − 2π L3L4 x4 − n3 −z3 2π  L4     × ˜u1 (x2 −n1L2, x4 −n3L4) = 0 . (A.24) (A.24) As already alluded to, we now recognize that the first order differential operators appearing above are the creation and annihilation operators of simple harmonic oscillators (SHO) of frequencies 2π/(L1L2) and 2π/(L3L4). Let hij p (x) be the normalized p-th state of the SHO of frequency 2 ωij = 2π LiLj . (A.25) (A.25) – 30 – – 30 – The relations that we need in what follows are the orthonormality relations ∞ Z −∞ dxhij n (x)hij m(x) = δnm , n, m = 0, 1, 2 . . . , (A.26) (A.26) as well as the raising and lowering operators which obey the usual equations s LiLj 4π " ∂x + 2π LiLj x # hij n (x) = √n hij n−1(x) ↔ Aij|n⟩ij = √n|n −1⟩ij, s LiLj 4π " −∂x + 2π LiLj x # hij n (x) = √ n + 1 hij n+1(x) ↔ A† ij|n⟩ij = √ n + 1|n + 1⟩ij , (A.27) JHEP01(2023)118 (A.27) where we have indicated that the differential operators in the middle and bottom line are the familiar lowering and raising operators Aij, A† ij of SHOs of frequencies ωij (A.25). In terms of A12, A† 12, A34, A† 34,33 we can rewrite (A.24) as √2ω34A34 √2ω12A† 12 √2ω12A12 −√2ω34A† 34 ! ˜u1  x2 −  n1 −z1 2π  L2, x4 −  n2 −z3 2π  L2  = 0 . A.1 Constructing the self-dual fractional instanton for small ∆ (A.31) (A.31) 33With appropriately shifted center, as in the argument of ˜u1 below, a fact which we do not make explicit for brevity. – 31 – One begins by noticing that c00 11 and c00 12 do not appear above (this is easy to see by inspection recalling the range of p, q, which ensure that terms containing the nonexistent coefficients, like c−1,∗ ∗∗ , are always multiplied by 0). Then, recursively solving the equations, one finds that their only solution is that all cnm ij vanish except for the two that do not appear in equations (A.31), the undetermined c00 11 and c00 12, called a and b in (A.29). Let us flesh out the argument. We consider the first and third equations in (A.31); the second and fourth can be considered similarly and are left as an exercise. First notice that (A.31) imply that c0,p 11 = cp,0 11 = 0 for p = 1, 2, 3 . . .. Further, denote δ = qω12 ω34 and shift the p’s and q’s in (A.31) such that both equations involve cp,q 11 we find JHEP01(2023)118 cp,q 11 √q + δcp−1,q−1 21 √p = 0, (A.32) cp,q 11 √p −1 δ cp−1,q−1 21 √q = 0. (A.32) Next, we multiply the top equation by √p and the bottom by √q, subtract them, and find q Next, we multiply the top equation by √p and the bottom by √q, subtract them, and find q cp−1,q−1 21 (pδ + q δ) = 0. (A.33) (A.33) Recalling that the appropriate range for p, q in (A.33) is 1, 2, 3 . . ., this implies that all c21’s vanish. Hence by (A.32), all cp,q 11 with (p, q) ̸= (0, 0) vanish as well. Recalling that the appropriate range for p, q in (A.33) is 1, 2, 3 . . ., this implies that all c21’s vanish. Hence by (A.32), all cp,q 11 with (p, q) ̸= (0, 0) vanish as well. We next turn to the first of the self-duality equations in (A.17). Since s1 is periodic, the r.h.s. of the equation has no constant Fourier mode. Thus, consistency implies that the constant mode of the r.h.s. vanishes as well; this will be seen to fix the coefficients a, b in terms of the volume of the torus up to an overall phase. A.1 Constructing the self-dual fractional instanton for small ∆ To determine them, let us collect everything — in reverse order, eqs. (A.29), (A.24), (A.23), (A.20), and (A.18)—and exhibit the full solution for w1 we found so far: w1 = F(x, z)C1 = F(x, z) a b 0 0 ! , (A.34) (A.34) where where F(x, z) = p L2L4 ∞ X n1,n3=−∞ e−i2π(n1 x1 L1 +n3 x3 L3 )e−i z2 L2 (x2−n1L2)−i z4 L4 (x4−n3L4) × h12 0  x2 −  n1 −z1 2π  L2  h34 0  x4 −  n3 −z3 2π  L4  , (A.35) F(x, z) = p L2L4 ∞ X n1 n3= ∞ e−i2π(n1 x1 L1 +n3 x3 L3 )e−i z2 L2 (x2−n1L2)−i z4 L4 (x4−n3L4) 1, 3 × h12 0  x2 −  n1 −z1 2π  L2  h34 0  x4 −  n3 −z3 2π  L4  , (A.35) with the normalization Z T 4 |F|2 = V, (A.36) Z T 4 |F|2 = V, (A.36) recalling (A.27). Note that F is dimensionless and a, b have dimension one. In addition, under the reflection of all xn and all zn, after relabeling n1, n3 →−n1, −n3 and noting that hij 0 are even functions of their arguments, we find recalling (A.27). Note that F is dimensionless and a, b have dimension one. In addition, under the reflection of all xn and all zn, after relabeling n1, n3 →−n1, −n3 and noting that hij 0 are even functions of their arguments, we find F(−x, −z) = F(x, z) . (A.37) (A.37) – 32 – – 32 – With (A.34), (A.35), we have that the vanishing constant mode of ∂s from equa- tion (A.17) implies that 2π √ V τ 3 = (C† cCc −C†C) Z T 4 d4x|F(x, z)|2 , or 2π √ V 1 0 0 −1 ! = |b|2 −|a|2 −2a∗b −2ab∗ |a|2 −|b|2 ! V . (A.38) 2π √ V 1 0 0 −1 ! = |b|2 −|a|2 −2a∗b −2ab∗ |a|2 −|b|2 ! V . (A.38) (A.38) We thus conclude that a = 0 while |b|2 = 2π V 1/2 . Thus, our solution has the form JHEP01(2023)118 w(x, z) = σnWn = √ ∆w1(x, z) = √ ∆F(x, z)eiα (2π)1/2 V 1/4 0 1 0 0 ! 34As stressed above, we shall not need its explicit form, but only the relations it satisfies, which are important to ensure self-duality. A.1 Constructing the self-dual fractional instanton for small ∆ (A.42) (A.42) – 33 – – 33 – The consistency of this equation (the absence of a constant Fourier mode of the r.h.s.) discussed above is yet again seen to follow from (A.36). We also note that equation (A.42) allows adding a constant to s1; this is a contribution to the constants zn, already included in our background (A.7). To solve (A.42), we multiply by σm∂m to obtain ∂n∂ns1 = −iσmτ 3 2π √ V (F ∗∂mF + F∂mF ∗) . (A.43) (A.43) This equation is solved by expanding both s1 and the r.h.s. in Fourier modes in x1 . . . x4 and equating the coefficients. This can be explicitly done and a unique s1 can be written down, but we shall not need the explicit form here. As we mentioned in section 1.3, understanding the higher orders in the ∆expansion is an interesting problem for future studies. JHEP01(2023)118 A.1 Constructing the self-dual fractional instanton for small ∆ + O(∆) , s(x, z) = σnSn = O(∆) , w(x, z) = σnWn = √ ∆w1(x, z) = √ ∆F(x, z)eiα (2π)1/2 V 1/4 0 1 0 0 ! + O(∆) , (A.39) with the phase α due to the gauge freedom to rotate around the τ 3 isospin direction. / with the phase α due to the gauge freedom to rotate around the τ 3 isospin direction. with the phase α due to the gauge freedom to rotate around the τ 3 isospin direction. Before we continue, let us exhibit the self-dual solution we found, eq. (A.39), w = ∆1/2w1 in terms of the 4-vector gauge potentials, Wn, Sn of (A.11): Before we continue, let us exhibit the self-dual solution we found, eq. (A.39), w = ∆1/2w1 in terms of the 4-vector gauge potentials, Wn, Sn of (A.11): Sn = O(∆) , W1(x, z, α) = −i 2 √ ∆F(x, z)eiα √ 2π V 1/4 + O(∆3/2) ≡−γeiαF(x, z), where γ ≡i 2 s 2π∆ √ V , W2(x, z, α) = 1 2 √ ∆F(x, z)eiα √ 2π V 1/4 + O(∆3/2) = iW1 + O(∆3/2), W3 = O(∆3/2), W4 = O(∆3/2). (A.40) W4 = O(∆3/2). (A.40) (A.40) We note that the above implies that the only gauge-field zero modes in our background are the one due to translations (corresponding to shifting zn) and constant gauge rotations around τ 3 (corresponding to shifts of α). The former are physical and gauge invariant quantities characterizing the solution will be seen to depend on zn, while the latter are gauge artifacts with no physical quantity exhibiting α-dependence. For calculating the action density and gauge-invariant “electric” and “magnetic” fields to leading nontrivial order, one also needs the expression for S1, which was not given in (A.40). Here we simply describe how this can be found. We have, with w1 from (A.39) w1 = F 0 b 0 0 ! , b = eiα √ 2π V 1 4 =⇒w† 1w1 = |F|2 0 0 0 |b|2 ! , w1c = F ∗ 0 0 −b∗0 ! =⇒w† 1cw1c = |F|2 |b|2 0 0 0 ! . (A.41) Hence, from the top equation in (A.17), we obtain the equation for s1: ¯σn∂ns1 = iτ 3 2π √ V  1 −|F(x, z)|2 . A.2 The field strength tensor of the fractional instanton to order ∆ Combining this with the results for F s mn from (A.46), we find F (0+1(s)) mn = τ 3 2            0 − 2π L1L2 + ∆F s 12 ∆F s 13 ∆F s 14 2π L1L2 −∆F s 12 0 ∆F s 14 −∆F13 −∆F s 13 −∆F s 14 0 − 2π L3L4 + ∆F s 34 −∆F s 14 ∆F s 13 2π L3L4 −∆F s 34 0            , (A.47) F (0+1(s)) mn = τ 3 2            0 − 2π L1L2 + ∆F s 12 ∆F s 13 ∆F s 14 2π L1L2 −∆F s 12 0 ∆F s 14 −∆F13 −∆F s 13 −∆F s 14 0 − 2π L3L4 + ∆F s 34 −∆F s 14 ∆F s 13 2π L3L4 −∆F s 34 0            , (A.47) (A.47) (A.47) JHEP01(2023)118 where F s 34 is understood to be expressed via F s 12 through the first equation in (A.46) 34 12 ( ) To study the complete field strength tensor in the τ 3 direction to order ∆, we must add to (A.47) the O(∆) contribution to the τ 3 field strength coming from the commu- tator F (1(w)) mn = i[Wmτ + + W ∗ mτ −, Wnτ + + W ∗ nτ −] = τ 3 2 2i(WmW ∗ n −W ∗ mWn). For the background (A.40), this is only nonzero for F (1(w)) 12 . We find F (1(w)) 12 = −F (1(w)) 21 = τ 3 2 2π∆ √ V |F(x, z)|2 , all other F (1(w)) mn = 0. (A.48) (A.48) Most of the terms in (A.47) obey self-duality because of F (0+1(s)) 13 = −F (0+1(s)) 24 and F (0+1(s)) 23 = F (0+1(s)) 14 as is evident from (A.47), (A.46). The only terms left to consider are the 12 and 34 entries. To study their self-duality, we write, using the top equation in (A.46) Most of the terms in (A.47) obey self-duality because of F (0+1(s)) 13 = −F (0+1(s)) 24 and F (0+1(s)) 23 = F (0+1(s)) 14 as is evident from (A.47), (A.46). A.2 The field strength tensor of the fractional instanton to order ∆ To find the gauge invariants of the solution to order ∆, we need the field strength of s1, namely34 F s nm ≡(∂nSm −∂mSn) , (A.44) (A.44) where for brevity we use Sn to denote the coefficient of the O(∆) part of Sn. The l.h.s. of (A.42) has the form where for brevity we use Sn to denote the coefficient of the O(∆) part of Sn. The l.h.s. of (A.42) has the form    −i∂3 + ∂4 −i∂1 −∂2 −i∂1 + ∂2 i∂3 + ∂4       iS3 + S4 iS1 + S2 iS1 −S2 −iS3 + S4       −i∂3 + ∂4 −i∂1 −∂2 −i∂1 + ∂2 i∂3 + ∂4       iS3 + S4 iS1 + S2 iS1 −S2 −iS3 + S4    =    ∂nSn + i(F s 12 −F s 34) −F s 13 −F s 24 + i(F s 23 −F s 14) F s 13 + F s 24 + i(F s 23 −F s 14) ∂nSn −i(F s 12 −F s 34)   . (A.45) =    ∂nSn + i(F s 12 −F s 34) −F s 13 −F s 24 + i(F s 23 −F s 14) F s 13 + F s 24 + i(F s 23 −F s 14) ∂nSn −i(F s 12 −F s 34)   . (A.45) (A.45) Comparing with the r.h.s. of (A.42), using ∂nSn = 0, we conclude that Comparing with the r.h.s. of (A.42), using ∂nSn = 0, we conclude that F s 12 −F s 34 = 2π √ V 1 −|F(x, z)|2, F s 13 + F s 24 = 0, F s 23 −F s 14 = 0. (A.46) (A.46) Note that these terms should be multiplied by ∆. Also note that these equations by themselves do not determine the individual F s 12, F s 34 (etc.) but only their non-self-dual parts. To find the individual F s mn, we need to solve (A.43) to first find s1. – 34 – The field strength of the O(1) abelian background (A.7) is F (0) mn, already given in (A.8). Combining this with the results for F s mn from (A.46), we find The field strength of the O(1) abelian background (A.7) is F (0) mn, already given in (A.8). A.2 The field strength tensor of the fractional instanton to order ∆ The only terms left to consider are the 12 and 34 entries. To study their self-duality, we write, using the top equation in (A.46) F (0+1(s)) 12 −F (0+1(s)) 34 = τ 3 2  −2πL3L4 −L1L2 V + ∆(F s 12 −F s 34)  = τ 3 2  −2π ∆ √ V + 2π ∆ √ V (1 −|F(x, z)|2  = −τ 3 2 2π∆ √ V |F(x, z)|2 . (A.49) F (0+1(s)) 12 −F (0+1(s)) 34 = τ 3 2  −2πL3L4 −L1L2 V + ∆(F s 12 −F s 34)  = τ 3 2  −2π ∆ √ V + 2π ∆ √ V (1 −|F(x, z)|2  3 2 ∆ = −τ 3 2 2π∆ √ V |F(x, z)|2 . (A.49) (A.49) This non-selfdual contribution to F (0+1(s)) mn is cancelled by the O(∆) contribution of the Wn shown in (A.48). Displayed in full glory, the Cartan part of the field strength to order ∆is given by the sum of (A.47) and (A.48): F (0+1) mn Cartan =          0 − 2π L1L2 +∆(F s 12+ 2π √ V |F(x,z)|2) ∆F s 13 ∆F s 14 2π L1L2 −∆(F s 12+ 2π √ V |F(x,z)|2) 0 ∆F s 14 −∆F13 −∆F s 13 −∆F s 14 0 − 2π L3L4 +∆F s 34 −∆F s 14 ∆F s 13 2π L3L4 −∆F s 34 0          . (A.50) F (0+1) mn Cartan = – 35 – We stress again that F s 34 is understood to be expressed via F s 12 through (A.46), a substitution we have not explicitly done for lack of space. Further, the above expression is understood to be multiplied by τ 3/2 and the undertermined F s mn are found by solving (A.43). We stress again that F s 34 is understood to be expressed via F s 12 through (A.46), a substitution we have not explicitly done for lack of space. Further, the above expression is understood to be multiplied by τ 3/2 and the undertermined F s mn are found by solving (A.43). The non-Cartan part of the solution, the Wn from (A.40) also produce a non-Cartan field strength. A.2 The field strength tensor of the fractional instanton to order ∆ The O( p ∆) field strength due to Wn is F (1) mn = (∂m + i ¯A3 m)Wnτ + + (∂m − i ¯A3 m)W ∗ nτ −−(m ↔n). It is self-dual by itself and the O( p ∆) field strength of Wn is the only non-Cartan contribution to order ∆(the next non-Cartan contribution is of order ∆3/2): F (1) mn =            0 0 F (1) 13 F (1) 14 0 0 F (1) 14 −F (1) 13 −F (1) 13 −F (1) 14 0 0 −F (1) 14 F (1) 13 0 0            . (A.51) F (1) mn =            0 0 F (1) 13 F (1) 14 0 0 F (1) 14 −F (1) 13 −F (1) 13 −F (1) 14 0 0 −F (1) 14 F (1) 13 0 0            . (A.51) JHEP01(2023)118 JHEP01(2023)118 (A.51) The nonzero entries of (A.51) are The nonzero entries of (A.51) are The nonzero entries of (A.51) are F (1) 13 = −iγ∗eiα rω34 2 G(x, z)τ + + iγe−iα rω34 2 G∗(x, z)τ −, (A.52) F (1) 14 = γ∗eiα rω34 2 G(x, z)τ + + γe−iα rω34 2 G∗(x, z)τ −, (A.52) where we shouldn’t forget that γ ∼ √ ∆, as γ = i 2 q 2π∆ √ V , as per (A.40). The function G(x, z) is G(x, z) = p L2L4 ∞ X n1,n3=−∞ e−i2π(n1 x1 L1 +n3 x3 L3 )e−i z2 L2 (x2−n1L2)−i z4 L4 (x4−n3L4) × h12 0  x2 −  n1 −z1 2π  L2  h34 1  x4 −  n3 −z3 2π  L4  , (A.53) (A.53) where, just like F(x, z), G is dimensionless. where, just like F(x, z), G is dimensionless. In conclusion, the full field strength tensor of our solution, to order ∆, is given by the Cartan part (A.50) and the non-Cartan part (A.51). Owing to the self-duality, the action of the solution is S0 = 4π2 g2 , as can also be explicitly inferred from the explicit form of the field strength. These properties of the solutions are useful in what follows. A.3 The gauge invariants of the fractional instanton background We now consider the zn-dependence of gauge invariants, both local and nonlocal (i.e. winding Wilson loops) characterizing the solution. We begin with the zn dependence of local gauge invariants, formed of traces of powers the field strength tensor. Using the data given above, we now compute ⟨E2 i ⟩≡ L3 Z 0 dx3 L4 Z 0 dx4 tr F 2 i4(x, z), (A.54) (A.54) – 36 – calling it the “i-th component of the electric field squared,” averaged over x3 and x4.35 Omitting overall constants, for i = 1, we find for the leading contribution to (A.54), which is O(∆): ⟨E2 1⟩∼ X n1,m1 e−i2π(n1−m1) 1 L1 x1−z2L1 2π  h12 0  x2 + z1L2 2π −n1L2  h12 0  x2 + z1L2 2π −m1L2  ∼ X n1,m1 e−i2π(n1−m1) 1 L1 x1−z2L1 2π  e − π L1L2 hx2+ z1L2 2π −n1L2 2+(x2+ z1L2 2π −m1L2)2i . (A.55) The sum over m, n is rapidly converging and can be seen to produce localized bumps on T4 when plotted, periodic on R2 with period L1, L2 (usually a limit of −4 ≤m, n ≤4 suffices to make the errors tiny and produces a periodic picture). The point of this discussion is to illustrate two facts: JHEP01(2023)118 1. That all local gauge invariants characterizing our fractional instanton depend on the combinations z2 −2πx1 L1 and z1 + 2πx2 L2 (this also holds for the dependence on z4 −2πx3 L2 and z3 + 2πx4 L4 , not shown above). 1. That all local gauge invariants characterizing our fractional instanton depend on the combinations z2 −2πx1 L1 and z1 + 2πx2 L2 (this also holds for the dependence on z4 −2πx3 L2 and z3 + 2πx4 L4 , not shown above). 2. That, furthermore, the local gauge invariants have 2π periodicity in these variables. 2. That, furthermore, the local gauge invariants have 2π periodicity in these variable Next, we consider the zn dependence of winding Wilson loops. To order ∆0, with the abelian background (A.7), this is a rather straightforward task. Consider a Wilson loop beginning at some x, going along the x1 direction n1 times (i.e. from x to x + ˆe1n1L1), then n2 times in the x2 direction, n3 times in the x3 direction, and n4 times in the x4 direction, with the final point being x + 4P k=1 ˆeknkLk. 35The averaging is done solely in order to shorten the formulae that we display. This was also done in [1], when comparing the analytic solution to the numerical minimization of the action at given ∆. A.3 The gauge invariants of the fractional instanton background As an explicit simple example, consider the O(∆) contribution to W(C1,0,0,0), obtained by expanding the path-ordered exponential and using the explicit form of the solution (A.40). Omitting the overall constant, we obtain36 JHEP01(2023)118 JHEP01(2023)118 W(C1,0,0,0) O(∆)−contribution (A.58) ∼cos ˆz1 2 X n3 ein3ˆz4 h34 0 ( ˆz3L4 2π −n3L4) 2 × X n1 e−in1ˆz2 h12 0 ( ˆz1L2 2π −n1L2) 1 Z 0 dt eit(ˆz1−2πn1) 2 + contribution of s1  . (A.58) The expression above illustrates the properties we mentioned earlier: as a function of ˆzn, the O(∆) contribution multiplying the overall cos ˆz1 2 factor is 2π periodic. The expression above illustrates the properties we mentioned earlier: as a function of ˆzn, the O(∆) contribution multiplying the overall cos ˆz1 2 factor is 2π periodic. A.3 The gauge invariants of the fractional instanton background The gauge invariant Wilson loop along the loop Cn1,n2,n3,n4, beginning at x and consisting of the winding straight segments described above, is given by W(Cn1,n2,n3,n4) = tr  Pe iR Cn1,n2,n3,n4 Ak(x′)dx′ k Ωn2 2 (x) Ωn4 4 (x)  , (A.56) (A.56) where the nontrivial transition functions are inserted to ensure gauge invariance. ¯ The path-ordering can be disregarded for an abelian background (A of (A.7)) and o can conclude that W ∆0 (Cn1,n2,n3,n4) (A.57) = 2 cos 1 2  n1  z1 + 2πx2 L2  + n2  z2 −2πx1 L1  + n3  z3 + 2πx4 L4  + n4  z4 −2πx4 L2  . (A.57) ( n1,n2,n3,n4) ( ) 2 cos 1 2  n1  z1 + 2πx2 L2  + n2  z2 −2πx1 L1  + n3  z3 + 2πx4 L4  + n4  z4 −2πx4 L2  . We now observe that the O(∆0) Wilson loops W ∆0 n1,n2,n3,n4 are periodic functions of the variables ˆz1 ≡z1 + 2πx2 L2 , ˆz2 ≡z2 −2πx1 L1 , ˆz3 ≡z3 + 2πx4 L4 , ˆz4 ≡z4 −2πx3 L3 . However, in contrast with the local gauge invariants, like the earlier (A.55), the periodicity in ˆzn is 4π, rather than 2π. Thus, while local gauge invariants can not distinguish values of ˆzn differing by 2π, nonlocal gauge invariant observables distinguish such values. These values are, therefore, not physically equivalent. We now observe that the O(∆0) Wilson loops W ∆0 n1,n2 – 37 – We are led to conclude that the range of values of ˆzn which are distinguished by gauge invariant quantities — and are thus physically distinct — is given by T4. In our description, the T4 has “circumference” 4π, ˆzn ≡ˆzn + 4π. This fact is important in the calculation of the gaugino condensate. It should be clear that the O(∆) (and higher) contributions to the Wilson loops (A.56), which require taking the path ordering into account, are proportional to the same overall factor as (A.57)—since they come upon expanding the path-ordered exponential. Thus, eq. (A.57), is multiplied by (1 + O(∆)). The O(∆) terms are 2π periodic functions of ˆzn, even with respect to their simultaneous reflection, not affecting our conclusion above. 37It should be clear that, to order O(∆0), the zero modes (B.1) already obey the background gauge condition: the leading-order background is in the Cartan algebra and thus commutes with Z0,(p) n and, furthermore, the leading-order zero modes (B.1) are constant. 36We indicated that there is an additional contribution of the Cartan-direction O(∆) component s1, which we have not computed. However, since it is found by solving (A.43), whose r.h.s. is (schematically) ∼F ∗F which has the same properties as the (also schematically) |W1|2 contribution shown in (A.58). B.1 Leading-order bosonic zero-modes and measure Here, we study the leading order bosonic zero modes and construct the O(∆0) bosonic zero mode measure. In the following sections, we shall argue that the measure remains the same to all orders in ∆. The bosonic zero modes are related to the dependence of the solution on zp. Their leading-order wave functions are particularly simple Z0,(p) n = ∂Acl. n ∂zp = δnp Lp τ3 2 + . . . (B.1) (B.1) As usual when performing semiclassical instanton calculations, we add a background Lorentz gauge fixing term to the bosonic action37 and expand to second order in fluctuations am, Am ≡Acl m + am, Dm ≡Dm(Acl) = ∂m + i[Acl m, ∗]. We stress that here Acl m is the classical As usual when performing semiclassical instanton calculations, we add a background Lorentz gauge fixing term to the bosonic action37 and expand to second order in fluctuations am, Am ≡Acl m + am, Dm ≡Dm(Acl) = ∂m + i[Acl m, ∗]. We stress that here Acl m is the classical 36We indicated that there is an additional contribution of the Cartan-direction O(∆) component s1, which we have not computed. However, since it is found by solving (A.43), whose r.h.s. is (schematically) ∼F ∗F which has the same properties as the (also schematically) |W1|2 contribution shown in (A.58). 37It should be clear that, to order O(∆0), the zero modes (B.1) already obey the background gauge condition: the leading-order background is in the Cartan algebra and thus commutes with Z0,(p) n and, furthermore, the leading-order zero modes (B.1) are constant. – 38 – solution on the asymmetric T4, taken to the desired order in ∆. Thus, we obtain the usual action of the bosonic fluctuations solution on the asymmetric T4, taken to the desired order in ∆. Thus, we obtain the usual action of the bosonic fluctuations Sb,g.f. = Z T 4  1 2g2 tr FmnFmn + 1 g2 tr (Dmam)2  (B.2) ≃4π2 g2 + 1 g2 Z T 4 tr [anOnmam] , where Onmam = −D2δnmam −2i[Fnm, am]. (B.2) We include the rather well-known details that follow in order to motivate the inner product of modes as well as to follow the factors of 2. Denote by Zk m the nonzero-eigenvalue eigenfunctions of Onm, i.e. B.1 Leading-order bosonic zero-modes and measure OnmZk m = ωkZk n and expand the nonzero-mode part of the fluctuation am (for brevity, using the same letter as the full fluctuation which includes the zero modes) as am = P k ζkZk m. Then we have that JHEP01(2023)118 Sb,g.f. −4π2 g2 = X l,k ωlζkζl 2  2 g2 Z T 4 tr Zk mZl m  ≡ X l,k ωlζkζl 2 Ukl, where the last equation defines the zero-mode norm matrix Ukl, explicitly spelled out in (B.3) below. We diagonalize the matrix Ukl with eigenvalues uk and define the measure of the path integral over the nonzero modes as Q k dζk √uk √ 2π , thus normalizing the path integral to simply produce the product Q k ω−1/2 k . The upshot is that we defined the inner product (or moduli space metric) Ukl = 2 g2 Z T 4 tr Zk nZl n (B.3) (B.3) which in a diagonal basis is simply Ukl = δlkul. which in a diagonal basis is simply Ukl = δlkul. ( ) We use the same inner product for the zero modes Z(0),p n of eq. (B.1), for which we find, neglecting the O( √ ∆) contributions u(0) k = V g2L2 k . (B.4) (B.4) As before, we expand the gauge field as An = Acl n + P4 p=1 ζ(0) p Z(0),p n + (nonzero modes), and define the measure over the zero modes as Q4 k=1 dζ(0) k r u(0) k 2π , the same as for the nonzero modes. Taken at face value, this integral is undetermined until we find the region of integration over ζ(0) k . To change variables ζ(0) k →zk, we note that to leading order in ∆this is quite straightforward, since the dependence of Acl(z) on zk is linear hence one simply replaces ζ(0) k by zk. These O(∆0) considerations allow us to obtain the bosonic zero- mode measure dµB ≡ d4z ( √ 2π)4 4 Y l=1 q u(0) l = V g4 dz1dz2dz3dz4 ( √ 2π)4 . (B.5) (B.5) As described earlier, section A.3, the zn are integrated over in the range from 0 to 4π modulo an overall reflection. We end this introductory discussion of bosonic zero modes with two comments: – 39 – 1. Eq. (B.5) was obtained by considering only the leading-order solution. B.1 Leading-order bosonic zero-modes and measure Our next task is to show that the zero modes of the O( √ ∆) (and higher) solution enjoy the same measure. We need to ensure that the background gauge condition can be satisfied and that the change of variables from ζ(0) k to zn results in the same measure. 2. An additional question that needs to be discussed is the fact that for ∆= 0, the self-dual abelian solution has extra non-Cartan zero modes, in addition to the constant modes, as was found long ago [46]. In contrast, the asymmetric T4 self-dual solution has only the zero modes discussed above, as we show below. JHEP01(2023)118 38All our notation regarding fermions is as in [25], save for the fact that ref. [25] uses antihermitean gauge fields, necessitating the replacement Athat ref. = iAthis paper. The four-vectors σn, ¯σn were already defined in (A.14). For futher use, notice, in particular, that σmn = (σm¯σn −σn¯σm)/4, and that these matrices are, explicitly, σ12 = σ34 = i 2σ3, σ13 = −σ24 = −i 2σ2, σ14 = σ23 = i 2σ1. As we already noted, we use σa to denote the usual Pauli matrices, not to be confused with the components of the four-vector σn of (A.14). 40This definition ensures that, upon perturbing with a zero-mode lifting mass term, δSm = m g2 tr λαλα, e obtains m for the zero-mode contribution to the path integral. B.2 Fermions and their zero-mode measure It is well-known (see e.g. [25, 26]) that there is a relation between the zero modes of the adjoint Dirac operator and the zero modes of the bosonic fluctuation operator Omn of eq. (B.2), to be exploited later. To this end, as well as because we are interested in the theory with adjoint fermions, we now consider the adjoint fermions and their path integral in the fractional instanton background. The Euclidean space Lagrangian density with the fermions included is 1 2g2 tr FmnFmn + 2 g2 tr (∂n¯λ ˙α + i[An, λ ˙α])¯σ ˙αα n λα), (B.6) (B.6) where λ and ¯λ are independent variables.38 For future use, we note that it is invariant under the supersymmetry δAn = ζα σn α ˙α ¯λ ˙α + ¯ζ ˙α ¯σ ˙αα n λα (B.7) δλα = −σ β mn α ζβ Fmn δ¯λ ˙α = −¯σ ˙α mn ˙β ¯ζ ˙β Fmn (B.7) δ¯λ ˙α = −¯σ ˙α mn ˙β ¯ζ ˙β Fmn δ¯λ ˙α = −¯σ ˙α mn ˙β ¯ζ ˙β Fmn where the σ’s are the ones of [25]. As usual for spinors, ξ1 = ξ2, ξ2 = −ξ1 and likewise for dotted. The procedure for the fermions we shall follow is to again start from the nonzero modes. We expand the fermions as eigenfunctions of the second order Hermitean operators The procedure for the fermions we shall follow is to again start from the nonzero mod We expand the fermions as eigenfunctions of the second order Hermitean operators D ¯D = D2 + iFmnσmn , −(D ¯D) β α λβ = ω2λβ (B.8) ¯DD = D2 + iFmn¯σmn = D2, D2¯λ ˙β = ω2¯λ ˙β , (B.8) where, in the second line, we used the self-duality of the background (A.15). To discuss the measure, begin by considering the contribution of a single (for brevity) nonzero eigenvalue ω to the fermion path integral. Let −(D ¯D) β α φi β = ω2φi α, where i labels the different eigenfunctions, the commuting functions φi α, with the same eigenvalue ω (we note that – 40 – there are at least two of them). We expand the nonzero-mode part of the fermion field (for brevity, denoting it with the same letter λ, ¯λ) there are at least two of them). B.2 Fermions and their zero-mode measure We expand the nonzero-mode part of the fermion field (for brevity, denoting it with the same letter λ, ¯λ) λα = X i χi φi α (B.9) 1 λα = X i χi φi α (B.9) ¯λ ˙α = X i ¯χi 1 ω ¯D ˙ααφi α, (B.9) where we used the fact that the nonzero eigenfunctions of D ¯D and ¯DD are related as shown and we attach the spinor index to the bosonic solution of the 2nd order equation and not to the Grassmann variable, χi or ¯χi (the fact that there is more than a single solution for every ω is accounted by the index i). We also indicate that the λ and ¯λ expansions have each their separate Grassmann variables χi, ¯χi. where we used the fact that the nonzero eigenfunctions of D ¯D and ¯DD are related as shown and we attach the spinor index to the bosonic solution of the 2nd order equation and not to the Grassmann variable, χi or ¯χi (the fact that there is more than a single solution for every ω is accounted by the index i). We also indicate that the λ and ¯λ expansions have each their separate Grassmann variables χi, ¯χi. JHEP01(2023)118 Plugging (B.9) into the fermionic action (B.6), we obtain after integration of parts and using the fact that φ is an eigenvector of D ¯D: SF = 2 g2 tr (Dn¯λ ˙α¯σ ˙αα n λα) = X ij ¯χjχiω  2 g2 Z tr φiαφj α  (B.10) = ω X ij ¯χjχi Uij F , (B.10) where the fermion mode inner product matrix is here the fermion mode inner product matrix is Uij F = 2 g2 Z T 4 tr φi 2φj 1 −φi 1φj 2 , U ij F = −Uji F , (B.11) (B.11) and again we remind ourselves that we are just looking at a single eigenvalue (one can imagine a sum over them). Then we define the fermion nonzero mode path integral so that it produces ω (the minimal number of eigenfunctions with the same eigenvalue is two, i.e. i, j = 1, 2, with UF generically a 2 × 2 matrix) Z Y i dχid¯χi (det UF )−1e−SF = ω . (B.12) (B.12) When all nonzero eigenvalues are taken into account, we obtain the square root of the product over all nonzero eigenvalues of ¯DD (or D ¯D). B.2.1 No zero modes of D2 = D ¯ D on the asymmetric T4 The reason to include this section is that in the ∆= 0 abelian self-dual background, i.e. in the symmetric-T4 case, the D2 (= ¯DD) operator has zero modes: an = cnτ 3, with arbitrary constant cn. These zero modes are also zero modes of Omn of (B.2), owing to the abelian nature of the background. The four Cartan zero modes of the ∆= 0 self-dual solution appear in addition to the two non-Cartan (complex) zero modes, also obeying Omnan = 0 but with an in the τ ± directions, found in [46]. Thus the ∆= 0 self-dual abelian background has 8, not 4 bosonic zero modes. While it is expected that interactions lift half of these zero modes, this has not been shown in any detail and is a problem for future studies. JHEP01(2023)118 In any case, since we find the ∆̸= 0 detuned T4 of greater physical interest, we proceed to show that in our self-dual background (A.40) the D2 operator has no zero modes. Furst, suppose that there exists an adjoint field φ (generally complex) obeying DnDnφ = 0 in our background; φ is, of course, assumed to obey the boundary conditions appropriate to adjoints, i.e. (A.4) without the nonhomogeneous term. This implies that R T4 tr φ†DnDnφ = 0, T or, after integration by parts, noting that the boundary terms vanish if (A.4) are obeyed, R T4 tr Dnφ†Dnφ = 0. This is only possible if Dnφ = 0, or writing explicitly the components of this equation: ∂nφ3 −2iA− n φ+ + 2iA+ n φ−= 0, ∂n −iA3 n φ−+ iA− n φ3 = 0, ∂n + iA3 n φ+ −iA+ n φ3 = 0, (B.15) (B.15) where A3,± n are to be substituted by the O( √ ∆) background fields (A.40). Eqs. (B.15) imply that the D2 zero mode φ0 of the abelian background (the ∼∆0 term with A± = 0) has components φ3 0 = c, φ± 0 = 0. One can show that there are no other zero mode solutions obeying the right boundary conditions (see [46], or perform a SHO analysis of (B.15) in the background (A.7), similar to the analysis in section A.1). We now want to argue that the O( √ ∆) perturbations around the abelian background of eq. (A.40) lift the zero eigenvalue of −D2. B.2.1 No zero modes of D2 = D ¯ D on the asymmetric T4 To this end, we use perturbation theory for the non-negative Hermitean operator −D2 and compute its matrix element in the unperturbed “eigenstate” found above, φ0 = cτ 3 2 . For the shift of the eigenvalue, this gives R T4 tr φ† 0(−D2)φ0 = |c|2 2 R T4 4A− n A+ n , where only the n = 1, 2 components are nonzero in the order √ ∆solution: A+ 1 = W1 and A+ 2 = W2 = iW1. The integral is positive definite, as it is easily seen to be proportional to R T4 |F|2, recall (A.36), showing that the zero eigenvalue is lifted in the detuned-T4 self-dual background. This is a welcome feature of this background, compared to the one in the symmetric T4 studied in [46]. B.2 Fermions and their zero-mode measure When all nonzero eigenvalues are taken into account, we obtain the square root of the product over all nonzero eigenvalues of ¯DD (or D ¯D). The definition of the integrals over the fermion zero modes are done in the same manner using the same mode normalization matrix, Uij F defined in (B.11). We imagine (as we shall argue to be the case in our background) that only the undotted spinors λα have zero modes, thus we expand39 λα = X i ηiφi α + nonzero modes, (B.13) (B.13) where we use ηi to denote the zero-mode Grassman variable. The fermion zero-mode measure is then taken to be the “square root” of (B.12):40 dµF = Y i dηi (det UF )−1/2 = Y i dηi (PfUF )−1 . (B.14) (B.14) 39Here and below, we use φi α to denote the zero-mode solutions of D ¯D, obeying (D ¯D) β α φi β = 0. The reader should forgive us for using the same letter as in the non-zero mode discussion near (B.9). 40 40This definition ensures that, upon perturbing with a zero-mode lifting mass term, δSm = m g2 tr λαλα, one obtains m for the zero-mode contribution to the path integral. – 41 – B.2.2 The zero modes of D on the asymmetric T4 via the Dirac equation In this section, we explicitly study the Dirac equation for the undotted fermions in the ∼ √ ∆background and show that they have two zero modes. Since, as shown above, D2 = ¯DD has no zero modes, the presence of two zero modes of D ¯D is guaranteed by the index theorem in the topological charge 1/2 background. Thus, we include this discussion – 42 – only for completeness. In the later section, we shall see that these zero modes can be obtained using supersymmetry. only for completeness. In the later section, we shall see that these zero modes can be obtained using supersymmetry. The Dirac equation for the zero mode is ¯D ˙ααλα = 0 yielding The Dirac equation for the zero mode is ¯D ˙ααλα = 0 yielding 0 = ¯σn ˙αα  ∂nλ3 α −2iW ∗ nλ+ α + 2iWnλ− α  , 0 = ¯σn ˙αα  ∂nλ− α −i ¯A3 nλ− α + iW ∗ nλ3 α  , 0 = ¯σn ˙αα  ∂nλ+ α + i ¯A3 nλ+ α −iWnλ3 α  . (B.16) (B.16) JHEP01(2023)118 In our leading-order background (A.40), these equations give, for the λ3 α components: (i∂1 + ∂2)λ3 2 + (i∂3 −∂4)λ3 1 = 4γ∗F(x, z)eiαλ− 2 , −(i∂1 −∂2)λ3 2 + (i∂3 + ∂4)λ3 1 = 4γF ∗(x, z)e−iαλ+ 1 . B.2.2 The zero modes of D on the asymmetric T4 via the Dirac equation Proceeding – 43 – thus, we find the leading-order fermion zero-modes: λ3(0) α = η3 α, λ3(0) α = η3 α, λ−(0) 1 = 0, λ−(0) 2 = −η3 1γe−iα s L3L4 π p L2L4 X n1,n3 e i2π  n1 x1 L1 +n3 x3 L3  e i  z2 L2 (x2−n1L2)+ z4 L4 (x4−n3L4)  × h12 0  x2 −n1 + z1 2π  h34 1  x4 −n3 + z3 2π  , λ+(0) 1 = η3 2γ∗eiα s L3L4 π p L2L4 X n1,n3 e −i2π  n1 x1 L1 +n3 x3 L3  e −i  z2 L2 (x2−n1)+ z4 L4 (x4−n3)  × h12 0  x2 −n1 + z1 2π  h34 1  x4 −n3 + z3 2π  , λ−(0) 1 = 0, JHEP01(2023)118 λ+(0) 1 = η3 2γ∗eiα s L3L4 π p L2L4 X n1,n3 e −i2π  n1 x1 L1 +n3 x3 L3  e −i  z2 L2 (x2−n1)+ z4 L4 (x4−n3)  × h12 0  x2 −n1 + z1 2π  h34 1  x4 −n3 + z3 2π  , λ+(0) 2 = 0. (B.20) λ+(0) 2 = 0. (B.20) λ+(0) 2 = 0. (B.20) That (B.20) are solutions to order √ ∆follows by direct substitution and use of (A.27). Consider, for example, the λ− α components of the zero modes. That λ− 2 satisfies the top equation in (B.18) follows from the fact that it is acted upon by the lowering operator of the ω12 SHO, while setting λ− 1 to zero is necessitated by its being acted upon by the raising operator of the ω34 oscillator as well as by the second equation in (B.18). The lowering operator of the ω34 oscillator acting on λ− 2 from (B.20) can be easily seen to produce the r.h.s. of the second eq. in (B.18), recalling the definition of F from (A.35). One similarly verifies that λ+(0) α solve the (B.19). Before we continue, let us write the fermion zero modes (B.20) in a more compact manner, in terms of the function G(x, z) of (A.53). The fermion zero modes (B.20), that ω34 = 2π/(L3L4), are now written as: λ(0) α = η3 1 η3 2 ! τ 3 2 + η3 2 0 ! γ∗eiα s 2 ω34 G(x, z)τ + + 0 −η3 1 ! B.2.2 The zero modes of D on the asymmetric T4 via the Dirac equation γe−iα s 2 ω34 G∗(x, z)τ − = η3 1 η3 2 ! τ 3 2 + η3 2 0 ! γ∗eiα V 1 4 π 1 2 G(x, z)τ + + 0 −η3 1 ! γe−iα V 1 4 π 1 2 G∗(x, z)τ −, (B.21) with the last equality being true to leading order in √ ∆. with the last equality being true to leading order in √ ∆. with the last equality being true to leading order in √ ∆. B.2.2 The zero modes of D on the asymmetric T4 via the Dirac equation (B.17) (B.17) On the other hand, the non-Cartan λ− α components satisfy the equations  i(∂1 −i z1 L1 ) + (∂2 −i z2 L2 ) + 2π L1L2 x2  λ− 2 +  i(∂3 −i z3 L3 ) −(∂4 −i z4 L4 ) + 2π L3L4 x4  λ− 1 = 0 ,  i(∂1 −i z1 L1 ) −(∂2 −i z2 L2 ) + 2π L1L2 x2  λ− 1 −  i(∂3 −i z3 L3 ) + (∂4 −i z4 L4 ) + 2π L3L4 x4  λ− 2 = 2γF ∗(x, z)e−iαλ3 1 , (B.18)  i(∂1 −i z1 L1 ) −(∂2 −i z2 L2 ) + 2π L1L2 x2  λ− 1 −  i(∂3 −i z3 L3 ) + (∂4 −i z4 L4 ) + 2π L3L4 x4  λ− 2 = 2γF ∗(x, z)e−iαλ3 1 , (B.18) hile the λ+ α components obey while the λ+ α components obey while the λ+ α components obey  −i(∂1 + i z1 L1 ) −(∂2 + i z2 L2 ) + 2π L1L2 x2  λ+ 2 +  −i(∂3 + i z3 L3 ) + (∂4 + i z4 L4 ) + 2π L3L4 x4  λ+ 1 = 2γ∗F(x, z)eiαλ3 2 ,  i(∂1 + i z1 L1 ) −(∂2 + i z2 L2 ) − 2π L1L2 x2  λ+ 1 +  −i(∂3 + i z3 L3 ) −(∂4 + i z4 L4 ) + 2π L3L4 x4  λ+ 2 = 0 . (B.19) = 0 . We now can follow exactly the same steps as in the study of the self-duality equation for w1, see discussion after (A.17): we introduce x1, x3 Fourier modes for λ± and the functions corresponding to (A.20); likewise, we can absorb the Wilson lines by a redefinition similar to (A.23). Proceeding thus, we can now solve the undotted fermion zero mode equations (B.17), (B.18), (B.19) in an expansion in √ ∆. Keeping in mind that γ ∼ √ ∆, it follows that the solution for λ3 α is of order ∆0 and is simply given by a two-component constant Grassmann spinor η3 α. This satisfies the λ3 α equation to leading order, since the r.h.s. of (B.17) is of order ( √ ∆)2 as the λ± solutions are themselves of order √ ∆. B.2.3 Zero modes of D and ¯ D on the symmetric T4 (B.23) That these are solutions of (B.17), (B.18), (B.19) with γ = 0 follows from observing that the annihilation operators of the ω12 and ω34 SHOs act on λ+ 1 and λ− 2 components only, while the other components are acted upon by creation operators and are thus set to zero. These four zero modes of ¯D ˙αα at ∆= 0 combine with the two dotted zero modes, obeying Dα ˙α¯λ ˙α = 0, which exist due to the fact that D2 has zero modes at ∆= 0 (recall section B.2.1):41 That these are solutions of (B.17), (B.18), (B.19) with γ = 0 follows from observing that the annihilation operators of the ω12 and ω34 SHOs act on λ+ 1 and λ− 2 components only, while the other components are acted upon by creation operators and are thus set to zero. These four zero modes of ¯D ˙αα at ∆= 0 combine with the two dotted zero modes, obeying Dα ˙α¯λ ˙α = 0, which exist due to the fact that D2 has zero modes at ∆= 0 (recall section B.2.1):41 ¯λ3(∆=0) ˙α = ¯η3 ˙α, ¯λ±(∆=0) ˙α = 0. (B.24) ¯λ±(∆=0) ˙α = 0. (B.24) (B.24) The presence of two dotted (B.24) and four undotted (B.23) fermion zero modes in the self-dual background on the symmetric T4 is, of course, in accord with the index theorem. The presence of extra zero modes is the fermionic counterpart of the existence of bosonic zero modes of D2 on the symmetric T4, as discussed after eq. (B.15) of section B.2.1. As mentioned in the main text, the extra zero modes — bosonic and fermionic — are expected to be lifted once fluctuations around the self dual background on the symmetric T4 and their interactions are taken into account, but this has not been yet demonstrated. 41As in our analysis leading to the bosonic solution of eq. (A.34), one can show that there are no normalizable zero modes of D or ¯D except for (B.23), (B.24). B.2.3 Zero modes of D and ¯ D on the symmetric T4 For completeness, let us consider the fermionic zero modes of the abelian self-dual in- stanton solution of the ∆= 0 symmetric T4. For the ¯Dλ = 0 equation, we can use (B.17), (B.18), (B.19) with γ set to zero, i.e. without r.h.s. Then, it immediately – 44 – follows that the zero modes on the symmetric T4 are follows that the zero modes on the symmetric T4 are λ3(∆=0) α = η3 α, (B.22) λ3(∆=0) α = η3 α, (B.22) λ−(∆=0) 1 = 0, λ−(∆=0) 2 = η− 2 p L2L4 X n1,n3 e i2π  n1 x1 L1 +n3 x3 L3  e i  z2 L2 (x2−n1L2)+ z4 L4 (x4−n3L4)  × h12 0  x2 −n1 + z1 2π  h34 0  x4 −n3 + z3 2π  , λ+(∆=0) 1 = η+ 1 p L2L4 X n1,n3 e −i2π  n1 x1 L1 +n3 x3 L3  e −i  z2 L2 (x2−n1)+ z4 L4 (x4−n3)  × h12 0  x2 −n1 + z1 2π  h34 0  x4 −n3 + z3 2π  , λ3(∆=0) α = η3 α, (B.22) λ−(∆=0) 1 = 0, (B.22) × h12 0  x2 −n1 + z1 2π  h34 0  x4 −n3 + z3 2π  , × h12 0  x2 −n1 + z1 2π  h34 0  x4 −n3 + z3 2π  , λ+(∆=0) 1 = η+ 1 p L2L4 X n1,n3 e −i2π  n1 x1 L1 +n3 x3 L3  e −i  z2 L2 (x2−n1)+ z4 L4 (x4−n3)  × h12 0  x2 −n1 + z1 2π  h34 0  x4 −n3 + z3 2π  , λ+(∆=0) 1 = η+ 1 p L2L4 X n1,n3 e −i2π  n1 x1 L1 +n3 x3 L3  e −i  z2 L2 (x2−n1)+ z4 L4 (x4−n3)  × h12  + z1  h34  + z3  JHEP01(2023)118 × h12 0  x2 −n1 + z1 2π  h34 0  x4 −n3 + z3 2π  , λ+(∆=0) 2 = 0. (B.23) λ+(∆=0) 2 = 0. B.2.4 The zero modes of D on the asymmetric T4 via supersymmetry We now check that the asymmetric T4 undotted fermion zero modes (B.20) can be obtained via supersymmetry of the O( √ ∆) bosonic background (A.7), (A.40). Consider the effect of the SUSY transforms (B.7) in the gauge field background (A.7), (A.40) with fermions set to zero, ¯λ = λ = 0. Since our solution is self-dual, i.e. obeys ¯σmnFmn = 0, the SUSY transform only produces λα variations. Computing δλ we obtain δλ = −(σmnF (0) mn + σmnF (1) mn)ζ + . . . (B.25) δλ = −(σmnF (0) mn + σmnF (1) mn)ζ + . . . (B.25) 41As in our analysis leading to the bosonic solution of eq. (A.34), one can show that there are no normalizable zero modes of D or ¯D except for (B.23), (B.24). 41As in our analysis leading to the bosonic solution of eq. (A.34), one can show that there are no normalizable zero modes of D or ¯D except for (B.23), (B.24). – 45 – where F (0) mn is the field strength (A.8) of the abelian background (A.7), and F (1) mn is the order √ ∆contribution from (A.51), (A.52). Thus, combining everything, plugging into (B.25), and recalling Footnote 38, we obtain δλ1 δλ2 ! = −2iF (0) 12 ζ1 −ζ2 ! +2F (1) 13 ζ2 −ζ1 ! −i2F (1) 14 ζ2 ζ1 ! = i 4π √ V " ζ1 −ζ2 ! τ 3 2 + V 1 4 π 1 2 γ∗eiαG(x,z)τ + −ζ2 0 ! + V 1 4 π 1 2 γe−iαG∗(x,z)τ − 0 −ζ1 !# (B.26) On the last line, we again used the small-∆relation ω34 ≃2πV −1 2 . Comparing (B.21) with (B.26), we see that they are identical provided the supersymmetry parameter in (B.26) is identified with the Grassmann coefficient in (B.21) as follows On the last line, we again used the small-∆relation ω34 ≃2πV −1 2 . Comparing (B.21) with (B.26), we see that they are identical provided the supersymmetry parameter in (B.26) is identified with the Grassmann coefficient in (B.21) as follows JHEP01(2023)118 η3 1 = 4πiV −1 2 ζ1 , (B.27) η3 2 = −4πiV −1 2 ζ2 , (B.27) showing that all is consistent with SUSY. B.3 The moduli space metric, to any order in ∆ Here we shall study the bosonic and fermionic moduli space to order ∆. It is well known that for every zero mode solution of the undotted Dirac equation φ(β) α , one can construct two zero mode eigenvalues of the operator Onm which obey the background gauge condition Dm(Acl)am = 0. We begin with our notation for the zero modes (B.25): we shall denote the corresponding commuting wave functions by φβ A α , where A = 1, 2, 3 denotes the SU(2) algebra index. These are the two solutions of the undotted Dirac equation considered above. Thus, with (β) = 1, 2 labeling the two zero modes, we have D ˙ααφ(β) = 0 (B 28) (B.28) φ(β) α = −(σmn)(β) α Fmn , with φ(β) α = 3 X A=1 φ (β) A α T A, (B.29) φ (β) A α = −(σmnF A mn)(β) α = −2i(σ3) (β) α F A 12+2i(σ2) (β) α F A 13−2i(σ1) (β) α F A 14 (B.30) = −2i (σa) (β) α V A a ,where V A a has components V A 3 = F A 12, V A 2 = −F A 13, V A 1 = F A 14. (B.29) φ (β) A α = −(σmnF A mn)(β) α = −2i(σ3) (β) α F A 12+2i(σ2) (β) α F A 13−2i(σ1) (β) α F A 14 (B.30) = −2i (σa) (β) α V A a ,where V A a has components V A 3 = F A 12, V A 2 = −F A 13, V A 1 = F A 14. (B.30) In the second equality, we used self-duality of the background and the explicit form of σmn given in Footnote 38. B.3.1 Fermion zero-mode measure to arbitrary order in ∆ (B.34) (B.34) The Pfaffian of the fermion mode matrix is thus PfUF = −U12 F = 4 × 4π2 g2 and the fermion zero-mode measure, defined via the Pfaffian in (B.14) is The Pfaffian of the fermion mode matrix is thus PfUF = −U12 F = 4 × 4π2 g2 and the fermion zero-mode measure, defined via the Pfaffian in (B.14) is dµF = dη1dη2 (PfUF )−1 = 4 × 4π2 g2 dη1dη2 . (B.35) (B.35) To obtain a nonzero result for the fermion zero mode integral, we insert the gaugino bilinear, tr λαλα = 1 2ηαηβφ(α)A γ φ(β)A δ ϵδγ+(nonzero modes), and obtain Z dη1dη2 (PfUF )−1 tr λαλα = g2 16π2 Z dη1dη2 1 2 ηαηβφ(α)A γ φ(β)A δ ϵδγ = g2 16π2 1 2  φ(2)A γ φ(1)A δ ϵδγ −φ(1)A γ φ(2)A δ ϵδγ , (B.36) (B.36) where we used (B.34) and the explicit form of the Pfaffian. We stress that the fermion zero mode measure (B.14) as well as (B.36) hold to arbitrary order in ∆. Furthermore, the measure and the result (B.36) are independent on ∆. B.3.1 Fermion zero-mode measure to arbitrary order in ∆ B.3.1 Fermion zero-mode measure to arbitrary order in ∆ In terms of the zero modes (B.28) the fermion zero-mode expansion (B.13), relabeling the index i (used there to label the different zero modes), i →β, we have λA α = ηβφ(β) A α , sum understood over β = 1, 2, λA α = ηβφ(β) A α , sum understood over β = 1, 2, Uβγ F = 1 g2 Z T 4  φ(β) A 2 φ(γ) A 1 −φ(β) A 1 φ(γ) A 2  , λA α = ηβφ(β) A α , sum understood over β = 1, 2, Uβγ F = 1 g2 Z T 4  φ(β) A 2 φ(γ) A 1 −φ(β) A 1 φ(γ) A 2  , (B.31) Uβγ F = 1 g2 Z T 4  φ(β) A 2 φ(γ) A 1 −φ(β) A 1 φ(γ) A 2  , (B.31) (B.31) – 46 – where again A = 1, 2, 3 is the Lie algebra index, summed over the definition of UF . The fermion zero mode norm matrix Uβγ F from (B.11) is antisymmetric and we have from (B.31) and (B.28) where again A = 1, 2, 3 is the Lie algebra index, summed over the definition of UF . The fermion zero mode norm matrix Uβγ F from (B.11) is antisymmetric and we have from (B.31) and (B.28) U12 F = 1 g2 Z T 4 V A a V A b (−4) h (σa) 1 2 (σb) 2 1 −(σa) 1 1 (τ b) 2 2 i = (−4) g2 Z T 4 V A a V A b Xab . (B.32) (B.32) Consider now the matrix Xab = (σa) 1 2 (σb) 2 1 −(σa) 1 1 (σb) 2 2 implicitly defined above. We have, from the explicit form of the Pauli matrices: JHEP01(2023)118 ||Xab|| =    1 −i 0 i 1 0 0 0 1   , (B.33) (B.33) thus U12 F = −4 g2 Z T 4 V A a V A a = −4 g2 Z T 4 F A 12 2 + F A 14 2 + F A 13 2 = −1 g2 Z T 4(F A mn)2 = −4 4π2 g2 since 1 4g2 Z T 4 F A mn 2 = 4π2 g2 ! . B.3.2 Bosonic zero-modes and moduli-space metric to any order in ∆ Now to the wave functions of the bosonic zero modes obtained from the fermionic modes and automatically obeying the gauge condition. For every fermionic zero mode φ (β) α , β = 1, 2, there are two bosonic zero modes. Thus, in total there are four independent bosonic zero modes. The advantage of the discussion that follows is that the bosonic zero modes thus obtained automatically obey the gauge condition and, furthermore, that their construction holds to arbitrary orders in ∆. – 47 – The four-vector expressions for the bosonic zero modes thus obtained are denoted by Z(β) A n and Z(β ′) A n , where β = 1, 2, A = 1, 2, 3. These modes are determined as follows (see e.g. [25, 26]). First one forms the quaternions made out of the zero-mode solutions of the undotted Dirac equation, explicitly: σnZ(β) A n = Z(β) 4 + iZ(β) 3 Z(β) 2 + iZ(β) 1 −Z(β) 2 + iZ(β) 1 Z(β) 4 −iZ(β) 3 !A = φ(β) 1 −φ(β) ∗ 2 φ(β) 2 φ(β) ∗ 1 !A , σnZ(β ′) A n = Z(β ′) 4 + iZ(β ′) 3 Z(β ′) 2 + iZ(β ′) 1 −Z(β ′) 2 + iZ(β ′) 1 Z(β ′) 4 −iZ(β ′) 3 !A = iφ(β) 1 iφ(β) ∗ 2 iφ(β) 2 −iφ(β) ∗ 1 !A . (B.37) (B.37) JHEP01(2023)118 Thus, each zero mode φ(β) α of the undotted Dirac equation can be used to build two four- vector bosonic zero modes, denoted by Z(β) n and Z(β ′) n . Their four-vector components are then inferred from (B.37): Z(β) A n = n ℑφ(β) A 2 , −ℜφ(β) A 2 , ℑφ(β) A 1 , ℜφ(β) A 1 o , Z(γ ′) A n = n ℜφ(γ) A 2 , ℑφ(γ) A 2 , ℜφ(γ) A 1 , −ℑφ(γ) A 1 o . (B.38) (B.38) Now, knowing the four-vector components of the zero modes, we can use (B.37) and (B.28) to find det Ukl and argue for its ∆-independence. We need to compute the 4 × 4 matrix of different overlaps (B.3) Now, knowing the four-vector components of the zero modes, we can use (B.37) and (B.28) to find det Ukl and argue for its ∆-independence. B.3.2 Bosonic zero-modes and moduli-space metric to any order in ∆ We need to compute the 4 × 4 matrix of different overlaps (B.3) Uβ,γ = 2 g2 Z T 4 tr Z(β) n Z(γ) n = 1 g2 Z T 4 Z(β) A n Z(γ) A n Uβ,γ+2 = Uγ+2,β = 2 g2 Z T 4 tr Z(β) n Z(γ ′) n = 1 g2 Z T 4 Z(β) A n Z(γ ′) A n , Uβ+2,γ+2 = 2 g2 Z T 4 tr Z(β ′) n Z(γ ′) n = 1 g2 Z T 4 Z(β ′) A n Z(γ ′) A n , (B.39) (B.39) where the trace is now in the Lie-algebra generator space. The four-vector inner products are Z(β) n Z(γ) n = Z(β ′) n Z(γ ′) n = ℑφ(β) 2 ℑφ(γ) 2 + ℜφ(β) 2 ℜφ(γ) 2 + ℑφ(β) 1 ℑφ(γ) 1 + ℜφ(β) 1 ℜφ(γ) 1 = 2 X α=1 1 2  φ(β) α φ(γ) ∗ α + φ(β) ∗ α φ(γ) α  , Z(β) n Z(γ ′) n = ℑφ(β) 2 ℜφ(γ) 2 −ℜφ(β) 2 ℑφ(γ) 2 + ℑφ(β) 1 ℜφ(γ) 1 −ℜφ(β) 1 ℑφ(γ) 1 = 2 X α=1 i 2  φ(β) α φ(γ) ∗ α −φ(β) ∗ α φ(γ) α  , (B.40 (B.40) where momentarily we omitted the group index A (to be restored below). Thus, using (B.28), where momentarily we omitted the group index A (to be restored below). Thus, using (B.28), – 48 – with the shorthand σ.F A ≡σmnF A mn, we find with the shorthand σ.F A ≡σmnF A mn, we find with the shorthand σ.F A ≡σmnF A mn, we find Uβ,γ = Uβ+2,γ+2 = 1 2g2 Z T 4 2 X α=1  φ(β) A α φ(γ) ∗A α + φ(β) ∗A α φ(γ) A α  = 1 2g2 Z T 4 2 X α=1 σ.F A (β) α σ.F A (γ) ∗ α + σ.F A (β) ∗ α σ.F A (γ) α  , Uβ,γ+2 = Uγ+2,β = i 2g2 Z T 4 2 X α=1  φ(β) A α φ(γ) ∗A α −φ(β) ∗A α φ(γ) A α  = i 2g2 Z T 4 2 X α=1 σ.F A (β) α σ.F A (γ) ∗ α − σ.F A (β) ∗ α σ.F A (γ) α  . 42The reader may notice that while we use the same letter, the moduli space metric U kl of (B.45) does not equal the one constructed earlier from the leading-order derivatives of the classical solution w.r.t. zn, the metric U kl of eqs. (B.3), (B.4). In fact, we have g8 det U kl eq. (B.45) = (4π)8 while g8 det U kl eq. (B.4) = V 2. This is accounted for by the difference in normalization of the respective zero modes; see section B.3.3 for explicit expressions. This difference contributes an extra factor of ( 4π √ V )8 Q k(L2 k) = (4π)8 V 2 to the determinant of eq. (B.4). B.3.2 Bosonic zero-modes and moduli-space metric to any order in ∆ JHEP01(2023)118 (B.41) (B.41) (B.41) ( ) Let us now study the matrix Let us now study the matrix Let us now study the matrix Aβγ = 1 2g2 Z T 4 2 X α=1 (σ.F A) (β) α (σ.F A) (γ) ∗ α . (B.42) (B.42) Using the notation of eq. (B.28), we rewrite it as Using the notation of eq. (B.28), we rewrite it as Using the notation of eq. (B.28), we rewrite it as Aβγ = 1 2g2 Z T 4 V A a V A b 4 (σa) (β) α ((σb)∗) (γ α ) = 2 g2 Z T 4 V A a V A b (σ2σaσbσ2) (γ) (β) = δγ β 2 g2 Z T 4 V A a V A a = 1 2g2 Z T 4(F A mn)2 . ( (B.43) Thus, the 4 × 4 matrix U with matrix elements (B.41), expressed through A of (B.42) is of the form U =       A11 + A∗ 11 A12 + A∗ 12 i(A11 −A∗ 11) i(A12 −A∗ 12) A12 + A∗ 12 A22 + A∗ 22 i(A12 −A∗ 12) i(A22 −A∗ 22) i(A11 −A∗ 11) i(A12 −A∗ 12) A11 + A∗ 11 A12 + A∗ 12 i(A12 −A∗ 12) i(A22 −A∗ 22) A12 + A∗ 12 A22 + A∗ 22       =       2A11 0 0 0 0 2A22 0 0 0 0 2A11 0 0 0 0 2A22       = diag(1, 1, 1, 1) 1 g2 Z T 4(F A mn)2 = diag(1, 1, 1, 1) 4 4π2 g2 since 1 4g2 Z T 4 F A mn 2 = 4π2 g2 ! , (B.44) (B.44) where we used the diagonal form of A form (B.43). where we used the diagonal form of A form (B.43). Thus, we have for the norm matrix (B.3) of the bosonic zero modes (to any arbitrary order in ∆to which the solution has been find): Ukl = δkl 4 4π2 g2 , k, l = 1, 2, 3, 4. q ( ) 43As these can be constructed from F cl. mn to any order in ∆, we shall call these “exact” zero modes. B.3.2 Bosonic zero-modes and moduli-space metric to any order in ∆ (B.45) (B.45) – 49 – – 49 – The point, so far, is to argue that the inner-product of the bosonic zero modes obeying the gauge condition — or the moduli space metric (B.45)—are ∆-independent.42 The careful reader may remark that the fact that the bosonic zero mode metric is proportional to the classical action, as in (B.45), is well-known, hence the ∆-independence follows from the fact that the action of the self-dual solution is ∆-independent. However, we presented the steps outlined above, especially the explicit relation between the undotted Dirac equation zero modes and the bosonic zero modes of eq. (B.38), in order to use them to verify that the derivatives of the O( √ ∆) classical solution we found with respect to zn are equal to the modes (B.38) obeying the background gauge condition, after an appropriate gauge transformation. This somewhat more involved procedure, compared to the similar task for the BPST instanton, is what we discuss next. JHEP01(2023)118 B.3.3 The derivatives of the O( √ ∆) solution and the gauge condition To this end, let us compute the zero modes (B.38) in the ∆expansion and compare to the derivatives of the classical solution, ∂Acl n /∂zk. The zero modes (B.38) obeying the gauge condition43 are determined by the matrices (B.28) ||ℜφ(β) A α || = 0 2F A 13 −2F A 13 0 ! , ||ℑφ(β) A α || = −2F A 12 −2F A 14 −2F A 14 2F A 12 ! . (B.46) (B.46) This yields for Z(β) n , Z(β)′ n of (B.38), This yields for Z(β) n , Z(β)′ n of (B.38), This yields for Z(β) n , Z(β)′ n of (B.38), This yields for Z(β) n , Z(β)′ n of (B.38), Y (3) A n ≡Z(1) A n = n ℑφ(1) A 2 ,−ℜφ(1) A 2 ,ℑφ(1) A 1 ,ℜφ(1) A 1 o = n −2F A 14,2F A 13,−2F A 12,0 o , Y (1) A n ≡−Z(2) A n = n −ℑφ(2) A 2 ,ℜφ(2) A 2 ,−ℑφ(2) A 1 ,−ℜφ(2) A 1 o = n −2F A 12,0,2F A 14,−2F A 13 o , Y (4) A n ≡−Z(1 ′) A n = n −ℜφ(1) A 2 ,−ℑφ(1) A 2 ,−ℜφ(1) A 1 ,ℑφ(1) A 1 o = n 2F A 13,2F A 14,0,−2F A 12 o , Y (2) A n ≡−Z(2 ′) A n = n −ℜφ(2) A 2 ,−ℑφ(2) A 2 ,−ℜφ(2) A 1 ,ℑφ(2) A 1 o = n 0,−2F A 12,−2F A 13,−2F A 14 o . (B.47) We relabelled the four zero modes Z(1) n , Z(2) n , Z(1)′ n , Z(2)′ n by Y (k) n , where k indicates that in our ∆-expanded solution these correspond to derivatives of the classical background with respect to zk (as we shall see shortly). The functions Y (k) n calculated in the leading ∼ √ ∆ solution are explicitly presented below. B.3.3 The derivatives of the O( √ ∆) solution and the gauge condition – 50 – Let us now also write our ∼ √ ∆self dual classical solution (A.40): Acl n (x, z) = 2πnnmxm LnLm + zn Ln  τ 3 2 + τ +(δn1 + iδn2)W + τ −(δn1 −iδn2)W ∗, Acl n (x, z) = 2πnnmxm LnLm + zn Ln  τ 3 2 + τ +(δn1 + iδn2)W + τ −(δn1 −iδn2)W ∗, W i √ π∆ iαF( ) ( Acl n (x, z) = 2πnnmxm LnLm + zn Ln  τ 3 2 + τ +(δn1 + iδn2)W + τ −(δn1 −iδn2)W ∗, W = −i √ π∆ √ 2V 1/2 eiαF(x, z), (B.4 W = −i √ π∆ √ 2V 1/2 eiαF(x, z), (B.48) (B.48) where for brevity we introduced the (not anti-symmetric!) tensor nnm where only n12 = n34 = 1 are nonzero. Consider now the derivative of the classical solution w.r.t. zp/Lp Lp ∂Acl n ∂zp = δnp τ 3 2 + τ +(δn1 + iδn2)Lp∂W ∂zp + τ −(δn1 −iδn2)Lp∂W ∗ ∂zp ). (B.49) Lp ∂Acl n ∂zp = δnp τ 3 2 + τ +(δn1 + iδn2)Lp∂W ∂zp + τ −(δn1 −iδn2)Lp∂W ∗ ∂zp ). (B.49) (B.49) JHEP01(2023)118 JHEP01(2023)118 The Cartan term is the one we considered before, see section B. To find the zero mode wave functions, an explicit computation using the SHO h0 and h1 properties from (A.27) shows that L1 ∂F ∂z1 = − s L1L2 4π ˜G , L2 ∂F ∂z2 = iL2z1 2π F −i s L1L2 4π ˜G , L3 ∂F ∂z3 = − s L3L4 4π G , L4 ∂F ∂z4 = iL4z3 2π F −i s L3L4 4π G . (B.50) (B.50) Here, we defined, in addition to F(x, z) (A.35) and G(x, z) (A.53), a new function ˜G(x, z), similar to G(x, z) but where the 1st-excited state is in the ω12 SHO instead: ˜G (x, z) = p L2L4 ∞ X n1,n3=−∞ e −i2π  n1 x1 L1 +n3 x3 L3  e−i z2 L2 (x2−n1L2)−i z4 L4 (x4−n3L4) ˜G (x, z) = p L2L4 ∞ X n1,n3=−∞ e −i2π  n1 x1 L1 +n3 x3 L3  e−i z2 L2 (x2−n1L2)−i z4 L4 (x4−n3L4) × h12 1  x2 −  n1 −z1 2π  L2  h34 0  x4 −  n3 −z3 2π  L4  . B.3.3 The derivatives of the O( √ ∆) solution and the gauge condition (B.51) × h12 1  x2 −  n1 −z1 2π  L2  h34 0  x4 −  n3 −z3 2π  L4  . (B.51) (B.51) Using these expressions, we find the derivatives of the classical solution w.r.t. zp: L1 ∂Acl n ∂z1 = δn1 τ 3 2 + " τ + (δn1 + iδn2) i √ ∆ 2 √ 2 eiα ˜G + h.c. # , L2 ∂Acl n ∂z2 = δn2 τ 3 2 +  τ + (δn1 + iδn2) −i √ π∆ √ 2V 1/2 eiα !  iL2z1 2π F −i s L1L2 4π ˜G  + h.c.  , L3 ∂Acl n ∂z3 = δn3 τ 3 2 + " τ + (δn1 + iδn2) i √ ∆ 2 √ 2 eiαG + h.c. # , L4 ∂Acl n ∂z4 = δn4 τ 3 2 +  τ + (δn1 + iδn2) −i √ π∆ √ 2V 1/2 eiα !  iL4z3 2π F −i s L3L4 4π G  + h.c.  . (B.52) ∂z4 2  √ 2V 1/2 !  2π s 4π   (B.52) – 51 – The expressions for the exact zero modes Y (k) n from (B.47) can also be computed using our knowledge of the field strength to order √ ∆, F (0) mn, F (1) mn of eqs. (A.8) and (A.52). Next, we use this information and (B.52) to determine the gauge transformations needed to bring the Lk ∂Acl n ∂zk zero modes into the background-Lorentz gauge. We shall see that on the T4 with twists, this is slightly different from the usual BPST instanton. To find these gauge transformations, we now consider the derivatives of the classical solution w.r.t. each zk in turn. Zero mode ∂ ∂z1 vs Y (1): here, we compare Y (1) n to the derivative w.r.t. z1. From the above we find that the four-vectors of the exact zero mode and the derivative of the classical solution are JHEP01(2023)118 Y (1) n = ( 4π √ V τ 3 2 , 0, τ + −i √ 2∆π √ V eiαG(x, z) ! + h.c., τ + √ 2∆π √ V eiαG(x, z) + h.c. ) , L1 ∂Acl n ∂z1 = ( τ 3 2 + τ + i √ ∆ 2 √ 2 eiα ˜G + h.c. ! B.3.3 The derivatives of the O( √ ∆) solution and the gauge condition (B.57) (B.57) Here, in contrast with (B.55), we find that the gauge transformation making the zero mode obey the background condition also has a Cartan-subalgebra piece ∼∆0, in addition to an O( √ ∆) piece which is proportional to (B.55): Here, in contrast with (B.55), we find that the gauge transformation making the zero mode obey the background condition also has a Cartan-subalgebra piece ∼∆0, in addition to an O( √ ∆) piece which is proportional to (B.55): JHEP01(2023)118 Λ(2)(x, z) = 2L2z1 √ V τ 3 2 + iΛ(1)+(x, z)τ + + h.c.  . (B.58) (B.58) Naturally, only terms of order √ ∆are to be kept on the r.h.s. of (B.57). Zero mode ∂ ∂z3 vs Y (3) : remarkably, here we find Y (3) n −4π √ V L3 ∂Acl n ∂z3 = 0 =⇒Λ(3) = 0, (B.59) (B.59) hence no compensating gauge transform is needed. This follows from the four-vector expressions for the zero modes Y (3) n = ( i √ 2∆π √ V eiαGτ + + h.c., − √ 2∆π √ V eiαGτ + + h.c., 4π √ V τ 3 2 , 0 ) , (B.60) L3 ∂Acl n ∂z3 = ( i √ ∆ 2 √ 2eiαGτ + + h.c., − √ ∆ 2 √ 2eiαGτ + + h.c., τ 3 2 , 0 ) . (B.61) (B.60) and and L3 ∂Acl n ∂z3 = ( i √ ∆ 2 √ 2eiαGτ + + h.c., − √ ∆ 2 √ 2eiαGτ + + h.c., τ 3 2 , 0 ) . (B.61) (B.61) Notice that x3 is the direction where Acl depends on x4 + z3L4/(2π) and where the classical √ ∆solution vanishes. Notice that x3 is the direction where Acl depends on x4 + z3L4/(2π) and where the classical √ ∆solution vanishes. B.3.3 The derivatives of the O( √ ∆) solution and the gauge condition , − τ + √ ∆ 2 √ 2eiα ˜G + h.c. ! , 0, 0 ) . (B.53) ( ! ! ) Their difference is  i ˜G( )  Their difference is Their difference is Their difference is Their difference is Y (1) n −4π √ V L1 ∂Acl n ∂z1 = τ + π √ 2∆eiα V 1/2       −i ˜G(x, z) ˜G(x, z) −iG(x, z) G(x, z)       + h.c. = Dn(Acl.)Λ(1) = ∂nΛ(1) + i h Acl. n ∆=0, Λ(1)i . (B.54) (B.54) After some algebra, we find that the gauge transformation making the derivative of the classical solution obey the gauge condition is O( √ ∆): After some algebra, we find that the gauge transformation making the derivative of the classical solution obey the gauge condition is O( √ ∆): Λ(1)(x, z) = − √ 2∆π V 1 4 eiαF(x, z)τ + + h.c. . (B.55) (B.55) Zero mode ∂ ∂z2 vs Y (2): here we have the four-vectors Y (2) n = ( 0, 4π √ V τ 3 2 , τ + √ 2∆π √ V eiαG(x, z) + h.c., τ + i √ 2∆π √ V eiαG(x, z) + h.c. ) , L2 ∂Acl n ∂z2 =   τ + √ ∆πeiα √ 2V 1 4  L2z1 2π F(x, z) − s L1L2 4π ˜G(x, z)  + h.c., τ 3 2 + τ +i √ ∆πeiα √ 2V 1 4  L2z1 2π F(x, z) − s L1L2 4π ˜G(x, z)  + h.c., 0, 0   . (B.56) (B.56) – 52 – – 52 – We again consider the difference We again consider the difference We again consider the difference Y (2) n −4π √ V L2 ∂Acl n ∂z2 = τ + π √ 2∆eiα √ V          −2√π V 1 4  L2z1 2π F(x, z) − q L1L2 4π ˜G(x, z)  −i2√π V 1 4  L2z1 2π F(x, z) − q L1L2 4π ˜G(x, z)  G(x, z) iG(x, z)          + h.c. = Dn(Acl.)Λ(2) = ∂nΛ(2) + i h Acl. n ∆=0 + Acl. n O( √ ∆), Λ(2)i . B.3.3 The derivatives of the O( √ ∆) solution and the gauge condition Zero mode ∂ ∂z4 vs Y (4): here, the four-vectors of the exact zero mode and the derivative of the classical solution are Y (4) n = ( − √ 2∆π √ V eiαGτ + + h.c., −i √ 2∆π √ V eiαGτ + + h.c., 0, 4π √ V τ 3 2 ) , (B.62) (B.62) and and L4 ∂Acl n ∂z4 =    √ π∆ √ 2V 1/2 eiα  L4z3 2π F − s L3L4 4π G  τ + + h.c., i √ π∆ √ 2V 1/2 eiα  L4z3 2π F − s L3L4 4π G  τ + + h.c., 0, τ 3 2   . (B.63)  √ 2V 1/2  2π s 4π  i √ π∆ √ 2V 1/2 eiα  L4z3 2π F − s L3L4 4π G  τ + + h.c., 0, τ 3 2   . (B.63) (B.63) – 53 – Their difference is Their difference is Their difference is Y (4) n −4π √ V L4 ∂Acl n ∂z4 = −τ + √ 2π∆ V 1/2 eiα L4z3 V 1 4       F(x, z) iF(x, z) 0 0       + h.c. = Dn(Acl.)Λ(4) = ∂nΛ(4) + i h Acl. n ∆=0 + Acl. n O( √ ∆), Λ(4)i . (B.64) (B.64) Here, we have that Λ(4)(x, z) = 2L4z3 √ V τ 3 2 (B.65) (B.65) JHEP01(2023)118 only has a ∆= 0 part. The claim that Λ(4) obeys (B.64) is straightforwardly verified Summary: in each case we have verified that to order √ ∆, 4π √ V Lk ∂Acl n ∂zk + Dn(Acl)Λ(k) = Y (k) n (B.66) (B.66) obeys the background gauge condition, where Λ(k), for k = 1, 2, 3, 4, are given in ((B.55), (B.58), (B.59), (B.65)), respectively. As follows from these explicit expressions, the gauge transformation Λ(k) which makes the derivative of the classical solution obey the background- gauge condition is Ω-periodic (recall the definition after (A.5)), i.e. obeys the same periodicity conditions (A.4) as the classical solution. In fact, the x-dependent part of Λ(k) is expressed through the O( √ ∆) component of the classical solution Acl k , similar to the BPST case. The Ω-periodicity of Λ(k) is important in what follows. B.3.3 The derivatives of the O( √ ∆) solution and the gauge condition We shall next argue that the measure in terms of the zn variables remains the one we found earlier by studying the leading-order zero modes, eq. (B.5). For use below, we also rewrite the zero modes (B.66) as ∂Acl n ∂zk + Dn(Acl)˜Λ(k) = √ V 4πLk Y (k) n . (B.67) (B.67) The motivation for the rescaling evident in (B.67) is that the zero modes are now directly proportional to the derivatives of Acl n with respect to zk. The compensating gauge transfor- mation ˜Λ(k) = √ V 4πLk Λ(k) is trivially related to Λ(k) appearing in (B.66) and appearing in ((B.55), (B.58), (B.59), (B.65)). The motivation for the rescaling evident in (B.67) is that the zero modes are now directly proportional to the derivatives of Acl n with respect to zk. The compensating gauge transfor- mation ˜Λ(k) = √ V 4πLk Λ(k) is trivially related to Λ(k) appearing in (B.66) and appearing in ((B.55), (B.58), (B.59), (B.65)). 44Of eigenvalues ωq, using the same notation as after eq. (B.2): OmnZ(q) n = ωqZ(q) n . 46Evaluating R T4 Acl. n Y (k) n using the explicit expressions of section B.3.3 and plugging into (B.70), we find that to leading-order in ∆the zero of fk occurs for zk = z∗ k, where z∗ k = −π(δk3 + δk4) + Lk ˜A3 k + O( √ ∆). Here, ˜A3 k is the constant T4-mode of the Cartan component of An. 45Recalling that (B.45) calculated Ukl = 2 g2 R T4 tr Y (k) n Y (l) n = 16π2 g2 δkl. (k) B.3.4 The Jacobian and the all-order bosonic measure We begin by shifting the bosonic field An(x), obeying (A.4), to be integrated over in the path integral by the classical solution Acl. n (x, z) of (B.48). We can choose to expand the fluctuation in terms of a complete set of eigenfunctions of the hermitean operator Omn(x, z) — the zero modes (B.67) and the nonzero modes Zq n:44 An(x) −Acl. n (x, z) = 4 X k=1 ζ(0) k √ V 4πLk Y (k) n (x, z) + X q ζq Z(q) n (x, z). (B.68) (B.68) 44Of eigenvalues ωq, using the same notation as after eq. (B.2): OmnZ(q) n = ωqZ(q) n . – 54 – The coefficients ζ(0) k and ζq are the projections of the gauge field fluctuation An(x) − Acl. n (x, z) onto the Y (k)(x, z) and Zq(x, z) directions in field space, thus they have implicit zk-dependence. In what follows, we trade the integration over ζ(0) k for integration over the zk. In our subsequent discussion we shall not explicitly write the contribution of the nonzero modes to the measure of the path integral, due to their cancellation with the contribution of the nonzero modes of the fermions and ghosts. With the expansion (B.68), the measure of the bosonic zero modes now takes the form, using (B.45)45 and taking into account the normalization of the zero modes dµB =  det V 16π2LkLl Ukl eq. (B.45)  1 2 4 Y k=1 " dζ(0) k √ 2π # = V g4 4 Y k=1 dζ(0) k √ 2π . (B.69) JHEP01(2023)118 JHEP01(2023)118 (B.69) In order to integrate over fields orthogonal to the Y (k) n (x, z) zero modes, we consider their inner product with (B.68) fk = 2 g2 tr Z T4(An(x) −Acl. n (x, z)) Y (k) n (x, z). B.3.4 The Jacobian and the all-order bosonic measure (B.70) (B.70) We then insert unity in the path integral, in the form 1 = Y k dzk Y p δ(fp) | det ∂fk ∂zl | , (B.71) (B.71) where ∂fk ∂zl is evaluated at the value of zn making delta function vanish.46 Then, using (B.68), the orthogonality of the zero and nonzero modes, we have that (B.45), that fp = √ V 4πLp 16π2 g2 ζ(0) p , (B.72) (B.72) so that the δ-function from (B.71) sets ζ(0) k = 0 after integrating over ζ(0) k with the measure (B.69) (to avoid confusion, recall that ζ(0) k has implicit z-dependence). On the other hand evaluating the derivative of (B 70) we find so that the δ-function from (B.71) sets ζ(0) k = 0 after integrating over ζ(0) k with the measure (B.69) (to avoid confusion, recall that ζ(0) k has implicit z-dependence). O th th h d l ti th d i ti f (B 70) fid On the other hand, evaluating the derivative of (B.70), we find ∂fk ∂zl = 2 g2 Z T4 tr ∂(An −Acl n ) ∂zl Y (k) n + (An −Acl n )∂Y (k) n ∂zl ! = 2 g2 Z T4 tr −∂Acl. n ∂zl Y (k) n + (An −Acl n )∂Y (k) n ∂zl ! . Next, we use (B.67) to replace ∂Acl. n ∂zl by Y (k) n . Using the fact that ˜Λ(k) is Ω-periodic allows us to integrate by parts on T4 without a boundary term, i.e. set R T4 tr Dn˜Λ(l) Y (k) n = 0, 45Recalling that (B.45) calculated Ukl = 2 g2 R T4 tr Y (k) n Y (l) n = 16π2 g2 δkl. l (k) 46Evaluating R T4 Acl. n Y (k) n using the explicit expressions of section B.3.3 and plugging into (B.70), we find that to leading-order in ∆the zero of fk occurs for zk = z∗ k, where z∗ k = −π(δk3 + δk4) + Lk ˜A3 k + O( √ ∆). Here, ˜A3 k is the constant T4-mode of the Cartan component of An. – 55 – since Y (k) n obeys the background gauge condition. We thus find ∂fk ∂zl = 2 g2 Z T4 tr − √ V 4πLl Y (l) n Y (k) n + (An −Acl n )∂Y (k) n ∂zl ! B.3.4 The Jacobian and the all-order bosonic measure = − √ V 4πLl 16π2 g2 δkl + 2 g2 Z T4 tr (An −Acl n )∂Y (k) n ∂zl . (B.73) (B.73) Thus, the unity insertion (B.71) becomes Thus, the unity insertion (B.71) becomes 1 = Y k dzk δ ζ(0) k √ V 4πLk 16π2 g2 ! det √ V 4πLl 16π2 g2 δkl −2 g2 Z T4 tr ζqZ(q) n ∂Y (k) n ∂zl ! , (B.74) (B.74) JHEP01(2023)118 where we used (B.68) and took the liberty to set ζ(0) k = 0 in the determinant, due to integrating the delta function with the measure (B.69). The nonzero mode part of the fluctuations can be ignored to leading order. Thus, collecting everything, we find that the Jacobian factors from the delta function and the determinant in (B.74) cancel out and the bosonic measure (B.69) becomes, after inserting (B.74) and integrating over ζ(0) k , where we used (B.68) and took the liberty to set ζ(0) k = 0 in the determinant, due to integrating the delta function with the measure (B.69). The nonzero mode part of the fluctuations can be ignored to leading order. Thus, collecting everything, we find that the Jacobian factors from the delta function and the determinant in (B.74) cancel out and the bosonic measure (B.69) becomes, after inserting (B.74) and integrating over ζ(0) k , dµB = V g4 4 Y k=1 dzk √ 2π . (B.75) (B.75) The bosonic zero mode measure is thus equal to the leading-order measure constructed earlier in (B.5). Open Access. This article is distributed under the terms of the Creative Commons Attribution License (CC-BY 4.0), which permits any use, distribution and reproduction in any medium, provided the original author(s) and source are credited. SCOAP3 supports the goals of the International Year of Basic Sciences for Sustainable Development. References [1] M. Garcia Perez, A. González-Arroyo and C. Pena, Perturbative construction of selfdual configurations on the torus, JHEP 09 (2000) 033 [hep-th/0007113] [INSPIRE]. [1] M. Garcia Perez, A. González-Arroyo and C. Pena, Perturbative construction of selfdual configurations on the torus, JHEP 09 (2000) 033 [hep-th/0007113] [INSPIRE]. [2] D. Gaiotto, A. Kapustin, N. Seiberg and B. Willett, Generalized Global Symmetries, JHEP 02 (2015) 172 [arXiv:1412.5148] [INSPIRE]. [2] D. Gaiotto, A. Kapustin, N. Seiberg and B. Willett, Generalized Global Symmetries, JHEP 02 (2015) 172 [arXiv:1412.5148] [INSPIRE]. [3] D. Gaiotto, A. Kapustin, Z. Komargodski and N. Seiberg, Theta, Time Reversal, and Temperature, JHEP 05 (2017) 091 [arXiv:1703.00501] [INSPIRE]. [3] D. Gaiotto, A. Kapustin, Z. Komargodski and N. Seiberg, Theta, Time Reversal, and Temperature, JHEP 05 (2017) 091 [arXiv:1703.00501] [INSPIRE]. [4] Y. Tanizaki, Anomaly constraint on massless QCD and the role of Skyrmions in chiral symmetry breaking, JHEP 08 (2018) 171 [arXiv:1807.07666] [INSPIRE]. [4] Y. Tanizaki, Anomaly constraint on massless QCD and the role of Skyrmions in chiral symmetry breaking, JHEP 08 (2018) 171 [arXiv:1807.07666] [INSPIRE]. [5] M.M. Anber and E. Poppitz, On the baryon-color-flavor (BCF) anomaly in vector-like theories, JHEP 11 (2019) 063 [arXiv:1909.09027] [INSPIRE]. [5] M.M. Anber and E. Poppitz, On the baryon-color-flavor (BCF) anomaly in vector-like theories, JHEP 11 (2019) 063 [arXiv:1909.09027] [INSPIRE]. [6] S. Bolognesi, K. Konishi and A. Luzio, Gauging 1-form center symmetries in simple SU(N) gauge theories, JHEP 01 (2020) 048 [arXiv:1909.06598] [INSPIRE]. [6] S. Bolognesi, K. Konishi and A. Luzio, Gauging 1-form center symmetries in simple SU(N) gauge theories, JHEP 01 (2020) 048 [arXiv:1909.06598] [INSPIRE]. [7] M.M. Anber and E. Poppitz, Generalized ’t Hooft anomalies on non-spin manifolds, JHEP 04 (2020) 097 [arXiv:2002.02037] [INSPIRE]. [7] M.M. Anber and E. Poppitz, Generalized ’t Hooft anomalies on non-spin manifolds, JHEP 04 (2020) 097 [arXiv:2002.02037] [INSPIRE]. – 56 – [8] T. Sulejmanpasic, Y. Tanizaki and M. Ünsal, Universality between vector-like and chiral quiver gauge theories: Anomalies and domain walls, JHEP 06 (2020) 173 [arXiv:2004.10328] [INSPIRE]. [9] M.M. Anber, Self-conjugate QCD, JHEP 10 (2019) 042 [arXiv:1906.10315] [INSPIRE]. [10] N. Lohitsiri and T. Sulejmanpasic, Comments on QCD3 and anomalies with fundamental and adjoint matter, JHEP 10 (2022) 081 [arXiv:2205.07825] [INSPIRE]. [11] S. Bolognesi, K. Konishi and A. Luzio, Dynamics from symmetries in chiral SU(N) gauge theories, JHEP 09 (2020) 001 [arXiv:2004.06639] [INSPIRE]. [12] M.M. Anber, S. Hong and M. References Son, New anomalies, TQFTs, and confinement in bosonic chiral gauge theories, JHEP 02 (2022) 062 [arXiv:2109.03245] [INSPIRE]. JHEP01(2023)118 JHEP01(2023)118 [13] A. Kapustin and N. Seiberg, Coupling a QFT to a TQFT and Duality, JHEP 04 (2014) 001 [arXiv:1401.0740] [INSPIRE]. [14] G. ’t Hooft, A Property of Electric and Magnetic Flux in Nonabelian Gauge Theories, Nucl. Phys. B 153 (1979) 141 [INSPIRE]. [15] G. ’t Hooft, Some Twisted Selfdual Solutions for the Yang-Mills Equations on a Hypertorus, Commun. Math. Phys. 81 (1981) 267 [INSPIRE]. [16] E. Witten, Constraints on supersymmetry breaking, Nucl. Phys. B 202 (1982) 253. [17] V.A. Novikov, M.A. Shifman, A.I. Vainshtein and V.I. Zakharov, Instanton Effects in Supersymmetric Theories, Nucl. Phys. B 229 (1983) 407 [INSPIRE]. [18] G.C. Rossi and G. Veneziano, Nonperturbative Breakdown of the Nonrenormalization Theorem in Supersymmetric QCD, Phys. Lett. B 138 (1984) 195 [INSPIRE]. [19] D. Amati, G.C. Rossi and G. Veneziano, Instanton Effects in Supersymmetric Gauge Theories, Nucl. Phys. B 249 (1985) 1 [INSPIRE]. [20] I. Affleck, M. Dine and N. Seiberg, Supersymmetry Breaking by Instantons, Phys. Rev. Lett. 51 (1983) 1026. [21] V.A. Novikov, M.A. Shifman, A.I. Vainshtein and V.I. Zakharov, Supersymmetric Instanton Calculus (Gauge Theories with Matter), Nucl. Phys. B 260 (1985) 157 [INSPIRE]. [22] D. Amati, K. Konishi, Y. Meurice, G. Rossi and G. Veneziano, Non-perturbative aspects in supersymmetric gauge theories, Phys. Rept. 162 (1988) 169. [23] M.A. Shifman and A.I. Vainshtein, Instantons versus supersymmetry: Fifteen years later, in ITEP lectures on particle physics and field theory. Vol. 1, 2, World Scientific Lecture Notes in Physics 62, World Scientific (1999), pp. 485–647 [hep-th/9902018] [INSPIRE]. [24] M.A. Shifman, Exact results in gauge theories: Putting supersymmetry to work. The 1999 Sakurai Prize Lecture, Int. J. Mod. Phys. A 14 (1999) 5017 [hep-th/9906049]. [25] N. Dorey, T.J. Hollowood, V.V. Khoze and M.P. Mattis, The Calculus of many instantons, Phys. Rept. 371 (2002) 231 [hep-th/0206063] [INSPIRE]. [26] S. Vandoren and P. van Nieuwenhuizen, Lectures on instantons, arXiv:0802.1862 [INSPIRE [27] J. Terning, Modern Supersymmetry: Dynamics and duality, Oxford University Press (2005), [DOI]. [28] A. Belavin, A. Polyakov, A. Schwartz and Y. Tyupkin, Pseudoparticle solutions of the Yang-Mills equations, Phys. Lett. B 59 (1975) 85. – 57 – [29] S.F. Cordes, The Instanton Induced Superpotential in Supersymmetric QCD, Nucl. Phys. B 273 (1986) 629 [INSPIRE]. [30] D. Finnell and P. Pouliot, Instanton calculations versus exact results in four-dimensional SUSY gauge theories, Nucl. Phys. References B 453 (1995) 225 [hep-th/9503115] [INSPIRE]. [31] N.M. Davies, T.J. Hollowood and V.V. Khoze, Monopoles, affine algebras and the gluino condensate, J. Math. Phys. 44 (2003) 3640 [hep-th/0006011] [INSPIRE]. [32] A. Kovner and M.A. Shifman, Chirally symmetric phase of supersymmetric gluodynamics, Phys. Rev. D 56 (1997) 2396 [hep-th/9702174] [INSPIRE]. [33] A. Ritz and A.I. Vainshtein, Instantons at strong coupling, averaging over vacua, and the gluino condensate, Nucl. Phys. B 566 (2000) 311 [hep-th/9909073] [INSPIRE]. JHEP01(2023)118 [34] F. Cachazo, M.R. Douglas, N. Seiberg and E. Witten, Chiral rings and anomalies in supersymmetric gauge theory, JHEP 12 (2002) 071 [hep-th/0211170]. [35] C. Csaki and H. Murayama, Discrete anomaly matching, Nucl. Phys. B 515 (1998) 114 [hep-th/9710105] [INSPIRE]. [36] T.J. Hollowood, V.V. Khoze, W.-J. Lee and M.P. Mattis, Breakdown of cluster decomposition in instanton calculations of the gluino condensate, Nucl. Phys. B 570 (2000) 241 [hep-th/9904116] [INSPIRE]. [37] N.M. Davies, T.J. Hollowood, V.V. Khoze and M.P. Mattis, Gluino condensate and magnetic monopoles in supersymmetric gluodynamics, Nucl. Phys. B 559 (1999) 123 [hep-th/9905015] [INSPIRE]. [38] B.J. Harrington and H.K. Shepard, Periodic Euclidean Solutions and the Finite Temperature Yang-Mills Gas, Phys. Rev. D 17 (1978) 2122 [INSPIRE]. [39] T.C. Kraan and P. van Baal, Periodic instantons with nontrivial holonomy, Nucl. Phys. B 533 (1998) 627 [hep-th/9805168] [INSPIRE]. [40] M. Atiyah, N. Hitchin, V. Drinfeld and Y. Manin, Construction of instantons, Phys. Lett. A 65 (1978) 185. [41] K.-M. Lee and P. Yi, Monopoles and instantons on partially compactified D-branes, Phys. Rev. D 56 (1997) 3711 [hep-th/9702107] [INSPIRE]. [42] K.-M. Lee and C.-h. Lu, SU(2) calorons and magnetic monopoles, Phys. Rev. D 58 (1998) 025011 [hep-th/9802108] [INSPIRE]. [43] G.V. Dunne and M. Ünsal, New Nonperturbative Methods in Quantum Field Theory: From Large-N Orbifold Equivalence to Bions and Resurgence, Ann. Rev. Nucl. Part. Sci. 66 (2016) 245 [arXiv:1601.03414] [INSPIRE]. [44] E. Poppitz, Notes on Confinement on R3 × S1: From Yang-Mills, Super-Yang-Mills, and QCD (adj) to QCD(F), Symmetry 14 (2022) 180 [arXiv:2111.10423] [INSPIRE]. [45] P. van Baal, Some Results for SU(N) Gauge Fields on the Hypertorus, Commun. Math. Phys. 85 (1982) 529 [INSPIRE]. [46] P. van Baal, SU(N) Yang-Mills Solutions With Constant Field Strength on T 4, Commun. Math. Phys. 94 (1984) 397 [INSPIRE]. [47] A. González-Arroyo and P. Martinez, Investigating Yang-Mills theory and confinement as a function of the spatial volume, Nucl. Phys. B 459 (1996) 337 [hep-lat/9507001] [INSPIRE]. – 58 – [48] A. González-Arroyo, P. References Martinez and A. Montero, Gauge invariant structures and confinement, Phys. Lett. B 359 (1995) 159 [hep-lat/9507006] [INSPIRE]. [49] A. González-Arroyo and A. Montero, Do classical configurations produce confinement?, Phys. Lett. B 387 (1996) 823 [hep-th/9604017] [INSPIRE]. [50] M. Garcia Perez, A. González-Arroyo and A. Sastre, From confinement to adjoint zero-modes, eCONF C0906083 (2009) 06 [arXiv:1003.5022] [INSPIRE]. [51] M. Luscher, Some Analytic Results Concerning the Mass Spectrum of Yang-Mills Gauge Theories on a Torus, Nucl. Phys. B 219 (1983) 233 [INSPIRE]. 2] P. van Baal, QCD in a finite volume, hep-ph/0008206 [INSPIRE]. [52] P. van Baal, QCD in a finite volume, hep-ph/0008206 [INSPIRE]. JHEP01(2023)118 JHEP01(2023)118 [53] M. Garcia Perez, A. González-Arroyo, A. Montero and P. van Baal, Calorons on the lattice: A New perspective, JHEP 06 (1999) 001 [hep-lat/9903022] [INSPIRE]. [54] P.J. Braam and P. van Baal, Nahm’s Transformation for Instantons, Commun. Math. Phys. 122 (1989) 267 [INSPIRE]. [55] M. Ünsal, Strongly coupled QFT dynamics via TQFT coupling, JHEP 11 (2021) 134 [arXiv:2007.03880] [INSPIRE]. [56] E. Cohen and C. Gomez, Chiral Symmetry Breaking in Supersymmetric Yang-Mills Theory, Phys. Rev. Lett. 52 (1984) 237. [57] A.A. Cox, E. Poppitz and F.D. Wandler, The mixed 0-form/1-form anomaly in Hilbert space: pouring the new wine into old bottles, JHEP 10 (2021) 069 [arXiv:2106.11442] [INSPIRE]. [58] A. González-Arroyo, Constructing SU(N) fractional instantons, JHEP 02 (2020) 137 [arXiv:1910.12565] [INSPIRE]. [59] A. González-Arroyo and A. Ramos, Expansion for the solutions of the Bogomolny equations on the torus, JHEP 07 (2004) 008 [hep-th/0404022] [INSPIRE]. [60] Y. Tanizaki and M. Ünsal, Center vortex and confinement in Yang-Mills theory and QCD with anomaly-preserving compactifications, PTEP 2022 (2022) 04A108 [arXiv:2201.06166] [INSPIRE]. [61] A. González Arroyo and C.P. Korthals Altes, The Spectrum of Yang-Mills Theory in a Small Twisted Box, Nucl. Phys. B 311 (1988) 433. [62] G. ’t Hooft, Computation of the Quantum Effects Due to a Four-Dimensional Pseudoparticle, Phys. Rev. D 14 (1976) 3432 [INSPIRE]. [63] M.M. Anber and E. Poppitz, Anomaly matching, (axial) Schwinger models, and high-T super Yang-Mills domain walls, JHEP 09 (2018) 076 [arXiv:1807.00093] [INSPIRE]. [64] G. ’t Hooft, Aspects of Quark Confinement, Phys. Scripta 24 (1981) 841. – 59 –
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Clinical Predictors of Response to Cognitive-Behavioral Therapy in Pediatric Anxiety Disorders: The Genes for Treatment (GxT) Study
Journal of the American Academy of Child and Adolescent Psychiatry
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University of Groningen University of Groningen Journal of the American Academy of Child and Adolescent Psychiatry IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2015 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Hudson, J. L., Keers, R., Roberts, S., Coleman, J. R. I., Breen, G., Arendt, K., Boegels, S., Cooper, P., Creswell, C., Hartman, C., Heiervang, E. R., Hoetzel, K., In-Albon, T., Lavallee, K., Lyne-Ham, H. J., Marin, C. E., McKinnon, A., Meiser-Stedman, R., Morris, T., ... Eley, T. C. (2015). Clinical Predictors of Response to Cognitive-Behavioral Therapy in Pediatric Anxiety Disorders: The Genes for Treatment (GxT) Study. Journal of the American Academy of Child and Adolescent Psychiatry, 54(6), 454-463. https://doi.org/10.1016/j.jaac.2015.03.018 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Download date: 24-10-2024 Clinical Predictors of Response to Cognitive-Behavioral Therapy in Pediatric Anxiety Disorders: The Genes for Treatment (GxT) Study Jennifer L. Hudson, PhD, Robert Keers, PhD, Susanna Roberts, MSc, Jonathan R.I. Coleman, MSc, Gerome Breen, PhD, Kristian Arendt, PhD, Susan B€ogels, PhD, Peter Cooper, DPhil, Cathy Creswell, DClinPsy, PhD, Catharina Hartman, PhD, Einar R. Heiervang, MD, PhD, Katrin H€otzel, PhD, Tina In-Albon, PhD, Kristen Lavallee, PhD, Heidi J. Lyneham, PhD, Carla E. Marin, PhD, Anna McKinnon, PhD, Richard Meiser-Stedman, PhD, Talia Morris, BPsych (Hons), Maaike Nauta, PhD, Ronald M. Rapee, PhD, Silvia Schneider, PhD, Sophie C. Schneider, BPsych(Hons), Wendy K. Silverman, PhD, Mikael Thastum, PhD, Kerstin Thirlwall, DClinPsy, Polly Waite, DClinPsy, Gro Janne Wergeland, MD, Kathryn J. Lester, DPhil, Thalia C. Eley, PhD lower rates of remission) than those with generalized anxiety disorder (GAD). Although individuals with specific phobia (SP) also had poorer outcomes than those with GAD at posttreatment, these differences were not maintained at follow-up. Both comorbid mood and externalizing disorders significantly pre- dicted poorer outcomes at posttreatment and follow- up, whereas self-reported parental psychopathology had little effect on posttreatment outcomes but signifi- cantly predicted response (although not remission) at follow-up. Objective: The Genes for Treatment study is an interna- tional, multisite collaboration exploring the role of genetic, demographic, and clinical predictors in response to cognitive-behavioral therapy (CBT) in pediatric anxiety disorders. The current article, the first from the study, examined demographic and clinical predictors of response to CBT. We hypothesized that the child’s gender, type of anxiety disorder, initial severity and comorbidity, and par- ents’ psychopathology would significantly predict outcome. lower rates of remission) than those with generalized anxiety disorder (GAD). Although individuals with specific phobia (SP) also had poorer outcomes than those with GAD at posttreatment, these differences were not maintained at follow-up. Both comorbid mood and externalizing disorders significantly pre- dicted poorer outcomes at posttreatment and follow- up, whereas self-reported parental psychopathology had little effect on posttreatment outcomes but signifi- cantly predicted response (although not remission) at follow-up. Method: A sampleof 1,519 children5 to 18 yearsofage with a primary anxiety diagnosis received CBT across 11 sites. Outcome was defined as response (change in diagnostic severity) and remission (absence of the primary diagnosis) at each time point (posttreatment, 3-, 6-, and/or 12-month follow-up) and analyzed using linear and logistic mixed models. Separate analyses were conducted using data from posttreatment and follow-up assessments to explore the relative importance of predictors at these time points. Clinical Predictors of Response to Cognitive-Behavioral Therapy in Pediatric Anxiety Disorders: The Genes for Treatment (GxT) Study Conclusion: SoAD, nonanxiety comorbidity, and parental psychopathology were associated with poorer outcomes after CBT. The results highlight the need for enhanced treatments for children at risk for poorer outcomes. Key Words: anxiety disorders, treatment, predictors, cognitive-behavioral therapy Results: Individuals with social anxiety disorder (SoAD) had significantly poorer outcomes (poorer response and J Am Acad Child Adolesc Psychiatry 2015;54(6):454–463. T T in life.1 Although CBT has been established as an efficacious treatment, roughly 40% of children retain their disorder after treatment.2,3 Identifying predictors of outcome, including both response (change in symptoms) and rates of remission, may allow clinicians to identify children at risk for poorer outcomes before they commence therapy4 and help guide the development of more effective treatments for these children. T his article presents the phenotypic analyses from the Genes for Treatment (GxT) study, an international multisite collaboration exploring the role of genetic and clinical predictors of response to cognitive-behavioral therapy (CBT) in pediatric anxiety disorders. Here we pre- sent analyses examining clinical predictors of outcome. Our research focuses on anxiety disorders, as these are the most prevalent mental disorders, and, when experienced early, are associated with increased risk of multiple disorders later There is some evidence to suggest that a diagnosis of social anxiety disorder (SoAD), and comorbid mood and externalizing disorder/symptoms are each associated with poorer treatment outcomes.5-8 Parental depression and anxiety have also been associated with poorer response and remission. Nevertheless, findings for each of these predictors are inconsistent. Indeed, the 2 most recent systematic re- views of the literature failed to find conclusive evidence for a role of any of these factors in treatment outcome.9,10 externalizing disorder/symptoms are each associate poorer treatment outcomes.5-8 Parental depressio anxiety have also been associated with poorer respon remission. Nevertheless, findings for each of these pre are inconsistent. Indeed, the 2 most recent system views of the literature failed to find conclusive eviden role of any of these factors in treatment outcome.9,10 Clinical guidance is available at the end of this article. Supplemental material cited in this article is available online. JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PS 454 www.jaacap.org VOLUME 54 NUMBER 6 JUN Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. Take-down policy Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. NEW RESEARCH Clinical Predictors of Response to Cognitive-Behavioral Therapy in Pediatric Anxiety Disorders: The Genes for Treatment (GxT) Study Jennifer L. Hudson, PhD, Robert Keers, PhD, Susanna Roberts, MSc, Jonathan R.I. Coleman, MSc, Gerome Breen, PhD, Kristian Arendt, PhD, Susan B€ogels, PhD, Peter Cooper, DPhil, Cathy Creswell, DClinPsy, PhD, Catharina Hartman, PhD, Einar R. Heiervang, MD, PhD, Katrin H€otzel, PhD, Tina In-Albon, PhD, Kristen Lavallee, PhD, Heidi J. Lyneham, PhD, Carla E. Marin, PhD, Anna McKinnon, PhD, Richard Meiser-Stedman, PhD, Talia Morris, BPsych (Hons), Maaike Nauta, PhD, Ronald M. Rapee, PhD, Silvia Schneider, PhD, Sophie C. Schneider, BPsych(Hons), Wendy K. Silverman, PhD, Mikael Thastum, PhD, Kerstin Thirlwall, DClinPsy, Polly Waite, DClinPsy, Gro Janne Wergeland, MD, Kathryn J. Lester, DPhil, Thalia C. Eley, PhD NEW RESEARCH NEW RESEARCH Clinical Predictors of Response to Cognitive-Behavioral Therapy in Pediatric Anxiety Disorders: The Genes for Treatment (GxT) Study JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY www.jaacap.org VOLUME 54 NUMBER 6 JUNE 2015 Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 ingen from ClinicalKey.com by Elsevier on June 27, 2019. . Copyright ©2019. Elsevier Inc. All rights reserved. JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 454 454 www.jaacap.org VOLUME 54 NUMBER 6 JUNE 2015 Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. PREDICTORS OF CBT OUTCOME IN PEDIATRIC ANXIETY DISORDERS It is likely that the absence of multivariate models, in conjunction with small samples, varied methodology, and the failure to consistently distinguish between response and remission, has contributed to the inconsistent results. The collaboration of multiple sites and trials can overcome these limitations. This study represents the largest collaboration to date of pediatric anxiety treatment data and provides significantly greater power to detect genetic, clinical, and demographic predictors of outcome than previously possible. The sample includes data from previously pub- lished studies,11,12 as well as data from ongoing trials yet to be published. The goal of the current article was to identify clinical and demographic predictors of outcome. We present results from a linear mixture model with a higher-order random effect allowing individuals to be nested within tri- als, thereby controlling for possible trial and site differences. The design allows for the simultaneous examination of multiple variables, resulting in the identification of unique predictors. Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. Clinical Predictors of Response to Cognitive-Behavioral Therapy in Pediatric Anxiety Disorders: The Genes for Treatment (GxT) Study In our prior analyses on a subset of the current sample, we found that being female, greater initial anxiety severity, and the presence of comorbid mood and external- izing disorders were uniquely associated with poorer response to CBT.13 Although these findings are largely consistent with the literature, the finding that girls do worse than boys in CBT for child anxiety has emerged in only 1 individual trial14 and requires further examination in a larger sample. We hypothesized that female gender, the presence of SoAD, comorbid mood disorder, or externalizing disorders, and greater parental psychopathology would predict poorer outcomes to CBT in pediatric anxiety. Bochum and Basel, where the Diagnostisches Interview bei psychi- schen Strungen im Kindes- und Jugendalter (Kinder-DIPS) was used.16 Participants were assessed before and immediately after treatment (posttreatment), with further assessments made 3, 6, or 12 months after treatment cessation where possible (follow-up). The presence and severity of the primary anxiety disorder was measured at each time point. Severity was assessed using the clinician severity rating (CSR) from the structured interview, which assigns a score of 0 to 8 (absent to very severe). A diagnosis was made when the child met the diagnostic criteria and received a CSR of 4 or more, usually based on a composite of parent and child report. Diagnoses were made according to DSM criteria.17 Ten sites (Sydney, Reading, Aarhus, Bochum, Basel, Groningen, Oxford, Florida, Cambridge, and Amsterdam) also assessed co- morbid mood (major depression or dysthymia) or externalizing disorders (oppositional defiant disorder, conduct disorder or attention-deficit/hyperactivity disorder [ADHD]) at baseline using the ADIS-C/P. In addition, at 8 sites (Sydney, Reading, Aarhus, Bergen, Bochum, Oxford, Florida, Amsterdam), parents completed the Depression Anxiety Stress Scales (DASS),18 assessing depression, anxiety, and stress symptoms experienced over the past week. For this study, the 3 subscales were summed to create an overall mea- sure of parental psychopathology. All assessments were completed by graduate assistants or clin- ical staff (mainly psychologists) trained in the administration of the instruments. Sites have previously reported good interrater reli- ability for the diagnostic instruments using these samples.11,19,20 METHOD Sample The Genes for Treatment study (GxT) sample comprises data from 1,519 children who received a course of CBT for anxiety at 1 of 11 sites: Sydney, Australia (n ¼ 706); Reading, UK (n ¼ 340); Aarhus, Denmark (n ¼ 124); Bergen, Norway (n ¼ 119); Bochum, Germany (n ¼ 57); Basel, Switzerland (n ¼ 49); Groningen, the Netherlands (n ¼ 37); Oxford, UK (n ¼ 21); Miami, Florida, USA (n ¼ 50); Cambridge, UK (n ¼ 12) and Amsterdam, the Netherlands (n ¼ 4). Participants were included if they were 5 to 18 years of age (94% were 5–13 years of age), met DSM-IV criteria for a primary diagnosis of an anxiety disorder, and provided a DNA sample. Parents gave written consent, and children gave written or verbal assent. Exclu- sion criteria were significant physical or intellectual impairment or psychosis. We conducted analyses using 2 treatment outcomes: response (change in diagnostic severity), and remission (absence of the pri- mary diagnosis). In response analyses, linear mixed-effects models were used to investigate the effects of baseline predictor variables on change in severity (CSR score) of the primary anxiety diagnosis from baseline at each time point. In these analyses, the b values of vari- ables predicting a more favorable response to treatment (i.e., greater reduction in severity) are negative, whereas variables predicting a less favorable response are positive. All participants received individual-based CBT involving a sin- gle child (with or without their parent; n ¼ 426, 28%; mean [SD] number sessions ¼ 11.8 [3.2]), group-based CBT (n ¼ 800, 52.7%; mean [SD] number sessions ¼ 10 [0]) or guided CBT self-help (n ¼ 293, 19.3%; mean [SD] number sessions ¼ 7.3 [1.5]) and provided at least 1 posttreatment assessment. In analyses of remission, similar logistic mixed effects models were used to investigate the effects of baseline predictor variables on absence of the primary anxiety diagnosis at each time point. In these analyses, odds ratios of variables predicting a higher likelihood of remission (a loss of the primary diagnosis) are greater than 1, whereas variables predicting a lower likelihood of remission have odds ratios of less than 1. All treatments were manualized, and treatment protocols across all sites were comparable for core elements of CBT including teaching of coping skills, cognitive restructuring, and exposure. Further details are provided in Supplement 1, available online. Statistical Analysis To make use of all available postbaseline assessments and to provide estimates in the presence of missing values, the effects of predictors on outcome were tested using mixed models fitted with full maximum likelihood. All models included the fixed effects of baseline severity (CSR score of the primary diagnosis at baseline, centered at the mean) and the linear and quadratic effects of time to account for the curvilinear slope of treatment outcome. To account for correlations between repeated measures from the same partici- pant, all models included the random effects of individual. We also included a higher-order random effect of trial to account for between-trial differences in outcome. As each trial was conducted at a single site, this random effect also accounted for between-site differences. Predictor variables were entered simultaneously. Thus, when a significant predictor is identified, it is significant over and above the other predictors in the model. Measures Initially, we considered response and remission using data from the entire duration of the trial. However, the power of the GxT sample also enabled us to compare the results from separate All sites administered the Anxiety Disorders Interview Schedule for DSM-IV, Parent and Child Versions (ADIS-IV-C/P15) except at JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 6 JUN 0 5 www.jaacap.o g 55 Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. Sample Characteristics p The baseline demographic and clinical characteristics of the sample overall and by site are given in Table 1. The most common primary diagnosis was GAD, followed by SoAD, SAD, and SP. The remaining participants met criteria for “other anxiety” disorders, which included panic disorder with and without agoraphobia and agoraphobia without panic disorder (n ¼ 38), obsessive-compulsive disorder (OCD; n ¼ 44), posttraumatic stress disorder (PTSD; n ¼ 17), selective mutism (in patients with primary selective mutism, a diagnosis of severe SoAD was also given; the selective mutism was considered by the clinician to be primary, the most interfering: n ¼ 4) or anxiety disorder not otherwise specified (n ¼ 10). CSR scores for the primary diagnosis indicated that the majority of the sample (79.1%) were rated 6 or above (either severe or very severe) at the start of treatment. Changes in severity scores grouped by primary diagnosis with the n for each time point are given in Figure 1. The 10 sites that measured comorbid mood and externalizing disorders found both to be common, with prevalence rates of 10.7% and 18.2%, respectively. Parental psychopathology was also common, with 114 (8.9%), 137 (10.6%), and 172 (13.3%) scoring above the cut-offs for se- vere depression (21þ), anxiety (15þ), and stress (26þ), respectively.22 Individuals treated with group CBT and those treated with self-help CBT had significantly more missing outcome data than those treated with individual Our primary analyses included only the clinical and de- mographic data collected in all of the participating sites as predictors of treatment outcome. These were treatment type (in which group- based and guided self-help CBT were each compared with individual-based CBT), age (centered at the mean), gender (0 ¼ male, 1 ¼ female), and primary diagnosis (in which SoAD, separa- tion anxiety disorder [SAD], specific phobia [SP], and “other anxi- ety” disorders were each compared with generalized anxiety disorder [GAD]). In secondary analyses, we also explored the effects of comorbid mood and externalizing disorders, and parental psy- chopathology as predictors of outcome in trials where these data were available. These analyses included the presence of a comorbid mood or externalizing disorder and standardized total score of the DASS to indicate parental depression, anxiety, and stress symptoms. To control for multiple testing (6 analyses), we considered predictors significant at a Bonferroni-corrected a level of 0.008 (0.05/6). RESULTS analyses predicting outcome at the posttreatment and follow-up assessments, respectively. To formally test whether predictors were specific to the posttreatment or follow-up time points, we also tested the significance of a time-by-predictor interaction in models using data from each time point in the study. Sample Characteristics JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 455 From Each Site Bergen Bochum Basel Groningen Oxford Florida Cambridge Amsterdam Total 2) 6.9 (1.1) 6.8 (1.1) 6 (0.8) 6.2 (1) 5.5 (1) 6.8 (1.2) 6.3 (1.2) 5.8 (1.7) 6.3 (1) 5) 64 (53.8) 33 (57.9) 27 (55.1) 17 (45.9) 13 (61.9) 21 (42.9) 8 (66.7) 0 (0) 783 (51.6) 4) 11.4 (2.1) 11.3 (2.5) 8.6 (2.2) 11.9 (3.1) 9 (1.8) 9.5 (2.2) 12.6 (2.8) 12 (1.8) 9.9 (2.2) 22 (18.5) 6 (10.5) 0 (0) 7 (18.9) 3 (14.3) 13 (26) 0 (0) 0 (0) 558 (36.7) 5) 54 (45.4) 15 (26.3) 0 (0) 15 (40.5) 7 (33.3) 13 (26) 0 (0) 1 (25) 341 (22.4) 3) 0 (0) 20 (35.1) 0 (0) 6 (16.2) 1 (4.8) 6 (12) 0 (0) 1 (25) 166 (10.9) 8) 43 (36.1) 13 (22.8) 49 (100) 6 (16.2) 9 (42.9) 12 (24) 0 (0) 2 (50) 341 (22.4) 3) 0 (0) 3 (5.3) 0 (0) 3 (8.1) 1 (4.8) 6 (12) 12 (100) 0 (0) 113 (7.4) 6) 58 (48.7) 57 (100) 49 (100) 37 (100) 0 (0) 50 (100) 12 (100) 1 (25) 426 (28) 4) 61 (51.3) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 3 (75) 800 (52.7) 0 (0) 0 (0) 0 (0) 0 (0) 21 (100) 0 (0) 0 (0) 0 (0) 293 (19.3) 9) —a 11 (19.3) 1 (2) 1 (2.7) 1 (4.8) 2 (4) 4 (36.4) 0 (0) 150 (10.7) ) —a 3 (5.3) 2 (4.1) 2 (5.4) 4 (19) 13 (26) 6 (54.5) 1 (25) 254 (18.2) 6) 13.5 (14.6) 28.2 (16.9) —a —a 33 (16.2) 28.4 (12.1) —a 22.2 (20.1) 30.8 (19.9) 3) 2.3 (4.2) 4.8 (5.3) —a —a 7.6 (6.2) 5.2 (4.9) —a 5.5 (6.4) 6.5 (6.5) 4) 4.3 (7.1) 7.7 (7.8) —a —a 9.4 (6.7) 7.4 (4.1) —a 3.8 (3.5) 9.1 (8) 8) 6.9 (5.5) 15.8 (7.7) —a —a 15.9 (6.7) 15.8 (7.1) —a 13 (11.3) 15.2 (8.4) goraphobia without panic disorder (n ¼ 38), obsessive-compulsive disorder (OCD; n ¼ 44), posttraumatic stress disorder (PTSD; n ¼ 17), selective ¼ cognitive-behavioral therapy; GAD ¼ generalized anxiety disorder; SAD ¼ separation anxiety disorder; SoAD ¼ social anxiety disorder; SP ¼ ) .6) .2) .7) .4) .9) .4) .4) ) .7) .3) PREDICTORS OF CBT OUTCOME IN PEDIATRIC ANXIETY DISORDERS Predictors of Response and Remission p Results of the linear and logistic mixed models used to explore the effects of demographic and clinical characteris- tics on response (change in diagnostic severity of the pri- mary diagnosis from baseline) and remission (absence of the primary diagnosis) are given in Tables 2 and 3. Outcome was considered first using data from all time points, then at the posttreatment or follow-up assessments specifically. To assess response (change in diagnostic severity), baseline severity of diagnosis was included in all models as a co- variate. Higher baseline severity was associated with higher severity scores and a lower likelihood of remission across all time points. Treatment Type Treatment type was not associated with response or remis- sion overall or in analyses conducted using the posttreat- ment or follow-up assessments separately. Sample Characteristics Finally, our approach to measuring outcome allowed us to include all of the available data and provided increased power to detect predictors of treatment outcome. To ensure that our findings were comparable to previous analyses of treatment outcome, we also conducted analyses exploring the effects of the factors included above on change in severity scores and absence of primary anxiety disorder for each time point separately, using linear and logistic regression, respectively. All statistical analyses were conducted using STATA version 12.0.21 FIGURE 1 Mean clinician severity rating (CSR) score by primary diagnosis at each time point. Note: Error bars represent 1 standard error of the mean; “other” includes panic disorder with and without agoraphobia and agoraphobia without panic disorder (n ¼ 38), obsessive-compulsive disorder (OCD; n ¼ 44), posttraumatic stress disorder (PTSD; n ¼ 17), selective mutism (n ¼ 4), or anxiety disorder not otherwise specified (n ¼ 10). GAD ¼ generalized anxiety disorder; SAD ¼ separation anxiety disorder; SoAD ¼ social anxiety disorder; SP ¼ specific phobia. JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 www.jaacap.org 457 Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 457 Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. HUDSON et al. Predictors of Response and Remission TABLE 2 Results of Linear Mixed Models Examining Predictors of Treatment Response (Change in Severity of the Primary Diagnosis From Baseline) Using Data From All Time Points, or Separately Using Only the Posttreatment or at Follow-Up Assessments r Mixed Models Examining Predictors of Treatment Response (Change in Severity of the Primary Diagnosis a From All Time Points, or Separately Using Only the Posttreatment or at Follow-Up Assessments ABLE 2 Results of Linear Mixed Models Examining Predictors of Treatment Response (Change in Severity rom Baseline) Using Data From All Time Points, or Separately Using Only the Posttreatment or at Follow TABLE 2 Results of Linear Mixed Models Examining Predictors of Treatment Response (Change in Severity of the Primary Diagnosis From Baseline) Using Data From All Time Points, or Separately Using Only the Posttreatment or at Follow-Up Assessments All Time Pointsa Posttreatment Assessment Follow-Up Assessmentsa b (95% CI) b (95% CI) b (95% CI) Severity of primary diagnosis at baseline 0.18 (0.14e0.21)* 0.20 (0.15e0.24)* 0.14 (0.10e0.19)* Treatment Individual-based CBT —b —b —b Group-based CBT 0.17 (e0.01e0.35) 0.18 (e0.01e0.38) 0.06 (e0.18e0.31) Guided self-help CBT e0.02 (e0.27e0.23) 0.02 (e0.23e0.28) e0.24 (e0.70e0.23) Gender 0.09 (0.02e0.16) 0.08 (0.00e0.16) 0.10 (0.01e0.19) Age 0.01 (e0.01e0.02) 0.01 (e0.01e0.03) 0.01 (e0.03e0.02) Primary diagnosis GAD —b —b —b SoAD 0.44 (0.34e0.53)* 0.48 (0.37e0.59)* 0.39 (0.27e0.51)* SP 0.13 (0.01e0.26) 0.22 (0.07e0.36)* 0.02 (e0.14e0.18) SAD 0.10 (0.00e0.20) 0.13 (0.01e0.24) 0.08 (e0.05e0.21) Other e0.18 (e0.32e0.03) e0.17 (e0.33e0.00) e0.16 (e0.34e0.03) Secondary analysesc Comorbid externalizing disorder 0.16 (0.06e0.27)* 0.23 (0.11e0.34)* 0.11 (e0.02e0.24) Comorbid mood disorder 0.19 (0.06e0.32)* 0.23 (0.08e0.37)* 0.15 (e0.02e0.31) Parental psychopathology 0.06 (0.02e0.10)* 0.04 (e0.01e0.09) 0.09 (0.03e0.14)* Note: All models included the random effects of trial. Regression weights (b) significantly greater than 0 indicate that this variable is associated with a poorer reduction in symptom severity after treatment. CBT ¼cognitive-behavioral therapy; GAD ¼ generalized anxiety disorder; Other ¼ other anxiety disorder; SAD ¼ separation anxiety disorder; SoAD ¼ social anxiety disorder; SP ¼ specific phobia. aTo account for data collected longitudinally, these models included the random effects of participant and the linear and quadratic effects of time. bReference category. cInclude comorbidity and parental psychopathology. *p < .008. JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 Gender and Age CBT (b ¼ 0.26, 95% CI ¼ 0.14–0.37, p < .001 and b ¼ 0.42, 95% CI ¼ 0.29–0.55, p < .001, respectively). However, missingness was not associated with baseline severity, age, gender, primary diagnosis, comorbid mood or exter- nalizing disorders, or parental psychopathology (all p values >.1). g Gender and age did not significantly predict response or remission after correction for multiple testing. Age-by- gender interactions were also nonsignificant. g Gender and age did not significantly predict response or remission after correction for multiple testing. Age-by- gender interactions were also nonsignificant. Primary Diagnosis Primary Diagnosis Primary diagnosis was significantly associated with both response and remission. In response analyses, individuals with SoAD showed significantly less change in their diag- nostic severity than those with GAD. Correspondingly, in analyses of remission, individuals with primary SoAD were significantly more likely to retain their diagnosis at post- treatment and follow-up assessments than those with GAD. Findings were similar regardless of time point. This suggests that this factor had similar effects on outcome at both the posttreatment and follow-up time points. The effects of SoAD were also similar regardless of treatment type. Results of response analyses for individual CBT, group CBT, and guided self-help respectively were as follows: b ¼ 0.36, 95% CI ¼ 0.16–0.56, p ¼ .001; b ¼ 0.54, 95% CI ¼ 0.37–0.70, p < .001; and b ¼ 0.37, 95% CI ¼ 0.13–0.62, p ¼ .003. Results of remission analyses for individual CBT, group CBT, and guided self-help respectively were as follows: OR ¼ 0.41, 95% CI ¼ 0.18–0.93, p ¼ .033; OR ¼ 0.16, 95% CI ¼ 0.07–0.33, p < .001; OR ¼ 0.08, 95% CI ¼ 0.01–0.84, p ¼ .035. This suggests that the poor outcomes for individuals with SoAD JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 458 www.jaacap.org Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. PREDICTORS OF CBT OUTCOME IN PEDIATRIC ANXIETY DISORDERS TABLE 3 Results of Logistic Mixed Models Examining Predictors of Remission (Absence of the Primary Diagnosis) Using Data From All Time Points, or Separately Using Only the Posttreatment or at Follow-Up Assessments TABLE 3 Results of Logistic Mixed Models Examining Predictors of Remission (Absence of the Primary Diagnosis) Using Data From All Time Points, or Separately Using Only the Posttreatment or at Follow-Up Assessments Characteristic All Time Pointsa Posttreatment Assessment Follow-Up Assessmentsa OR (95% CI) OR (95% CI) OR (95% CI) Severity of primary diagnosis at baseline 0.54 (0.44e0.65)* 0.69 (0.61e0.78)* 0.50 (0.36e0.69)* Treatment Individual-based CBT —b —b —b Group-based CBT 0.49 (0.21e1.13) 0.60 (0.32e1.09) 0.87 (0.24e3.13) Guided self-help CBT 0.33 (0.10e1.04) 0.47 (0.23e0.98) 1.80 (0.13e25.57) Gender 0.76 (0.55e1.05) 0.84 (0.67e1.05) 0.78 (0.47e1.29) Age 1.00 (0.92e1.08) 0.98 (0.93e1.04) 1.05 (0.92e1.19) Primary diagnosis GAD —b —b —b SoAD 0.18 (0.11e0.28)* 0.31 (0.23e0.42)* 0.18 (0.08e0.39)* SP 0.59 (0.33e1.04) 0.58 (0.40e0.86)* 0.90 (0.37e2.17) SAD 0.76 (0.47e1.21) 0.70 (0.51e0.96) 1.02 (0.50e2.12) Other 1.99 (0.99e3.99) 1.55 (0.95e2.53) 1.76 (0.60e5.16) Secondary analysesc Comorbid externalizing disorder 0.57 (0.35e0.94) 0.66 (0.48e0.91) 0.70 (0.35e1.43) Comorbid mood disorder 0.43 (0.23e0.80)* 0.58 (0.39e0.87) 0.43 (0.17e1.06) Parental psychopathology 0.80 (0.65e0.98) 0.91 (0.79e1.04) 0.71 (0.52e0.97) Note: All models included the random effects of trial. Regression weights (b) significantly greater than 0 indicate that this variable is associated with a poorer reduction in symptom severity after treatment. CBT ¼ cognitive-behavioral therapy; GAD ¼ generalized anxiety disorder; Other ¼ other anxiety disorder; OR ¼ odds ratio; SAD ¼ separation anxiety disorder; SoAD ¼ social anxiety disorder; SP ¼ specific phobia. aTo account for data collected longitudinally, these models included the random effects of participant and the linear and quadratic effects of time. bReference category. cIncludes comorbidity and parental psychopathology. *p < .008. type, age, gender, and diagnosis were similar to those in the previous models (see Table S2, available online, for estimates from the full model). were not driven by a poor response to a particular treatment type. Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. Comorbid Mood or Externalizing Disorders Comorbid Mood or Externalizing Disorders g Using the same models and covariates as above (that is, baseline severity as a covariate and gender, age, primary diagnosis, and treatment type as predictors), we conducted secondary analyses, exploring the effects of comorbid mood or externalizing disorders, and parental psychopathology on remission and response in trials that measured these factors (lower portion of Tables 2 and 3). Effect sizes for treatment JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 We also found that the presence of SoAD anywhere in the child’s profile significantly worsened his/her outcome (see Table S1, available online). The presence of a comorbid externalizing disorder was associated with a poorer response to treatment (less change in severity). Although these effects appeared to be smaller in the follow-up than in the posttreatment as- sessments, externalizing disorder by study period in- teractions were nonsignificant (all p values >.1), indicating that this factor had similar effects at both outcome time points. Although findings were nominally significant (p < .05) for remission, they did not withstand correction for multiple testing. Individuals with a primary diagnosis of SP showed significantly poorer response (less change in severity) and lower rates of remission than those with GAD. However, these findings were specific to outcome at the posttreatment assessment. To test the statistical significance of these effects, we included a diagnosis by study period interaction in an- alyses using data from all time points. This interaction was significant for both response and remission outcomes (b ¼ –0.17, 95% CI ¼ –0.31 to 0.02, p ¼ .025 and OR ¼ 2.33, 95% CI ¼ 1.15–4.71, p ¼ .035, respectively), indicating that SP becomes a less important predictor of outcome in the later stages of the study. The presence of a comorbid mood disorder was also associated with poorer response (especially at posttreat- ment) and lower likelihood of remission using data from all time points. However, as with externalizing disorders, a mood disorder by study period interaction was nonsignifi- cant for response and remission (all p values >.1), suggest- ing that the effects of mood disorders did not differ across time. Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. VOLUME 54 NUMBER 6 JUNE 2015 www.jaacap.org 459 Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. Parental Psychopathology Parental psychopathology (total DASS score) was associ- ated with significantly poorer response, particularly in the JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 RICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY MBER 6 JUNE 2015 www.jaacap.org 459 Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. 459 HUDSON et al. follow-up assessment. There was a significant parental psychopathology by study period interaction (b ¼ 0.11, 95% CI ¼ 0.06–0.15, p < .001), indicating that these effects were specific to follow-up. Although findings were in a similar direction for remission, these results did not with- stand correction for multiple testing. disorders was also significantly associated with lower like- lihood of remission, and although findings were only nominally significant (p < .05) for mood disorders and parental psychopathology, they followed the same pattern as we observed in our original analysis. Our longitudinal approach to measuring outcome allowed us to include all of the available data, providing increased power to detect predictors of outcome. To enable direct comparisons with other studies, we also conducted analyses of remission of the primary diagnosis and change in the severity of primary diagnosis at each time point in the study (see Tables S7 and S8, available online). Although findings did not reach statistical significance at all time points because of the lower power inherent to subgroup analyses, the results are similar to those from the mixture model approach. Parental Involvement and Treatment Length A recent individual-level meta-analysis combining data from published child anxiety treatment trials suggested that the level of parental involvement in treatments may have an impact on outcome. Specifically, treatments that involved parents and used contingency management strategies and/or a transfer of control model showed better outcomes than treatments that included other types of parental involvement.23 To account for these effects in the current study, we coded parental involvement in each trial using the same approach as in this previous study (i.e., low involvement, active involvement without emphasis on contingency management, and transfer of control or active involvement with emphasis on contin- gency management or transfer of control) and reanalyzed the data using parental involvement as a covariate (see Supplement 1 Methods and Table S3, available online). Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. Parental Psychopathology The results indicated that the level of parental involve- ment was not associated with either response or remission, and the inclusion of this variable did not affect our pre- vious findings. As the included trials differed in the number of planned sessions, we also explored whether treatment length explained our previous findings (see Table S4, available online). These analyses suggested that treatment length was not associated with either response or remission and did not confound the relationship be- tween diagnosis, comorbidity, and parental psychopa- thology and outcome. Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. Comparison With Previous Analyses Comparison With Previous Analyses We previously reported on clinical and demographic pre- dictors of treatment outcome at follow-up for a subset (n ¼ 384) of this sample. These analyses suggested that female gender, greater initial anxiety severity, and comorbid mood and externalizing disorders were all associated with poorer response to CBT.13 To ensure that the findings in the current report were not driven entirely by data from these previous analyses, we reanalyzed the GxT data excluding this subset. The results were similar to those from the entire sample (see Table S5, available online). 460 www.jaacap.org VOLUME 54 NUMBER 6 JUNE 2015 Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY ww.jaacap.org VOLUME 54 NUMBER 6 JUNE 2015 Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. without permission. Copyright ©2019. Elsevier Inc. All rights reserved. Sensitivity Analyses W b d d f We combined data from multiple trials including patients with a wide age range with a variety of different primary disorders. This approach provided us with increased po- wer to detect small effects and to identify robust predictors with the highest potential clinical utility. Nevertheless, the resulting heterogeneity may have affected the results. To address this we conducted a series of sensitivity analyses in which we attempted to reduce the heterogeneity of the sample to include only individuals within a narrower age range (5–13, n ¼ 1,429, 94.1%: see Table S9, available on- line), only those with the 4 most common diagnoses (GAD, SoAD, SAD, and SP; n ¼ 1,406, 92.5%; see Table S10, available online), or only those who received a treatment that was not diagnosis specific (n ¼ 1,423, 93.7%; see Table S11, available online). In each of these analyses, findings were equivalent to those from the full analysis, suggesting that they were not the result of excessive het- erogeneity in the sample. DISCUSSION This is the first article to emerge from an international multisite collaboration exploring the role of genetic and clinical predictors of outcome after CBT for pediatric anxiety disorders. We identified several clinical predictors of outcome, some of which showed effects only at specific time points. As our study examined multiple treatment pre- dictors, we were able to identify variables that contributed unique variance over and above other predictors, such as baseline severity. y In support of previous research,5,6 children with pri- mary SoAD had the poorest outcomes and were nearly twice as likely as children with primary GAD to still have a diagnosis at the end of the study. This is not to say that CBT is ineffective for children with SoAD but, rather, it suggests that CBT is less effective than for children with other types of anxiety disorders. These results cannot be explained by initial severity, comorbidity, or parental psychopathology. Currently we do not fully understand why children with SoAD have poorer outcomes. Future research must endeavor to understand the mechanisms We chose to focus on outcomes for the primary anxiety disorder in the current article, as this is typically the main outcome measure used in clinical trials and is typically the target of treatment. Nevertheless, some previous studies have considered remission as an absence of all anxiety di- agnoses. When we conducted analyses using this stricter definition, the results were comparable to our previous findings of remission from the primary diagnosis (see Table S6, available online). That is, individuals with a diagnosis of SoAD were significantly less likely to experi- ence remission. The presence of comorbid externalizing 460 ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 PREDICTORS OF CBT OUTCOME IN PEDIATRIC ANXIETY DISORDERS underlying these poorer outcomes for children with SoAD and to develop and evaluate enhanced treatments. Of particular note, the treatment delivered in the trials re- ported here were typically of a generic format targeting a heterogeneous group of children with anxiety disorders (with the exception of patients with PTSD from the Cambridge site and patients with SAD from the Bochum and Basel sites). Treatments tailored specifically to target SoAD (e.g., increased social skills training, video feed- back, attention training) such as Social Effectiveness Training24 may enhance outcomes for this more intrac- table disorder. DISCUSSION As all variables were modeled simultaneously, predictor effects are significant over and above all other predictors in the model. Thus we can conclude, for instance, that SoAD is a signifi- cant predictor of poorer response and remission, over and above comorbid mood disorders. This study represents the largest of its kind and was made possible through sharing of data and procedures. Despite these strengths, there are a number of limitations. First, there is considerable heterogeneity in the sample. We included trial as a covariate in our analyses and used broadly common assessment tools; yet each trial and site in which it was conducted had subtle differences in recruit- ment, assessment, and treatment. We also had very few adolescents in our sample, limiting generalization of our findings to preadolescent children. Future research needs to determine whether these predictors are also important for adolescents receiving treatment for anxiety disorders. As we were interested in predictors of poor outcome in children who received a full course of CBT, a control group was not appropriate. Yet it is possible that the predictors identified in this article may also be predictive of poorer outcomes even in the absence of treatment. Finally, these data suggest that parental psychopa- thology may have an impact on outcomes, specifically during the follow-up period, although this varies depending on the measure of outcome used. Parental psychopathology did not predict remission of child anxi- ety disorder. In contrast, when outcome was measured as change in diagnostic severity, children of parents with elevated symptoms of anxiety, depression, and stress showed poorer response at follow-up. Previous research has shown, albeit inconsistently, that increased parental psychopathology reduces the efficacy of treatment for anxious youth.9,25 However, the temporal effects observed here are novel and may explain why not all studies report a significant association. Moreover, these findings indicate that parental psychopathology may exert increasing influence on the child’s symptom presentation even after a child’s treatment has been completed. At the completion of treatment, children no longer rely on the therapist to monitor the successful execution of exposure tasks but, rather, become increasingly reliant on parents or themselves. DISCUSSION Unexpectedly, children with a primary diagnosis of SP also showed poorer outcomes immedi- ately after treatment than children with a primary diagnosis of GAD, but this difference disappeared by follow-up. This suggests that children with a primary diagnosis of SP take longer to demonstrate equivalent outcomes to children with GAD. It is possible that, given the graded approach to exposure, severe fears were tackled toward the end of therapy after other, less severe comorbid fears were reduced. majority of evidence shows comparable outcomes for treatments with limited versus increased parental involvement. However, a recent individual patient data meta-analysis showed enhanced long-term outcomes for treatments with greater parent involvement and increased focus on parenting factors such as contingency manage- ment.23 Furthermore, there is some evidence to suggest that, in the long term, providing additional parent anxiety management may lead to enhanced outcomes for children with anxiety.27 Treatment modality was not a significant predictor of outcome, suggesting that treatment change is influenced by factors common to the programs included in this study. Consistent with a recent meta-analysis,28 age also was not a significant predictor of outcome, suggesting that CBT works just as well for younger and older children, although the majority of our sample was less than 13 years of age; thus, our conclusions with respect to adolescence are limited. Our lack of evidence for a unique effect of gender is in contrast to a previous analysis of a small subset of these data.13 Children presenting with comorbid mood or external- izing disorders were approximately twice as likely as those without to retain their primary anxiety disorder across all outcome time points. These children also demonstrated reduced levels of symptom change. These results support the growing body of evidence that suggests that comorbidity affects outcomes of CBT for anxious youth.7,8 There was weak support for a temporal effect of comorbidity on outcome, with the importance of comorbid disorders reduced by the follow-up time point. Although this could be explained by reduced power within these secondary ana- lyses, it could also suggest that children with comorbid disorders take longer to improve compared to those without, suggesting that treatments could be developed that bring about more efficient change. Of note, the significance of the predictors identified cannot be explained by the child’s baseline severity of the primary diagnosis, as this was included in the models. Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 www.jaacap.org 461 Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. 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Elsevier Inc JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 Clinical Guidance Havik, PhD, and Krister Fjermestad, PhD, of University of Bergen; Elisa Kulewski, MSc, Jonas Großekath€ofer, MSc, Nora Dirks, BSc, Evelyn Kmelnitski, BSc, Sabrina Heuser, Dipl Psych, Karen Krause, Dipl Psych, of Bochum University; Adrian Boyle, MD, FCEM, Clare Dixon, BSc, MSc, Patrick Smith, MA, MSc, PhD, and Tim Dalgleish, MA, PhD, MSc, of University of Cambridge; Harma Moorlag, PhD, Nienke Boersma, MSc, and Sanne Hogendoorn, MSc, of University of Groningen; Sue Cruddace, PhD, Marie Weber, student, Zoe Hughes, BSc, Liz White, BSc, Francoise Hentges, PhD, DClinPsy, and Kiri Clarke, MSc, of Reading University; Nynke Wagenaar, MSc, of University of Amsterdam; Luci Motoca, PhD, Yesenia Rodriguez, MS, Klaudia Pereira, MSc, Cristina Del Busto, MS, Erin Hede- mann, MS, and Yasmin Rey, PhD, of Florida International University; and Gillian O’Neill, BSc (Hons), Lucy Lindley, BSc (Hons), Rachel Banham, BSc (Hons), and Nora Delvendahl, BSc (Hons), of King’s College London for their contributions. This article was reviewed under and accepted by deputy editor John Pia- centini, PhD. Drs. Hudson, Lyneham, Rapee, and Ms. Morris and Ms. Schneider are with the Centre for Emotional Health, Macquarie University, Sydney, Australia. Drs. Keers, Breen, and Eley and Ms. Roberts and Mr. Coleman are with King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Med- ical Research Council (MRC) Social, Genetic and Developmental Psychiatry (SGDP) Centre, London. Drs. Arendt and Thastum are with University of Aar- hus, Denmark. Dr. Bogels is with the Research Institute Child Development and Education, University of Amsterdam. Drs. Cooper, Creswell, Thirlwall, and Waite are with the School of Psychology and Clinical Language Sciences, University of Reading, UK. Drs. Hartman and Nauta are with University Medical Center Groningen, University of Groningen, The Netherlands. Dr. Heiervang is with the Institute of Clinical Medicine, University of Oslo, Nor- way and Anxiety Research Network, Haukeland University Hospital, Bergen, Norway. Dr. H€otzel is with Ruhr-Universit€at Bochum, Germany. Dr. In-Albon is with University Koblenz-Landau, Landau, Germany. Dr. Lavallee is with Uni- versity of Basel, Switzerland. Drs. Marin and Silverman are with Yale Uni- versity, New Haven, CT. Drs. McKinnon and Meiser-Stedman are with the MRC Cognition and Brain Sciences Unit, Cambridge, UK. Dr. Schneider is with Ruhr-Universit€at Bochum, Germany. Dr. Wergeland is with Anxiety Research Network, Haukeland University Hospital. Dr. Lester is with the School of Psychology, University of Sussex, UK. Disclosure: Dr. Clinical Guidance NIHR on behalf of the MRC-NIHR partnership. Dr. Lester is supported by an MRC research grant (MR/J011762/1) and Jacobs Foundation Young Scholar Award. Dr. Keers is supported by an MRC Population Health Scientist Award (MR/K021281/1). This study presents independent research partly funded by the NIHR Biomedical Research Centre at South London and Maudsley, NHS Foundation Trust, and King’s College London. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, or the Department of Health. NIHR on behalf of the MRC-NIHR partnership. Dr. Lester is supported by an MRC research grant (MR/J011762/1) and Jacobs Foundation Young Scholar Award. Dr. Keers is supported by an MRC Population Health Scientist Award (MR/K021281/1). This study presents independent research partly funded by the NIHR Biomedical Research Centre at South London and Maudsley, NHS Foundation Trust, and King’s College London. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, or the Department of Health.  CBT works irrespective of a child’s age and gender.  Children with SoAD had poorer outcomes compared to children with other anxiety disorders.  Parent involvement did not impact treatment outcome.  Parent involvement did not impact treatment outcome. Drs. Hudson and Keers contributed equally to the work. Drs. Lester and Eley also contributed equally to the work.  There is some evidence that the presence of comorbid mood disorders and parental psychopathology may lead to poorer outcomes  There is some evidence that the presence of comorbid mood disorders and parental psychopathology may lead to poorer outcomes Dr. Keers served as the statistical expert for this research. The authors thank Irma Knuistingh Neven, BEd, MSc, Kathryn Preece, BSc(Psych) PGDip, Annabel Price, BSc (Hons), and Julia White, BCom, BSc-Psych (Hons), Grad Dip Psych, of Macquarie University; Marianne Bjerregaard Madsen, administrator, Hjalti Jonsson, PhD, and Lisbeth Jørgensen, MSc, of Aarhus University; Carmen Adornetto, DPhil, Judith Blatter- Meunier, DPhil, Chantal Herren, DPhil, of University of Basel; Kristine Fonnes Griffin, administrator, Odd E. DISCUSSION Given this, it is possible that parental psychopathology could exert greater interference on the child’s symptom reduction during this period.26 The In summary, these findings suggest that CBT is effective for children irrespective of whether treatment is delivered in individual or group format and irrespective of the child’s age and gender. CBT is more effective for children without primary SoAD or comorbid mood disorders. Children with primary specific phobia or comorbid externalizing disorders may show slower response; however, in the long term, there should be no significant difference in outcome. Finally, the impact of having a parent with elevated levels of psycho- pathology will have an increasingly important impact on the child’s outcomes after treatment is complete. The next step is to develop and to evaluate enhanced treatments for children at risk for poorer outcome. & JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 461 HUDSON et al. REFERENCES REFERENCES 5. Ginsburg GS, Kendall PC, Sakolsky D, et al. Remission after acute treat- ment in children and adolescents with anxiety disorders: findings from the CAMS. J Consult Clin Psychol. 2011;79:806-813. 1. Rapee RM, Schniering CA, Hudson JL. Anxiety disorders during child- hood and adolescence: origins and treatment. Ann Rev Clin Psychol. 2009;5:311-341. 2. James AC, James G, Cowdrey FA, Soler A, Choke A. Cognitive behav- ioural therapy for anxiety disorders in children and adolescents. Cochrane Database System Rev. 2013;6:CD004690. y 6. Compton SN, Peris TS, Almirall D, et al. Predictors and moderators of treatment response in childhood anxiety disorders: results from the CAMS trial. J Consult Clin Psychol. 2014;82:212-224. y 7. Rapee RM, Lyneham HJ, Hudson JL, Kangas M, Wuthrich VM, Schniering CA. Effect of comorbidity on treatment of anxious children and adolescents: results from a large, combined sample. J Am Acad Child Adolesc Psychiatry. 2013;52:47-56. 3. Silverman WK, Pina AA, Viswesvaran C. Evidence-based psychosocial treatments for phobic and anxiety disorders in children and adolescents. J Clin Child Adolesc Psychol. 2008;37:105-130. y 4. Kendall PC, Settipani CA, Cummings CM. No need to worry: the promising future of child anxiety research. J Clin Child Adolesc Psychol. 2012;41:103-115. y y 8. Berman SL, Weems CF, Silverman WK, Kurtines WM. Predictors of outcome in exposure-based cognitive and behavioral treatments for JOURNAL OF THE AMERICAN ACADEMY OF CHILD & ADOLESCENT PSYCHIATRY VOLUME 54 NUMBER 6 JUNE 2015 462 www.jaacap.org Clinical Guidance Hudson is an author of the Cool Kids program but receives no direct payment from it. Dr. Creswell is joint author of a book used in treatment within the Overcoming trial and receives royalties from sales of the book. Dr. Lyneham is an author of the Cool Kids program but receives no direct payment from it. Dr. Rapee is an author of the Cool Kids program but receives no direct payment from it. Dr. Schneider is an author of the Diagnostisches Interview bei psychischen St€orungen im Kindes- und Jugendalter, from which she receives royalties. Dr. Silverman is an author of the Anxiety Disorders Interview Schedule for Children, from which she receives royalties. Drs. Keers, Breen, Arendt, Bogels, Cooper, Hartman, Heiervang, H€otzel, In-Albon, Lav- allee, Marin, McKinnon, Meiser-Stedman, Nauta, Thastum, Thirlwall, Waite, Wergeland, Lester, Eley, Ms. Roberts, Mr. Coleman, Ms. Morris, and Ms. Schneider report no biomedical financial interests or potential conflicts of in- terest. Combined study supported by UK MRC grant G0901874/1 (T.C.E.). In- dividual trials support by Australian Research Council grant DP0878609 (J.L.H., Jenny Donald, PhD, R.M.R., T.C.E.); Australian National Health and Medical Research Council grants (1027556: R.M.R., J.L.H., H.J.L., Cathy Mihalopolous, BSc[Hons], PhD), (488505: H.J.L., J.L.H., R.M.R.), and (382008: J.L.H. and R.M.R.); TrygFonden grant (7-10-1391: M.T. and Esben Hougaard, PhD); Edith og Godtfred Kirk Christiansens Fond grant (21- 5675: M.T.); Swiss National Science Foundation grant (105314-116517: S.S.); Western Norway Regional Health Authority grants (911253: Odd E. Havik, PhD) and (911366: E.H.); UK MRC Clinical Fellowship (G0802821: R.M.-S.); National Institute of Mental Health R01MH079943 (W.K.S.); UK National Institute for Health Research (NIHR) grants (PB-PG-0110-21190: C.C.) and (PB-PG-0107-12042: P.C.); UK MRC grants (09-800-17: P.C. and C.C.; G0802326: K.T., P.C., and C.C.; G1002011: P.W., C.C., and P.C.; and G0601874; C.C.). Grant 09-800-17 was managed by Correspondence to Thalia Eley, PhD, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, SGDP Centre, Box P080, De Crespingy Park, London, SE5 8AF UK; e-mail: thalia.eley@kcl.ac.uk, or Kathryn Lester, DPhil, School of Psychology, University of Sussex, pevensey Building, Falmer, Brighton, BN1 9QH, UK; e-mail: k.lester@sussex.ac.uk 0890-8567/$36.00/ª2015 American Academy of Child and Adolescent Psychiatry. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). http://dx.doi.org/10.1016/j.jaac.2015.03.018 www.jaacap.org Downloaded for Anonymous User (n/a) at University of Groningen from ClinicalKey.com by Elsevier on June 27, 2019. For personal use only. No other uses without permission. Copyright ©2019. Elsevier Inc. All rights reserved. PREDICTORS OF CBT OUTCOME IN PEDIATRIC ANXIETY DISORDERS 18. Lovibond SH, Lovibond PF. Manual for the Depression Anxiety Stress Scales. 2nd ed. Sydney: Psychology Foundation; 1995. phobic and anxiety disorders in children. Behav Ther. 2000;31: 713-731. 9. Knight A, Hudson J, McLellan L, Jones M. Pre-treatment predictors of outcome in childhood anxiety disorders: a systematic review. Psycho- pathol Rev. 2014;1:52. y y y gy 19. Creswell C, Apetroaia A, Murray L, Cooper P. Cognitive, affective, and behavioral characteristics of mothers with anxiety disorders in the context of child anxiety disorder. J Abnorm Psychol. 2012; 122:26-38. p 10. Lundkvist-Houndoumadi I, Hougaard E, Thastum M. Pre-treatment child and family characteristics as predictors of outcome in cognitive behavioural therapy for youth anxiety disorders. Nord J Psychiatry. 2014; 68:524-535. 20. Lyneham HJ, Abbott MJ, Rapee RM. Interrater Reliability of the Anxiety Disorders Interview Schedule for DSM-IV: Child and Parent Version. J Am Academy Child Adolesc Psychiatry. 2007;46:731-736. 11. Hudson JL, Newall C, Rapee RM, et al. The impact of brief parental anxiety management on child anxiety treatment outcomes: a controlled trial. J Clin Child Adolesc Psychol. 2014;43:370-380. y y y 21. StataCorp. Stata statistical software: release 12. StataCorp; 2011. 22. Lovibond PF, Lovibond SH. The structure of negative emotional states: comparison of the Depression Anxiety Stress Scales (DASS) with the Beck Depression and Anxiety Inventories. Behav Res Ther. 1995;33: 335-343. y 12. Rapee RM, Abbott MJ, Lyneham HJ. Bibliotherapy for children with anxiety disorders using written materials for parents: a randomized controlled trial. J Consult Clin Psychol. 2006;74:436-444. 23. Manassis K, Lee TC, Bennett K, et al. Types of parental involvement in CBT with anxious youth: a preliminary meta-analysis. J Consult Clin Psychol. 2014;82:1163-1172. y 13. Hudson JL, Lester KJ, Lewis CM, et al. Predicting outcomes following cognitive behaviour therapy in child anxiety disorders: the influence of genetic, demographic and clinical information. J Child Psychol Psychia- try. 2013;54:1086-1094. y 24. Beidel DC, Turner SM, Morris TL. Behavioral treatment of childhood social phobia. J Consult Clin Psychol. 2000;68:1072-1080. y 14. Legerstee JS, Tulen JH, Dierckx B, et al. CBT for childhood anxiety dis- orders: differential changes in selective attention between treatment re- sponders and non-responders. J Child Psychol Psychiatry Allied Discipl. 2010;51:162-172. www.jaacap.org 25. Bodden DH, Bogels SM, Nauta MH, et al. Child versus family cognitive- behavioral therapy in clinically anxious youth: an efficacy and partial effectiveness study. J Am Acad Child Adolesc Psychiatry. 2008;47: 1384-1394. 15. Silverman WK, Albano AM. The Anxiety Disorders Interview Schedule for Children-IV (Child and Parent Versions). New York: Oxford Uni- versity Press; 1996. 26. Schneider S, In-Albon T, Nuendel B, Margraf J. Parental panic treatment reduces children’s long-term psychopathology: a prospective longitudi- nal study. Psychother Psychosom. 2013;82:346-348. 16. Schneider S, Unnewehr S, Margraf J. Kinder-DIPS fur DSM-IV-TR. Diagnostisches Interview bei psychischen Strungen im Kindes- und Jugendalter. Heidelberg: Springer; 2009. 27. Cobham VE, Dadds MR, Spence SH, McDermott B. Parental anxiety in the treatment of childhood anxiety: a different story three years later. J Clin Child Adolesc Psychol. 2010;39:410-420. y 28. Bennett K, Manassis K, Walter SD, et al. Cognitive behavioral therapy age effects in child and adolescent anxiety: an individual patient data meta- analysis. Depress Anxiety. 2013;30:829-841. 17. American Psychiatric Association. Diagnostic and Statistical Manual of Mental Disorders. 4th edition. Arlington, VA: American Psychiatric Association; 1994:97-327. 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https://openalex.org/W2804810112
https://www.frontiersin.org/articles/10.3389/fonc.2018.00125/pdf
English
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Multimodal Light Microscopy Approaches to Reveal Structural and Functional Properties of Promyelocytic Leukemia Nuclear Bodies
Frontiers in oncology
2,018
cc-by
20,706
Multimodal Light Microscopy Approaches to Reveal Structural and Functional Properties of Promyelocytic Leukemia Nuclear Bodies The promyelocytic leukemia (pml) gene product PML is a tumor suppressor localized mainly in the nucleus of mammalian cells. In the cell nucleus, PML seeds the formation of macromolecular multiprotein complexes, known as PML nuclear bodies (PML NBs). While PML NBs have been implicated in many cellular functions including cell cycle regulation, survival and apoptosis their role as signaling hubs along major genome main- tenance pathways emerged more clearly. However, despite extensive research over the past decades, the precise biochemical function of PML in these pathways is still elusive. It remains a big challenge to unify all the different previously suggested cellular functions of PML NBs into one mechanistic model. With the advent of genetically encoded fluores- cent proteins it became possible to trace protein function in living specimens. In parallel, a variety of fluorescence fluctuation microscopy (FFM) approaches have been developed which allow precise determination of the biophysical and interaction properties of cel- lular factors at the single molecule level in living cells. In this report, we summarize the current knowledge on PML nuclear bodies and describe several fluorescence imaging, manipulation, FFM, and super-resolution techniques suitable to analyze PML body assembly and function. These include fluorescence redistribution after photobleaching, fluorescence resonance energy transfer, fluorescence correlation spectroscopy, raster image correlation spectroscopy, ultraviolet laser microbeam-induced DNA damage, erythrocyte-mediated force application, and super-resolution microscopy approaches. Since most if not all of the microscopic equipment to perform these techniques may be available in an institutional or nearby facility, we hope to encourage more researches to exploit sophisticated imaging tools for their research in cancer biology. Citation: Hoischen C, Monajembashi S, Weisshart K and Hemmerich P (2018) Multimodal Light Microscopy Approaches to Reveal Structural and Functional Properties of Promyelocytic Leukemia Nuclear Bodies. Front. Oncol. 8:125. doi: 10.3389/fonc.2018.00125 Keywords: live cell imaging, fluorescence fluctuation microscopy, super-resolution, promyelocytic leukemia, tumor suppressor, oncogene Edited by: Elisa Ferrando-May, Universität Konstanz, Germany Reviewed by: Lothar Schermelleh, University of Oxford, United Kingdom Graham Dellaire, Dalhousie University, Canada Don C. Lamb, Ludwig-Maximilians-Universität München, Germany *Correspondence: Peter Hemmerich peter.hemmerich@leibniz-fli.de Specialty section: This article was submitted to Cancer Genetics, a section of the journal Frontiers in Oncology Received: 17 November 2017 Accepted: 05 April 2018 Published: 25 May 2018 Review Review published: 25 May 2018 doi: 10.3389/fonc.2018.00125 published: 25 May 2018 doi: 10.3389/fonc.2018.00125 Edited by: Edited by: Elisa Ferrando-May, Universität Konstanz, Germany PML AND PML NUCLEAR BODIES The pml gene product (PML) is a member of the tripartite motif (TRIM)-containing protein superfamily. In human cells, six nuclear PML isoforms (I–VI) are expressed. The various isoforms originate from alternative mRNA splicing of exons 7–9 while exons 1–6 are shared by all isoforms (Figure 1A) (21). This primary sequence complexity of PML protein expression allows for common as well as individual functional modalities among the isoforms (22). PML I is the longest isoform (882 amino acids), while PML VI (552 amino acids) is the shortest isoform in the cell nucleus. Similar to other members of the TRIM family, all nuclear PML protein isoforms contain a conserved TRIM/RBCC motif consisting of a RING domain, two B-box domains and a coiled-coil domain (RBCC) (Figure 1A) (23). A nuclear localiza- tion signal (NLS) mediates predominant nuclear localization of PML. All PML isoforms contain three well-characterized small ubiquitin-related modifier (SUMO) modification sites at position 65, 160, and 490 of the PML primary sequence (Figure 1A) (24). Generally, SUMO modification of proteins plays important roles in diverse cellular processes, including chromatin organization, transcription, DNA repair, macromolecular assembly, protein i A better understanding of the biophysical and biochemical mechanisms by which PML and/or the PML nuclear bodies participate in genome maintenance is expected to facilitate the development of therapeutic strategies for the treatment of PML- related diseases (19). Novel microscopy methods have become key tools for study- ing biological systems over the past decades. Deep insight with unprecedented spatial and time resolution has been obtained for many cellular factors as a result of the rapid development of optical microscopy, fluorescent probes, and new labeling tech- niques (20). Since most biochemical mechanisms on the cellular level are dynamic by nature and cannot be fully understood by simply measuring fixed structures it is desirable to investigate the molecule of interest in real time, in living cells, at single-molecule, nanometer, and nanosecond resolution. Is this feasible? We think the answer is yes and the purpose of this report is explaining why. Figure 1 | Promyelocytic leukemia (PML) protein isoforms. (A) Schematic depiction of the six nuclear PML isoforms (I to VI). Exons 1–6 are shared by all isoforms while their C-termini are individually different due to alternative splicing of exons 7–9. R, RING domain, B, B box; CC, coiled coil domain; NLS, nuclear localization sequence; SIM, SUMO-interacting motif; S, SUMOylation sites at arginine positions K65, K160, and K490. INTRODUCTION At the physiological level, PML has been functionally linked to anti-inflammatory and antiviral response pathways, metabolism, stem cell maintenance, and aging, while more mechanistically, PML’s role in tumor suppression is linked to control of the cell cycle, apoptosis/ senescence, cell migration, angiogensis, and the DNA damage response (9, 10). Since upon DNA damage PML NBs accumulate various DNA damage response factors and physically associate with damaged chromatin, they have also been suggested to play important roles in genome maintenance, probably by supporting specific aspects of DNA repair pathways (11–18). We set out here to summarize our view of PML nuclear body function and assembly, the current status of powerful imaging methods and describe in some detail how the new imaging tools work in deciphering structural and functional aspects of PML nuclear bodies. Many of these tools may be accessible at a near-by imaging facility of most laboratories. We therefore wish to encour- age those researchers in the fields of cancer biology to exploit the new methods more rigorously. Ultimately, the combination of classical biochemical approaches with dynamic methods and live cell imaging platforms may make it possible to fully elucidate the biophysical mechanisms underlying the structure, function, and networks of tumor suppressors and oncogenes, thus aiding the development of new therapeutic approaches. INTRODUCTION The promyelocytic leukemia (pml) gene is a target of the t(15;17) chromosomal translocation, which fuses pml reciprocally with retinoic acid receptor α (RARα) (1). PML protein is the major build- ing unit of the so-called PML nuclear bodies (PML NBs). PML NBs appear as nuclear dot-shaped structures that are interspersed between chromatin (2). PML NBs are heterogeneous and dynamic May 2018  |  Volume 8  |  Article 125 Frontiers in Oncology  |  www.frontiersin.org 1 Advanced Bioimaging of PML Bodies Hoischen et al. structures, ranging in size from 0.1 to 1.0 µm, and typically there are 5–30 bodies per nucleus, depending on the cell type, phase of cell cycle, and the cellular stress level (3–5). Overexpression of PML in cancer cell lines induces cell cycle arrest and apoptosis (6). PML knock-out mice develop a range of cancers including papillomas, carcinomas, and lymphomas after exposure to car- cinogens (7). Furthermore, loss of PML is a hallmark of human cancers from diverse tissues (8). Therefore, PML is regarded as a potent tumor suppressor in in vitro (biochemistry, cell culture experiments) and in vivo (model organisms). At the physiological level, PML has been functionally linked to anti-inflammatory and antiviral response pathways, metabolism, stem cell maintenance, and aging, while more mechanistically, PML’s role in tumor suppression is linked to control of the cell cycle, apoptosis/ senescence, cell migration, angiogensis, and the DNA damage response (9, 10). Since upon DNA damage PML NBs accumulate various DNA damage response factors and physically associate with damaged chromatin, they have also been suggested to play important roles in genome maintenance, probably by supporting specific aspects of DNA repair pathways (11–18). structures, ranging in size from 0.1 to 1.0 µm, and typically there are 5–30 bodies per nucleus, depending on the cell type, phase of cell cycle, and the cellular stress level (3–5). Overexpression of PML in cancer cell lines induces cell cycle arrest and apoptosis (6). PML knock-out mice develop a range of cancers including papillomas, carcinomas, and lymphomas after exposure to car- cinogens (7). Furthermore, loss of PML is a hallmark of human cancers from diverse tissues (8). Therefore, PML is regarded as a potent tumor suppressor in in vitro (biochemistry, cell culture experiments) and in vivo (model organisms). PML AND PML NUCLEAR BODIES Additional posttranslational modifications (PTMs) of PML include phosphorylation, acetylation, and ubiquitination, all of which may serve to fine-tune PML (nuclear body) function through multiple mechanisms (28). A common feature of TRIM/RBCC proteins is homo-multimerization which generates a variety of subcellular structures including ribbon-like structures, cytoplasmic or nucleopasmic filaments, as well as cytoplasmic or nucleoplasmic bodies (23). Indeed, all six nuclear PML isoforms, when ectopically overexpressed, individually form nuclear bodies even in the absence of endogenous PML (29), with some isoforms contributing not only to nuclear body morphology (27, 30) but also function (31–33). By immunofluorescence light microscopy, normal PML bod- ies display as spherical structures, ranging in size from 0.2 µm up to 1 µm (Figure 2A). By electron or super-resolution light microscopy, PML protein is concentrated in a ~100  nm thick shell in the periphery of the nuclear bodies with no chromatin or RNA inside them (34–37). The shell also contains SUMO isoforms and other PML body components, such as SP100 (Figure  2B) (35). This structural arrangement provokes the question on the nature and biological function of the inner core of a PML NB. Within the nuclear body shell, PML’s branched SUMO chains stabilize protein complexes as a “molecular glue” (see next section). In functionally specialized PML bodies, such as in alternative lengthening of telomeres-associated PML nuclear bodies (APBs) and in immunodeficiency, centromeric instability, and facial dysmorphy (ICF) syndrome cells, the inner core of PML bodies contains chromatin, namely telomeric DNA in APBs or Figure 2 | Structure and function of promyelocytic leukemia (PML) nuclear bodies. (A) Distribution of PML protein in a cell nucleus of a MRC-5 (primary human lung fibroblast) cell. The micrograph shows the immunofluorecence signal of an antibody directed to all PML isoforms (green, monoclonal antibody E-11, sc-377390, Santa Cruz Biotechnology, Heidelberg, Germany) along with DAPI fluorescence (red) of a mid-confocal section of the nucleus. Bar; 5 µm. (B) Structure of PML nuclear bodies. SUMOylated PML protein subunits are the building blocks of a shell-like structure in the periphery of the nuclear body. Additional PML body- interacting proteins may bind to PML, specifically to the C-termini of the various PML isoforms, to the poly-small ubiquitin-related modifier (poly-SUMO) chains or to SUMO-interaction motifs. PML nuclear bodies’ are in direct contact with chromatin fibers, which contribute to the bodies physical stability. See Figure 3 for more information on the assembly mechanism. PML AND PML NUCLEAR BODIES (B) PML protein expression in various cell lines. Western blot of whole cell lysates derived from MRC-5 (primary human lung fibroblasts), U2OS (Osteosarcoma-derived ALT cell line), and HEp-2 (human epithelial non-ALT cancer cell line) using a rabbit-anti-PML antibody (ABD-030, Jena Bioscience, Germany) at 1:500 dilution. Non-SUMOylated PML isoforms are detectable between 55 kDa and 110 kDa. Poly-SUMOylated PML isoforms are detected above 110–250 kDa. Figure 1 | Promyelocytic leukemia (PML) protein isoforms. (A) Schematic depiction of the six nuclear PML isoforms (I to VI). Exons 1–6 are shared by all isoforms while their C-termini are individually different due to alternative splicing of exons 7–9. R, RING domain, B, B box; CC, coiled coil domain; NLS, nuclear localization sequence; SIM, SUMO-interacting motif; S, SUMOylation sites at arginine positions K65, K160, and K490. (B) PML protein expression in various cell lines. Western blot of whole cell lysates derived from MRC-5 (primary human lung fibroblasts), U2OS (Osteosarcoma-derived ALT cell line), and HEp-2 (human epithelial non-ALT cancer cell line) using a rabbit-anti-PML antibody (ABD-030, Jena Bioscience, Germany) at 1:500 dilution. Non-SUMOylated PML isoforms are detectable between 55 kDa and 110 kDa. Poly-SUMOylated PML isoforms are detected above 110–250 kDa. May 2018  |  Volume 8  |  Article 125 2 Advanced Bioimaging of PML Bodies Hoischen et al. homeostasis, trafficking, and signal transduction (25). In the case of PML, SUMO-2 and SUMO-3 can form heteropolymeric poly-SUMO chains (26). PML isoforms as well as their poly- SUMOylated variants can be easily detected by Western blotting (Figure  1B) (27). Additional posttranslational modifications (PTMs) of PML include phosphorylation, acetylation, and ubiquitination, all of which may serve to fine-tune PML (nuclear body) function through multiple mechanisms (28). A common feature of TRIM/RBCC proteins is homo-multimerization which generates a variety of subcellular structures including ribbon-like structures, cytoplasmic or nucleopasmic filaments, as well as cytoplasmic or nucleoplasmic bodies (23). Indeed, all six nuclear PML isoforms, when ectopically overexpressed, individually form nuclear bodies even in the absence of endogenous PML (29), with some isoforms contributing not only to nuclear body morphology (27, 30) but also function (31–33). homeostasis, trafficking, and signal transduction (25). In the case of PML, SUMO-2 and SUMO-3 can form heteropolymeric poly-SUMO chains (26). PML isoforms as well as their poly- SUMOylated variants can be easily detected by Western blotting (Figure  1B) (27). PML NUCLEAR BODY FUNCTION Systems biological analyses based on online repositories, most notably the Nuclear Protein Database1 (43) have predicted, that more than 150 nuclear proteins have the ability to interact with PML bodies (44, 45). The “Biological General Repository for Interaction Datasets” (BioGRID) lists 243 unique protein interactions.2 Resident factors of PML NBs include, beside all PML isoforms, SUMO paralogs, Daxx, and SP100 (46). Most other factors only transiently accumulate at PML bodies under specific stress conditions or in specialized PML bodies, such as APBs or the giant PML bodies in ICF cells (39). In addition to the telomeric chromatin and shelterin core components, APBs accumulate DNA recombination and repair factors such as the MRN complex, RAD (radiation sensitivity) family members, RPA and WRN (38, 47).h The functional diversity of transient PML NB components is likely the basis of the many different biological roles ascribed to these nuclear structures (Figure 2C) (5, 48). PML NBs have been functionally linked to apoptosis (49), nuclear proteolysis (50), senescence (51), stem cell renewal (52, 53), regulation of gene expression (54), tumor suppression (55), the DNA dam- age response (40, 41, 56), telomere elongation and stability (47, 57), epigenetic regulation (37, 58), and antiviral responses (59) (Figure  2C). Not surprisingly, functional annotation of PML nuclear body proteins show an enrichment of terms related to cell cycle control, cellular stress response, DNA repair, and protein modification processes (44). More globally, the various aspects of PML NB functions mainly point to their role in genome maintenance (18). The iterative nature of the multiple binding sites creates a multivalency, which has now been suggested to be responsible for the compartmentalization activity of PML NBs through the biophysical mechanism of phase-separation (67). Although only inferred as probable from GFP-SUMO/RFP-SIM phase- separation data obtained in vitro, the Banani et al. report suggests that that the polySUMO/polySIM interfaces in PML NBs may form phase-separated liquid droplet structures in living cells (68). Thus PML NBs belong to the family of viscous liquid, mem- brane less nuclear compartments, which may function as phase separating condensates equivalent to lipid droplets (69). PML AND PML NUCLEAR BODIES (C) Proposed functions of PML nuclear bodies. Probably more than 100 proteins permanently or transiently bind to PML NBs. According to these protein’s function, many different physiological roles as depicted have been proposed for PML NBs. Figure 2 | Structure and function of promyelocytic leukemia (PML) nuclear bodies. (A) Distribution of PML protein in a cell nucleus of a MRC-5 (primary human lung fibroblast) cell. The micrograph shows the immunofluorecence signal of an antibody directed to all PML isoforms (green, monoclonal antibody E-11, sc-377390, Santa Cruz Biotechnology, Heidelberg, Germany) along with DAPI fluorescence (red) of a mid-confocal section of the nucleus. Bar; 5 µm. (B) Structure of PML nuclear bodies. SUMOylated PML protein subunits are the building blocks of a shell-like structure in the periphery of the nuclear body. Additional PML body- interacting proteins may bind to PML, specifically to the C-termini of the various PML isoforms, to the poly-small ubiquitin-related modifier (poly-SUMO) chains or to SUMO-interaction motifs. PML nuclear bodies’ are in direct contact with chromatin fibers, which contribute to the bodies physical stability. See Figure 3 for more information on the assembly mechanism. (C) Proposed functions of PML nuclear bodies. Probably more than 100 proteins permanently or transiently bind to PML NBs. According to these protein’s function, many different physiological roles as depicted have been proposed for PML NBs. May 2018  |  Volume 8  |  Article 125 Frontiers in Oncology  |  www.frontiersin.org 3 Advanced Bioimaging of PML Bodies Hoischen et al. pericentric satellite heterochromatin of chromosome 1 in the giant PML bodies of ICF cells (38, 39).h reactions or complex formation between low-abundance nuclear factors, as was also suggested for other subnuclear structures such as Cajal bodies or nucleoli (62). More specifically, PML NBs may be SUMOylation hot spots. This hypothesis is driven by the observation that most components of the SUMOylation machinery concentrate in PML NBs (45). The number of PML NBs varies between 5 and 30 depend- ing on the cell-type, the cellular differentiation status, and the cell cycle. During interphase PML bodies are positionally stable through their physical and probably functional interplay with the surrounding chromatin (Figure 2B) (2). Yet, PML NBs are also dynamic structures that undergo significant changes in number, size, and position particularly in response to cellular stress (4). One example is fission of PML bodies into smaller bodies in early S phase (40, 41, 42). 1 http://npd.hgu.mrc.ac.uk/ (Accessed: November 17, 2017). 2 https://thebiogrid.org/111384/summary/homo-sapiens/pml.html (Accessed: November 17, 2017). PML AND PML NUCLEAR BODIES PML NBs may lose their structural integrity based on modifications or structural alterations in adjacent chromatin associated with DNA replication. PML NUCLEAR BODY ASSEMBLY The formation and structural integrity of PML NBs relies on at least five basic mechanistic principles: (i) oxidation-driven intermo- lecular disulfide cross-linking of PML, (ii) the self-oligomerizing properties of PML’s RBCC motif, (iii) the poly-SUMO chains on the three major target lysines, (iv) the non-covalent interac- tion of SUMO with SUMO interacting motifs (SIM) in nuclear body-associated factors, and (v) specific sequences in various PML protein isoforms (Figure 3). In the initial step of nuclear body assembly, oxidized PML monomers allow the formation of disulfide-crosslinked covalent multimers that self-organize into the NB outer shell (9, 63). Non-covalent homodimerization mediated by the RBCC domain may be similarly important for the early PML NB assembly step, since the isolated RING domain of PML very efficiently forms multimeres in vitro (64). Subsequently, UBC9-mediated poly-SUMOylation, SUMO/SIM interactions (9, 65) and addition of SUMO and/or SIM-containing binding partners create a mature PML body with a peripheral scaffold consisting of the six different PML isoforms, their SIM motifs and the poly-SUMO chains (Figure 3). Recently, it was demonstrated that certain regions in the C-terminal domains of specific PML isoforms are also important for NB assembly and function (32, 33). These findings add an additional layer of complexity in the structural and functional maintenance of PML NB integrity. The PML nuclear body scaffold offers a multitude of potential sites to which an assortment of PML-interacting, SIM-containing, and/ or SUMOylated partner proteins may bind transiently to a more or less extent. The varying residence times (Rts) of binding part- ners at PML NBs would be expected to depend on the number and strength of their individual interaction modules (66). This is in line with the presence of several SUMOylation sites and SIMs in major PML-NB components including PML, SP100, DAXX, HIPK2, UBC9, PIASy, and RNF4 (9).h PML NUCLEAR BODY FUNCTION The biochemical environment within a phase-separating PML body is different from that in the surrounding nucleoplasm, and this difference could enable unique strategies for regulating nuclear response pathways, including (a) regulation of enzyme reaction kinetics (i.e., posttranslational modifications), (b) regulation of One hypothesis for the integration of all of these functions in a unifying concept is based on the idea that PML NBs provide a stable protein scaffold onto which binding partners associate for their efficient PTM or sequestration (Figure 2C) (28, 60, 61). Controlled accumulation at or release of specific nuclear factors from the nuclear bodies may enhance their functional interaction based on mass-law action, thereby fine-tuning signaling cascades through the nucleoplasm. This mechanism may enable chemical May 2018  |  Volume 8  |  Article 125 Frontiers in Oncology  |  www.frontiersin.org 4 Hoischen et al. Advanced Bioimaging of PML Bodies Figure 3 | Assembly of promyelocytic leukemia (PML) nuclear bodies. The assembly of PML nuclear bodies is initiated by oligomerization of non-SUMOylated PML monomers. Oligomerization occurs via weak non-covalent interactions through the RBCC motif and covalent di-sulfide bonds between cystein residues. The E2-small ubiquitin-related modifier (SUMO) ligase UBC9 then promotes (poly-)SUMOylation of the PML moieties which allows for multiple SUMO–SUMO interacting motifs (SIM) interaction possibilities to form larger aggregates. Binding partners carrying SIMs and or SUMO residues can bind to the preassembled aggregates to form a normal PML body based on self-organization. Figure 3 | Assembly of promyelocytic leukemia (PML) nuclear bodies. The assembly of PML nuclear bodies is initiated by oligomerization of non-SUMOylated PML monomers. Oligomerization occurs via weak non-covalent interactions through the RBCC motif and covalent di-sulfide bonds between cystein residues. The E2-small ubiquitin-related modifier (SUMO) ligase UBC9 then promotes (poly-)SUMOylation of the PML moieties which allows for multiple SUMO–SUMO interacting motifs (SIM) interaction possibilities to form larger aggregates. Binding partners carrying SIMs and or SUMO residues can bind to the preassembled aggregates to form a normal PML body based on self-organization. genesis itself, suggesting that tightly controlled PTMs are required for full maturation of functional PML bodies in early G1 (71). the specificity of biochemical reactions, (c) sequestration of mol- ecules, and (d) buffering cellular concentration of molecules (67). Cell cycle-dependent disassembly of PML NBs begins upon de-SUMOylation of PML at the onset of mitosis. PML NUCLEAR BODY FUNCTION The spherical shell structure of PML NBs breaks down and other NB compo- nents such as SUMO, SP100, and DAXX detach or are removed. During mitosis PML aggregates into so-called mitotic accumu- lations of PML protein (MAPPs) (40, 41). Interestingly, PML bodies form stable interactions with early endosomes throughout mitosis and the two compartments dissociate in the cytoplasm of newly divided daughter cells (70). When followed through the telophase/G1 transition, Chen et al. observed that GFP-tagged MAPPs become trapped in the newly formed nuclei but also that many PML NBs are formed de novo at different sites in daughter nuclei. This suggests that PML NBs can assemble from both, MAPPs as well as soluble PML monomers in G1 (71). At the M/ G1 border of the cell cycle, MAPPs also complex with FG repeat- containing peripheral components of the nuclear pore complex to become CyPNs (cytoplasmic assemblies of PML and nucleop- orins) (72). Within CyPNs, PML appears to be instrumental in a novel, nuclear pore-independent, mechanism of nucleoporin and nuclear cargo protein targeting to the reforming G1 cell nucleus (73). The recruitment of SP100 and DAXX into newly formed PML NBs occurs considerably (ca. 30 min) later than PML NB PML IN TUMORIGENESIS So far, we have summarized some aspects of PML NB biology derived from microscopic, cell, and molecular biology approaches. Another branch of PML research has tackled questions on PML protein function by means of genetics. These approaches uncov- ered PML’s role in cancer biology. PML was originally identified as a potential gene of interest in tumorigenesis due to its associa- tion with acute promyelocytic leukemia (APL). APL is a rare but aggressive subtype of white blood cell cancer, characterized by an accumulation of promyelocytes in the bone marrow and periph- eral blood (74). The majority of APL patients are characterized by the t(15;17) chromosomal translocation that reciprocally joins the PML and retinoic acid receptor α (RARα) genes, resulting in bal- anced expression of PML-RARα and RARα-PML fusion proteins (1). While PML-RARα blocks differentiation of promyelocytes by suppressing the transcriptional function of RARα, PML-RARα disrupts the structure of PML nuclear bodies through formation of PML-RARα/PML heterodimers. This phenotype was observed in 99% of APL patients (75). Treatment of APL for many years was retinoic acid, arsenic trioxide or a combination of the two, May 2018  |  Volume 8  |  Article 125 Frontiers in Oncology  |  www.frontiersin.org 5 Advanced Bioimaging of PML Bodies Hoischen et al. which, fortunately, seemed to cure most APL patients. It is now known that the mechanism of this therapy involves targeting of the PML/RARα fusion protein to proteasomal degradation (76). Strikingly, drug treatment reverses the pathological microspeck- led PML distribution in the nucleus of APL cells toward the regular morphology of PML nuclear bodies (77). defective localization of Brca1 and Rad51 to sites of DNA damage (89). Thus, although the physiological function of PML and the nuclear bodies have not been thoroughly elucidated, their tumor- suppressive role by supporting DNA damage response pathways may be common to all of these potential functions (19, 89).h The lack of PML is not necessarily a tumor-promoting event. Functional analysis of the hematopoietic stem cell compartment in mice have uncovered that PML is required for leukemia initiating cell maintenance (90). The authors suggest a new therapeutic approach for eradication of cancer-initiating cells in leukemia through pharamacological inhibition of PML. This and other reports have lead to the suggestion that PML may act as both a tumor suppressor and an oncogene, depending on the cellular context (91). TUMOR SUPPRESSOR AND ONCOGENIC FUNCTIONS OF PML Beside the correlative connection between carcinogenesis and PML expression, there is plenty of experimental evidence for a direct tumor-suppressive role of PML. Several independent studies have demonstrated that overexpression of PML can slow down or block cell cycle progression in a variety of cancer cell lines (6, 81, 84). Likewise, in primary human or mouse fibroblasts overexpression of PML isoform IV induces a stable senescence- associated cell cycle arrest (85, 86). Further analyses of typical stress-response pathways revealed the involvement of the tumor suppressors pRb and p53 in PML overexpression-induced cellular senescence (86, 87). However, the molecular details of PML action along the pRB and/or p53 tumor suppressive pathways remain elusive. Besides in cellular senescence, PML has an essential functional role in apoptosis (49). This is based on initial observations on the first reported PML knock-out mouse model, where splenic lymphocytes and thymocytes from Pml−/− mice show barely half the capacity of wild-type cells to initiate apoptosis after ionizing radiation or after induction of the cytokine death-receptor pathway (88). As already pointed out, PML loss correlates with the progression of many cancers and in most cases low PML expression is associated with poor prognosis. The tumor suppressor function of PML NBs may be linked to their ability to accumulate many proteins involved in DNA dam- age response and repair pathways, which is believed to stabilize DNA repair complexes and enhance their activities (4, 13, 60). In support of this hypothesis, it was shown recently in a knock-in mouse model, that intact PML bodies are critical for DNA dam- age responses. Functional assays in mice expressing PML but lacking PML NBs showed impaired homologous recombination (HR) and non-homologous end-joining repair pathways, with Inter- and intracellular mechanisms of molecular communication may be better understood through direct visualization. In the past decades, advancements in imaging technologies have expanded our ability to access and analyze in living specimen the morphol- ogy of tissues and cellular components. These enabled analyses of fine-structural features at the nanoscale level, precise localization, and the dynamic interplay of single and macromolecular assem- blies that drive cell growth, the cell cycle, differentiation, and cell death (20–37). Super-resolution light microscopy delivered images with unprecedented sensitivity and clarity allowing the exploration of interactions between individual molecules with a distance resolution as low as 20  nm (94). PML IN TUMORIGENESIS Along these lines it was also demonstrated that PML targeting impacts on breast cancer (BCa)-initiating cell function, and hence on cancer initiation and dissemination in BCa (92). Furthermore, in triple- negative breast cancer cell and mouse models PML promotes cell migration, invasion, and metastasis through binding to regulatory regions of HIF1A target genes (93). These initially unexpected findings clearly suggest a previously underestimated importance of PML in the maintenance of some tumors. Another link between cancer and PML became evident by comparing PML protein expression in normal and neoplastic human tissues. Such studies documented loss of PML expression in breast carcinoma (78), gastric cancer (79), small cell lung car- cinoma (80), and in invasive epithelial tumors (81). Furthermore, microarray analyses of PML mRNA expression showed complete loss of or strongly reduced PML transcript expression in many different human neoplasms, including colon, prostate, and breast adenocarcinomas, as well as in lung, CNS, germ cell, and non- Hodgkin’s tumors/lymphomas (8). The same study reported that PML protein is also frequently overexpressed in carcinomas of larynx and thyroid, epithelial thymomas, Kaposi’s sarcoma, and in Hodgkin cells, a tumor of cytokine-producing cells. The latter phenomenon may be attributable to strong upregulation of the PML gene after Interferon induction (82). Taken together, loss of expression in many (but not all) cancer types have suggested that PML works as a tumor suppressor (83). Frontiers in Oncology  |  www.frontiersin.org TUMOR SUPPRESSOR AND ONCOGENIC FUNCTIONS OF PML New fluorescence fluctuation microscopy (FFM) approaches provided the basis for determining the biophysical and interaction properties of single molecules in living cells (95, 96). Laser-based FFM analysis tools are outlined below but many more exist, all of which unfortunately cannot be covered by this overview, including single particle tracking (SPT), light sheet microscopy, total internal reflection microscopy just to name a few. To acquire the full picture of live cell laser-based imaging technologies, we refer to recent excel- lent reviews on these topics (20, 97–99). Altogether, a plethora of new live cell imaging techniques have been developed which even large research groups are unable to establish to a broad extent in their departments. To address this, dedicated advanced light microscopy imaging facilities are extremely helpful as their members are usually microscope experts (100). However, we believe that research laboratories are still reluctant in exploiting the full potential of microscopy facilities. We therefore provide an introductory overview on some imaging instrumentation which May 2018  |  Volume 8  |  Article 125 Frontiers in Oncology  |  www.frontiersin.org 6 Advanced Bioimaging of PML Bodies Hoischen et al. the creation of photobleached spots of fluorescent molecules in solution or in living cells by the application of a laser beam. By monitoring the redistribution of the fluorescent molecules from the unbleached volume, their diffusion or transport properties can be assessed (101). FRAP and related techniques such as point continuous photobleaching, fluorescence loss in photobleaching, inverse-FRAP, and photoactivation/conversion have been devel- oped in the past, each suitable to quantitatively assess specific biophysical properties of the molecule under investigation (97). However, the limitations and pitfalls of FRAP experiments, in particular when they are employed to extract biophysical param- eters also, have to be considered. Things to consider include the complete set-up of the FRAP experiment (103), knowledge on the bleach volume profile (104), as well as the potential phototoxic effects elicited by the bleaching laser beam (105). are covered by such facilities and provide specific examples in PML biology to encourage cancer cell biologists and biochemists to extend their experimental approaches toward the exciting new imaging technologies. FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING (FRAP) A third circled unbleached region at the bottom of this nucleus is shown as a positive control. One particular bleach spot is shown in a magnified view in the bottom panels. (B) Quantitation of FRAP experiments. After background subtraction, compensation for imaging-induced photobleaching and normalization, typical FRAP curves are obtained. FRAP curve A shows full recovery to prebleach fluorescence values indicating complete exchange of the GFP-tagged protein in the bleached spot within the observation time. In FRAP curve B, fluorescence recovery is not complete within observation time indicating an immobile fraction of molecules or a fraction with a very slow exchange rate. (C) FRAP curve fitting using exponential functions. FRAP curves for GFP-tagged PML-I (left) and PML-II (right) were fitted with one-component (red) or two-component (green) exponential functions. (D) Table showing the residence time (Rt) in minutes of GFP-tagged PML isoforms I to VI derived from fitting FRAP curves employing different mathematical models (See text for details). * numbers in red letters represent Rt values derived from one component modeling which failed to precisely fit to the measured FRAP curve as shown for GFP-PML-II in (C). Figure 4 | Fluorescence recovery after photobleaching (FRAP) to assess component exchange at promyelocytic leukemia (PML) nuclear bodies. (A) A typical FRAP experiment is shown. Two circular regions in the nucleus of a GFP-PML-V expressing U2OS cell were exposed to a short 488 nm laser bleach pulse and fluorescence redistribution was monitored over time. A third circled unbleached region at the bottom of this nucleus is shown as a positive control. One particular bleach spot is shown in a magnified view in the bottom panels. (B) Quantitation of FRAP experiments. After background subtraction, compensation for imaging-induced photobleaching and normalization, typical FRAP curves are obtained. FRAP curve A shows full recovery to prebleach fluorescence values indicating complete exchange of the GFP-tagged protein in the bleached spot within the observation time. In FRAP curve B, fluorescence recovery is not complete within observation time indicating an immobile fraction of molecules or a fraction with a very slow exchange rate. (C) FRAP curve fitting using exponential functions. FRAP curves for GFP-tagged PML-I (left) and PML-II (right) were fitted with one-component (red) or two-component (green) exponential functions. (D) Table showing the residence time (Rt) in minutes of GFP-tagged PML isoforms I to VI derived from fitting FRAP curves employing different mathematical models (See text for details). Figure 4 | Fluorescence recovery after photobleaching (FRAP) to assess component exchange at promyelocytic leukemia (PML) nuclear bodies. (A) A typical FRAP experiment is shown. Two circular regions in the nucleus of a GFP-PML-V expressing U2OS cell were exposed to a short 488 nm laser bleach pulse and fluorescence redistribution was monitored over time. A third circled unbleached region at the bottom of this nucleus is shown as a positive control. One particular bleach spot is shown in a magnified view in the bottom panels. (B) Quantitation of FRAP experiments. After background subtraction, compensation for imaging-induced photobleaching and normalization, typical FRAP curves are obtained. FRAP curve A shows full recovery to prebleach fluorescence values indicating complete exchange of the GFP-tagged protein in the bleached spot within the observation time. In FRAP curve B, fluorescence recovery is not complete within observation time indicating an immobile fraction of molecules or a fraction with a very slow exchange rate. (C) FRAP curve fitting using exponential functions. FRAP curves for GFP-tagged PML-I (left) and PML-II (right) were fitted with one-component (red) or two-component (green) exponential functions. (D) Table showing the residence time (Rt) in minutes of GFP-tagged PML isoforms I to VI derived from fitting FRAP curves employing different mathematical models (See text for details). * numbers in red letters represent Rt values derived from one component modeling which failed to precisely fit to the measured FRAP curve as shown for GFP-PML-II in (C). FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING (FRAP) Arguably, one of the most commonly used approaches to study dynamic cellular processes in living cells is FRAP (101). FRAP is able to access average dynamics of diffusing molecules within the observation volume. The original description of FRAP was coined continuous fluorescence microphotolysis, which itself has been established for more than three decades (102). When subjected to repeated cycles of excitation and emission, fluorescent mol- ecules eventually lose their ability to emit fluorescence, enabling f Figure 4A shows a typical FRAP experiment for GFP-tagged PML (isofom V) at nuclear bodies. Measuring the redistribution Figure 4 | Fluorescence recovery after photobleaching (FRAP) to assess component exchange at promyelocytic leukemia (PML) nuclear bodies. (A) A typical FRAP experiment is shown. Two circular regions in the nucleus of a GFP-PML-V expressing U2OS cell were exposed to a short 488 nm laser bleach pulse and fluorescence redistribution was monitored over time. A third circled unbleached region at the bottom of this nucleus is shown as a positive control. One particular bleach spot is shown in a magnified view in the bottom panels. (B) Quantitation of FRAP experiments. After background subtraction, compensation for imaging-induced photobleaching and normalization, typical FRAP curves are obtained. FRAP curve A shows full recovery to prebleach fluorescence values indicating complete exchange of the GFP-tagged protein in the bleached spot within the observation time. In FRAP curve B, fluorescence recovery is not complete within observation time indicating an immobile fraction of molecules or a fraction with a very slow exchange rate. (C) FRAP curve fitting using exponential functions. FRAP curves for GFP-tagged PML-I (left) and PML-II (right) were fitted with one-component (red) or two-component (green) exponential functions. (D) Table showing the residence time (Rt) in minutes of GFP-tagged PML isoforms I to VI derived from fitting FRAP curves employing different mathematical models (See text for details). * numbers in red letters represent Rt values derived from one component modeling which failed to precisely fit to the measured FRAP curve as shown for GFP-PML-II in (C). Figure 4 | Fluorescence recovery after photobleaching (FRAP) to assess component exchange at promyelocytic leukemia (PML) nuclear bodies. (A) A typical FRAP experiment is shown. Two circular regions in the nucleus of a GFP-PML-V expressing U2OS cell were exposed to a short 488 nm laser bleach pulse and fluorescence redistribution was monitored over time. FLUORESCENCE (CROSS) CORRELATION SPECTROSCOPY Fluorescence correlation spectroscopy (FCS) is an in  vivo method that analyses diffusing particles in a diffraction-limited illumination ellipsoid (114, 115). The FCS detection volume is created by a laser beam in a pinhole-adjustable confocal optical system focused through a high numerical aperture objective (Figure 5A). The FCS detection volume is defined by the point spread function of the objective and the confocal pinhole. The excitation laser beam determines how much of the detection volume is excited and the final observation volume is deter- mined by the overlap of excitation and detection volumes. For objectives with a high numerical aperture (i.e., NA = 1.4) the effective measuring volume is ~1 fl (116). Photons emitted from diffusing fluorescent particles are counted continuously over time through the same optics using sensitive avalanche photodiodes (APDs) or galliumarsenidephosphide (GaAsP) hybrid detectors at single molecule resolution (Figure 5A) (117). The fluorescence intensity fluctuations are recorded over time (Figure 5B). Particle concentration is reflected by the fluctuation amplitude, whereas the frequency gives information on the diffusion times of the fluorescent particles. For quantitative evaluation, the photon trace is correlated with a time-shifted replica of itself (autocor- relation) at different time values (Figure 5C). The amplitude of the autocorrelation curve is inversely proportional to the average number of fluorescent molecules in the confocal volume allow- ing determination of particle concentration (Figure 5C). A more detailed overview on the theory, history, and application of FCS can be found here: (118, 119).l g gi g To obtain a complete picture we collected the Rts of all PML isoforms after fitting to one- and two-component exponential functions (Figure  4D). This approach delivers the Rt of the protein under investigation (110). One-component exponential fits were successful for GFP-tagged PML-I and PML-V, while FRAP curves for the other isoforms could only be fitted with two-component exponential fits (Figure  4C and data not shown). For comparison, the table includes the data we previ- ously obtained by application of a binding-diffusion model based on more sophisticated differential equation modeling to analyze the FRAP curves (66). The table shows that the Rts of PML isoforms at nuclear bodies as deduced from one-component exponential fits, is convincingly close to those obtained from assuming a binding-diffusion model (Figure 4D) although the fits are not satisfactory for PML-II, -III, -IV, and -VI (values in red letters). In particular, the very long Rt of PML-V (~50 min) is confirmed. FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING (FRAP) * numbers in red letters represent Rt values derived from one component modeling which failed to precisely fit to the measured FRAP curve as shown for GFP-PML-II in (C). May 2018  |  Volume 8  |  Article 125 7 Advanced Bioimaging of PML Bodies Hoischen et al. of fluorescence into the bleached region then yields the FRAP recovery curve (Figure  4B). During the observation time of the FRAP experiment, the fluorescence in the bleached region may return to the prebleach value (Figure 4B, curve A) or not (Figure 4B, curve B). Incomplete recovery even after long obser- vation (>1 h) has been observed for some chromatin-binding proteins, which suggests the presence of immobile or very slow exchanging populations of molecules (106, 107). FRAP data can be analyzed using mathematical models to yield kinetic parameters (108). Today, many FRAP models of processes in the cell nucleus assume that the proteins undergo diffusion as well as binding/unbinding events at chromatin or other more static subnuclear structures such as nuclear bodies. Importantly, both diffusion and binding/unbinding events contribute to the spatial dynamics of nuclear proteins (109, 110). of fluorescence into the bleached region then yields the FRAP recovery curve (Figure  4B). During the observation time of the FRAP experiment, the fluorescence in the bleached region may return to the prebleach value (Figure 4B, curve A) or not (Figure 4B, curve B). Incomplete recovery even after long obser- vation (>1 h) has been observed for some chromatin-binding proteins, which suggests the presence of immobile or very slow exchanging populations of molecules (106, 107). FRAP data can be analyzed using mathematical models to yield kinetic parameters (108). Today, many FRAP models of processes in the cell nucleus assume that the proteins undergo diffusion as well as binding/unbinding events at chromatin or other more static subnuclear structures such as nuclear bodies. Importantly, both diffusion and binding/unbinding events contribute to the spatial dynamics of nuclear proteins (109, 110). In conclusion, Figure 4 suggests that different FRAP modeling approaches, despite subtle differences, arrive at overall similar Rts for PML isoforms at nuclear bodies. It should be noted however that these long Rts do not necessarily reflect the time in which one PML molecule stays bound to one and the same specific binding site. FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING (FRAP) Long Rts may also originate from PML molecules under- going rapid binding and unbinding events at multiple adjacent binding sites (in our case at the nuclear body) without leaving the observation volume (110). If binding/unbinding events do not occur on well-separated time scales, the interaction parameters may not be readily extractable from the FRAP curves (111). A combination of different FFM approaches may be required for accurate determination of binding parameters (112). To assess binding/unbinding events at PML NBs at higher resolution, the tool kit should be extended to single particle tracking (SPT) since this approach is able to quantitatively describe several popula- tions of molecules with distinct binding properties (113). With respect to PML protein exchange at nuclear bodies it is safe to assume a binding-dominant behavior because of the very slow exchange rates as observed by FRAP (Figure 4A). Previously, the residence time (Rt) at nuclear bodies of all PML isoforms had been determined by FRAP using a binding-diffusion model based on differential equations (29, 66). It was therefore interesting to compare different modeling approaches. Figure 4C shows two examples of fitting FRAP data obtained for GFP-tagged PML isoforms I and II. Interestingly both, one- and two-exponential functions delivered good fits to the FRAP curve for GFP-PML-I but not for GFP-PML-II, where only a two-component exponen- tial function gave good fit results (Figure 4C). FLUORESCENCE (CROSS) CORRELATION SPECTROSCOPY These statistical fluctuations are mathematically processed using an autocorrelation algorithm, from which biophysical parameters such as the particle concentration, the diffusion coefficient and complex formation properties can readily be assessed (C). (D) Confocal live cell image of a U2OS nucleus coexpressing EGFP-SP100 and mRFP-PML-III (bar: 5 µm). The FCCS laser beam (light-blue) can be positioned anywhere in the cell. (E) By fitting the measured FCS data points (solid lines) to appropriate diffusion models (dashed lines), one can extract from the reciprocal of the amplitude and the decay half-time value the number of particles in the detection volume (concentration) and the diffusion time, respectively. The cross-correlation (CC) result of EGFP-SP100 and mRFP-PML-III are also shown. (F) CC results in the nucleus of living cells for a GFP–RFP fusion protein (positive control, high CC), GFP and RFP as individual proteins (negative control, no CC) and the measurement performed in (D,E). An example of FCCS measurements of PML body components is shown in Figure 5D. The image shows a live-cell confocal snap- shot of a U2OS cell nucleus transiently expressing EGFP-SP100 and mRFP-PML III. The FCS laser spot was parked at a position in the nucleoplasm where the fluorescence signals of the fusion proteins are extremely low (Figure 5D, blue arrow). EGFP and mRFP fluorescence fluctuation was then recorded over time (10  ×  10  s measurements) and the fluctuation data correlated for each fluorophore (Figure 5E). By fitting theoretical model functions to the measured autocorrelation curves, the diffusion coefficient and the concentration of the diffusing species can be extracted. In this particular cell nucleus (Figure  5D), the concentration of EGFP-SP100 and mRFP-PML-III was 8.0 nM and 2.5  nM, respectively, demonstrating the power of FCS to work at extremely low expression levels (Figure 5E). The diffu- sion coefficient in the nucleoplasm outside nuclear bodies for these PML body components had been determined previously (DSP100 = 1.23 µm2 s−1, DPML-III = 1.63 µm2 s−1) (66). Cross-correlation analysis between EGFP-SP100 and mRFP- PML-III revealed a small but significant amplitude above the value of 1.0 (Figure 5E, blue curve indicated with GFP-SP100 and RFP-PML), indicating the formation of complexes between these fusion proteins. To evaluate this observation, the CC was compared with values obtained for individually expressed GFP and RFP molecules (negative control) as well as a GFP-RFP fusion protein (positive control) (Figures  5E,F). Experiments with these fluorochromes determine the dynamic range of the FCCS set-up. FLUORESCENCE (CROSS) CORRELATION SPECTROSCOPY This observation is fully consistent with the presence of a strong homo-dimerization domain we found in the unique C-terminus of PML isofom V (32). Obviously, this domain in PML-V confers additional binding strength toward PML bodies. Fitting with two-component exponential functions assumes the presence of two populations of molecules exchanging at PML bodies with different on/off rates. These functions provided per- fect fits for all PML isoforms (Figure 4C, green curves, and data not shown), and the Rts are shown in Figure 4D. Interestingly, the two-component fits deliver considerably large populations of PML isoforms IV (61%) and VI (66%) with a Rt of ~half an hour (Figure 4D). This suggests that a subfraction of these isoforms may contribute to the structural integrity of nuclear bodies through stable incorporation. In fluorescence cross-correlation spectroscopy (FCCS), two spectrally distinct fluorophores are measured in the same detection volume at the same time (Figures 5A,B, red and green lines) and correlated by cross-correlation (CC) (Figure 5C, blue curve). The amplitude of the CC curve is directly proportional to the degree of complex formation and/or direct interaction between the two fluorescent particles (120). A practical guide to set up FCS and FCCS experiments in living cells can be found here (121–123). May 2018  |  Volume 8  |  Article 125 Frontiers in Oncology  |  www.frontiersin.org 8 Advanced Bioimaging of PML Bodies Hoischen et al. Figure 5 | Fluorescence cross-correlation spectroscopy (FCCS) analysis of promyelocytic leukemia (PML) nuclear body components. (A) Schematic side view of a living cell with the FCS laser beam focused to a position within the nucleus. The objective creates a laser light-illuminated subfemtoliter measuring volume in which single fluorescent molecules are excited to emit photons. The photons are counted on an avalanche photodiode (APD) or a galliumarsenidphosphid (GaAsP) detector as a time series of fluorescence intensity (B). These statistical fluctuations are mathematically processed using an autocorrelation algorithm, from which biophysical parameters such as the particle concentration, the diffusion coefficient and complex formation properties can readily be assessed (C). (D) Confocal live cell image of a U2OS nucleus coexpressing EGFP-SP100 and mRFP-PML-III (bar: 5 µm). The FCCS laser beam (light-blue) can be positioned anywhere in the cell. FLUORESCENCE (CROSS) CORRELATION SPECTROSCOPY (E) By fitting the measured FCS data points (solid lines) to appropriate diffusion models (dashed lines), one can extract from the reciprocal of the amplitude and the decay half-time value the number of particles in the detection volume (concentration) and the diffusion time, respectively. The cross-correlation (CC) result of EGFP-SP100 and mRFP-PML-III are also shown. (F) CC results in the nucleus of living cells for a GFP–RFP fusion protein (positive control, high CC), GFP and RFP as individual proteins (negative control, no CC) and the measurement performed in (D,E). Figure 5 | Fluorescence cross-correlation spectroscopy (FCCS) analysis of promyelocytic leukemia (PML) nuclear body components. (A) Schematic side view of a living cell with the FCS laser beam focused to a position within the nucleus. The objective creates a laser light-illuminated subfemtoliter measuring volume in which single fluorescent molecules are excited to emit photons. The photons are counted on an avalanche photodiode (APD) or a galliumarsenidphosphid (GaAsP) detector as a time series of fluorescence intensity (B). These statistical fluctuations are mathematically processed using an autocorrelation algorithm, from which biophysical parameters such as the particle concentration, the diffusion coefficient and complex formation properties can readily be assessed (C). (D) Confocal live cell image of a U2OS nucleus coexpressing EGFP-SP100 and mRFP-PML-III (bar: 5 µm). The FCCS laser beam (light-blue) can be positioned anywhere in the cell. (E) By fitting the measured FCS data points (solid lines) to appropriate diffusion models (dashed lines), one can extract from the reciprocal of the amplitude and the decay half-time value the number of particles in the detection volume (concentration) and the diffusion time, respectively. The cross-correlation (CC) result of EGFP-SP100 and mRFP-PML-III are also shown. (F) CC results in the nucleus of living cells for a GFP–RFP fusion protein (positive control, high CC), GFP and RFP as individual proteins (negative control, no CC) and the measurement performed in (D,E). Figure 5 | Fluorescence cross-correlation spectroscopy (FCCS) analysis of promyelocytic leukemia (PML) nuclear body components. (A) Schematic side view of a living cell with the FCS laser beam focused to a position within the nucleus. The objective creates a laser light-illuminated subfemtoliter measuring volume in which single fluorescent molecules are excited to emit photons. The photons are counted on an avalanche photodiode (APD) or a galliumarsenidphosphid (GaAsP) detector as a time series of fluorescence intensity (B). FÖRSTER RESONANCE ENERGY TRANSFER (FRET) The FRET process is a dipole–dipole interaction in which an excited donor fluorophore transfers energy to an acceptor mol- ecule in nanometer vicinity without absorption and emission of a photon (128). FRET is therefore commonly employed to measure the spatial distance between two fluorophores in fixed as well as in living cells (129). The FRET efficiency depends on the distance between two adjacent fluorescent molecules. At the Förster radius distance between a FRET pair (typically around 5 nm), the FRET efficiency is 50% (130). This size regime is comparable to the size of many proteins, the distance within which proteins interact, and the distance between sites on multisubunit proteins. Therefore, FRET can deliver parameters on the distance between two distinct sites on a macromolecule, the distance between two fluorophore- tagged proteins, and hence if and how these two proteins interact (131). Basically five different FRET detection methods have been developed for light microscopy, including acceptor photobleach- ing, donor photobleaching, ratio imaging, sensitized emission, and fluorescence lifetime measurements (132). Raster image correlation spectroscopy thereby expands the accessible timescales of FCS as it can resolve dynamics in the range of microseconds to seconds with still a sufficient spatial resolution (125). Data in cells are most conveniently acquired as a time series stack by raster scanning of images of selected cell areas. Due to its broad dynamic access by analyzing the fluctua- tions between neighboring pixels in the x- and y-direction, nearly all diffusion processes that take place in cellular subregions can be studied (125). A major advantage of the RICS technology is that it can be used in principle on any commercial confocal micro- scope with analog detection (126). The software and application tutorials developed by the Enrico Gratton lab can be found as downloads here.3 l In the past, we have mainly used acceptor photobleach- ing FRET (abFRET) to analyze spatial proximities within chromatin-interacting complexes (133). In abFRET, the accep- tor chromophore is photobleached, thereby preventing FRET from the donor to the acceptor (Figure 7A). If the donor and acceptor were in sufficient proximity for energy transfer, pho- tobleaching the acceptor results in an observable increase in donor fluorescence (Figure 7B). The measurement of abFRET only generates positive values when the distance between the donor and acceptor (in our case EGFP and mRFP, respec- tively) is between 3 and 8 nm. RASTER IMAGE CORRELATION SPECTROSCOPY (RICS) The examples shown illustrate the power of RICS to determine spatial maps of concentrations, aggregation, diffusion and bind- ing of mobile molecules in living cells using readily accessible instrumentation (125). Ideally, in the assessment of biophysical parameters of mobile molecules in living specimens, one wants to know the space- resolved behavior of single molecules in terms of their kinetics and interactions and without the disturbance of the equilibrium state, as occurs in FRAP. All of these parameters are provided by RICS (125). Data acquisition in RICS is quite simple as only a 2D confocal image or time series analysis is required. The scanning encodes dynamic information within a single image, which can then be extracted using RICS. The processing of the resulting images, however, is not trivial: RICS data are computed from the power spectrum of the spatial autocorrelation function that is obtained from the intensity images by 2D fast Fourier transfor- mation algorithms (125). FLUORESCENCE (CROSS) CORRELATION SPECTROSCOPY The mathematical delineation of the CC values is described elsewhere (124). Analyzing EGFP and mRFP as single molecules in our system resulted in CC = 1.001, indicating 0% complex formation while for the mRFP-EGFP fusion protein we observed a CC amplitude of 1.029, corresponding to 45% complex formation. The CC value for EGFP-SP100 and mRFP-PML-III was CC = 1.010, indicating that in this cell nucleus ca. 13% of SP100 molecules reside in a complex with PML (Figures 5E,F). These analyses demonstrate that FCS and FCCS, although May 2018  |  Volume 8  |  Article 125 Frontiers in Oncology  |  www.frontiersin.org 9 Advanced Bioimaging of PML Bodies Hoischen et al. technically somewhat more demanding than for example FRAP experiments, provide an extremely powerful tool to precisely extract biophysical and interaction data on diffusing molecules of interest in living cells. suggests incorporation of PML into larger complexes and/ or interaction with an immobile structure (i.e., chromatin), or both. RICS can also be performed on large (but not small) PML nuclear bodies (Figures  6J–M). The resulting diffusion map reveals very slow diffusion of GFP-PML-IV at or within PML NBs (Figure 6L), suggesting that binding events predominante PML molecule mobility at or in the nuclear body.h 3 http://www.lfd.uci.edu/globals/ (Accessed: November 17, 2017). FÖRSTER RESONANCE ENERGY TRANSFER (FRET) An abFRET example is shown in Figure  7C, where EGFP-Sumo-1 (green) and mRFP-PML I (red) are coexpressed in living cells. Two PML bodies were selected for analysis and acceptor photobleaching performed in region 1 but not in region 2 which served as internal control for non-FRET effects (Figure 7C). For quantitation, FRET efficien- cies in bleached and unbleached regions are then plotted in a bar diagram (Figure 7D). The plot indicates that FRET between EGFP-SUMO-1 and mRFP-PML-I occurred in most of the cases (mean of FRET = 5.5%; black bars in Figure 7D), while the unbleached control spots show a FRET mean value of −1.4% (gray bars in Figure 7C). The FRET efficiency distribution is significantly different from that in control regions (p < 0.001, n = 88) (Figure 7D). Thus, Sumo-1 is in close proximity to PML To measure RICS we have used a Zeiss LSM710 which conveniently provides a built-in RICS module in the ZEN microscope software. Some examples of RICS measurements are shown in Figure 6. As a positive control, a confocal time series was acquired in a subregion of a U2OS cell expressing EGFP (Figure 6A). RICS analysis then delivers a spatial correlation of this region (Figure 6B). By fitting of the correlation data with a 3D-free diffusion model, a spatially resolved diffusion coefficient map is generated (Figure 6C). This map shows that EGFP diffuses throughout the cellular volume with variable diffusion coeffi- cients ranging between 5 µm2 s−1 and 50 µm2 s−1. The mean value for EGFP in the nucleus by RICS was 25 (± 5) μm2 s−1 (n = 12) consistent with FCS data (127). The RICS approach also delivers a map of the number of detected mobile molecules in the diffu- sion analysis (Figure 6D). RICS was then applied to a U2OS cell nucleus expressing EGFP-PML (isoform IV) (Figures  6E–M). Two subregions of the 2D confocal time stack were selected for RICS analysis. RICS analysis in the nucleoplasm (Figures 6F–I) showed that the diffusion coefficient of GFP-tagged PML-IV is about one order of magnitude smaller than that of GFP alone (Figure  6H), consistent with FCS measurements (66). This May 2018  |  Volume 8  |  Article 125 Frontiers in Oncology  |  www.frontiersin.org 10 Hoischen et al. Advanced Bioimaging of PML Bodies Figure 6 | Spatial mapping of promyelocytic leukemia (PML) protein mobility in the nucleus by raster image correlation spectroscopy (RICS). FÖRSTER RESONANCE ENERGY TRANSFER (FRET) (A–D) As an introductory example, RICS was performed in a U2OS cell expressing EGFP alone. (A) Shows a subregion of the cell containing nuclear (nuc.) and cytoplasmic (cyt.) parts. The nuclear outshape is indicated by a black dashed line. For RICS analysis, a time series of GFP fluorescence images was acquired by confocal microscopy. Thus, the fluorescence intensity of each pixel is collected and the spatial autocorrelation is obtained per image (B). The image stack serves to increase the SNR and to be able to remove immobile and slow molecules. This analysis generates spatial maps of the diffusion coefficient (C) and the number of free molecules which contributed to the assessment (D). Since the shape of the spatial autocorrelation image indicates mostly freely diffusing species, the RICS data were fitted with a one-component 3D-free diffusion model yielding diffusion coefficients for EGFP in the nucleus between 10 µm2 s−1 and 50 µm2 s−1 (C). RICS was then performed similarly in a EGFP-PML-I-expressing U2OS cell (E–M). In the nucleoplasm, the diffusion coefficient of EGFP-tagged PML-I ranged between 1 µm2 s−1 and 4 µm2 s−1 (H). RICS in a region containing a large PML NB (J) still delivered acceptable spatial autocorrelation quality (K). This approach revealed a diffusion coefficient of EGFP-PML-I in or at PML bodies which was one order of magnitude lower than in the nucleoplasm (L). Bars; 5 µm. Figure 6 | Spatial mapping of promyelocytic leukemia (PML) protein mobility in the nucleus by raster image correlation spectroscopy (RICS). (A–D) As an introductory example, RICS was performed in a U2OS cell expressing EGFP alone. (A) Shows a subregion of the cell containing nuclear (nuc.) and cytoplasmic (cyt.) parts. The nuclear outshape is indicated by a black dashed line. For RICS analysis, a time series of GFP fluorescence images was acquired by confocal microscopy. Thus, the fluorescence intensity of each pixel is collected and the spatial autocorrelation is obtained per image (B). The image stack serves to increase the SNR and to be able to remove immobile and slow molecules. This analysis generates spatial maps of the diffusion coefficient (C) and the number of free molecules which contributed to the assessment (D). FÖRSTER RESONANCE ENERGY TRANSFER (FRET) Since the shape of the spatial autocorrelation image indicates mostly freely diffusing species, the RICS data were fitted with a one-component 3D-free diffusion model yielding diffusion coefficients for EGFP in the nucleus between 10 µm2 s−1 and 50 µm2 s−1 (C). RICS was then performed similarly in a EGFP-PML-I-expressing U2OS cell (E–M). In the nucleoplasm, the diffusion coefficient of EGFP-tagged PML-I ranged between 1 µm2 s−1 and 4 µm2 s−1 (H). RICS in a region containing a large PML NB (J) still delivered acceptable spatial autocorrelation quality (K). This approach revealed a diffusion coefficient of EGFP-PML-I in or at PML bodies which was one order of magnitude lower than in the nucleoplasm (L). Bars; 5 µm. binding properties of repair factors at DNA lesions (138). Live cell imaging of DNA damage foci has been used to reveal the mobility of repair proteins, their assembly timing into repair sites, and the movement of damaged chromatin (139–141). DNA damage can be induced globally by ionizing radiation or radiomimetic drugs allowing for bulk analysis of the DNA damage response at multiple sites of DNA damage in the nucleus (142). Generation of single focal spots of DNA damage is instrumental to analyze single repair sites and became possible by targeted expression of endonucle- ases or microirradiation (143). Coupling of UV-A light-emitting lasers into confocal microscopes resulted in the development of laser-microirradiation technologies (Figure 8A) (144, 145). Laser lines in the visible range spectrum (405–514 nm) as well as mul- tiphoton excitation (>750 nm) have been implemented in such devices (146). The advantages and disadvantages of the different laser systems to study cellular responses to DNA damage has been assessed (147). By fine-tuning the microirradiation system it is possible to discriminate between induction of base lesions, sin- gle–strand and double-strand DNA breaks. Special UV-suitable lenses (i.e., quartz glass) must be used to avoid energy loss and destroying the lenses. Objectives with a high numerical aperture I at PML NBs which was expected because of the covalent con- jugation of SUMO-1 to PML in nuclear bodies (134). A similar abFRET approach has previously been used to document the functional interaction between the CHFR mitotic checkpoint protein and PML within PML NBs (135). FÖRSTER RESONANCE ENERGY TRANSFER (FRET) By expanding this abFRET approach, the individual spatial relationships between many PML NB components and probably even the degree of PML SUMOylation could now be determined to obtain a full picture of the molecular interaction landscape within PML NBs. This kind of approach proved successful in detecting the spatial inter-relationships within the large human kinetochore complex (136) as well as in smaller complexes such as the nucleosome (137). Thus, adding FRET techniques to the experimental tool kits in many laboratories would significantly increase the understanding of protein-protein interaction net- works in cancer biology. LASER MICROIRRADIATION (B) Time courses of the fluorescence intensity of donor and acceptor during abFRET. Bleaching of the acceptor results in a fluorescence intensity increases of the donor indicating FRET (arrow). (C) Cell nucleus showing the location of EGFP-Sumo-1 and mRFP-PML I in PML-bodies. Two of them, spot1 and spot2, were selected for fluorescence intensity analysis before and after acceptor- photobleaching (see enlargements below). At spot 1, the acceptor fluorophore mRFP was bleached (compare prebleach and postbleach), whereas spot 2 was not bleached and served as control. (D) The donor fluorescence intensity variation observed during acceptor-photobleaching was determined for 89 not bleached control PML-bodies (see spot 2) yielding Evar (gray bars) and for 89 acceptor-photobleaching PML bodies (see spot 1) yielding EFRET (black bars). The numbers of observed single cases (grouped into Evar or EFRET value ranges of 4%) are displayed versus the values of Evar and EFRET. should be employed to achieve diffraction-limited focusing and fine micromanipulation. A starting point to plan the application of microirradiation techniques can be found here: (148, 149).h NBS1 has detached from the irradiated area and the number of PML NBs returned to preirradiation levels (Figure 8B, 4 h). The repair process has most likely been successfully completed by that time although direct evidence for successful repair is lacking. All these observations are consistent with previously reported data (40, 41). When DNA damage becomes irreparable, repair foci become permanent, as demonstrated for damaged telomeres (151). PML bodies stay stably associated with such irreparable DNA breaks (152). This phenomenon is illustrated in Figure 8C, where a U2OS cell was microirradiated at multiple locations in the nucleus with a high UV-A laser dose (40 μJ pulse−1) and stained for PML and gH2AX 24 h after damage induction. Interestingly, UV-induced DNA damage foci that colocalize with PML NBs are positionally more stable than non-colocalizing (14), suggesting that PML NBs may function to support topographic stability of DNA repair foci within chromatin. The involvement of PML NBs in cellular DNA damage response/repair pathways became evident upon the demonstra- tion of their colocalization with experimentally induced DNA damage foci (12, 13, 56, 150). UV laser microirradiation was also used in the initial studies to analyze in more detail the behavior of PML NBs in the vicinity of DNA damage in live cells (40, 41). LASER MICROIRRADIATION Experimental induction of DNA damage foci in living cells became an ideal method to analyze in time and space the recruitment and May 2018  |  Volume 8  |  Article 125 Frontiers in Oncology  |  www.frontiersin.org 11 Advanced Bioimaging of PML Bodies Hoischen et al. Figure 7 | Complex formation assessment of promyelocytic leukemia (PML) body components by acceptor-photobleaching Förster resonance energy transfer (FRET). (A) Schematic explanation of acceptor-photobleaching Förster resonance energy transfer (abFRET). The energy donor EGFP and the energy acceptor mRFP are fused to proteins X and Y, which are sufficiently close (<10 nm) to each other to allow for FRET. Left side: the acceptor mRFP absorbs radiation-free energy from the exited donor EGFP resulting in decreased donor fluorescence intensity. Right side: acceptor mRFP is bleached and energy is no longer transferred from donor EGFP to acceptor mRFP resulting in an increase of donor fluorescence intensity. (B) Time courses of the fluorescence intensity of donor and acceptor during abFRET. Bleaching of the acceptor results in a fluorescence intensity increases of the donor indicating FRET (arrow). (C) Cell nucleus showing the location of EGFP-Sumo-1 and mRFP-PML I in PML-bodies. Two of them, spot1 and spot2, were selected for fluorescence intensity analysis before and after acceptor- photobleaching (see enlargements below). At spot 1, the acceptor fluorophore mRFP was bleached (compare prebleach and postbleach), whereas spot 2 was not bleached and served as control. (D) The donor fluorescence intensity variation observed during acceptor-photobleaching was determined for 89 not bleached control PML-bodies (see spot 2) yielding Evar (gray bars) and for 89 acceptor-photobleaching PML bodies (see spot 1) yielding EFRET (black bars). The numbers of observed single cases (grouped into Evar or EFRET value ranges of 4%) are displayed versus the values of Evar and EFRET. Figure 7 | Complex formation assessment of promyelocytic leukemia (PML) body components by acceptor-photobleaching Förster resonance energy transfer (FRET). (A) Schematic explanation of acceptor-photobleaching Förster resonance energy transfer (abFRET). The energy donor EGFP and the energy acceptor mRFP are fused to proteins X and Y, which are sufficiently close (<10 nm) to each other to allow for FRET. Left side: the acceptor mRFP absorbs radiation-free energy from the exited donor EGFP resulting in decreased donor fluorescence intensity. Right side: acceptor mRFP is bleached and energy is no longer transferred from donor EGFP to acceptor mRFP resulting in an increase of donor fluorescence intensity. Frontiers in Oncology  |  www.frontiersin.org LASER MICROIRRADIATION The laser-microbeam is focused into the middle of the field of view by a 100×, NA 1.3 Plan Neofluar oil immersion objective (Zeiss). The Nd:YLF laser can be frequency-tripled delivering 20 ns duration pulses at 350 nm with user-defined energies from 1 µJ to 200 µJ at user defined repetition rates 1–1000 Hz. (B) A living U2OS cell expressing EGFP-tagged NBS1 and mRFP-tagged PML-IV was irradiated at a single defined spot with approx. 5 µJ of energy using the set-up described above (yellow arrow). Confocal stacks were acquired across the nucleus before and at indicated time points after the damage pulse. In (C), U2OS cells were microirradiated at multiple positions with high laser power (40 µJ per site). Twenty-four hours after DNA damage induction cells were fixed and stained to detect the DNA damage marker gH2AX (green) and endogenous PML (red). Scale bars, 5 µm. perform homologeous recombination (HR) repair (15, 16), and it should also be mentioned that permanent lack of PML induces genomic instability and increased susceptibility to cancer (11). Thus it would be now interesting to fine-dissect the molecular mechanisms by which the presence of a PML NB is supportive to DNA repair events at particular DNA damage foci. A straight- forward model would be a scaffold or platform function of the bodies for efficient biochemical repair activities nearby damaged chromatin. A combination of super-resolution techniques with live cell imaging after microirradiation is an attractive approach to further study this phenomenon. and multiple traps or as optical strecher (156–159). OTs are excellent nanotools with which manipulation in a living cell or a living organism is possible without perforating the cell membrane. Further information on OT technologies can be found in Ref. (160–162). Generally OTs are used either to trap biological objects directly with light or as indirect force trans- ducers to exert linear forces via trapped microbeads. In EMFA, polyethylenimine-coated erythrocytes are used instead of beads as the “force transmitting device” for axial force application on cells (Figure 9A) (161). Here, we used EMFA to recapitulate some of the published data on PML NB behavior after global nuclear stress. Previously it had been observed that PML NBs disintegrate into many small PML-containing structures during heat shock or exposure to Cadmium2+ ions, implying that these structures undergo a stress response to altered chromatin organization or topology (163, 164). LASER MICROIRRADIATION These studies revealed intriguing morphological changes of PML NBs near the damaged chromatin, including moving toward the breaks, coalescing, and loss of positional stability. A recapitulation of these observations is shown in Figure 8B. In this experiment, a short pulse of 350 nm UV light was focused into the nucleus of a U2OS cell expressing GFP-tagged NBS1 (A DNA damage sensor protein) (green) and mRFP-tagged PML (red). As expected, NBS1 accumulates focally at the microirradiated chromatin spot within minutes. Shortly after, new PML bodies appear at the periphery of the damage focus (30 min). After 4 h, Of course, these fascinating microscopic observations remain descriptive without supporting functional studies. Previously it was shown that depletion of PML indeed decreases the ability to May 2018  |  Volume 8  |  Article 125 Frontiers in Oncology  |  www.frontiersin.org 12 Advanced Bioimaging of PML Bodies Hoischen et al. Figure 8 | Behavior of promyelocytic leukemia (PML) bodies at UV-A microbeam induced DNA damage foci. (A) For laser damage induction, a pulsed 350 nm Nd:YLF (neodymium-doped yttrium lithium fluoride) UV-A laser (Spectra Physics) was coupled into a confocal laser scanning microscope (LSM 510) via the epifluorescence illumination path. The laser-microbeam is focused into the middle of the field of view by a 100×, NA 1.3 Plan Neofluar oil immersion objective (Zeiss). The Nd:YLF laser can be frequency-tripled delivering 20 ns duration pulses at 350 nm with user-defined energies from 1 µJ to 200 µJ at user defined repetition rates 1–1000 Hz. (B) A living U2OS cell expressing EGFP-tagged NBS1 and mRFP-tagged PML-IV was irradiated at a single defined spot with approx. 5 µJ of energy using the set-up described above (yellow arrow). Confocal stacks were acquired across the nucleus before and at indicated time points after the damage pulse. In (C), U2OS cells were microirradiated at multiple positions with high laser power (40 µJ per site). Twenty-four hours after DNA damage induction cells were fixed and stained to detect the DNA damage marker gH2AX (green) and endogenous PML (red). Scale bars, 5 µm. Figure 8 | Behavior of promyelocytic leukemia (PML) bodies at UV-A microbeam induced DNA damage foci. (A) For laser damage induction, a pulsed 350 nm Nd:YLF (neodymium-doped yttrium lithium fluoride) UV-A laser (Spectra Physics) was coupled into a confocal laser scanning microscope (LSM 510) via the epifluorescence illumination path. LASER MICROIRRADIATION When EMFA is applied on living cells expressing GFP- tagged PML, force is applied on chromatin located just below the erythrocyte (Figure  9A). This physical pressure induces the appearance of PML-containing microstructures within the region of force application (Figure 9B). Eventually, such micro- structures fuse with each other to form larger structures, while the native PML NBs remain positionally stable (Figure 9B). This behavior of PML microstructures occurs on a minute scale and was interpreted as evidence for a supramolecular assembly/disas- sembly model in which PML NBs are not a uniform, homogene- ous polymer, but rather are composed of units or modules that are linked together as supramolecular assemblies (4, 41). This view is supported by super-resolution analyses of the PML NB archi- tecture which revealed distinct occupation rather than uniform distribution of various PML body components in a shell-like structure (35) (Figure 10). Rapid disassembly/reassembly cycles of PML nuclear bodies upon cellular stress may be instrumental in their function as damage sensors and in genome maintenance. Frontiers in Oncology  |  www.frontiersin.org OPTICAL TWEEZER (OT): ERYTHROCYTE- MEDIATED FORCE APPLICATION (EMFA) In phase contrast (PhC) imaging, the position of the nucleus relative to erythrocytes can be monitored during the course of the experiment (upper panels). The behavior of PML nuclear bodies was monitored by confocal sectioning (middle panels, images show maximum intensity projections). The nuclear region of force application is shown as a magnified view in the bottom panels. Arrowheads indicate de novo formation of PML NBs. Scale bar, 5 µm. Figure 9 | Optical tweezer (OT) as a tool to analyze PML nuclear body assembly. (A) Schematic depiction of erythrocyte-mediated force application (EMFA) based on OTs. Polyethylenimine coated erythrocytes attach unspecifically to the surfaces of the adherent target cells. Erythrocytes serve as very efficient “force transmitting devices” for axial force application on cells. The cell layer is moved into the region of the desired position in such a way that the laser focus (yellow ellipse) locates slightly below the erythrocyte. Immediately after switching on the laser the erythrocyte is pulled toward the focus due to the gradient force of the laser light, which causes a brief physical force onto the cell. The experimental setup used here consists of a continuous wave (cw) diode pumped Nd-YAG-laser (Spectra Physics) emitting at 1064 nm. The laser beam is coupled into an inverted confocal laser scanning microscope (LSM 510, Carl Zeiss Jena) and was focused via a high numerical aperture objective (100×, 1.30 NA) into the object plane. (B) U2OS cells expressing EGFP-tagged PML-IV were subjected to EMFA as shown in (A). In phase contrast (PhC) imaging, the position of the nucleus relative to erythrocytes can be monitored during the course of the experiment (upper panels). The behavior of PML nuclear bodies was monitored by confocal sectioning (middle panels, images show maximum intensity projections). The nuclear region of force application is shown as a magnified view in the bottom panels. Arrowheads indicate de novo formation of PML NBs. Scale bar, 5 µm. Figure 10 | Super-resolution imaging of promyelocytic leukemia (PML) nuclear bodies. (A) Principle of stimulated emission depletion (STED) microscopy. In STED, two lasers are focused through a high numerical aperture objective lens. The excitation laser (green) serves to excite the fluorophore of interest similar to confocal imaging. Excitation light pulses are immediately followed by a high energy red-shifted STED beam with circularly polarized light (red). OPTICAL TWEEZER (OT): ERYTHROCYTE- MEDIATED FORCE APPLICATION (EMFA) The STED light de-excites the excited fluorescence except for a small central spot due to the donut-like shape of the STED beam. This results in a subdiffraction size illumination excitation beam which can be scanned across the sample with a confocal scanner to produce super-resolved images. (B–D) Example of 3-color STED imaging of PML NBs using a Leica STED microscope. Fixed U2OS cells were immunofluorescently labeled to detect SUMO, SP100, and PML with secondary antibodies coupled to STAR-635P (green), STAR-580 (red), and Atto-490LS (blue), respectively. All dyes were depleted using the 770 nm STED laser. (B) shows one confocal section in the center of the nucleus recorded in confocal mode. (C) shows the same focal section as in (B) but recorded with the depletion laser switched on followed by deconvolution of the fluorescence signals using Huygens software (STED/decon.). (D) The DAPI signal was also acquired in the same focal section employing the HyVolution II mode of the Leica LSM (= confocal mode with the pinhole closed to 0.5 Airy units followed by deconvolution) (Confocal/decon.). (E) 3D-STORM imaging of a PML nuclear body in U2OS cells immunofluorescently labeled with an anti-PML antibody (Secondary antibody: Alexa-647N). (F) Super-resolution SIM imaging of a PML nuclear body in U2OS cells immunofluorescently labeled with an anti-PML antibody (Secondary antibody: Cy3). STORM and SIM imaging was performed using a Zeiss Elyra system. Figure 10 | Super-resolution imaging of promyelocytic leukemia (PML) nuclear bodies. (A) Principle of stimulated emission depletion (STED) microscopy. In STED, two lasers are focused through a high numerical aperture objective lens. The excitation laser (green) serves to excite the fluorophore of interest similar to confocal imaging. Excitation light pulses are immediately followed by a high energy red-shifted STED beam with circularly polarized light (red). The STED light de-excites the excited fluorescence except for a small central spot due to the donut-like shape of the STED beam. This results in a subdiffraction size illumination excitation beam which can be scanned across the sample with a confocal scanner to produce super-resolved images. (B–D) Example of 3-color STED imaging of PML NBs using a Leica STED microscope. Fixed U2OS cells were immunofluorescently labeled to detect SUMO, SP100, and PML with secondary antibodies coupled to STAR-635P (green), STAR-580 (red), and Atto-490LS (blue), respectively. All dyes were depleted using the 770 nm STED laser. OPTICAL TWEEZER (OT): ERYTHROCYTE- MEDIATED FORCE APPLICATION (EMFA) Since their introduction in 1986 by Ashkin et al. (153), OTs have developed rapidly over the past decades (154). OTs are today widely used tools in physics, chemistry, biological, and medical research (155). OTs are applicable to objects at nanometer up to several micrometer size ranges. The simplest form to use OTs is by focusing a laser beam using an objective lens of high numerical aperture (Figure 9A). As the rear pupil of the objective must be entirely illuminated, the diameter of the laser beam is expanded by telescope optics before directed to the microscope. Dielectric particles such as small biological objects near the focus will mainly experience two forces: radiation pressure in the direction of light propagation and gradient forces in the direction of the spatial light gradient. The balancing of both forces is required. The equilibrium position of particles in the focus is given if gradi- ent force dominates over the scattering force.h There are also several setup variants: conventional OT with standard Gaussian laser beam, non-Gaussian laser beams based on a Bessel beam or a Laguerre–Gaussian mode, dual beams, May 2018  |  Volume 8  |  Article 125 13 Advanced Bioimaging of PML Bodies Hoischen et al. Figure 9 | Optical tweezer (OT) as a tool to analyze PML nuclear body assembly. (A) Schematic depiction of erythrocyte-mediated force application (EMFA) based on OTs. Polyethylenimine coated erythrocytes attach unspecifically to the surfaces of the adherent target cells. Erythrocytes serve as very efficient “force transmitting devices” for axial force application on cells. The cell layer is moved into the region of the desired position in such a way that the laser focus (yellow ellipse) locates slightly below the erythrocyte. Immediately after switching on the laser the erythrocyte is pulled toward the focus due to the gradient force of the laser light, which causes a brief physical force onto the cell. The experimental setup used here consists of a continuous wave (cw) diode pumped Nd-YAG-laser (Spectra Physics) emitting at 1064 nm. The laser beam is coupled into an inverted confocal laser scanning microscope (LSM 510, Carl Zeiss Jena) and was focused via a high numerical aperture objective (100×, 1.30 NA) into the object plane. (B) U2OS cells expressing EGFP-tagged PML-IV were subjected to EMFA as shown in (A). OPTICAL TWEEZER (OT): ERYTHROCYTE- MEDIATED FORCE APPLICATION (EMFA) (B) shows one confocal section in the center of the nucleus recorded in confocal mode. (C) shows the same focal section as in (B) but recorded with the depletion laser switched on followed by deconvolution of the fluorescence signals using Huygens software (STED/decon.). (D) The DAPI signal was also acquired in the same focal section employing the HyVolution II mode of the Leica LSM (= confocal mode with the pinhole closed to 0.5 Airy units followed by deconvolution) (Confocal/decon.). (E) 3D-STORM imaging of a PML nuclear body in U2OS cells immunofluorescently labeled with an anti-PML antibody (Secondary antibody: Alexa-647N). (F) Super-resolution SIM imaging of a PML nuclear body in U2OS cells immunofluorescently labeled with an anti-PML antibody (Secondary antibody: Cy3). STORM and SIM imaging was performed using a Zeiss Elyra system. SUPER-RESOLUTION MICROSCOPY (SRM) several SRM approaches have been established over past decade which improve resolution by a factor of 2–10, depending on the technique. Meanwhile, three main super-resolution technolo- gies are commercially available, namely structured illumination microscopy (SIM), single molecule localization (SML), and stimulated emission depletion (STED) (94). The resolution of a light microscope is limited to about 200 nm by diffraction (165). The microscopic images of small cellular orga- nelles or nuclear bodies in this size range therefore appear blurred and their morphological details go undetected. Fortunately, May 2018  |  Volume 8  |  Article 125 Frontiers in Oncology  |  www.frontiersin.org 14 Advanced Bioimaging of PML Bodies Hoischen et al. Structured illumination microscopy is a versatile and the most gentle super-resolution approach which increases the resolution by up to twofold in lateral and axial direction (166, 167). This is achieved by illuminating the sample with a grid pattern. The pat- tern can for example be generated by laser light passing through a movable optical grating which is projected via the objective onto the sample (168). The interference of the pattern with sample structures allows access to high frequency or in other words high-resolution information that would be otherwise obscured in a normal wide field image. SIM requires at least 9 images (2D- SIM) or 15 images (3D-SIM) to be taken for each optical section, whereby the illumination pattern is phase shifted and rotated in order to access the high-resolution information by sophisticated algorithms (168). The advantage of SIM is that it is compatible with all fluorescent dyes, making even super-resolved multicolor live-cell imaging feasible (169).l subdiffraction-sized fluorescence spot in the center of the donut (179, 180) (Figure 10A). Interestingly, the first report on super- resolution light microscopy of PML nuclear bodies was not based on the three SRM methods described above but was realized with the so-called 4Pi microscope developed by Hell et al. (179). Four-Pi fluorescence laser-scanning microscopy studies revealed that during interphase PML NBs adopt a spherical organization characterized by the assembly of different PML body components into distinct, partially overlapping patches within a 50–100-nm thick shell (35). The spherical organization of PML NBs had been observed already before by electron microscopy (36, 48), but 4Pi allowed for simultaneous pair-wise detection of two PML body components. One example of STED nanoscopy on PML NBs is shown in Figures 10B–D. SUPER-RESOLUTION MICROSCOPY (SRM) The three major PML NB constituents SUMO, SP100 and PML were immunolabeled in U2OS cells with differ- ent fluorophores and imaged in confocal as well as in STED mode to visualize the improvement in optical resolution through STED (Figures 10B,C, respectively). As expected, STED reveals that these proteins decorate distinct, yet partially overlapping patches in the peripheral shell of the PML NB (Figure  10C). Super- imposition of the STED image with the DAPI pattern of the same confocal section confirms the absence of chromatin in the core of normal PML NBs (Figure 10D) (36). We also applied STORM and SIM imaging of PML in U2OS cells. STORM is similarly well suited to reveal the shell morphology of PML protein distribution (Figure 10E) while the resolution in SIM is, as expected, consider- ably lower than in STED or STORM (Figure 10F). However, since the laser load is much less, SIM would be better suited for live cell super-resolved imaging of PML nuclear body morphology, i.e., in the analyses of fission and fusion events of PML microstructures in stress conditions (Figure 9) or DNA at damage foci (Figure 8). In conclusion, this section shows that with commercially avail- able SRM microscopes the analysis of biomolecules can be lifted to a new optical dimension. In SML switching of molecules between two distinct fluores- cent states, normally an “on” and an “off” state is used to determine the exact position of a fluorescent molecule by determining the center of mass within the blurry fluorescent spot. The blinking is thereby adjusted to have at average only one molecule in its fluorescent state within the diffraction limited spot. The concept of blinking was realized using photoactivatable dyes, such as paGFP in photoactivated localization microscopy (PALM) and fluorescence PALM, or by using photoswitchable dye pairs (such as Cy3–Cy5 or EosFPs) as in stochastic optical reconstruction microscopy (STORM). Although PALM was established using fluorescence proteins, it was soon realized that any organic dye under appropriate reducing conditions can be brought to on and off switch cycles, a technology termed dSTORM (170). In PALM/STORM, a series of several thousand images from the blinking specimen are recorded and mathematically pro- cessed into high-resolution images reaching resolutions below 30 nm in the lateral direction (171, 172). SML approaches have the inherent disadvantage that typically (ten)thousands of frames need to be acquired to reconstruct a single super-resolved image. SUPER-RESOLUTION MICROSCOPY (SRM) The entailed low temporal resolution, extended exposure with high excitation power and associated phototoxicity render these methods less suitable for live cell imaging.l 4 http://www.eurobioimaging.eu/ (Accessed: January 12, 2018). 5 http://www.eurobioimaging.eu/global-bioimaging (Accessed: January 12, 2018). Frontiers in Oncology  |  www.frontiersin.org OUTLOOK We believe that many biochemical or molecular biology ori- ented research labs are still not aware of the multitude of new and exciting microscopic methods and their capabilities. The aim of this contribution was to present recent advances in bio- imaging in combination with selected application examples in PML nuclear body biology. Here we have illustrated the power of imaging methods and provide a guide to these techniques to make them more accessible to a larger number of labs involved in oncogene or tumor suppressor research. We have presented several experimental examples feasible in our imaging facil- ity, yet the number of additional techniques is much higher. Bioimaging facility networks have been established in several countries worldwide and these can be approached with specific imaging requests. A source for comprehensive bioimaging methodology is available Europe-wide4 and a global bioimaging network project may be realized in the near future.5 More recently developed fluctuation microscopy (SOFI, SIRF) approaches in part overcome these limitations at the expense of much lower resolution increase (173, 174). Nevertheless, live cell imaging using SML has been reported (175). Optical resolution in STED usually is well below 50 nm in fixed samples and ca. 70 nm in live-cell experiments (94). A more in depth explanation on the theory and on practical applications of SIM, SML, and STED can be found here: (176, 177). Possible practical limita- tions and compromises that must be considered when designing super-resolution experiments have been pointed out by Lambert and Waters (178). Stimulated emission depletion is based on the application of two laser beams in a confocal (point-scanning) set-up. The STED depletion laser is delivered into the optical path through a phase filter, which creates a donut-shaped beam on the confocal fluorescence spot by controlled de-excitation of the previously excited fluorophore (Figure  10A). The high intensity STED beam extinguishes the peripheral fluorescence signal, leaving a May 2018  |  Volume 8  |  Article 125 15 Advanced Bioimaging of PML Bodies Hoischen et al. in certain stem cell niches, these nuclear bodies could be imaged and functionally analyzed in various living spheroid or organoid stem cell systems using a combination of multicolor lightsheet and super-resolution approaches (187, 188). In the same experimental setting, laser-assisted ablation of single PML NB-expressing cells could help to identify PML-mediated mechanisms of stem cell plasticity (189). REFERENCES 8. Gurrieri C, Capodieci P, Bernardi R, Scaglioni PP, Nafa K, Rush LJ, et  al. Loss of the tumor suppressor PML in human cancers of multiple histologic origins. J Natl Cancer Inst (2004) 96:269–79. doi:10.1093/jnci/ djh043 1. Melnick A, Licht JD. Deconstructing a disease: RARα, its fusion partners, and their roles in the pathogenesis of acute promyelocytic leukemia. Blood (1999) 93:3167–215. 1. Melnick A, Licht JD. Deconstructing a disease: RARα, its fusion partners, and their roles in the pathogenesis of acute promyelocytic leukemia. Blood (1999) 93:3167–215. 9. Sahin U, Ferhi O, Jeanne M, Benhenda S, Berthier C, Jollivet F, et al. Oxidative stress-induced assembly of PML nuclear bodies controls sumoylation of part- ner proteins. J Cell Biol (2014) 204(6):931–45. doi:10.1083/jcb.201305148 h 2. Eskiw CH, Dellaire G, Bazett-Jones DP. Chromatin contributes to structural integrity of promyelocytic leukemia bodies through a SUMO-1- independent mechanism. J Biol Chem (2004) 279:9577–85. doi:10.1074/jbc. M312580200 10. Guan D, Kao HY. The function, regulation and therapeutic implications of the tumor suppressor protein, PML. Cell Biosci (2015) 5:60. doi:10.1186/ s13578-015-0051-9 3. Hodges M, Tissot C, Howe K, Grimwade D, Freemont PS. Structure, organi- zation, and dynamics of promyelocytic leukemia protein nuclear bodies. Am J Hum Genet (1998) 63:297–304. doi:10.1086/301991 3. Hodges M, Tissot C, Howe K, Grimwade D, Freemont PS. Structure, organi- zation, and dynamics of promyelocytic leukemia protein nuclear bodies. Am J Hum Genet (1998) 63:297–304. doi:10.1086/301991 11. Zhong S, Hu P, Ye TZ, Stan R, Ellis NA, Pandolfi PP. A role for PML and the nuclear body in genomic stability. Oncogene (1999) 18:7941–7. doi:10.1038/ sj.onc.1203367 4. Dellaire G, Bazett-Jones DP. PML nuclear bodies: dynamic sensors of DNA damage and cellular stress. Bioessays (2004) 26:963–77. doi:10.1002/ bies.20089 i 4. Dellaire G, Bazett-Jones DP. PML nuclear bodies: dynamic sensors of DNA damage and cellular stress. Bioessays (2004) 26:963–77. doi:10.1002/ bies.20089 12. Carbone R, Pearson M, Minucci S, Pelicci PG. PML NBs associate with the hMre11 complex and p53 at sites of irradiation induced DNA damage. Oncogene (2002) 21(11):1633–40. doi:10.1038/sj.onc.1205227 5. Bernardi R, Pandolfi PP. Structure, dynamics and functions of promyelo- cytic leukaemia nuclear bodies. Nat Rev Mol Cell Biol (2007) 8:1006–16. doi:10.1038/nrm2277 5. Bernardi R, Pandolfi PP. Structure, dynamics and functions of promyelo- cytic leukaemia nuclear bodies. Nat Rev Mol Cell Biol (2007) 8:1006–16. doi:10.1038/nrm2277 13. Bøe SO, Haave M, Jul-Larsen A, Grudic A, Bjerkvig R, Lønning PE. OUTLOOK Seeing is believing and therefore we look forward to monitor PML nuclear body biochemistry through new imaging set-ups in real time in living cells in the future. Local, regional, national, and supranational imaging networks will continue to develop with the aim to provide access, service and training to state-of-the-art imaging technologies. Only such dedicated facility infrastructures and/or very specialized imaging research labs will be able to cope with the fast development of novel microscopy techniques. Although probably a demanding task, both, the facility members as well as basic research scientists are now in charge to synergistically work together to fully exploit the powerful imaging tools in the study of molecular and cellular mechanisms. FUNDING This work was supported by grant HE 2484/3-1 to PH from the Deutsche Forschungsgemeinschaft. This work was supported by grant HE 2484/3-1 to PH from the Deutsche Forschungsgemeinschaft. ACKNOWLEDGMENTS We apologize to all authors who’s excellent articles in the field of PML body biology and microscopy techniques could not be cited in this contribution due to space limitations. We would like to thank the following colleagues for their time and effort in helping to establish the microscopy techniques described in our facility: Stephanie Weidtkamp-Peters, Lars Schmiedeberg, Almut Horch, Sandra Münch, Sandra Orthaus, Karolin Klement, Paulius Grigaravicius, Daniela Hellwig, Tobias Ulbricht, Volker Döring, Otto Greulich, Friedrich Haubensak, Eberhard Schmitt, Frank Große, and Stephan Diekmann. We would like to thank Debra Weih for proof-reading of the manuscript. More physiologically, it would be seminal to investigate PML NBs in their most physiological setting, the living model organism. A combination of confocal microscopy and/or nanoscopy with adaptive optics for better tissue penetration (185, 186) would enable monitoring of fluorescent PML NBs in living tissue such as skin or brain of GFP-PML knock-in mice under normal vs. stress condi- tions (irradiation, chemicals). Since PML has an established role AUTHOR NOTE We have also summarized the current knowledge on the potential functions and assembly of PML nuclear bodies. PML has been analyzed using wet-lab and genetic techniques on one hand and imaging methods on the other. With the new microscopy methods now at hand it will be exciting to see the two different approaches merging. For example, a combination of STED and FCS (STED-FCS) (181), should make it possible to assess biophysical and binding properties of PML-interacting partners within PML NBs. This would help (i) to understand the molecular/biochemical events occurring molecularly at PML NBs at sites of DNA damage and (ii) to better visualize/understand the proposed phase separation function of PML NBs (68). For exam- ple, single-molecule tracking at nanoscale resolution has recently been employed to demonstrate the liquid droplet nature of stress granules in the cell nucleus (182). As nanoscopy will become less phototoxic in the future (183), super-resolution imaging of APBs in living cells will shed more light on the mechanisms of DNA recombination events which occur in PML NBs during telomere elongation in ALT cancer cells (184). This contribution is dedicated to Jörg Langowski. AUTHOR CONTRIBUTIONS CH, SM, KW, and PH prepared the figures and wrote the text. REFERENCES PML body meets telomere: the begin- ning of an ALTernate ending? Nucleus (2012) 3:263–75. doi:10.4161/nucl.20326 h 26. Tatham MH, Jaffray E, Vaughan OA, Desterro JM, Botting CH, Naismith JH, et al. Polymeric chains of SUMO-2 and SUMO-3 are conjugated to protein substrates by SAE1/SAE2 and Ubc9. J Biol Chem (2001) 276:35368–74. doi:10.1074/jbc.M104214200 48. Lallemand-Breitenbach V, de Thé H. PML nuclear bodies. Cold Spring Harb Perspect Biol (2010) 2(5):a000661. doi:10.1101/cshperspect.a000661 i 49. Bernardi R, Papa A, Pandolfi PP. Regulation of apoptosis by PML and the PMLNBs. Oncogene (2008) 27:6299–631. doi:10.1038/onc.2008.305 27. Condemine W, Takahashi Y, Zhu J, Puvion-Dutilleul F, Guegan S, Janin A, et al. Characterization of endogenous humanpromyelocyticl eukemia iso- forms. Cancer Res (2006) 66:6192–8. doi:10.1158/0008-5472.CAN-05-3792 50. Lallemand-Breitenbach V, Zhu J, Puvion F, Koken M, Honorè N, Doubeikovsky A, et al. Role of promyelocytic leukemia (PML) sumolation in nuclear body formation, 11S proteasome recruitment, and As2O3-induced PML or PML/retinoic acid receptor alpha degradation. J Exp Med (2001) 193(12):1361–71. doi:10.1084/jem.193.12.1361 h 28. Schmitz ML, Grishina I. Regulation of the tumor suppressor PML by sequen- tial post-translational modifications. Front Oncol (2012) 2:204. doi:10.3389/ fonc.2012.00204 51. Ivanschitz L, De Thè H, Le Bras M. PML, SUMOylation, and senescence. Front Oncol (2013) 3:171. doi:10.3389/fonc.2013.00171 f 29. Brand P, Lenser T, Hemmerich P. Assembly dynamics of PML nuclear bodies in living cells. PMC Biophys (2010) 3:3. doi:10.1186/1757-5036-3-3 52. Salomoni P. Stemming out of a new PML era? Cell Death Differ (2009) 16(8):1083–92. doi:10.1038/cdd.2009.63 30. Beech SJ, Lethbridge KJ, Killick N, McGlincy N, Leppard KN. Isoforms of the promyelocytic leukemia protein differ in their effects on ND10 organization. Exp Cell Res (2005) 307:109–17. doi:10.1016/j.yexcr.2005.03.012 53. Zhou W, Bao S. PML-mediated signaling and its role in cancer stem cells. Oncogene (2014) 33(12):1475–84. doi:10.1038/onc.2013.111 ih 31. Cuchet D, Sykes A, Nicolas A, Orr A, Murray J, Sirma H, et al. PML isoforms I and II participate in PML-dependent restriction of HSV-1 replication. J Cell Sci (2011) 124:280–91. doi:10.1242/jcs.075390 54. Zhong S, Salomoni P, Pandolfi PP. The transcriptional role of PML and the nuclear body. Nat Cell Biol (2000) 2(5):E85–90. doi:10.1038/35010583 55. Hofmann TG, Will H. Body language: the function of PML nuclear bodies in apoptosis regulation. Cell Death Differ (2003) 10(12):1290–9. doi:10.1038/ sj.cdd.4401313 32. Geng Y, Monajembashi S, Shao A, Cui D, He W, Chen Z, et al. Contribution of the C-terminal regions of promyelocytic leukemia protein (PML) isoforms II and V to PML nuclear body formation. REFERENCES Promyelocytic leukemia nuclear bodies are predetermined processing sites for damaged DNA. J Cell Sci (2006) 119(Pt 16):3284–95. doi:10.1242/ jcs.03068 6. Mu ZM, Le XF, Vallian S, Glassman AB, Chang KS. Stable overexpression of PML alters regulation of cell cycle progression in HeLa cells. Carcinogenesis (1997) 18:2063–9. doi:10.1093/carcin/18.11.2063 6. Mu ZM, Le XF, Vallian S, Glassman AB, Chang KS. Stable overexpression of PML alters regulation of cell cycle progression in HeLa cells. Carcinogenesis (1997) 18:2063–9. doi:10.1093/carcin/18.11.2063 14. Foltánková V, Matula P, Sorokin D, Kozubek S, Bártová E. Hybrid detectors improved time-lapse confocal microscopy of PML and 53BP1 nuclear body colocalization in DNA lesions. Microsc Microanal (2013) 19:360–9. doi:10.1017/S1431927612014353 7. Wang ZG, Delva L, Gaboli M, Rivi R, Giorgio M, Cordon-Cardo C, et al. Role of PML in cell growth and the retinoic acid pathway. Science (1998) 279:1547–51. doi:10.1126/science.279.5356.1547 7. Wang ZG, Delva L, Gaboli M, Rivi R, Giorgio M, Cordon-Cardo C, et al. Role of PML in cell growth and the retinoic acid pathway. Science (1998) 279:1547–51. doi:10.1126/science.279.5356.1547 May 2018  |  Volume 8  |  Article 125 Frontiers in Oncology  |  www.frontiersin.org 16 Hoischen et al. Advanced Bioimaging of PML Bodies 15. Boichuk S, Hu L, Makielski K, Pandolfi PP, Gjoerup OV. Functional connec- tion between Rad51 and PML in homology-directed repair. PLoS One (2011) 6(10):e25814. doi:10.1371/journal.pone.0025814 38. Yeager TR, Neumann AA, Englezou A, Huschtscha LI, Noble JR, Reddel RR. Telomerase-negative immortalized human cells contain a novel type of promyelocytic leukemia (PML) body. Cancer Res (1999) 59:4175–9. 16. Yeung PL, Denissova NG, Nasello C, Hakhverdyan Z, Chen JD, Brenneman MA. Promyelocytic leukemia nuclear bodies support a late step in DNA dou- ble-strand break repair by homologous recombination. J Cell Biochem (2012) 113:1787–99. doi:10.1002/jcb.24050 39. Luciani JJ, Depetris D, Usson Y, Metzler-Guillemain C, Mignon-Ravix C, Mitchell MJ, et al. PML nuclear bodies are highly organised DNA-protein structures with a function in heterochromatin remodelling at the G2 phase. J Cell Sci (2006) 119:2518–31. doi:10.1242/jcs.02965 17. Legartová S, Sehnalová P, Malyšková B, Küntziger T, Collas P, Cmarko D, et  al. Localized movement and levels of 53BP1 protein are changed by γ-irradiation in PML deficient cells. J Cell Biochem (2016) 117:2583–96. doi:10.1002/jcb.25551 40. Dellaire G, Eskiw CH, Dehghani H, Ching RW, Bazett-Jones DP. Mitotic accumulations of PML protein contribute to the re-establishment of PML nuclear bodies in G1. J Cell Sci (2006) 119(Pt 6):1034–42. doi:10.1242/ jcs.02817 18. REFERENCES Chang HR, Munkhjargal A, Kim MJ, Park SY, Jung E, Ryu JH, et al. The functional roles of PML nuclear bodies in genome maintenance. Mutat Res (2017). doi:10.1016/j.mrfmmm.2017.05.002 41. Dellaire G, Ching RW, Ahmed K, Jalali F, Tse KC, Bristow RG, et  al. Promyelocytic leukemia nuclear bodies behave as DNA damage sensors whose response to DNA double-strand breaks is regulated by NBS1 and the kinases ATM, Chk2, and ATR. J Cell Biol (2006) 175:55–66. doi:10.1083/jcb.200604009 h j 19. Gamell C, Jan Paul P, Haupt Y, Haupt S. PML tumour suppression and beyond: therapeutic implications. FEBS Lett (2014) 588:2653–62. doi:10.1016/j. febslet.2014.02.007 42. Ching G, Dehghani RW, Ren HY, Bazett-Jones DP. The number of PML nuclear bodies increases in early S phase by a fission mechanism. J Cell Sci (2006) 119:1026–33. doi:10.1242/jcs.02816 h 20. Liu Z, Lavis LD, Betzig E. Imaging live-cell dynamics and structure at the single-molecule level. Mol Cell (2015) 58:644–59. doi:10.1016/j. molcel.2015.02.033 43. Dellaire G, Farrall R, Bickmore WA. The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome. Nucleic Acids Res (2003) 31:328–30. doi:10.1093/nar/gkg018 h 21. Jensen K, Shiels C, Freemont PS. PML protein isoforms and the RBCC/TRIM motif. Oncogene (2001) 20:7223–33. doi:10.1038/sj.onc.1204765 f 44. Mohamad N, Bodén M. The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression. BMC Syst Biol (2010) 4:44. doi:10.1186/1752-0509-4-44 22. Nisole S, Maroui MA, Mascle XH, Aubry M, Chelbi-Alix MK. Differential roles of PML isoforms. Front Oncol (2013) 3:1–17. doi:10.3389/fonc.2013.00125 h 23. Reymond A, Meroni G, Fantozzi A, Merla G, Cairo S, Luzi L, et al. The tripar- tite motif family identifies cell compartments. EMBO J (2001) 20:2140–51. doi:10.1093/emboj/20.9.2140 45. Van Damme E, Laukens K, Dang TH, Van Ostade X. A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics. Int J Biol Sci (2010) 6:51–67. doi:10.7150/ijbs.6.51 24. Kamitani T, Kito K, Nguyen HP, Wada H, Fukuda-Kamitani T, Yeh ET. Identification of three major sentrinization sites in PML. J Biol Chem (1998) 273:26675–82. 46. Negorev D, Maul GG. Cellular proteins localized at and interacting within ND10/PML nuclear bodies/PODs suggest functions of a nuclear depot. Oncogene (2001) 20:7234–42. doi:10.1038/sj.onc.1204764 25. Flotho A, Melchior F. Sumoylation: a regulatory protein modification in health and disease. Annu Rev Biochem (2013) 82:357–85. doi:10.1146/ annurev-biochem-061909-093311 47. Chung I, Osterwald S, Deeg KI, Rippe K. REFERENCES J Biol Chem (2012) 287(36):30729–42. doi:10.1074/jbc.M112.374769 56. Varadaraj A, Dovey CL, Laredj L, Ferguson B, Alexander CE, Lubben N, et al. Evidence for the receipt of DNA damage stimuli by PML nuclear domains. J Pathol (2007) 211(4):471–80. doi:10.1002/path.2126 33. Li C, Peng Q, Wan X, Sun H, Tang J. C-terminal motifs in promyelocytic leukemia protein isoforms critically regulate PML nuclear body formation. J Cell Sci (2017) 130:3496–506. doi:10.1242/jcs.202879 57. Marchesini M, Matocci R, Tasselli L, Cambiaghi V, Orleth A, Furia L, et al. PML is required for telomere stability in non-neoplastic human cells. Oncogene (2016) 35:1811–21. doi:10.1038/onc.2015.246 h 34. de Thè G, Riviére M, Bernhard W. Examen au microscope e’lectronique de la tumeur VX2 du lapin domestique de´rive´e du papillome de Shope. Bull Cancer (1960) 47:570–84. h 58. Salomoni P. The PML-interacting protein DAXX: histone loading gets into the picture. Front Oncol (2013) 3:152. doi:10.3389/fonc.2013.00152 35. Lang M, Jegou T, Chung I, Richter K, Münch S, Udvarhelyi A, et al. Three- dimensional organization of promyelocytic leukemia nuclear bodies. J Cell Sci (2010) 123:392–400. doi:10.1242/jcs.053496 59. Tavalai N, Stamminger T. New insights into the role of the subnuclear struc- ture ND10 for viral infection. Biochim Biophys Acta (2008) 1783(11):2207–21. doi:10.1016/j.bbamcr.2008.08.004 36. Boisvert FM, Hendzel MJ, Bazett-Jones DP. Promyelocytic leukemia (PML) nuclear bodies are protein structures that do not accumulate RNA. J Cell Biol (2000) 148:283–92. doi:10.1083/jcb.148.2.283 60. Dellaire G, Bazett-Jones DP. Beyond repair foci: subnuclear domains and the cellular response to DNA damage. Cell Cycle (2007) 15:1864–72. doi:10.4161/ cc.6.15.4560 37. Torok D, Ching RW, Bazett-Jones DP. PML nuclear bodies as sites of epigen- etic regulation. Front Biosci (2009) 14:1325–36. doi:10.2741/3311 61. Borden KL, Culjkovic B. Perspectives in PML: a unifying framework for PML function. Front Biosci (Landmark Ed) (2009) 14:497–509. doi:10.2741/3258 May 2018  |  Volume 8  |  Article 125 Frontiers in Oncology  |  www.frontiersin.org 17 Advanced Bioimaging of PML Bodies Hoischen et al. 62. Rajendra TK, Praveen K, Matera AG. Genetic analysis of nuclear bodies: from nondeterministic chaos to deterministic order. Cold Spring Harb Symp Quant Biol (2010) 75:365–74. doi:10.1101/sqb.2010.75.043h 85. Bischof O, Kirsh O, Pearson M, Itahana K, Pelicci PG, Dejean A. Deconstructing PMLinduced premature senescence. EMBO J (2002) 21:3358–69. doi:10.1093/emboj/cdf341 63. Sahin U, Lallemand-Breitenbach V, de The H. PML nuclear bodies: regu- lation, function and therapeutic perspectives. J Pathol (2014) 234:289–91. doi:10.1002/path.4426 86. Mallette FA, Goumard S, Gaumont-Leclerc MF, Moiseeva O, Ferbeyre G. REFERENCES Chen YC, Kappel C, Beaudouin J, Eils R, Spector DL. Live cell dynamics of promyelocytic leukemia nuclear bodies upon entry into and exit from mitosis. Mol Biol Cell (2008) 19(7):3147–62. doi:10.1091/mbc.E08-01-0035 72. Jul-Larsen A, Grudic A, Bjerkvig R, Bøe SO. Cell cycle regulation and dynamics of cytoplasmic compartments containing the promyelocytic leu- kemia protein and nucleoporins. J Cell Sci (2009) 122:1201–10. doi:10.1242/ jcs.040840 94. Sahl SJ, Hell SW, Jakobs S. Fluorescence nanoscopy in cell biology. Nat Rev Mol Cell Biol (2017) 18:685–701. doi:10.1038/nrm.2017.71 l 95. Weidemann T, Mücksch J, Schwille P. Fluorescence fluctuation microscopy: a diversified arsenal of methods to investigate molecular dynamics inside cells. Curr Opin Struct Biol (2014) 28:69–76. doi:10.1016/j.sbi.2014.07.008 ll 73. Lång A, Eriksson J, Schink KO, Lång E, Blicher P, Połeć A, et al. Visualization of PML nuclear import complexes reveals FG-repeat nucleoporins at cargo retrieval sites. Nucleus (2017) 8:404–20. doi:10.1080/19491034.2017.1306161 96. Bag N, Wohland T. Imaging fluorescence fluctuation spectroscopy: new tools for quantitative bioimaging. Annu Rev Phys Chem (2014) 65:225–48. doi:10.1146/annurev-physchem-040513-103641 74. Hillestad LK. Acute promyelocytic leukemia. Acta Med Scand (1957) 159:189–94. doi:10.1111/j.0954-6820.1957.tb00124.x 97. Wachsmuth M, Conrad C, Bulkescher J, Koch B, Mahen R, Isokane M, et al. High-throughput fluorescence correlation spectroscopy enables analysis of proteome dynamics in living cells. Nat Biotechnol (2015) 33(4):384–9. doi:10.1038/nbt.3146 75. Goddard AD, Borrow J, Freemont PS, Solomon E. Characterization of a zinc finger gene disrupted by the t(15,17) in acute promyelocytic leukemia. Science (1991) 254:1371–4. doi:10.1126/science.1720570 76. de Thè H, Chen Z. Acute promyelocytic leukaemia: novel insights into the mechanisms of cure. Nat Rev Cancer (2010) 10:775–83. doi:10.1038/nrc2943 98. Thorn K. A quick guide to light microscopy in cell biology. Mol Biol Cell (2016) 27(2):219–22. doi:10.1091/mbc.E15-02-0088 77. Zhu J, Koken MHM, Quignon F, Chelbi-Alix MK, Degos L, Wang ZY, et al. Arsenic-induced PML targeting onto nuclear bodies: implications for the treatment of acute promyelocytic leukemia. Proc Natl Acad Sci U S A (1997) 94:3978–83. doi:10.1073/pnas.94.8.3978 99. Follain G, Mercier L, Osmani N, Harlepp S, Goetz JG. Seeing is believing – multi-scale spatio-temporal imaging towards in vivo cell biology. J Cell Sci (2017) 130(1):23–38. doi:10.1242/jcs.189001 100. Ferrando-May E, Hartmann H, Reymann J, Ansari N, Utz N, Fried HU, et al. Advanced light microscopy core facilities: balancing service, science and career. German BioImaging network. Microsc Res Tech (2016) 79(6):463–79. doi:10.1002/jemt.22648 78. Gambacorta M, Flenghi L, Fagioli M, Pileri S, Leoncini L, Bigerna B, et al. REFERENCES Human fibroblasts require the Rb family of tumor suppressors, but not p53, for PML-induced senescence. Oncogene (2004) 23:91–9. doi:10.1038/ sj.onc.1206886 64. Kentsis A, Gordon RE, Borden KL. Control of biochemical reactions through supramolecular RING domain self-assembly. Proc Natl Acad Sci U S A (2002) 99(24):15404–9. doi:10.1073/pnas.202608799 87. de Stanchina E, Querido E, Narita M, Davuluri RV, Pandolfi PP, Ferbeyre G, et al. PML is a direct p53 target that modulates p53 effector functions. Mol Cell (2004) 13:523–35. doi:10.1016/S1097-2765(04)00062-0 65. Matunis MJ, Zhang XD, Ellis NA. SUMO: the glue that binds. Dev Cell (2006) 11(5):596–7. doi:10.1016/j.devcel.2006.11.011 88. Wang ZG, Ruggero D, Ronchetti S, Zhong S, Gaboli M, Rivi R, et al. PML is essential for multiple apoptotic pathways. Nat Genet (1998) 20:266–72. doi:10.1038/3073 66. Weidtkamp-Peters S, Lenser T, Negorev D, Gerstner N, Hofmann TG, Schwanitz G, et al. Dynamics of component exchange at PMLnuclear bodies. J Cell Sci (2008) 121:2731–43. doi:10.1242/jcs.031922 89. Voisset E, Moravcsik E, Stratford EW, Jaye A, Palgrave CJ, Hills RK, et al. Pml nuclear body disruption cooperates in APL pathogenesis and impairs DNA damage repair pathways in mice. Blood (2018) 131:636–48. doi:10.1182/ blood-2017-07-794784 67. Banani SF, Lee HO, Hyman AA, Rosen MK. Biomolecular condensates: orga- nizers of cellular biochemistry. Nat Rev Mol Cell Biol (2017) 18(5):285–98. doi:10.1038/nrm.2017.7 68. Banani SF, Rice AM, Peeples WB, Lin Y, Jain S, Parker R, et al. Compositional control of phase-separated cellular bodies. Cell (2016) 166(3):651–63. doi:10.1016/j.cell.2016.06.010 90. Ito K, Bernardi R, Morotti A, Matsuoka S, Saglio G, Ikeda Y, et al. PML targeting eradicates quiescent leukaemia-initiating cells. Nature (2008) 453:1072–8. doi:10.1038/nature07016 69. Uversky VN. Intrinsically disordered proteins in overcrowded milieu: mem- brane-less organelles, phase separation, and intrinsic disorder. Curr Opin Struct Biol (2017) 44:18–30. doi:10.1016/j.sbi.2016.10.015 91. Mazza M, Pelicci PG. Is PML a tumor suppressor? Front Oncol (2013) 3:174. doi:10.3389/fonc.2013.00174 92. Martín-Martín N, Piva M, Urosevic J, Aldaz P, Sutherland JD, Fernández- Ruiz S, et al. Stratification and therapeutic potential of PML in metastatic breast cancer. Nat Commun (2016) 7:12595. doi:10.1038/ncomms12595 70. Palibrk V, Lång E, Lång A, Schink KO, Rowe AD, Bøe SO. Promyelocytic leukemia bodies tether to early endosomes during mitosis. Cell Cycle (2014) 13(11):1749–55. doi:10.4161/cc.28653 93. Ponente M, Campanini L, Cuttano R, Piunti A, Delledonne GA, Coltella N, et  al. PML promotes metastasis of triple-negative breast cancer through transcriptional regulation of HIF1A target genes. JCI Insight (2017) 2:e87380. doi:10.1172/jci.insight.87380 71. REFERENCES Ultrasensitive detection of single molecules by fluo- rescence correlation spectroscopy. Bioscience (1990) 3:180–3. 138. Karanam K, Loewer A, Lahav G. Dynamics of the DNA damage response: insights from live-cell imaging. Brief Funct Genomics (2013) 12(2):109–17. doi:10.1093/bfgp/els059 116. Rüttinger S, Buschmann V, Krämer B, Erdmann R, Macdonald R, Koberling F. Comparison and accuracy of methods to determine the confocal volume for quantitative fluorescence correlation spectroscopy. J Microsc (2008) 232:343–52. doi:10.1111/j.1365-2818.2008.02105.x 139. Essers J, Houtsmuller AB, van Veelen L, Paulusma C, Nigg AL, Pastink A, et al. Nuclear dynamics of RAD52 group homologous recombination pro- teins in response to DNA damage. EMBO J (2002) 21(8):2030–7. doi:10.1093/ emboj/21.8.2030 117. Becker W, Su B, Holub O, Weisshart K. FLIM and FCS detection in laser-scanning microscopes: increased efficiency by GaAsP hybrid detectors. Microsc Res Tech (2011) 74(9):804–11. doi:10.1002/jemt.20959 140. Bekker-Jensen S, Mailand N. Assembly and function of DNA double-strand break repair foci in mammalian cells. DNA Repair (Amst) (2010) 9(12):1219– 28. doi:10.1016/j.dnarep.2010.09.010 118. Elson EL. Fluorescence correlation spectroscopy: past, present, future. Biophys J (2011) 101(12):2855–70. doi:10.1016/j.bpj.2011.11.012 141. Lemaître C, Soutoglou E. DSB (Im)mobility and DNA repair compartmen- talization in mammalian cells. J Mol Biol (2015) 427(3):652–8. doi:10.1016/j. jmb.2014.11.014 119. Ries J, Schwille P. Fluorescence correlation spectroscopy. Bioessays (2012) 34(5):361–8. doi:10.1002/bies.201100111 120. Schwille P, Meyer-Almes FJ, Rigler R. Dual-color fluorescence cross-cor- relation spectroscopy for multicomponent diffusional analysis in solution. Biophys J (1997) 72(4):1878–86. doi:10.1016/S0006-3495(97)78833-7 h 142. Rothkamm K, Barnard S, Moquet J, Ellender M, Rana Z, Burdak-Rothkamm S. DNA damage foci: meaning and significance. Environ Mol Mutagen (2015) 56(6):491–504. doi:10.1002/em.21944 121. Thews E, Gerken M, Eckert R, Zäpfel J, Tietz C, Wrachtrup J. Cross talk free fluorescence cross correlation spectroscopy in live cells. Biophys J (2005) 89:2069–76. doi:10.1529/biophysj.104.057919 143. Polo SEP, Jackson SP. Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications. Genes Dev (2011) 25(5):409–33. doi:10.1101/gad.2021311 122. Bacia K, Kim SA, Schwille P. Fluorescence cross-correlation spectroscopy in living cells. Nat Methods (2006) 3(2):83–9. doi:10.1038/nmeth822 144. Kim JS, Heale JT, Zeng W, Kong X, Krasieva TB, Ball AR Jr, et al. In situ analysis of DNA damage response and repair using laser microirradiation. Methods Cell Biol (2007) 82:377–407. doi:10.1016/S0091-679X(06)82013-3 123. Weidtkamp-Peters S, Weisshart K, Schmiedeberg L, Hemmerich P. Fluorescence correlation spectroscopy to assess the mobility of nuclear proteins. Methods Mol Biol (2009) 464:321–41. doi:10.1007/978-1-60327-461-6_18 145. Ferrando-May E, Tomas M, Blumhardt P, Stöckl M, Fuchs M, Leitenstorfer A. REFERENCES Heterogeneous nuclear expression of the promyelocytic leukemia (PML) protein in normal and neoplastic human tissues. Am J Pathol (1996) 149:2023–35. 101. Carrero G, McDonald D, Crawford E, de Vries G, Hendzel MJ. Using FRAP and mathematical modeling to determine the in  vivo kinetics of nuclear proteins. Methods (2003) 29:14–28. l 79. Lee HE, Jee CD, Kim MA, Lee HS, Lee YM, Lee BL, et al. Loss of promy- elocytic leukemia protein in human gastric cancers. Cancer Lett (2007) 247:103–9. doi:10.1016/j.canlet.2006.03.034 102. Peters R, Brünger A, Schulten K. Continuous fluorescence microphotolysis: a sensitive method for study of diffusion processes in single cells. Proc Natl Acad Sci U S A (1981) 78(2):962–6. doi:10.1073/pnas.78.2.962 80. Zhang P, Chin W, Chow LT, Chan AS, Yim AP, Leung SF, et al. Lack of expres- sion for the suppressor PML in human small cell lung carcinoma. Int J Cancer (2000) 85:599–605. doi:10.1002/(SICI)1097-0215(20000301)85:5<599:: AID-IJC1>3.0.CO;2-# 103. Mueller F, Mazza D, Stasevich TJ, McNally JG. FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know? Curr Opin Cell Biol (2010) 22(3):403–11. doi:10.1016/j.ceb.2010.03.002 81. Koken MH, Linares-Cruz G, Quignon F, Viron A, Chelbi-Alix MK, Sobczak- Thépot J, et  al. The PML growthsuppressor has an altered expression in human oncogenesis. Oncogene (1995) 10:1315–24. h 104. Blumenthal D, Goldstien L, Edidin M, Gheber LA. Universal approach to FRAP analysis of arbitrary bleaching patterns. Sci Rep (2015) 5:11655. doi:10.1038/srep11655 82. Lavau C, Marchio A, Fagioli M, Jansen J, Falini B, Lebon P, et al. The acute promyelocytic leukaemia-associated PML gene is induced by interferon. Oncogene (1995) 11(5):871–6. 105. Dobrucki JW, Feret D, Noatynska A. Scattering of exciting light by live cells in fluorescence confocal imaging: phototoxic effects and relevance for FRAP studies. Biophys J (2007) 93:1778–86. doi:10.1529/biophysj.106. 096636 g 83. Salomoni P, Pandolfi PP. The role of PML in tumor suppression. Cell (2002) 108:165–70. doi:10.1016/S0092-8674(02)00626-8 84. Le XF, Yang P, Chang KS. Analysis of the growth and transformation sup- pressor domains of promyelocytic leukemia gene, PML. J Biol Chem (1996) 271:130–5. doi:10.1074/jbc.271.1.130 106. Hemmerich P, Schmiedeberg L, Diekmann S. Dynamic as well as stable protein interactions contribute to genome function and maintenance. Chromosome Res (2011) 19(1):131–51. doi:10.1007/s10577-010-9161-8 May 2018  |  Volume 8  |  Article 125 Frontiers in Oncology  |  www.frontiersin.org 18 Advanced Bioimaging of PML Bodies Hoischen et al. 130. Clegg RM. FRET tells us about proximities, distances, orientations and dynamic properties. J Biotechnol (2002) 82(3):177–9. REFERENCES doi:10.1016/ S1389-0352(01)00044-7 107. van Royen ME, Zotter A, Ibrahim SM, Geverts B, Houtsmuller AB. Nuclear proteins: finding and binding target sites in chromatin. Chromosome Res (2011) 19(1):83–98. doi:10.1007/s10577-010-9172-5 131. Jares-Erijman EA, Jovin TM. Imaging molecular interactions in living cells by FRET microscopy. Curr Opin Chem Biol (2006) 10(5):409–16. doi:10.1016/j. cbpa.2006.08.021 108. McNally JG. Quantitative FRAP in analysis of molecular binding dynamics in  vivo. Methods Cell Biol (2008) 85:329–51. doi:10.1016/ S0091-679X(08)85014-5 109. Beaudouin J, Mora-Bermúdez F, Klee T, Daigle N, Ellenberg J. Dissecting the contribution of diffusion and interactions to the mobility of nuclear proteins. Biophys J (2006) 90:1878–94. doi:10.1529/biophysj.105.071241 132. Padilla-Parra S, Tramier M. FRET microscopy in the living cell: different approaches, strengths and weaknesses. Bioessays (2012) 34(5):369–76. doi:10.1002/bies.201100086 133. Diekmann S, Hoischen C. Biomolecular dynamics and binding studies in the living cell. Phys Life Rev (2014) 11(1):1–30. doi:10.1016/j.plrev.2013. 11.011 110. Sprague BL, Pego RL, Stavreva DA, McNally JG. Analysis of binding reactions by fluorescence recovery after photobleaching. Biophys J (2004) 86:3473–95. doi:10.1529/biophysj.103.026765 111. Erdel F, Müller-Ott K, Baum M, Wachsmuth M, Rippe K. Dissecting chroma- tin interactions in living cells from protein mobility maps. Chromosome Res (2011) 19(1):99–115. doi:10.1007/s10577-010-9155-6 134. Müller S, Matunis MJ, Dejean A. Conjugation with the ubiquitin-related modifier SUMO-1 regulates the partitioning of PML within the nucleus. EMBO J (1998) 17(1):61–70. doi:10.1093/emboj/17.1.61 112. Baum M, Erdel F, Wachsmuth M, Rippe K. Retrieving the intracellular topol- ogy from multi-scale protein mobility mapping in living cells. Nat Commun (2014) 24(5):4494. doi:10.1038/ncomms5494 135. Daniels MJ, Marson A, Venkitaraman AR. PML bodies control the nuclear dynamics and function of the CHFR mitotic checkpoint protein. Nat Struct Mol Biol (2004) 11(11):1114–21. doi:10.1038/nsmb837 113. Gebhardt JC, Suter DM, Roy R, Zhao ZW, Chapman AR, Basu S, et al. Single- molecule imaging of transcription factor binding to DNA in live mammalian cells. Nat Methods (2013) 10(5):421–6. doi:10.1038/nmeth.2411 hl 136. Hellwig D, Hoischen C, Ulbricht T, Diekmann S. Acceptor-photobleaching FRET analysis of core kinetochore and NAC proteins in living human cells. Eur Biophys J (2009) 38(6):781–91. doi:10.1007/s00249-009-0498-x 114. Magde D, Elson E, Webb WW. Thermodynamic fluctuations in a reacting system – measurement by fluorescence correlation spectroscopy. Phys Rev Lett (1972) 29:705–8. doi:10.1103/PhysRevLett.29.705 137. Bui M, Dimitriadis EK, Hoischen C, An E, Quénet D, Giebe S, et al. Cell- cycle-dependent structural transitions in the human CENP-A nucleosome in vivo. Cell (2012) 150(2):317–26. doi:10.1016/j.cell.2012.05.035 115. Rigler R, Widengren J. REFERENCES Superresolution optical fluctuation imaging (SOFI). Adv Exp Med Biol (2012) 733:17–21. doi:10.1007/978-94-007-2555-3_2 152. Münch S, Weidtkamp-Peters S, Klement K, Grigaravicius P, Monajembashi S, Salomoni P, et  al. The tumor suppressor PML specifically accumulates at RPA/Rad51-containing DNA damage repair foci but is nonessential for DNA damage-induced fibroblast senescence. Mol Cell Biol (2014) 34:1733–46. doi:10.1128/MCB.01345-13 174. Gustafsson N, Culley S, Ashdown G, Owen DM, Pereira PM, Henriques R. Fast live-cell conventional fluorophore nanoscopy with ImageJ through super-resolution radialfluctuations. Nat Commun (2016) 7:12471. doi:10.1038/ncomms12471 153. Ashkin A, Dziedzic JM, Bjorkholm JE, Chu S. Observation of a single-beam gradient force optical trap for dielectric paricles. Opt Lett (1986) 11:288–90. doi:10.1364/OL.11.000288 175. Hess ST, Gould TJ, Gudheti MV, Maas SA, Mills KD, Zimmerberg J. Dynamic clustered distribution of hemagglutinin resolved at 40 nm in living cell mem- branes discriminates between raft theories. Proc Natl Acad Sci U S A (2007) 104:17370–5. doi:10.1073/pnas.0708066104 154. Greulich KO. Selected applications of laser scissors and tweezers and new applications in heart research. Methods Cell Biol (2008) 82:59–80. doi:10.1016/S0091-679X(06)82002-9 176. Blom H, Widengren J. Stimulated emission depletion microscopy. Chem Rev (2017) 117:7377–427. doi:10.1021/acs.chemrev.6b00653 155. Greulich KO, Pilarczyk G, Hoffmann A, Meyer Zu Hörste G, Schäfer B, Uhl V, et  al. Micromanipulation by laser microbeam and optical twee- zers: from plant cells to single molecules. J Microsc (2000) 198:182–7. doi:10.1046/j.1365-2818.2000.00698.x 177. Fornasiero EF, Opazo F. Super-resolution imaging for cell biologists: con- cepts, applications, current challenges and developments. Bioessays (2015) 37:436–51. doi:10.1002/bies.201400170 178. Lambert TJ, Waters JC. Navigating challenges in the application of superresolution microscopy. J Cell Biol (2017) 216:53–63. doi:10.1083/ jcb.201610011 156. MCGloin D, Dholakia K. Bessel beams: diffraction in a new light. Contemp Phys (2005) 46:15–28. doi:10.1080/0010751042000275259 157. Nie Z, Shi G, Li D, Zhang X, Wang Y, Song Y. Tight focusing of a radially polarized Laguerre–Bessel–Gaussian beam and its application to manipula- tion of two types of particles. Phys Lett A (2015) 379:857–63. doi:10.1016/j. physleta.2014.11.029 179. Hell SW, Stelzer EH, Lindek S, Cremer C. Confocal microscopy with an increased detection aperture: type-B 4Pi confocal microscopy. Opt Lett (1994) 19:222–32. doi:10.1364/OL.19.000222 f 180. Hell SW, Wichmann J. Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt Lett (1994) 19:780–2. doi:10.1364/OL.19.000780 158. Diekmann R, Wolfson DL, Spahn C, Heilemann M, Schuttpelz M, Huser T. Nanoscopy of bacterial cells immobilized by holographic optical tweezers. Nat Commun (2016) 7:13711–4. doi:10.1038/ncomms13711 181. REFERENCES Highlighting the DNA damage response with ultrashort laser pulses in the near infrared and kinetic modeling. Front Genet (2013) 16(4):135. doi:10.3389/fgene.2013.00135 124. Bacia K, Schwille P. A dynamic view of cellular processes by in vivo fluores- cence auto- and cross-correlation spectroscopy. Methods (2003) 29(1):74–85. doi:10.1016/S1046-2023(02)00291-8 146. Gassman NR, Wilson SH. Micro-irradiation tools to visualize base excision repair and single-strand break repair. DNA Repair (Amst) (2015) 31:52–63. doi:10.1016/j.dnarep.2015.05.001 125. Digman MA, Brown CM, Sengupta P, Wiseman PW, Horwitz AR, Gratton E. Measuring fast dynamics in solutions and cells with a laser scanning microscope. Biophys J (2005) 89(2):1317–27. doi:10.1529/biophysj.105. 062836 147. Kong X, Mohanty SK, Stephens J, Heale JT, Gomez-Godinez V, Shi LZ, et al. Comparative analysis of different laser systems to study cellular responses to DNA damage in mammalian cells. Nucleic Acids Res (2009) 37(9):68. doi:10.1093/nar/gkp221 126. Brown CM, Dalal RB, Hebert B, Digman MA, Horwitz AR, Gratton E. Raster image correlation spectroscopy (RICS) for measuring fast protein dynamics and concentrations with a commercial laser scanning confocal microscope. J Microsc (2008) 229:78–91. doi:10.1111/j.1365-2818.2007.01871.x 148. Holton NW, Andrews JF, Gassman NR. Application of laser micro-irradia- tion for examination of single and double strand break repair in mammalian cells. J Vis Exp (2017) (127). doi:10.3791/56265 127. Chen Y, Müller JD, Ruan Q, Gratton E. Molecular brightness characterization of EGFP in vivo by fluorescence fluctuation spectroscopy. Biophys J (2002) 82(1 Pt 1):133–44. doi:10.1016/S0006-3495(02)75380-0 149. Lukas C, Bartek J, Lukas J. Imaging of protein movement induced by chromosomal breakage: tiny ‘local’ lesions pose great ‘global’ challenges. Chromosoma (2005) 114(3):146–54. doi:10.1007/s00412-005-0011-y 128. Förster T. Zwischenmolekulare Energiewanderung und Fluoreszenz. Ann Phys (1948) 437:55–75. doi:10.1002/andp.19484370105 150. Bischof O, Kim SH, Irving J, Beresten S, Ellis NA, Campisi J. Regulation and localization of the Bloom syndrome protein in response to DNA damage. J Cell Biol (2001) 153(2):367–80. doi:10.1083/jcb.153.2.367 129. Sun Y, Rombola C, Jyothikumar V, Periasamy A. Förster resonance energy transfer microscopy and spectroscopy for localizing protein-protein interactions in living cells. Cytometry A (2013) 83(9):780–93. doi:10.1002/ cyto.a.22321 151. Fumagalli M, Rossiello F, Clerici M, Barozzi S, Cittaro D, Kaplunov JM, et  al. Telomeric DNA damage is irreparable and causes persistent DNA- May 2018  |  Volume 8  |  Article 125 Frontiers in Oncology  |  www.frontiersin.org 19 Hoischen et al. Advanced Bioimaging of PML Bodies damage-response activation. Nat Cell Biol (2012) 14(4):355–65. doi:10.1038/ ncb2466 173. Dertinger T, Colyer R, Vogel R, Heilemann M, Sauer M, Enderlein J, et al. REFERENCES Mueller V, Honigmann A, Ringemann C, Medda R, Schwarzmann G, Eggeling C. FCS in STED microscopy: studying the nanoscale of lipid membrane dynamics. Methods Enzymol (2013) 519:1–38. doi:10.1016/ B978-0-12-405539-1.00001-4 159. Guck J, Ananthakrishnan R, Mahmood H, Moon TJ, Cunningham CC, Käs J. The optical stretcher: a novel laser tool to micromanipulate cells. Biophys J (2001) 81:767–84. doi:10.1016/S0006-3495(01)75740-2 160. Greulich KO. Manipulation of cells with laser microbeam scissors and optical tweezers: a review. Rep Prog Phys (2017) 80(2):026601. doi:10.1088/1361-6633/80/2/026601 182. Niewidok B, Igaev M, Pereira da Graca A, Strassner A, Lenzen C, Richter CP, et  al. Single-molecule imaging reveals dynamic biphasic partition of RNA-binding proteins in stress granules. J Cell Biol (2018) 217(4):1303–18. doi:10.1083/jcb.201709007 161. Grigaravicius P, Greulich KO, Monajembashi S. Laser microbeams and optical tweezers in ageing research. Chemphyschem (2009) 10:79–85. doi:10.1002/cphc.200800725 183. Balzarotti F, Eilers Y, Gwosch KC, Gynnå AH, Westphal V, Stefani FD, et al. Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes. Science (2017) 355:606–12. doi:10.1126/science. aak9913 162. Zhang H, Liu K-K. Optical tweezers for single cells. J R Soc Interface (2008) 5:671–90. doi:10.1098/rsif.2008.0052 163. Maul GG, Yu E, Ishov AM, Epstein AL. Nuclear domain 10 (ND10) associ- ated proteins are also present in nuclear bodies and redistribute to hundreds of nuclear sites after stress. J Cell Biochem (1995) 59:498–513. doi:10.1002/ jcb.240590410 184. Osterwald S, Deeg KI, Chung I, Parisotto D, Wörz S, Rohr K, et al. PML induces compaction, TRF2 depletion and DNA damage signaling at telomeres and promotes their alternative lengthening. J Cell Sci (2015) 128:1887–900. doi:10.1242/jcs.148296 164. Eskiw CH, Dellaire G, Mymryk JS, Bazett-Jones DP. Size, position and dynamic behavior of PML nuclear bodies following cell stress as a paradigm for supramolecular trafficking and assembly. J Cell Sci (2003) 116:4455–66. doi:10.1242/jcs.00758 185. Booth M, Andrade D, Burke D, Patton B, Zurauskas M. Aberrations and adaptive optics in super-resolution microscopy. Microscopy (Oxf) (2015) 64:251–61. doi:10.1093/jmicro/dfv033 186. Heine J, Reuss M, Harke B, D’Este E, Sahl SJ, Hell SW. Adaptive-illumination STED nanoscopy. Proc Natl Acad Sci U S A (2017) 114:9797–802. doi:10.1073/ pnas.1708304114 165. Abbe E. Beiträge zur Theorie des Mikroskops und der mikroskopischen Wahrnehmung. Arch für Mikroskopische Anat (1873) 9:413–8. doi:10.1007/ BF02956173 187. Valm AM, Cohen S, Legant WR, Melunis J, Hershberg U, Wait E, et  al. Applying systems-level spectral imaging and analysis to reveal the organelle interactome. Nature (2017) 546:162–7. doi:10.1038/nature22369 166. Gustafsson MG. REFERENCES Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J Microsc (2000) 198:82–7. doi:10.1046/j.1365-2818.2000.00710.x 188. Gustavsson AK, Petrov PN, Lee MY, Shechtman Y, Moerner WE. 3D single-molecule super-resolution microscopy with a tilted light sheet. Nat Commun (2018) 9:123. doi:10.1038/s41467-017-02563-4 167. Gustafsson MG, Shao L, Carlton PM, Wang CJ, Golubovskaya IN, Cande WZ, et  al. Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophys J (2008) 94:4957–70. doi:10.1529/biophysj.107.120345 189. Engelbrecht CJ, Greger K, Reynaud EG, Krzic U, Colombelli J, Stelzer EH. Three-dimensional laser microsurgery in light-sheet based microscopy (SPIM). Opt Express (2007) 15:6420–30. doi:10.1364/OE.15.006420 168. Heintzmann R, Huser T. Super-resolution structured illumination micros- copy. Chem Rev (2017) 117(23):13890–908. doi:10.1021/acs.chemrev.7b00218 169. Shao L, Kner P, Rego EH, Gustafsson MG. Super-resolution 3D microscopy of live whole cells using structured illumination. Nat Methods (2011) 8:1044–6. doi:10.1038/nmeth.1734 Conflict of Interest Statement: KW was employed by Carl Zeiss Microscopy GmbH (ZEISS Group, Carl-Zeiss-Promenade 1007745 Jena, Germany). All other authors declare no competing interests. 170. van de Linde S, Löschberger A, Klein T, Heidbreder M, Wolter S, Heilemann M, et al. Direct stochastic optical reconstruction microscopy with standard flu- orescent probes. Nat Protoc (2011) 6:991–1009. doi:10.1038/nprot.2011.336 Copyright © 2018 Hoischen, Monajembashi, Weisshart and Hemmerich. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. 171. Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, Bonifacino JS, et  al. Imaging intracellular fluorescent proteins at nanometer resolution. Science (2006) 313:1642–5. doi:10.1126/science.1127344 172. Hess ST, Girirajan TP, Mason MD. Ultra-high resolution imaging by fluores- cence photoactivation localization microscopy. Biophys J (2006) 91:4258–72. doi:10.1529/biophysj.106.091116 172. Hess ST, Girirajan TP, Mason MD. Ultra-high resolution imaging by fluores- cence photoactivation localization microscopy. Biophys J (2006) 91:4258–72. doi:10.1529/biophysj.106.091116 May 2018  |  Volume 8  |  Article 125 Frontiers in Oncology  |  www.frontiersin.org 20
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English
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Childhood MMR vaccination and the incidence rate of measles infection: a ten year longitudinal cohort study of American children born in the 1990s
BMC pediatrics
2,019
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Open Access © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Childhood MMR vaccination and the incidence rate of measles infection: a ten year longitudinal cohort study of American children born in the 1990s David A. Geier1,2, Janet K. Kern1,2* and Mark R. Geier1,2 David A. Geier1,2, Janet K. Kern1,2* and Mark R. Geier1,2 Abstract Background: Measles (rubeola) is a highly contagious disease with significant morbidity/mortality. Measles-Mumps- Rubella (MMR) is a live-attenuated vaccine used in the United States (US) since the early 1970s to prevent measles infection. This retrospective longitudinal cohort study examined childhood MMR vaccination effectiveness (VE) on preventing diagnosed measles cases. Methods: The Independent Healthcare Research Database (IHRD) is composed of non-identifiable linked eligibility and claim healthcare records prospectively generated from the Florida Medicaid system. The SAS system was utilized to examine a cohort of 101,736 persons eligible for Florida Medicaid from 1990 to 2009 and continuously eligible with ≥10 outpatient office visits during the 120-month period following birth. There were 32,870 persons (224,492 person-years) in the cohort receiving a single dose of childhood MMR vaccine (vaccinated) and 43,538 persons (434,637 person-years) in an unvaccinated cohort (no exposures to measles-containing vaccine). The frequency of diagnosed measles (ICD-9 code: 055xxx) was examined. Cox proportional hazards models evaluated MMR vaccination and diagnosed measles over time. Results: MMR vaccinated cohort members were at significantly reduced risk of measles in the unadjusted (VE = 83.6, 95% CI = 67.2–91.8%) and adjusted (VE = 80.7, 95% CI = 61.5–83.9%) models as compared to the unvaccinated cohort. VE = 80% among younger MMR recipients (12–15 months), whereas VE = 90% among older MMR recipients (16–20 months) as compared to the unvaccinated cohort. Conclusion: Routine childhood MMR vaccination significantly reduced the incidence rate of childhood measles infections, and the VE was greater in the older recipients (16–20 months) than in the younger recipients (12–15 months). Conclusion: Routine childhood MMR vaccination significantly reduced the incidence rate of childhood measles infections, and the VE was greater in the older recipients (16–20 months) than in the younger recipients (12–15 months). Keywords: Cohort, Measles, MMR vaccine, Pediatric, Rubeola Background occur in epidemic cycles and virtually all people acquired measles before adulthood in the US prior to the imple- mentation of the national measles vaccine program in 1963. It was described prior to the national measles vaccine program in the US, annually about 500,000 cases of measles were reported, of whom 500 persons died, 48, 000 were hospitalized, and about 1000 cases of encephal- itis with permanent brain damage were observed [2]. As described by the United States (US) Centers for Dis- ease Control and Prevention (CDC), measles (rubeola) is highly contagious (90% of exposed susceptible persons develop measles) rash illness that is transmitted by direct contact with respiratory droplets or airborne spread between person to person [1]. Measles was observed to In the US, measles vaccination was initially recom- mended for administration at 9 months in 1963, 12 months in 1965, and 15 months in 1967 [1]. During the * Correspondence: jkern@dfwair.net 1Institute of Chronic Illnesses, Inc, 14 Redgate Ct, Silver Spring, MD 20905, USA 2CoMeD, Inc, 14 Redgate Ct, Silver Spring, MD 20905, USA * Correspondence: jkern@dfwair.net 1Institute of Chronic Illnesses, Inc, 14 Redgate Ct, Silver Spring, MD 20905, Institute of Chronic Illnesses, Inc, 14 Redgate Ct, Silver Spri USA 2CoMeD, Inc, 14 Redgate Ct, Silver Spring, MD 20905, USA USA 2CoMeD, Inc, 14 Redgate Ct, Silver Spring, MD 20905, USA Geier et al. BMC Pediatrics (2019) 19:325 https://doi.org/10.1186/s12887-019-1710-5 Geier et al. BMC Pediatrics (2019) 19:325 https://doi.org/10.1186/s12887-019-1710-5 Independent healthcare research database (IHRD) Independent healthcare research database (IHRD) The Independent Healthcare Research Database (IHRD) is composed of non-identifiable healthcare records generated from the Florida Medicaid system. The data contained within the IHRD were obtained from the Agency for Health Care Administration (AHCA) of the state of Florida and included eligibility and claim files. It is possible to link a person’s eligibility and claim records by a unique recipient identifier code. The eligibility records included detailed information for each person regarding their month and year of enrollment, gender, date of birth, and county level residency. The claims records included detailed information for each person regarding their diagnosis status using the International Study participants Fi 1 y p p Figure 1 presents a schematic flowchart of the IHRD data examined in the present study. A cohort of 8,440, 941 persons of all ages with no changes or missing gen- ders or dates of birth and eligible at specific times for Florida Medicaid from July 1990 through June 2009 was initially evaluated in this study. Among this cohort, a total of 1,871,728 persons were eligible for Florida Medicaid from their date of birth and among those persons a total of 193,453 persons were continuously eligible for Florida Medicaid for 120 months following birth. Finally, among the cohort of 193,453 persons continuously eligible for Florida Medicaid for 120 months following birth, a sub-cohort of 101,736 persons with ≥10 outpatient office visits during the 120-month period following birth was identified. Since, the late 1980s/early 1990s, the Advisory Commit- tee on Immunization Practices (ACIP), the American Academy of Pediatrics (AAP), and American Academy of Family Practitioners (AAFP) have recommended that the first dose of MMR vaccine should be given to children aged 12 through 15 months (with administration between 6 and 12 months under special circumstances) [1]. The measles vaccine program in the US was so success- ful against measles infections that it is the largest country in the world to have ended endemic measles transmission [6]. Therefore, it would be ethically unacceptable to con- duct placebo-controlled trials to assess measles vaccine effectiveness in the US, and as a result, current epidemio- logical research on the effectiveness of MMR vaccine needs to focus on retrospective studies of populations to optimize protection by modifying immunization schedules [7]. Vaccination status h The exposure variable examined in this study was identi- fied from the healthcare procedure codes filed on claims for each cohort member examined. The procedure codes examined, included: measles vaccination (codes: 9945, W1941, 90705), MMR vaccine (codes: 90707, W1943, 9948), measles and rubella vaccine (code: 90708), mea- sles, mumps, rubella, and varicella (MMRV) vaccine (code: 90710). Only persons receiving a single dose of MMR vaccine were included in the vaccinated cohort (codes: 90707, W1943, or 9948) and persons were con- sidered unvaccinated, if they did not receive any mea- sles-containing vaccine (codes: 9945, W1941, 90705, 90707, W1943, 9948, 90708, or 90710) during the study period examined. All persons receiving more than 1 dose of MMR vaccination or other measles-containing vac- cines were excluded from the present study. Among those vaccinated with MMR, the date of service for the first claim in chronological order with a procedure code specifying MMR vaccine was assumed to be the date of vaccine administration. Overall, it was observed that 32, 916 persons were in the MMR vaccinated cohort and 43, 538 persons were in the unvaccinated cohort. The purpose of the present retrospective longitudinal cohort study was to examine the vaccine effectiveness of childhood MMR vaccination to reduce the incidence rate of childhood measles infections in the US during the 1990s/2000s. In addition, this study examined the relationship between the age of childhood MMR vaccin- ation and its impact on the effectiveness of the vaccine. Page 2 of 11 Page 2 of 11 Geier et al. BMC Pediatrics (2019) 19:325 Geier et al. BMC Pediatrics (2019) 19:325 Code for Disease, 9th revision (ICD-9) codes, healthcare procedure codes (medical, dental, etc.), and administered drugs using National Drug Codes (NDC). The data in the IHRD were assembled and accessed under approval by the Liberty Institutional Review Board (IRB) (Deland, FL). The SAS system for Windows, version 9.4 (Cary, NC, USA) was used to examine the IHRD. 1970s combined measles-mumps-rubella (MMR) vaccine was introduced in the US [3, 4]. The MMR vaccine used in the US since the 1980s is the M-M-R® II vaccine (Merck & Co, Inc., Whitehouse Station, NJ), and is a sterile lyophilized preparation of (1) ATTENUVAX® (Measles Virus Vaccine Live), a more attenuated line of measles virus, derived from Enders’ attenuated Edmon- ston strain and propagated in chick embryo cell culture; (2) MUMPSVAX® (Mumps Virus Vaccine Live), the Jeryl Lynn™(B level) strain of mumps virus propagated in chick embryo cell culture; and (3) MERUVAX® II (Ru- bella Virus Vaccine Live), the Wistar RA 27/3 strain of live attenuated rubella virus propagated in WI-38 human diploid lung fibroblasts [5]. Outcomes The outcome variable examined in this study was identi- fied from the ICD-9 codes filed on claims for each cohort member examined. All measles-related diagnoses (code: 055xxx) were examined, including: measles (055), Page 3 of 11 Geier et al. BMC Pediatrics (2019) 19:3 Geier et al. BMC Pediatrics Fig. 1 A schematic flowchart of the data examined in the present study. Persons in the MMR vaccinated cohort received only 1 dose of MMR vaccine and includes only persons diagnosed with measles post-MMR vaccine administration (43 persons were excluded with measles diagnoses pre-MMR vaccine administration and 3 persons were diagnosed measles within 30 days of vaccine administration, which are most likely measles vaccine-associated adverse events) Fig. 1 A schematic flowchart of the data examined in the present study. Persons in the MMR vaccinated cohort received only 1 dose of MMR vaccine and includes only persons diagnosed with measles post-MMR vaccine administration (43 persons were excluded with measles diagnoses pre-MMR vaccine administration and 3 persons were diagnosed measles within 30 days of vaccine administration, which are most likely measles vaccine-associated adverse events) vaccination were included in the final MMR vaccinated cohort. As a result, the overall size of the MMR vaccinated cohort was reduced to 32,870 persons. post-measles encephalitis (code: 055.0), post-measles pneumonia (code: 055.1), post-measles otitis media (code: 055.2), measles with other specified complications (code: 055.7), measles keratoconjunctivitis (code: 055.71), mea- sles with other specified complications (code: 055.79), measles with unspecified complication (code: 055.8), and measles without mention of complication (code: 055.9). No information was available regarding whether measles cases were laboratory confirmed or not. Persons were considered to have measles if they had any of the measles- related diagnoses and persons were not considered to have measles if they did not have any of the measles-related diagnoses during the study period examined. Among those with a measles diagnosis, the date of service for the first claim in chronological order with a measles diagnosis was assumed to be the date of onset of measles infection. Only those persons either not diagnosed with measles or diagnosed with measles more than 30 days post-MMR Statistical analyses In all statistical analyses, the statistical package in SAS was utilized, and a two-sided p-value < 0.05 was considered statistically significant. The null hypothesis was that MMR vaccination would have no impact on the incidence rate of measles diagnoses. It was also assumed in this study that chances of exposure to wild type measles virus were equal in the vaccinated and unvaccinated cohorts. In order to evaluate the relationship between MMR vac- cination and diagnosed measles, person-years of follow-up were calculated in the vaccinated and unvaccinated co- horts examined in this study. In the unvaccinated cohort, person-years of follow-up began on the date of birth and continued until the end of eligibility (a maximum of 120 Geier et al. BMC Pediatrics (2019) 19:325 Page 4 of 11 Page 4 of 11 months after birth) or until the date of the first measles diagnosis. In the vaccinated cohort, person-years of fol- low-up began on the date of MMR vaccine administration and continued until the end of eligibility (a maximum of 120 months after birth) or until the date of the first mea- sles diagnosis. cohort contributing a total of 224,492 person-years and 43,538 persons in the unvaccinated cohort contributing a total of 434,637 person-years. The gender distribution was similar in the MMR vaccinated cohort (male/female ratio: 1.13) and unvaccinated cohort (male/female ratio = 1.14). In addition, overall mean dates of birth were similar in both the vaccinated and unvaccinated cohorts. g A regression analysis of diagnosed measles cases based on the Cox proportional hazards model was used to evalu- ate overtime in years the potential relationship between MMR vaccination and the outcome of a measles diagno- sis. Ties in the failure times were handled using the exact method. In addition, an evaluation of the potential impact of young (< 1 year-old) persons in the unvaccinated cohort being diagnosed with measles at an age prior to the earli- est age when MMR vaccine is first recommended at 12 months-old was undertaken. MMR vaccine effectiveness was examined in modeling by only counting cases of measles diagnosed at ≥12 months-old in the unvaccinated cohort and only examining persons receiving MMR vac- cine at ≥12 months-old in the vaccinated cohort. Finally, modeling was conducted to evaluate the potential impact of age of MMR vaccine administration (≥12 months, ≥ 16 months, and ≥20 months) on the effectiveness of the vaccine to prevent cases of measles. Statistical analyses All models were con- structed without adjustment for covariates (Model I) and with adjustment for the covariates of gender (categorical variable), date of birth (continuous variable), and county of residence (as a continuous variable) (Model II). Overall, vaccine effectiveness was determined as ((1 – hazard ratio) × 100). Table 2 shows the demographic characteristics of the 85 persons diagnosed with measles examined this study. Slightly more males than females were diagnosed with measles (male/female ratio = 1.15), but the ratio was consistent with those observed in the vaccinated and unvaccinated cohorts examined. The mean date of birth among persons diagnosed with measles was slightly earlier in chronological time in the unvaccinated cohort (1993) as compared to vaccinated cohort (1994). Most diagnosed cases of measles (> 90%) were without complications. Table 3 reveals the Cox proportional hazards model results examining the impact of childhood MMR vaccin- ation on the incidence rate of diagnosed measles. It was observed regardless of the age of childhood MMR vac- cination that the vaccine effectiveness was 83.6% (95% confidence interval = 67.2 to 91.8%) in the unadjusted and 80.7% (95% confidence interval = 61.5 to 90.4%) in the adjusted models. MMR vaccine effectiveness remained significant when only counting cases of mea- sles diagnosed at ≥1 year-old in the unvaccinated cohort and only examining persons receiving MMR vaccine at ≥1 year-old in the vaccinated cohort in the unadjusted (vaccine effectiveness = 70.9, 95% confidence interval = 37.8 to 86.4%) and adjusted (vaccine effectiveness = 65.4, 95% confidence interval = 25.6 to 83.9%) models. ICD-9 International Code of Disease, 9th revision, MMR Measles, mumps, rubella, std. Standard deviation a All persons examined in this study were enrolled from their date of birth for 120 consecutive months. All persons had non-changing dates of birth and gender status. All persons had ≥10 outpatient office visits b Persons received only 1 dose of MMR vaccine and includes only persons diagnosed with measles post-MMR vaccine administration (43 persons were excluded with measles diagnoses pre-MMR vaccine administration and 3 persons were diagnosed measles within 30 days of vaccine administration, which are most likely measles vaccine-associated adverse events) c P i d d f l i i i Results Table 1 displays the demographic characteristics of the population of persons examined in this study. Overall, there were a total 32,870 persons in the MMR vaccinated Figure 2 is a Cox proportional hazards survival plot evaluating the incidence of measles cases diagnosed over Table 1 Demographic characteristics of the persons examined in this studya Parameter Examined MMR Vaccinated Cohortb (n = 32,870) Unvaccinated Cohortc (n = 43,538) Person-Years 224,492 434,637 Gender (%) Male 17,468 (53.14%) 23,202 (53.29%) Female 15,402 (46.86%) 20,336 (46.71%) Date of Birth mean ± std. (range) 1995 ± 2.5 (1990–1999) 1994 ± 2.5 (1990–1999) Number Diagnosed with Measles (ICD-9 Code: 055xxx) 9 76 Number Diagnosed with Measles (ICD-9 Code: 055xxx) ICD-9 International Code of Disease, 9th revision, MMR Measles, mumps, rubella, std. Standard deviation a All persons examined in this study were enrolled from their date of birth for 120 consecutive months. All persons had non-changing dates of birth and gender status. All persons had ≥10 outpatient office visits b Persons received only 1 dose of MMR vaccine and includes only persons diagnosed with measles post-MMR vaccine administration (43 persons were excluded with measles diagnoses pre-MMR vaccine administration and 3 persons were diagnosed measles within 30 days of vaccine administration, which are most likely measles vaccine-associated adverse events) c d d f l c Persons received no doses of any measles-containing vaccine Page 5 of 11 Geier et al. BMC Pediatrics (2019) 19:325 Table 2 Demographic summary of the persons diagnosed with measles examined in this studya Parameter Examined All Persons Diagnosed with Measles (n = 85) Vaccinated Persons Diagnosed with Measles (n = 9)c Unvaccinated Persons with Diagnosed Measles (n = 76)d Gender (%) Male 45 (53.41%) 5 (55.56%) 40 (52.63%) Female 40 (47.06%) 4 (44.44%) 36 (47.37%) Date of Birth mean ± std. (range) 1993 ± 2.1 (1990–1999) 1994 ± 1.26 (1992–1996) 1993 ± 2.2 (1990–1999) Age at Measles Diagnosis mean ± std. (range) 1.65 ± 1.69 (0.15–7.08) 1.27 ± 1.72 (0.15–5.39) 1.69 ± 1.7 (0.18–7.08) Year of Measles Diagnosis mean ± std. (range) 1995 ± 2.78 (1991–2003) 1996 ± 1.9 (1993–1999) 1994 ± 2.8 (1991–2003) Measles Diagnosis-Associated Complications No Complications 78 (91.77%) 8 (88.89%) 70 (92.11%) Complications Specifiedb 5 (5.88%) 1 (11.11%) 4 (5.26%) Unknown Complication Status 2 (2.35%) 0 (0%) 2 (2.63%) aAll persons examined in this study were enrolled from their date of birth for 120 consecutive months. Results The unvac- cinated cohort revealed the most significant increases in the number of measles cases diagnosed in the first 2 years of follow-up in the present study. This was then followed by a period of still increasing numbers of mea- sles case diagnoses from the 2nd to the 6th year of fol- low-up, but at a slower rate than the initial 2-year period of follow-up. Finally, in the last period from the 6th to 10th year of follow-up, there were relatively few measles cases diagnosed as compared to the previous follow-up periods. Results All persons had non-changing dates of birth and gender status. All persons had ≥10 outpatient office visits bThis includes persons with post-measles otitis media (n = 2), measles keratoconjunctivitis (n = 1), measles with other specified complications (n = 1), measles with unspecified complication (n = 1) cPersons received only 1 dose of MMR vaccine and includes only persons diagnosed with measles post-MMR vaccine administration (43 persons were excluded with measles diagnoses pre-MMR vaccine administration and 3 persons were diagnosed measles within 30 days of vaccine administration, which are most likely measles vaccine-associated adverse events) dPersons received no doses of measles-containing vaccine when examining the MMR vaccinated cohort at the older ages examined with receipt at ≥16 months-old or ≥ 20 months-old vaccine effectiveness was about 90% or more. the period of years persons were followed in the MMR vaccinated cohort and the unvaccinated cohort. The plot reveals that in the initial period post-MMR vaccination (< 6 months) there were a greater number of measles cases diagnosed than in the unvaccinated cohort, but in the later periods post-MMR vaccination (> 6 months) there relatively few measles cases diagnosed as compared to the initial 6-month follow-up period in the MMR vac- cinated cohort or the unvaccinated cohort. The unvac- cinated cohort revealed the most significant increases in the number of measles cases diagnosed in the first 2 years of follow-up in the present study. This was then followed by a period of still increasing numbers of mea- sles case diagnoses from the 2nd to the 6th year of fol- low-up, but at a slower rate than the initial 2-year period of follow-up. Finally, in the last period from the 6th to 10th year of follow-up, there were relatively few measles cases diagnosed as compared to the previous follow-up periods. the period of years persons were followed in the MMR vaccinated cohort and the unvaccinated cohort. The plot reveals that in the initial period post-MMR vaccination (< 6 months) there were a greater number of measles cases diagnosed than in the unvaccinated cohort, but in the later periods post-MMR vaccination (> 6 months) there relatively few measles cases diagnosed as compared to the initial 6-month follow-up period in the MMR vac- cinated cohort or the unvaccinated cohort. Discussion The results of this retrospective longitudinal cohort study of prospectively collected healthcare data provide important and compelling new epidemiological quantita- tive data regarding the vaccine effectiveness of the child- hood MMR vaccine routinely administered to American children. Further, the vaccine effectiveness of childhood MMR vaccination remained when considering covariates such as gender, date of birth, and county of residence. In considering the results observed in the present study with previous studies, the Cochrane Collaboration recently published an extensive review examining MMR vaccine effectiveness [7]. Of three MMR vaccine effect- iveness studies examined by the Cochrane Collaboration, all three were cohort studies that observed childhood MMR vaccine administration was significantly effective in preventing clinical cases of measles [8–10]. In addition, the Cochrane Collaboration review also described that vaccine effectiveness = 97% for MMR vaccine administered in US vaccine programs [11]. Table 4 reveals the impact of the age of MMR vaccine administration on vaccine effectiveness in comparison to the unvaccinated cohort. Among those persons receiving MMR vaccine at the younger ages examined with receipt at ≥12 months-old was the least effective with a vaccine effectiveness ranging from about 80 to 85%. By contrast, Page 6 of 11 Geier et al. BMC Pediatrics (2019) 19:325 Table 3 Cox proportional hazards model results examining the relationship between MMR vaccination and diagnosed measles Model Variable Hazard Ratio (95% CI) VE (95% CI) p-value χ2 I Vaccinateda vs Unvaccinatedb (all ages) 0.164 (0.082 to 0.328) 83.6% (67.2 to 91.8%) < 0.0001 26.2 Vaccinated vs Unvaccinated (≥12 months-old)c 0.291 (0.136 to 0.622) 70.9% (37.8 to 86.4%) 0.0015 10.1 II Vaccinated vs Unvaccinated (all ages) 0.193 (0.096 to 0.385) 80.7% (61.5% to 90.4) < 0.0001 21.7 Gender (Female vs Male) 1.01 (0.659 to 1.544) 0.97 0.002 County of Residence 0.993 (0.982 to 1.004) 0.24 1.40 Date of Birth 0.999 (0.999 to 0.999) < 0.0001 30.2 Vaccinated vs Unvaccinated (≥12 months-old)c 0.346 (0.161 to 0.744) 65.4% (25.6 to 83.9%) 0.00065 7.39 Gender (Female vs Male) 0.959 (0.544 to 1.692) 0.89 0.02 County of Residence 0.997 (0.982 to 1.011) 0.65 0.21 Date of Birth 0.999 (0.999 to 0.999) < 0.0001 18.8 Italicized results are statistically significant. Discussion Model I = unadjusted, Model II = adjusted for gender, county of residence, and date of birth CI Confidence interval, VE Vaccine effectiveness aPersons received only 1 dose of MMR vaccine bPersons received no doses of measles-containing vaccine cOnly persons diagnosed with measles at ≥12 months-old were included in the unvaccinated cohort and only examining persons receiving MMR vaccine at ≥12 months-old in the vaccinated cohort, so as to ensure direct overlap in ages with the vaccinated and unvaccinated cohorts Table 3 Cox proportional hazards model results examining the relationship between MMR vaccination and diagnosed measles Persons received only 1 dose of MMR vaccine bPersons received no doses of measles-containing vaccine cOnly persons diagnosed with measles at ≥12 months-old were included in the unvaccinated cohort and only examining persons receiving MMR vaccine at ≥12 months-old in the vaccinated cohort, so as to ensure direct overlap in ages with the vaccinated and unvaccinated cohorts Fig. 2 A Cox proportional hazards survival plot evaluating cases of measles diagnosed over the period of follow-up in the MMR vaccinated cohort1 (1) in comparison to the unvaccinated cohort2 (0). 1 Persons received only 1 dose of MMR vaccine. 2 Persons received no doses of measles-containing vaccine Fig. 2 A Cox proportional hazards survival plot evaluating cases of measles diagnosed over the period of follow-up in the MMR vaccinated cohort1 (1) in comparison to the unvaccinated cohort2 (0). 1 Persons received only 1 dose of MMR vaccine. 2 Persons received no doses of measles-containing vaccine Fig. 2 A Cox proportional hazards survival plot evaluating cases of measles diagnosed over the period of follow-up in the MMR vaccinated cohort1 (1) in comparison to the unvaccinated cohort2 (0). 1 Persons received only 1 dose of MMR vaccine. 2 Persons received no doses of measles-containing vaccine Page 7 of 11 Geier et al. BMC Pediatrics (2019) 19:325 Geier et al. Discussion BMC Pediatrics Table 4 An evaluation of the impact of the age of MMR vaccine administration on the effectiveness of the vaccine to prevent cases of measles Model Variable Hazard Ratio (95% CI) VE (95% CI) p-value χ2 I Vaccinateda vs Unvaccinatedb (≥12 months-old) 0.147 (0.071 to 0.305) 85.3% (69.5 to 92.9%) < 0.0001 26.5 Vaccinated vs Unvaccinated (≥16 months-old) 0.100 (0.036 to 0.273) 90% (72.7 to 86.4%) < 0.0001 20.2 Vaccinated vs Unvaccinated (≥20 months-old) 0.061 (0.015 to 0.247) 93.9% (75.3 to 98.5%) < 0.0001 15.3 II Vaccinated vs Unvaccinated (≥12 months-old) 0.173 (0.083 to 0.360) 82.7% (64 to 91.7%) < 0.0001 22.1 Gender (Female vs Male) 1.032 (0.673 to 1.584) 0.89 0.02 County of Residence 0.994 (0.983 to 1.005) 0.27 1.20 Date of Birth 0.999 (0.999 to 0.999) < 0.0001 30 Vaccinated vs Unvaccinated (≥16 months-old) 0.111 (0.040 to 0.303) 88.9% (69.7 to 96%) < 0.0001 18.4 Gender (Female vs Male) 1.109 (0.718 to 1.715) 0.64 0.22 County of Residence 0.995 (0.984 to 1.007) 0.42 0.66 Date of Birth 0.999 (0.999 to 0.999) < 0.0001 28.1 Vaccinated vs Unvaccinated (≥20 months-old) 0.070 (0.017 to 0.287) 93% (71.3 to 98.3%) < 0.0001 13.7 Gender (Female vs Male) 1.027 (0.658 to 1.602) 0.91 0.01 County of Residence 0.996 (0.985 to 1.008) 0.49 0.47 Date of Birth 0.999 (0.999 to 1.000) < 0.0001 27.4 Italicized results are statistically significant. Model I = unadjusted, Model II = adjusted for gender, county of residence, and date of birth CI Confidence interval, VE Vaccine effectiveness a Persons received only 1 dose of MMR vaccine b Persons received no doses of measles-containing vaccine Table 4 An evaluation of the impact of the age of MMR vaccine administration on the effectiveness of the vaccine to prevent cases of measles Italicized results are statistically significant. Model I = unadjusted, Model II = adjusted for gender, county of residence, and date of birth CI Confidence interval, VE Vaccine effectiveness a Persons received only 1 dose of MMR vaccine b Persons received no doses of measles-containing vaccine The results of the present study also revealed that vac- cine effectiveness was greatest for those children admin- istered a single dose of MMR vaccine between 16 and 20 months of age as compared to those receiving a single dose of MMR vaccine between 12 and 15 months. Discussion It is also worth considering in countries where the risk of measles infection is high and low MMR vaccine uptake, especially for the second dose of MMR vaccine, that administration of MMR vaccine at ≥15 months maybe a means to improve long-term protection against measles infection for many children. examined were generated completely separate from the current study design. The healthcare providers submit- ting claims for MMR vaccine administration and measles diagnoses were most likely not thinking about the possible relationship between MMR vaccination and measles diagnoses. The study design utilized to examine the IHRD was another important strength of the present study. All persons examined in this study were eligible for Florida Medicaid from birth for 120 months (no gaps in eligibil- ity were allowed). In addition, in order to ensure that the cohort of persons examined was actively utilizing healthcare services from the Florida Medicaid system, all persons examined in this study had to have ≥10 out- patient office visit claims submitted (that averages to at least one outpatient office visit per person per year). These requirements helped to significantly reduce possible enrollment factors or differences in healthcare- seeking behaviors among the persons examined in this study. Another interesting aspect of the present study was that there were three measles disease diagnoses made within 30 days post-MMR vaccine (these were excluded from analyses undertaken in the present study to deter- mine MMR vaccine effectiveness). It was previously re- ported the usual incubation period of measles is 8 to 12 days [21]. All three measles diagnoses appeared to occur within the biologically appropriate time for the incuba- tion and manifestation of measles infection (one on day 11 and two on day 13), and as a result are most likely MMR vaccine-associated adverse events. It is unclear whether any previous epidemiological studies were large enough to observe this phenomenon following child- hood MMR vaccine administration, but a previous day- to-day reactogenicity study of MMR vaccine versus a placebo administered to 14 to 18 months-old in a twin study revealed apparently mild measles-associated symp- toms commenced 5 to 7 days post-MMR vaccine admin- istration and peaked on day 10 [21]. The results of the present study support that MMR vaccine-associated measles adverse events are rare with a rate of 0.91 per 10,000 recipients (95% confidence interval = 0.19 to 2.67 per 10,000 recipients) within 30 days of MMR vaccin- ation. Discussion It would be interesting in future studies to use microbiological tests to determine whether such poten- tial measles adverse events are truly vaccine-associated or the result of wild-type measles infections. Further, vaccination status was determined with preci- sion for each person because detailed information regard- ing procedure codes and dates of service for claims submitted on behalf of each person were examined. In order for a person to become a member of the vaccinated cohort, the claims records for a person revealed that only a single dose of MMR vaccine was administered. Those persons with procedure codes specifying other measles- containing vaccine(s) or multiple doses of MMR vaccine were excluded from the present analyses. Similarly, members of the unvaccinated cohort were confirmed to have no claims submitted on their behalf specifying receipt of any type of measles-containing vaccine. The outcome status was also determined with precision for each person because detailed information regarding outcomes using ICD-9 diagnosis coding and dates of ser- vice for claims submitted on behalf of each person were examined. In order for a person to be recognized as having a measles diagnosis, the initial date of service speci- fying a measles diagnosis (055xxx) was identified. Finally, the use of Cox proportional hazards survival plot modeling to evaluate cases of measles diagnosed over a period of many years in the vaccinated and unvaccinated cohorts allowed for us to draw inferences regarding the relationship between vaccination and out- comes as a function of follow-up time. It is possible that a potential limitation of this study was that the findings observed were the result of statistical chance or cofounders/unknown biases in the data. Statis- tical chance seems unlikely given that a limited number of statistical tests were performed, and most results were highly statistically significant. In addition, it was observed that the significant effects observed in unadjusted models remained significant even when adjusting for potential Discussion This type of age dependent MMR vaccine effectiveness was described in previous epidemiological studies [18]. The ACIP reported that measles vaccine is at least 95% effective for children vaccinated at ≥15 months of age, whereas a lower efficacy was observed for children vacci- nated between 12 and 14 months of age. They commen- ted that measles vaccine efficacy maybe lower because of trans-placental maternal antibody persists beyond the first birthday in some children, which, interferes with re- sponse to vaccination [19]. The biological plausibility of age dependent MMR vaccine effectiveness is supported by a previous study that revealed higher proportion of The results observed in this study regarding the vaccine effectiveness of childhood MMR to significantly reduce the incidence rate of measles cases for many years post-vaccin- ation are biologically plausible. For example, it was reported as early as 1971 that among 715 children (with no initial antibody to measles) that MMR vaccination induced a posi- tive measles antibody response in 96% of the children [12]. It was subsequently reported that among children administered a single dose of MMR vaccine at 15 months- old and evaluated for antibodies against measles at 6–7 years-old that > 90% were still positive for antibodies against measles [13]. Other studies in different populations revealed that measles antibodies may persistent more than a decade post-MMR vaccination [14, 15]. In addition, it was even revealed in long-term longitudinal cohort studies of measles vaccine recipients that persistent antibodies were observed in > 90% of the persons examined [16, 17]. Page 8 of 11 Geier et al. BMC Pediatrics (2019) 19:325 Page 8 of 11 those vaccinated with MMR vaccine at younger ages had undetectable or low levels of measles antibody 5–6 years post-immunization [20]. As a consequence, there is a potential delicate balance to weigh between ensuring the best possible long-term immunological response to MMR vaccine administration in vaccine recipients ver- sus the potential of measles exposure and measles-asso- ciated disease among children. It would seem, at least in the US, in more recent years with the end of endemic measles transmission that for most children administration of MMR vaccine at ≥15 months would be more appropriate than < 15 months, although the impact maybe limited because most children will subsequently receive a second childhood dose of MMR vaccine. Strengths/limitations It is possible that there may be differences in the chances of wild type measles virus exposure in different geographical areas over different years. This potential phenomenon should be further examined in future studies. An additional potential limitation of this study was that measles cases were not uniformly diagnosed during the study period from 1990 to 2009. As revealed in Table 5, it was observed that most cases of measles were diagnosed in the early 1990s period, and by the 2000s virtually no cases of measles were diagnosed, regardless of vaccination status. This phenomena most probably re- flects increasing “herd immunity” from increasing MMR vaccine coverage in the overall population. As described previously about “herd immunity” [22], the consequence is that the chance of exposure to measles throughout the study period examined significantly decreased regardless of vaccination status, and as a result, this may have reduced the vaccine effectiveness observed in the present study in comparison with previous studies examining measles vaccine effectiveness. Namely, unvaccinated persons were deriving a benefit of protection against measles infection from vaccinated persons. It would be interesting in future studies to evaluate the impact of increasing “herd immunity” on population measles disease patterns. The ACIP recommends that a second dose of MMR vac- cination should be administered during childhood [1]. It is possible that additional doses of MMR vaccination may further improve vaccine effectiveness to prevent cases of measles. It is recommended that future studies further explore the impact of additional doses of MMR vaccination on vaccine effectiveness to prevent measles cases. The ACIP recommends that a second dose of MMR vac- cination should be administered during childhood [1]. It is possible that additional doses of MMR vaccination may further improve vaccine effectiveness to prevent cases of measles. It is recommended that future studies further explore the impact of additional doses of MMR vaccination on vaccine effectiveness to prevent measles cases. Another potential limitation of the present study was that the better vaccine effectiveness associated with older age of receiving MMR vaccination might associated with missing data on the first vaccination (i.e., perhaps the first documented MMR vaccination was really a second MMR vaccination, because the first was not docu- mented). Strengths/limitations An important strength of this study was that retrospect- ive observations made in the IHRD were derived from eligibility and claims records prospectively generated as part of the routine healthcare provided for persons in the Florida Medicaid system. Therefore, the data Geier et al. BMC Pediatrics (2019) 19:325 Page 9 of 11 Table 5 A summary of diagnosed measles cases by year of diagnosis Year of Diagnosis All Measles Cases MMR Vaccinated Cohorta Diagnosed with Measles Unvaccinated Cohortb Diagnosed with Measles 1991 18 0 18 1992 14 0 14 1993 11 1 10 1994 11 2 6 1995 8 1 7 1996 8 2 6 1997 6 1 5 1998 5 1 4 1999 4 1 3 2000 2 0 2 2001 0 0 0 2002 0 0 0 2003 1 0 1 2004 0 0 0 2005 0 0 0 2006 0 0 0 2007 0 0 0 2008 0 0 0 2009 0 0 0 Total 85 9 76 aPersons received only 1 dose of MMR vaccine bPersons received no doses of measles-containing vaccine covariates such as gender, date of birth, and county of residence. The results observed this study were consistent with previous epidemiological observations on different populations and were biologically plausible. Table 5 A summary of diagnosed measles cases by year of diagnosis It is also possible that some of the persons examined in the IHRD may have had symptoms of measles that were so slight that they were not noted by their healthcare pro- viders, or healthcare providers may have misdiagnosed or misclassified vaccination status for some persons. How- ever, these potential limitations, while possible, should not have affected the results appreciably because it is uncer- tain how differential application would have occurred in the vaccinated and unvaccinated cohorts examined. Im- portantly, any misclassification with respect to diagnostic or vaccination status, would in all likelihood bias the find- ings towards the null hypothesis because persons exam- ined would have been put into the wrong vaccination and/ or diagnostic category and result in diminished statistical power to establish the accurate relationship between vaccination and outcomes. Another potential limitation of this study was that limited information was available regarding the area of residence of persons over the multiple years of this study. It was assumed that chances of exposure to wild type measles virus were equal in the vaccinated and un- vaccinated cohorts examined. AAFP: American Academy of Family Practitioners; AAP: American Academy of Pediatrics; ACIP: Advisory Committee on Immunization Practices; AHCA: Agency for Health Care Administration; CA: California; FL: Florida; ICD-9: International Code for Disease, 9th revision; IHRD: Independent Healthcare Research Database; IRB: Institutional Review Board; MMR: Measles-mumps-rubella; NDC: National Drug Codes; NJ: New Jersey; US: United States; USA: United States of America; VE: Vaccination effectiveness; WA: Washington Consent for publication Not applicable. Consent for publication Not applicable. Consent for publication Not applicable. Funding Th This research was funded by the non-profit organizations, CoMeD, Inc. and Institute of Chronic Illnesses, Inc. Dr. Mark Geier and Mr. David Geier are directors of the non-profit Institute of Chronic Illnesses, Inc. and the non-profit CoMeD, Inc. The funding organizations did not influence the design, data collection, analyses, data interpretation, or the writing of this manuscript. 16. Kremer JR, Schneider F, Muller CP. Waning antibodies in measles and rubella vaccines-a longitudinal study. Vaccine. 2006;24(14):2594–601. 16. Kremer JR, Schneider F, Muller CP. Waning antibodies in measles and rubella vaccines-a longitudinal study. Vaccine. 2006;24(14):2594–601. 17. Kato H, Mori M, Oba M, Kawahara H, Kaneko T. Persistence and half-lives of anti-measles and anti-rubella antibodies in Japanese hospital workers: a longitudinal study. Intern Med. 2016;55(18):2587–94. 17. Kato H, Mori M, Oba M, Kawahara H, Kaneko T. Persistence and half-lives of anti-measles and anti-rubella antibodies in Japanese hospital workers: a longitudinal study. Intern Med. 2016;55(18):2587–94. 18. Orenstein WA, Markowitz L, Preblud SR, Hinman AR, Tomasi A, Bart KJ. Appropriate age for measles vaccination in the United States. Dev Biol Stand. 1986;65:13–21. 18. Orenstein WA, Markowitz L, Preblud SR, Hinman AR, Tomasi A, Bart KJ. Appropriate age for measles vaccination in the United States. Dev Biol Stand. 1986;65:13–21. Acknowledgements None. 12. Stokes J Jr, Weibel RE, Villarejos VM, Arguedas JA, Buynak EB, Hilleman MR. Trivalent combined measles-mumps-rubella vaccine. Findings in clinical- laboratory studies. JAMA. 1971;218(1):57–61. 12. Stokes J Jr, Weibel RE, Villarejos VM, Arguedas JA, Buynak EB, Hilleman MR. Trivalent combined measles-mumps-rubella vaccine. Findings in clinical- laboratory studies. JAMA. 1971;218(1):57–61. Authors’ contributions l d d 13. Gil Miguel A, Astasio Arbiza P, Ortega Molina P, Dominguez Rojas V, Gonzalez Lope A. Seroprevalence of antibodies against measles, rubella, mumps and varicella among school children in Madrid. An Esp Pediatr. 1999;50(5):459–62. 13. Gil Miguel A, Astasio Arbiza P, Ortega Molina P, Dominguez Rojas V, Gonzalez Lope A. Seroprevalence of antibodies against measles, rubella, mumps and varicella among school children in Madrid. An Esp Pediatr. 1999;50(5):459–62. DAG conceptualized and designed the study, carried out the initial analyses, drafted the initial manuscript, and approved the final manuscript as submitted. JKK critically reviewed and revised the manuscript, and approved the final manuscript as submitted. MRG conceptualized and designed the study, drafted the initial manuscript, and approved the final manuscript as submitted. All authors read and approved the final manuscript. 14. Seagle EE, Bednarczyk RA, Hill T, Fiebelkorn AP, Hickman CJ, Icenogle JP, Belongia EA, McLean HQ. Measles, mumps, and rubella antibody patters of persistence and rate of decline following the second dose of the MMR vaccine. Vaccine. 2018;36(6):818–26. 14. Seagle EE, Bednarczyk RA, Hill T, Fiebelkorn AP, Hickman CJ, Icenogle JP, Belongia EA, McLean HQ. Measles, mumps, and rubella antibody patters of persistence and rate of decline following the second dose of the MMR vaccine. Vaccine. 2018;36(6):818–26. 15. Davidkin I, Jokinen S, Broman M, Leinikki P, Peltola H. Persistence of measles, mumps, and rubella in an MMR-vaccinated cohort: a 20-year follow-up. J Infect Dis. 2008;197(7):950–6. Conclusion Seagle EE, Bednarczyk RA, Hill T, Fiebelkorn AP, Hickman CJ, Icenogle JP, Belongia EA, McLean HQ. Measles, mumps, and rubella antibody patters of persistence and rate of decline following the second dose of the MMR vaccine. Vaccine. 2018;36(6):818–26. 15. Davidkin I, Jokinen S, Broman M, Leinikki P, Peltola H. Persistence of measles, mumps, and rubella in an MMR-vaccinated cohort: a 20-year follow-up. J Infect Dis. 2008;197(7):950–6. 16. Kremer JR, Schneider F, Muller CP. Waning antibodies in measles and rubella vaccines-a longitudinal study. Vaccine. 2006;24(14):2594–601. 17. Kato H, Mori M, Oba M, Kawahara H, Kaneko T. Persistence and half-lives of anti-measles and anti-rubella antibodies in Japanese hospital workers: a longitudinal study. Intern Med. 2016;55(18):2587–94. 18. Orenstein WA, Markowitz L, Preblud SR, Hinman AR, Tomasi A, Bart KJ. Appropriate age for measles vaccination in the United States. Dev Biol Stand. 1986;65:13–21. Received: 7 September 2018 Accepted: 3 September 2019 Received: 7 September 2018 Accepted: 3 September 2019 References Measles transmission and vaccine effectiveness during a large outbreak on a densely populated island: implications for vaccination policy. Clin Infect Dis. 2006;42(3):315–9. 8. Marin M, Nguyen HQ, Langidrik JR, Edwards R, Briand K, Papania MJ, et al. Measles transmission and vaccine effectiveness during a large outbreak on a densely populated island: implications for vaccination policy. Clin Infect Dis. 2006;42(3):315–9. 8. Marin M, Nguyen HQ, Langidrik JR, Edwards R, Briand K, Papania MJ, et al. Measles transmission and vaccine effectiveness during a large outbreak on a densely populated island: implications for vaccination policy. Clin Infect Dis. 2006;42(3):315–9. Ethics approval and consent to participate Ethics approval and consent to participate References 1. McLean HQ, Fiebelkorn AP, Temte JL, Wallace GS. Centers for Disease Control and Prevention. Prevention of measles, rubella, congenital rubella syndrome and mumps, 2013: summary recommendations of the advisory committee on immunization practices (ACIP). MMWR Recomm Rep. 2013; 62(RR-04:1–34. 2. Bloch AB, Orenstein WA, Stetler HC, et al. Health impact of measles vaccination in the United States. Pediatrics. 1985;76:524–32. 2. Bloch AB, Orenstein WA, Stetler HC, et al. Health impact of measles vaccination in the United States. Pediatrics. 1985;76:524–32. 3. Redd SC, Markowitz LE, Katz SL. Measles vaccine. In: Plotkin SA, Orenstein WA, editors. Vaccines. Philadelphia: WB Saunders; 1999. p. 222–66. 4. Schwarz AJ, Jackson JE, Ehrenkranz NJ, Ventura A, Schiff GM, Walters VW. Clinical evaluation of a new measles-mumps-rubella trivalent vaccine. Am J Dis Child. 1975;129(12):1408–12. 2. Bloch AB, Orenstein WA, Stetler HC, et al. Health impact of measles vaccination in the United States. Pediatrics. 1985;76:524–32. 3. Redd SC, Markowitz LE, Katz SL. Measles vaccine. In: Plotkin SA, Orenstein WA, editors. Vaccines. Philadelphia: WB Saunders; 1999. p. 222–66. 3. Redd SC, Markowitz LE, Katz SL. Measles vaccine. In: Plotkin SA, Orenstein WA, editors. Vaccines. Philadelphia: WB Saunders; 1999. p. 222–66. 4. Schwarz AJ, Jackson JE, Ehrenkranz NJ, Ventura A, Schiff GM, Walters VW. Clinical evaluation of a new measles-mumps-rubella trivalent vaccine. Am J Dis Child. 1975;129(12):1408–12. 5. MERCK & CO., INC., M-M-R-II, Measles Mumps, and Rubella Virus Vaccine Live. http://www.merck.com/product/usa/pi_circulars/m/mmr_ii/mmr_ii_pi. pdf. Revised 5/2017; Accessed 18 July 2018. Overall, the results of the present study support the ongoing successful use of routine MMR vaccination as an important public health tool to reduce the incidence rate of diagnosed measles. Future studies should con- tinue to monitor how long and how robust the protect- ive effects of MMR vaccine(s) can be expected to persist. 6. Strebel PM, Henao-Restrepo AM, Hoekstra E, Olive JM, Papania MJ, Cochi SL. Global measles elimination efforts: the significance of measles elimination in the United States. J Infect Dis. 2004;189(Suppl 1):S251–7. 7. Demicheli V, Rivetti A, Debalini MG, Di Pietrantonj C. Vaccines for measles, mumps, and rubella in children. Cochrane Database Syst Rev. 2012;15(2): CD004407. 7. Demicheli V, Rivetti A, Debalini MG, Di Pietrantonj C. Vaccines for measles, mumps, and rubella in children. Cochrane Database Syst Rev. 2012;15(2): CD004407. 8. Marin M, Nguyen HQ, Langidrik JR, Edwards R, Briand K, Papania MJ, et al. Competing interests Th h d l h This retrospective cohort study of prospectively collected healthcare data from the IHRD provides new evidence con- sistent with and extending results from previous epidemio- logical studies revealing that routine childhood MMR vaccination in the US significantly reduced the incidence rate of diagnosed measles cases. Furthermore, MMR vac- cine administration at 16–20 months-old was associated with greater vaccine effectiveness relative to MMR vaccine administration at 12–15 months-old. It was also revealed that on rare occasions in the 30-day post-MMR vaccine administration period about 1 in 10,000 doses of MMR vac- cine developed MMR vaccine-associated measles adverse events. Finally, the results observed in this study help to establish that the IHRD is an important epidemiological resource to help quantitatively evaluate important public health issues. The authors declare that they have no competing interests. Received: 7 September 2018 Accepted: 3 September 2019 Abbreviations AAFP A i AAFP: American Academy of Family Practitioners; AAP: American Academy of Pediatrics; ACIP: Advisory Committee on Immunization Practices; AHCA: Agency for Health Care Administration; CA: California; FL: Florida; ICD-9: International Code for Disease, 9th revision; IHRD: Independent Healthcare Research Database; IRB: Institutional Review Board; MMR: Measles-mumps-rubella; NDC: National Drug Codes; NJ: New Jersey; US: United States; USA: United States of America; VE: Vaccination effectiveness; WA: Washington 9. Marolla F, Baviera G, Cacciapuoti CV, Cannavavo R, Clemente A, et al. A field study on vaccine efficacy against mumps of three MMR vaccines [Efficacia verso la parotite di tre diversi vaccini a tripla componente: studio sul campo]. Riv Ital Pediatr. 1998;24(3):466–72. 10. Ong G, Rasidah N, Wan S, Cutter J. Outbreak of measles in primary school students with high first dose MMR vaccination coverage. Singap Med J. 2007;48(7):656–61. 11. Orenstein WA, Bernier RH, Dondero TJ, Hinman AR, Marks JS, Bart KJ, et al. Field evaluation of vaccine efficacy. Bull World Health Org. 1985;63(6):1055–68. 11. Orenstein WA, Bernier RH, Dondero TJ, Hinman AR, Marks JS, Bart KJ, et al. Field evaluation of vaccine efficacy. Bull World Health Org. 1985;63(6):1055–68. Conclusion Competing interests The authors declare that they have no competing interests. Received: 7 September 2018 Accepted: 3 September 2019 References 1. McLean HQ, Fiebelkorn AP, Temte JL, Wallace GS. Centers for Disease Control and Prevention. Prevention of measles, rubella, congenital rubella syndrome and mumps, 2013: summary recommendations of the advisory committee on immunization practices (ACIP). MMWR Recomm Rep. 2013; 62(RR-04:1–34. 2. Bloch AB, Orenstein WA, Stetler HC, et al. Health impact of measles vaccination in the United States. Pediatrics. 1985;76:524–32. 3. Redd SC, Markowitz LE, Katz SL. Measles vaccine. In: Plotkin SA, Orenstein WA, editors. Vaccines. Philadelphia: WB Saunders; 1999. p. 222–66. 4. Schwarz AJ, Jackson JE, Ehrenkranz NJ, Ventura A, Schiff GM, Walters VW. Clinical evaluation of a new measles-mumps-rubella trivalent vaccine. Am J Dis Child. 1975;129(12):1408–12. 5. MERCK & CO., INC., M-M-R-II, Measles Mumps, and Rubella Virus Vaccine Live. http://www.merck.com/product/usa/pi_circulars/m/mmr_ii/mmr_ii_pi. pdf. Revised 5/2017; Accessed 18 July 2018. 6. Strebel PM, Henao-Restrepo AM, Hoekstra E, Olive JM, Papania MJ, Cochi SL. Global measles elimination efforts: the significance of measles elimination in the United States. J Infect Dis. 2004;189(Suppl 1):S251–7. 7. Demicheli V, Rivetti A, Debalini MG, Di Pietrantonj C. Vaccines for measles, mumps, and rubella in children. Cochrane Database Syst Rev. 2012;15(2): CD004407. 8. Marin M, Nguyen HQ, Langidrik JR, Edwards R, Briand K, Papania MJ, et al. Measles transmission and vaccine effectiveness during a large outbreak on a densely populated island: implications for vaccination policy. Clin Infect Dis. 2006;42(3):315–9. 9. Marolla F, Baviera G, Cacciapuoti CV, Cannavavo R, Clemente A, et al. A field study on vaccine efficacy against mumps of three MMR vaccines [Efficacia verso la parotite di tre diversi vaccini a tripla componente: studio sul campo]. Riv Ital Pediatr. 1998;24(3):466–72. 10. Ong G, Rasidah N, Wan S, Cutter J. Outbreak of measles in primary school students with high first dose MMR vaccination coverage. Singap Med J. 2007;48(7):656–61. 11. Orenstein WA, Bernier RH, Dondero TJ, Hinman AR, Marks JS, Bart KJ, et al. Field evaluation of vaccine efficacy. Bull World Health Org. 1985;63(6):1055–68. 12. Stokes J Jr, Weibel RE, Villarejos VM, Arguedas JA, Buynak EB, Hilleman MR. Trivalent combined measles-mumps-rubella vaccine. Findings in clinical- laboratory studies. JAMA. 1971;218(1):57–61. 13. Gil Miguel A, Astasio Arbiza P, Ortega Molina P, Dominguez Rojas V, Gonzalez Lope A. Seroprevalence of antibodies against measles, rubella, mumps and varicella among school children in Madrid. An Esp Pediatr. 1999;50(5):459–62. 14. Strengths/limitations This would appear to be unlikely, since the ages examined for receipt of MMR vaccination were all before the second birthday, and the ACIP does not recommend administration of a second dose of MMR vaccine at such a young age [1]. A final potential limitation of the present study was that it is unknown how many cases were reported to the national notifiable disease system from Florida in this time period compared to what was observed in the A still further potential limitation of the present study was that only persons receiving a single dose of MMR vaccination were examined in the vaccinated cohort. Page 10 of 11 Geier et al. BMC Pediatrics (2019) 19:325 Geier et al. BMC Pediatrics (2019) 19:325 Florida Medicaid system. It is possible that there may be some sort of selection bias, although it would probably not have a large impact on the observations made in this study. Ethics approval and consent to participate The data in the IHRD were assembled and accessed under approval by the Liberty Institutional Review Board (IRB) (Deland, FL). Availability of data and materials This database is publicly available through the US Medicaid system. This database is publicly available through the US Medicaid system. Page 11 of 11 Geier et al. BMC Pediatrics (2019) 19:325 Geier et al. BMC Pediatrics (2019) 19:325 19. Centers for Disease Control (CDC). Measles prevention. MMWR Suppl. 1989; 38(9):1–18. 20. Boulianne N, Serres GD, Ratnam S, Ward BJ, Joly JR, Duval B. Measles, mumps, and rubella antibodies in children 5-6 years after immunization: effect of vaccine type and age at vaccination. Vaccine. 1995;13(16):1611–6. 20. Boulianne N, Serres GD, Ratnam S, Ward BJ, Joly JR, Duval B. Measles, mumps, and rubella antibodies in children 5-6 years after immunization: effect of vaccine type and age at vaccination. Vaccine. 1995;13(16):1611–6. 21. Virtanen M, Petola H, Paunio M, Heinonen OP. Day-to-day reactogenicity and the healthy vaccine effect of measles-mumps-rubella vaccination. Pediatrics. 2000;106(5):E62. 21. Virtanen M, Petola H, Paunio M, Heinonen OP. Day-to-day reactogenicity and the healthy vaccine effect of measles-mumps-rubella vaccination. Pediatrics. 2000;106(5):E62. 22. Fing P, Earnes K, Heymann DL. “Herd immunity”: a rough guide. Clin Infect Dis. 2011;52(7):911–6. 22. Fing P, Earnes K, Heymann DL. “Herd immunity”: a rough guide. Clin Infect Dis. 2011;52(7):911–6. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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“The Great Mimicker”: An Unusual Etiology of Cytopenia, Diffuse Lymphadenopathy, and Massive Splenomegaly
Case reports in medicine
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Hindawi Publishing Corporation Case Reports in Medicine Volume 2015, Article ID 637965, 6 pages http://dx.doi.org/10.1155/2015/637965 Hindawi Publishing Corporation Case Reports in Medicine Volume 2015, Article ID 637965, 6 pages http://dx.doi.org/10.1155/2015/637965 Hindawi Publishing Corporation Case Reports in Medicine Volume 2015, Article ID 637965, 6 pages http://dx.doi.org/10.1155/2015/637965 Correspondence should be addressed to Mazen Zaarour; mfzaarour@gmail.com Correspondence should be addressed to Mazen Zaarour; mfzaarour@gmail.com Received 11 August 2015; Accepted 4 October 2015 Academic Editor: Masahiro Kohzuki Copyright © 2015 Mazen Zaarour et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Sarcoidosis is an idiopathic multisystem disease characterized by the formation of noncaseating granulomas. It frequently presents with pulmonary infiltrates and bilateral hilar and mediastinal lymphadenopathy. Splenic involvement is common, but massive splenomegaly is a rare occurrence. Sarcoidosis is known as “the great mimicker” (or “the great imitator”) since it exhibits a myriad of symptoms, mimicking other inflammatory, infectious, and neoplastic conditions, including lymphoma. Herein, we report the case of a 44-year-old male patient who was found to have bicytopenia, hypercalcemia, diffuse lymphadenopathy, and massive splenomegaly, a constellation of findings suggestive of underlying lymphoma. Interestingly, lymph node biopsy showed noncaseating granulomas suggestive of sarcoidosis, without evidence of malignancy. 1. Introduction Herein, we report the case of a 44-year-old male patient who was found to have bicytopenia, hypercalcemia, diffuse lymphadenopathy, and massive splenomegaly, a constellation of findings suggestive of underlying lymphoma. Surprisingly, lymph node biopsy showed noncaseating granulomas sugges- tive of sarcoidosis, without evidence of malignancy. Sarcoidosis is a chronic inflammatory disorder of unknown origin which occurs mainly in young people [1, 2]. It is characterized by the presence of noncaseating granulomas. Although the lung is the most common organ involved, the disease can affect any organ, including the spleen [1]. Granulomatous infiltration of the spleen is common in sarcoidosis and is often asymptomatic [2]. Splenomegaly is unusual, and massive splenomegaly is very rare [3].hi Case Report (The Great Mimicker): An Unusual Etiology of Cytopenia, Diffuse Lymphadenopathy, and Massive Splenomegaly Mazen Zaarour,1 Chanudi Weerasinghe,1 Elias Moussaly,1 Shafinaz Hussein,2 and Jean-Paul Atallah3 1Department of Medicine, Staten Island University Hospital, North Shore-LIJ Health System, Staten Island, New York, NY 10305, USA 2Department of Pathology, Staten Island University Hospital, North Shore-LIJ Health System, Staten Island, New York, NY 10305, USA 3Division of Hematology and Oncology, Department of Medicine, Staten Island University Hospital, North Shore-LIJ Health System, Staten Island, New York, NY 10305, USA Mazen Zaarour,1 Chanudi Weerasinghe,1 Elias Moussaly,1 Shafinaz Hussein,2 and Jean-Paul Atallah3 Shafinaz Hussein,2 and Jean-Paul Atallah3 1Department of Medicine, Staten Island University Hospital, North Shore-LIJ Health System, Staten Island, New York, NY 10305, USA 2Department of Pathology, Staten Island University Hospital, North Shore-LIJ Health System, Staten Island, New York, NY 10305, USA 3Division of Hematology and Oncology, Department of Medicine, Staten Island University Hospital, North Shore-LIJ Health System, Staten Island, New York, NY 10305, USA 1Department of Medicine, Staten Island University Hospital, North Shore-LIJ Health System, Staten Island, New York, NY 10305, USA 2Department of Pathology, Staten Island University Hospital, North Shore-LIJ Health System, Staten Island, New York, NY 10305, USA 3Division of Hematology and Oncology, Department of Medicine, Staten Island University Hospital, North Shore-LIJ Health System, Staten Island, New York, NY 10305, USA 2. Case Presentation We report the case of a 44-year-old Caucasian male who was referred to our hospital by his primary physician for abnor- mal outpatient laboratory test values. The patient had been healthy until 5 months prior to admission, when he started to have progressively worsening fatigue. Outpatient blood tests revealed kidney injury, hypercalcemia, and anemia, findings that required hospitalization. The symptoms of sarcoidosis, if present, are nonspecific. The presence of noncaseating granulomas is also not pathog- nomonic of the disease, as it can be seen in malignancy [1]. Moreover, the involvement of the reticuloendothelial system in sarcoidosis, as evidenced by enlarged lymph nodes and splenomegaly, often mandates tissue examination to exclude an underlying masked lymphoma. Sarcoidosis is well known to be “the great mimicker” (or “the great imitator”), since it exhibits a myriad of symptoms, mimicking other inflammatory, infectious, and neoplastic conditions, includ- ing lymphoma. On the day of admission, the patient’s only complaint was severe fatigue. Upon further questioning, he admitted having a 70-pound unintentional weight loss over the last 18 months. He denied any fever, chills, night sweats, cough, rash, or joint or abdominal pain. His prior medical history consisted of 2 2 Case Reports in Medicine (a) (b) Figure 1: Massive splenomegaly. (a) Sagittal sonographic view of the spleen showing a markedly enlarged and diffuse heterogeneous spleen (blue arrow) measuring 30 cm in length. (b) Coronal noncontrast CT of the abdomen and pelvis showing enlarged spleen reaching 33.6 cm in length. (a) (b) (a) (b) Figure 1: Massive splenomegaly. (a) Sagittal sonographic view of the spleen showing a markedly enlarged and diffuse heterogeneous spleen (blue arrow) measuring 30 cm in length. (b) Coronal noncontrast CT of the abdomen and pelvis showing enlarged spleen reaching 33.6 cm in length. (a) (b) Figure 2: Diffuse lymphadenopathy. (a) Transverse CT of the abdomen showing enlarged para-aortic lymph nodes (blue arrows) reaching 14 mm in the shortest axis. (b) Transverse CT of the pelvis showing enlarged inguinal lymph nodes reaching 15 mm in the shortest axis. (b) (a) (a) (b) Figure 2: Diffuse lymphadenopathy. (a) Transverse CT of the abdomen showing enlarged para-aortic lymph nodes (blue arrows) reaching 14 mm in the shortest axis. (b) Transverse CT of the pelvis showing enlarged inguinal lymph nodes reaching 15 mm in the shortest axis. 2. Case Presentation hypercalcemia of 13.7 mg/dL was noted, along with a blood urea nitrogen (BUN) of 33 mg/dL and a serum creatinine of 2.39 mg/dL, findings consistent with kidney injury. The renal function was normal three years ago. Liver enzymes were normal. An abdominal sonogram showed a markedly enlarged and diffusely heterogeneous spleen measuring 30 cm in length (Figure 1(a)). Enlarged kidneys with normal echogenicity were found as well (right kidney 13 cm, left kidney 15.5 cm). A noncontrast computed tomography (CT) scan of the abdomen and pelvis confirmed the presence of massive splenomegaly (Figure 1(b)), along with multiple mildly enlarged paraaortic, mesenteric, and bilateral iliac chain lymph nodes (Figure 2). A chest radiograph was unre- markable; however, a CT chest revealed diffuse mediastinal, lower cervical, and axillary adenopathy. diabetes mellitus, gout, and hyperlipidemia. The patient was a nonsmoker and had no allergies. His family history was noncontributory. On physical exam, the patient’s body temperature was 98.6∘F, blood pressure was 159/92 mmHg, and heart rate was 100/min. Cardiovascular and pulmonary exams were unremarkable. Left upper quadrant tenderness was noted on the abdominal exam, as well as a firm and enlarged spleen, which was palpable below the umbilicus. No rash, cervical, or axillary lymphadenopathy was identified. i Laboratory analysis showed a normocytic anemia with a hemoglobin of 6.7 g/dL, a hematocrit of 21.4%, and a mean corpuscular volume (MCV) of 82.3 𝜇m3. The rest of the hematologic panel was as follows: white blood cell count of 3.93 × 109/L, platelet count of 254 × 109/L, and erythrocyte sedimentation rate (ESR) of 93 mm/h. A periph- eral blood smear was within normal limits. In addition, The patient received packed red blood cells transfusions to maintain his hemoglobin level around 8 mg/dL. He was 3 Case Reports in Medicine (a) (b) Figure 3: Nonnecrotizing granulomata. Low- (a) and high-magnification (b) photomicrograph of a section from an inguinal lymph node. It shows that the lymph node is replaced by numerous small compact nonnecrotizing granulomata. (b) (a) (b) (a) Figure 3: Nonnecrotizing granulomata. Low- (a) and high-magnification (b) photomicrograph of a section from an inguinal lymph node. It shows that the lymph node is replaced by numerous small compact nonnecrotizing granulomata. Table 1: Laboratory findings. 2. Case Presentation Extrathoracic sarcoidosis is also common, with liver and spleen involvement described in half of autopsy cases [2, 3]. Other commonly involved organs are the skin, the joints, and the eyes. Extrathoracic sarcoidosis is also common, with liver and spleen involvement described in half of autopsy cases [2, 3]. Other commonly involved organs are the skin, the joints, and the eyes. y Sarcoidosis can be asymptomatic in some patients. If present, symptoms are both systemic (fever, weight loss, and fatigue) and/or organ-specific (shortness of breath, chest pain, and cough) [1]. There is no single laboratory test for the diagnosis. However, cytopenia, eosinophilia, and hyper- gammaglobulinemia are common findings. Hypercalcemia and/or hypercalciuria are also found in some cases. ACE, produced by the epithelial cells of granulomas, is detected in the serum of 60% of patients; however, its value in diagnosing ormanaging sarcoidosis remains controversial [4]. Soluble interleukin-2 receptor (sIL-2R) concentration, a marker of T-cell activation, is considered to reflect disease activity. A biopsy from the involved organ that is most easily accessed is 2. Case Presentation Parameter Value Total protein (g/dL) 8.1 (6–8.3) Albumin (g/dL) 3.2 (3.0–5.5) Serum iron (𝜇g/dL) 34 (35–150) Total iron binding capacity (𝜇g/dL) 241 (260–400) Ferritin (ng/mL) 608 (30–400) Percent saturation (%) 14.1 (15–50) Reticulocyte count (%) 1.88 (0.5–1.5) ESR (mm/h) 93 (0–10) Vitamin B12 (pg/mL) 215 (243–894) Lactate dehydrogenase (IU/L) 97 (60–200) Inorganic phosphorus (mg/dL) 2.5 (2.1–4.9) Intact PTH (pg/mL) 5 (15–65) PTH related protein (pg/mL) 22 (14–27) Thyroid stimulating hormone (𝜇IU/mL) 2.72 (0.27–4.2) Vitamin D 1,25(OH)2 total (pg/mL) 248 (18–72) Vitamin D 25-OH total (ng/mL) 26 (30–100) Uric acid (mg/dL) 6.3 (4.8–8.7) Serum protein electrophoresis (SPEP) Normal Free kappa/lambda ratio 1.01 (0.26–1.65) Urine protein electrophoresis (UPEP) Normal Table 1: Laboratory findings. also given intravenous fluids to treat the hypercalcemia and received one dose of pamidronate, which helped to lower the calcium level to as low as 11 mg/dL over the next few days.hf The presence of massive splenomegaly and diffuse lymph node enlargement was concerning lymphoma. Further workup showed anemia of chronic disease and elevated vitamin D 1,25(OH)2 levels (with low PTH levels). Anti- nuclear antibody, HIV test, monospot test, and purified protein derivative (PPD) were negative. Additional studies are listed in Table 1. A bone marrow biopsy revealed a hypercellular marrow with negative cultures and cytogenetic analysis. PCR analyses for Bcr/Abl and JAK2 mutation were both negative. An excisional biopsy of a left inguinal lymph node showed that the lymph node was extensively involved with small compact nonnecrotizing granulomata (Figure 3). Gomori methenamine silver (GMS) and acid- fast bacillus (AFB) staining showed no fungal organisms or acid-fast organisms, respectively. There was no morphologic or immunophenotypic evidence of malignancy. Additional serum studies showed an angiotensin-converting enzyme (ACE) level of 73 U/L (reference range 9–67). These findings led to a diagnosis of sarcoidosis, for which the patient was started on prednisone 40 mg/day and discharged home few days later.t Four weeks after the initiation of therapy, the patient’s calcium level was 10.3 mg/dL, along with a hemoglobin of 9.4 g/dL and a creatinine of 1.38 mg/dL. 2 weeks later, ACE level was 31 mg/dL. 8 weeks after hospital discharge, a fluorine-18 fluorodeoxyglucose (FDG) PET imaging, done while the patient was still on treatment, showed no focal FDG avid lesions, along with stable non-FDG avid thoracic and abdominal adenopathy. The patient continued to be in good health 9 months after his diagnosis and had shown no progression of sarcoidosis. 3. Discussion Patients with splenomegaly may have a higher incidence of constitutional symptoms and more disseminated disease [11]. Splenic sarcoidosis may cause hypersplenism, as evidenced by anemia, leukopenia, thrombocytopenia, or any such combination. The radiographic features of splenic sar- coidosis are variable. Splenomegaly is usually homogeneous; however, the sarcoid granulomas, often small, can coalesce to produce macroscopically visible nodules. Therefore, in up to 15% of patients, the disease may manifest as multiple low- attenuation and diffusely scattered nodules, ranging in size from 1 to 30 mm [2, 12, 13]. This pattern may mimic other worrisome diagnoses, such as lymphoma, metastases from solid tumor, and tuberculosis [2, 3].h The crux of sarcoidosis is its ability to masquerade as other diseases, most significantly lymphoma. As such, for clinicians, distinguishing these entities can make the difference between life and death for patients. In addition to the nonspecific clinical, radiological, and histological features in sarcoidosis, the lymphocyte activation and the reticu- loendothelial system involvement (lymph nodes, spleen, and liver) make the distinction of sarcoidosis from lymphoma extremely challenging. In fact, hypercalcemia and increased serum ACE levels have also been described in patients with lymphoma [14]. Moreover, multiple reports confirmed the presence of sarcoid-like (noncaseating epithelioid) granulo- mas in patients with lymphoma, even without a history of “true” sarcoidosis [15]. Brincker concluded that a sarcoid- like granulomatous reaction occurred in 4% of cancers, in 14% of patients with Hodgkin’s lymphoma, and in 7% of patients with non-Hodgkin’s lymphoma [15]. In our patient, the combination of bicytopenia, hypercalcemia, diffuse lym- phadenopathy, and massive splenomegaly favored a diagnosis of lymphoma. Moreover, the patient had no clinical or radiological evidence of respiratory system involvement to suggest sarcoidosis as a “likely” diagnosis. g [ ] Splenic involvement in sarcoidosis is defined as the histologic presence of noncaseating granulomas in the spleen. Autopsy studies show that the spleen is the second most commonly affected organ in sarcoidosis, with the lung being first [3]. Clinical evidence of splenomegaly is however uncommon, present only in up to 27% of cases. Moreover, the occurrence of massive splenomegaly in sarcoidosis is limited to case reports. Although there is no consensus regarding the definition of massive splenomegaly, most authors describe it as when the spleen reaches the pelvis or has crossed the midline into the right lower or right upper abdominal quadrants. 3. Discussion Sarcoidosis is a chronic idiopathic granulomatous disease which can affect all age groups [1]. It has a slight predilection for women in the third to fifth decades of life. Sarcoidosis can affect virtually any organ system, with the lungs and mediastinal lymphatic system being affected in up to 90% of patients. In this setting, bilateral hilar adenopathy, with or without interstitial lung disease, is a common finding. 4 Case Reports in Medicine Lymphoma (usually indolent). Lymphoma (usually indolent). recommended and is the only way to establish the diagnosis [4, 5].h Hairy cell leukemia. The diagnosis of sarcoidosis is based on criteria from the American Thoracic Society (ATS), the European Respiratory Society (ERS), and the World Association of Sarcoidosis and Other Granulomatous Disorders (WASOG) [6]. These crite- ria include the following: the presence of clinicoradiological findings suggestive of sarcoidosis, the presence of histological evidence of noncaseating epithelioid cell granulomas, and the exclusion of known causes of granulomatous reactions [5, 6]. In fact, noncaseating granulomas are nonspecific for sarcoidosis and are associated with some infections (such as tuberculosis and histoplasmosis), occupational and environ- mental exposures (such as beryllium), autoimmune disorders (such as Wegener’s granulomatosis), and malignancy (such as lymphoma and solid tumors) [1]. Gaucher disease. Beta thalassemia major. Schistosomiasis. Kala-azar (visceral leishmaniasis). Sarcoidosis (rarely). Hyperreactive malarial splenomegaly syndrome (tropical splenomegaly syndrome). AIDS with mycobacterium avium complex. Splenic vein thrombosis. y p Some patients with sarcoidosis are not disabled by the illness and therefore do not require treatment [4]. In general, treatment is initiated when impairment of organ function is imminent. Oral prednisone at a dose of 20 to 40 mg daily is the recommended regimen. In the case of adequate response after 1 to 3 months, the prednisone dose should be tapered to 5 to 15 mg daily, with treatment planned for at least 6 additional months [4]. Sarcoidosis associated with massive splenomegaly can be treated with either splenectomy or corticosteroids, with no clear superiority of one modality over the other [2, 7]. Splenectomy has not been shown to alter the course of sarcoid progression. The indications for splenectomy include intractable abdominal pain from splenomegaly, functional asplenia, splenic rupture, hema- tologic abnormalities, massive splenomegaly refractory to medical therapy, or a strong suspicion of an alternative diagnosis [8].i Splenic involvement in sarcoidosis is usually asymp- tomatic, although left upper quadrant pain is occasionally present. 3. Discussion Other authors define it as when the spleen weights more than 1000–1500 g or if the largest dimension is greater than 20 cm (Poulin et al.). The most common etiologies of massive splenomegaly include hematological disorders (such as myeloproliferative disease and lymphomas), infectious diseases (such as visceral leishmaniasis and malaria), and infiltrative conditions (such as Gaucher disease) [9]. Massive splenomegaly remains a rare manifestation of sarcoidosis. In fact, in a large review by Fordice et al. of 6074 cases of sarcoidosis, only 20 patients (3%) had massive splenomegaly [10]. Differential diagnosis of massive splenomegaly is as follows: In some cases, the coexistence of “true” sarcoidosis and lymphoproliferative disease has been reported in the literature. In most of these cases, sarcoidosis preceded the diagnosis of lymphoma, but in few other reports, lymphopro- liferative disease occurred first [16]. This possible association Myelofibrosis (primary or secondary). Chronic myeloid leukemia. 5 Case Reports in Medicine between these two entities led to the so-called “sarcoidosis- lymphoma syndrome,” first suggested by Brincker in 1989 [17]. Since the diagnosis of sarcoidosis preceded the occur- rence of the lymphoproliferative disease in most cases, he suggested that sarcoidosis might be a paraneoplastic syn- drome [17]. The causal relation between these two entities is still a subject of speculation. It has been suggested that the impairment of the immune system in sarcoidosis, in the form of altered cell reaction and increased mitogenesis of B and T lymphocytes, can predispose to the development of lymphoid malignancies [18]. Moreover, the treatment of sarcoidosis with steroids can further compromise the immune system and may represent another predisposing factor for lymphoma development [15]. between these two entities led to the so-called “sarcoidosis- lymphoma syndrome,” first suggested by Brincker in 1989 [17]. Since the diagnosis of sarcoidosis preceded the occur- rence of the lymphoproliferative disease in most cases, he suggested that sarcoidosis might be a paraneoplastic syn- drome [17]. The causal relation between these two entities is still a subject of speculation. It has been suggested that the impairment of the immune system in sarcoidosis, in the form of altered cell reaction and increased mitogenesis of B and T lymphocytes, can predispose to the development of lymphoid malignancies [18]. Moreover, the treatment of sarcoidosis with steroids can further compromise the immune system and may represent another predisposing factor for lymphoma development [15]. [4] M. C. Iannuzzi, B. A. Rybicki, and A. S. The authors declared no conflict of interests. [17] H. Brincker, “Coexistence of sarcoidosis and malignant disease: causality or coincidence?” Sarcoidosis, vol. 6, no. 1, pp. 31–43, 1989. Consent Informed consent was obtained from the patient for publica- tion of this case report and any accompanying images. [15] H. Brincker, “Sarcoid reactions in malignant tumours,” Cancer Treatment Reviews, vol. 13, no. 3, pp. 147–156, 1986. [16] J. London, A. Grados, C. Ferm´e et al., “Sarcoidosis occurring after lymphoma: report of 14 patients and review of the literature,” Medicine, vol. 93, no. 21, article e121, 2014. 3. Discussion Teirstein, “Sarcoidosis,” The New England Journal of Medicine, vol. 357, no. 21, pp. 2108– 2165, 2007. [5] N. Sharma, H. Tariq, K. Uday, Y. Skaradinskiy, M. Niazi, and S. Chilimuri, “Hypercalcemia, anemia, and acute kidney injury: a rare presentation of sarcoidosis,” Case Reports in Medicine, vol. 2015, Article ID 565243, 6 pages, 2015. [6] American Thoracic Society, “Statement on sarcoidosis: joint statement of the American Thoracic Society (ATS), the Euro- pean Respiratory Society (ERS) and the World Association of Sarcoidosis and Other Granulomatous Disorders (WASOG) adopted by the ATS Board of Directors and by the ERS Executive Committee, February 1999,” American Journal of Respiratory and Critical Care Medicine, vol. 160, no. 2, pp. 736– 755, 1999. p FDG PET imaging remains an essential modality in the management of lymphoma. One of many advantages it offers over conventional imaging is the ability to detect occult lesions. However, its specificity is limited by multiple false- positive conditions, including infections, inflammations, and sarcoidosis [19, 20]. In fact, in the setting of sarcoidosis, PET imaging has been suggested to monitor disease progression and response to therapy [21]. Since both sarcoidosis and lymphoma are FDG avid, PET imaging cannot differentiate these two conditions, and therefore histological verification remains mandatory [20, 22]. [7] S. Kawano, J. Kato, N. Kawano et al., “Sarcoidosis manifesting as cardiac sarcoidosis and massive splenomegaly,” Internal Medicine, vol. 51, no. 1, pp. 65–69, 2012. [8] O. P. Sharma, V. Vucinic, and D. G. James, “Splenectomy in sarcoidosis: indications, complications, and long-term follow- up,” Sarcoidosis Vasculitis and Diffuse Lung Diseases, vol. 19, no. 1, pp. 66–70, 2002. [9] H. L. Paz-Y-Mar, A. Gonzalez-Estrada, and M. C. Alraies, “Massive splenomegaly,” BMJ Case Reports, vol. 2013, 2013. [10] J. Fordice, T. Katras, R. E. Jackson et al., “Massive splenomegaly in sarcoidosis,” Southern Medical Journal, vol. 85, no. 7, pp. 775– 778, 1992. [11] R. Palade, D. Voiculescu, E. Suliman, and G. Simion, “Splenic sarcoidosis—a case report,” Chirurgia, vol. 109, no. 5, pp. 670– 674, 2012. 4. Conclusion This report illustrates an unusual case of sarcoidosis that pre- sented as bicytopenia, hypercalcemia, diffuse lymphadenopa- thy, and massive splenomegaly, mimicking lymphoma. Physi- cians should be aware of this atypical presentation and accordingly should consider sarcoidosis in their differential diagnosis, after excluding other worrisome diagnoses, such as lymphoma. [12] F. Ufuk and D. Herek, “CT of hepatic sarcoidosis: small nodular lesions simulating metastatic disease,” Polish Journal of Radiology, vol. 80, pp. 945–954, 2015. [13] D. M. Warshauer and J. K. T. Lee, “Imaging manifestations of abdominal sarcoidosis,” American Journal of Roentgenology, vol. 182, no. 1, pp. 15–28, 2004. [14] R. A. DeRemee and P. M. Banks, “Non-Hodgkin’s lymphoma associated with hypercalcemia and increased activity of serum angiotensin-converting enzyme,” Mayo Clinic Proceedings, vol. 61, no. 9, pp. 714–718, 1986. Conflict of Interests The authors declared no conflict of interests. References [18] H. Brincker, “Coexistence of sarcoidosis and myeloproliferative disease: a case of sarcoidosis preceding polycythaemia vera with a literature review,” Journal of Internal Medicine, vol. 225, no. 5, pp. 355–357, 1989. [1] L. S. Newman, C. S. Rose, and L. A. Maier, “Sarcoidosis,” The New England Journal of Medicine, vol. 336, no. 17, pp. 1224–1234, 1997. [19] M. E. Juweid and B. D. Cheson, “Role of positron emission tomography in lymphoma,” Journal of Clinical Oncology, vol. 23, no. 21, pp. 4577–4580, 2005. [2] Z. Pavlovi´c-Popovi´c, B. Zari´c, Z. Kosjerina, and D. Petrovi´c, “Splenomegaly in sarcoidosis: frequency, treatment, prognosis and long-term follow-up,” Srpski Arhiv za Celokupno Lekarstvo, vol. 143, no. 5-6, pp. 279–283, 2015. [20] T. Acar, R. Savas, K. Kocacelebi, and E. S. Ucan, “Corticosteroid responsive sarcoidosis with multisystemic involvement years after initial diagnosis: a lymphoma mimicker on 18-FDG PET/CT,” Journal of Clinical Imaging Science, vol. 5, article 40, 2015. [3] I. Patel, M. Ismajli, and A. Steuer, “Sarcoidosis presenting as massive splenic infarction,” Case Reports in Rheumatology, vol. 2012, Article ID 834758, 2 pages, 2012. Case Reports in Medicine 6 [21] H. Zhuang and A. Alavi, “18-Fluorodeoxyglucose positron emission tomographic imaging in the detection and monitoring of infection and inflammation,” Seminars in Nuclear Medicine, vol. 32, no. 1, pp. 47–59, 2002. [22] P. Spagnolo, F. Luppi, P. Roversi, S. Cerri, L. M. Fabbri, and L. Richeldi, “Sarcoidosis: challenging diagnostic aspects of an old disease,” The American Journal of Medicine, vol. 125, no. 2, pp. 118–125, 2012.
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Tubgcp3 Is Required for Retinal Progenitor Cell Proliferation During Zebrafish Development
Frontiers in molecular neuroscience
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ORIGINAL RESEARCH published: 24 May 2019 doi: 10.3389/fnmol.2019.00126 Tubgcp3 Is Required for Retinal Progenitor Cell Proliferation During Zebrafish Development Guobao Li1,2, Daqing Jin1,2* and Tao P. Zhong1,2* 1 State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China, 2 Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, China The centrosomal protein γ-tubulin complex protein 3 (Tubgcp3/GCP3) is required for the assembly of γ-tubulin small complexes (γ-TuSCs) and γ-tubulin ring complexes (γ-TuRCs), which play critical roles in mitotic spindle formation during mitosis. However, its function in vertebrate embryonic development is unknown. Here, we generated the zebrafish tubgcp3 mutants using the CRISPR/Cas9 system and found that the tubgcp3 mutants exhibited the small eye phenotype. Tubgcp3 is required for the cell cycle progression of retinal progenitor cells (RPCs), and its depletion caused cell cycle arrest in the mitotic (M) phase. The M-phase arrested RPCs exhibited aberrant monopolar spindles and abnormal distributed centrioles and γ-tubulin. Moreover, these RPCs underwent apoptosis finally. Our study provides the in vivo model for the functional study of Tubgcp3 and sheds light on the roles of centrosomal γ-tubulin complexes in vertebrate development. Edited by: Christian Gonzalez-Billault, Universidad de Chile, Chile Edited by: Christian Gonzalez-Billault, Universidad de Chile, Chile Reviewed by: Jaerak Chang, Ajou University, South Korea Ann C. Morris, University of Kentucky, United States *Correspondence: Tao P. Zhong taozhong@fudan.edu.cn; tzhong@bio.ecnu.edu.cn Daqing Jin dqjin@fudan.edu.cn; dqjin@bio.ecnu.edu.cn Reviewed by: Jaerak Chang, Ajou University, South Korea Ann C. Morris, University of Kentucky, United States Keywords: γ-TuSC, γ-TuRC, tubgcp3, cell cycle, ciliary marginal zone, zebrafish INTRODUCTION Centrosome, the major microtubule-organizing center (MTOC) in vertebrate cells, provides a major site for microtubule (MT) nucleation and plays key roles in bipolar spindle assembly during mitosis (Kellogg et al., 1994). A typical centrosome consists of a pair of centrioles surrounded by the pericentriolar matrix (PCM) (Bornens, 2002). Many proteins, including γ-tubulin (GCP1), γ-tubulin complex proteins (GCPs) and a large number of other centrosome-associated proteins, localize to PCM and are involved in the formation of mitotic spindles. Together with other GCPs, γ-tubulin forms two distinctly sized complexes: the γ-tubulin small complex (γ-TuSC) and the γ-tubulin ring complex (γ-TuRC). The γ-TuSC is a heterotetramer consisting of two copies of γ-tubulin and one copy each of GCP2 and GCP3/Tubgcp3. Seven γ-TuSCs with GCP4, GCP5, GCP6 and other accessory proteins assemble into the γ-TuRC, which facilitates MT nucleation by capping the minus ends of MTs and protecting them from depolymerization (Zheng et al., 1995). Centrosomes have critical roles in brain development, and mutations in genes encoding for centrosome-associated proteins have been shown to be genetically linked to neurodevelopmental disorders (Novorol et al., 2013; Chavali et al., 2014; Morris-Rosendahl and Kaindl, 2015; Buchwalter et al., 2016). Received: 24 December 2018 Accepted: 29 April 2019 Published: 24 May 2019 Citation: Li G, Jin D and Zhong TP (2019) Tubgcp3 Is Required for Retinal Progenitor Cell Proliferation During Zebrafish Development. Front. Mol. Neurosci. 12:126. doi: 10.3389/fnmol.2019.00126 Received: 24 December 2018 Accepted: 29 April 2019 Published: 24 May 2019 Zebrafish Maintenance Zebrafish (Danio rerio) were maintained and bred under standard conditions as previously described (Westerfield, 2000). Stages of embryonic development were determined according to their morphology (Westerfield, 2000). Embryos were treated with 0.003% 1-phenyl-2-thiourea (PTU) in egg water to prevent the production of pigment. The transgenic line Tg(HuC:GFP) was used in this study, in which the zebrafish brain is labeled with green fluorescent protein (GFP) (Park et al., 2000). All animal experiments were approved by the Institutional Animal Care and Use Committee, Fudan University. Among vertebrate models, the zebrafish provides many unique advantages over other rodents for gene functional study during early embryonic development. For example, owing to its external fertilization and rapid development, zebrafish early embryos can be easily visualized and manipulated. In addition, maternal gene products, synthesized during oogenesis and supplied to the egg, play essential roles in the earliest stages of zebrafish embryonic development (Pelegri, 2003). With disruption of any of the maternal-effect genes, the embryos continue to develop until the maternal supply is exhausted, which facilitates the functional study of these genes at relatively late developmental stages. The zebrafish retina is part of the central nervous system (CNS), and its neuroanatomy is well characterized. The ciliary marginal zone (CMZ), a proliferative region located at the periphery of the retina, provides an excellent model for the study of neurodevelopment (Novorol et al., 2013). The retina grows continuously throughout life and almost all retina neurogenesis comes from CMZ after the embryogenesis of retina is completed at 60 hpf (Marcus et al., 1999). The CMZ contains retinal stem cells (RSCs) and retinal progenitor cells (RPCs), exhibiting a peripheral-to- central arrangement pattern. The RSCs were located nearest to the periphery, the proliferative RPCs resided in the middle, and the post-mitotic RPC cells were positioned at the most central of the CMZ (Wehman et al., 2005; Cerveny et al., 2010; Valdivia et al., 2016; Wan et al., 2016). In CMZ, cell proliferation and differentiation are precisely coordinated for the growth of zebrafish eyes. Many cell proliferation and Citation: In Saccharomyces cerevisiae, cells overexpressing the wild-type Spc98p/GCP3 or carrying the temperature-sensitive allele spc98-1 arrest in mitosis with a defective spindle (Geissler et al., 1996). The duplication and separation of spindle pole body (SPB; yeast centrosome) are not affected in these cells. Disruption of gcpC/GCP3 in Aspergillus nidulans results in absent functional spindles and defective mitosis (Xiong and Oakley, 2009). In Drosophila mutants for disks-degenerate 4 (dd4, which encodes GCP3), cells exhibit reduced density of spindle microtubules and delayed cell cycle progression from mitosis (Barbosa et al., 2000). Centriole duplication and separation are defective in some of the dd4 mutant cells. In addition, γ-tubulin is missing from the spindle poles and becomes dispersed throughout the cell. Mitotic arrest has been observed in Hela, T98, and U87MG cell lines after depletion of GCP3 using siRNA (Draberova et al., 2015; Farache et al., 2016; Cota et al., 2017). However, Mikule et al. (2007) found that cells harboring wild-type p53 (RPE-1, BJ-1, HME-1, and HCT-116) arrest in G1 phase in a p53-dependent manner after being transfected with siRNA against GCP3. Given that U87MG cells expressing wild-type p53 show mitotic arrest, it remains unclear which types of cell cycle defects will happen in the GCP3-deleted cells with wild-type p53 gene. These different cell cycle defects may occur in a cell type-specific manner as these studies were carried out using different cell lines. Moreover, there have been no functional studies of GCP3 in vivo in a vertebrate system. differentiation-associated genes have been studied using the zebrafish model (Wehman et al., 2005; Cerveny et al., 2010; Valdivia et al., 2016). In this study, we explored the in vivo function of tubgcp3 using the zebrafish model. We found that Tubgcp3 is essential for the development of zebrafish retina. Knockout of the tubgcp3 gene resulted in the small eye phenotype exhibiting CMZ defects due to the abnormal cell cycle progression. Depletion of Tubgcp3 in RPCs caused mitotic arrest and apoptosis. Our findings reveal the critical roles of GCP3 in cell cycle progression, providing insights into the function of its associated complexes, γ-TuSC and γ-TuRC, in development, and establish a vertebrate model for further study. Citation: Li G, Jin D and Zhong TP (2019) Tubgcp3 Is Required for Retinal Progenitor Cell Proliferation During Zebrafish Development. Li G, Jin D and Zhong TP (2019) Tubgcp3 Is Required for Retinal Progenitor Cell Proliferation During Zebrafish Development. Front. Mol. Neurosci. 12:126. doi: 10.3389/fnmol.2019.00126 Many studies have shown that γ-TuSC is involved in MT nucleation and mitotic spindle assembly, and every component of γ-TuSC is indispensable for cell cycle progression May 2019 | Volume 12 | Article 126 1 Frontiers in Molecular Neuroscience | www.frontiersin.org Tubgcp3 in Zebrafish Retinal Development Li et al. (Oakley et al., 1990; Geissler et al., 1996; Knop et al., 1997; Yuba-Kubo et al., 2005; Xiong and Oakley, 2009; Pouchucq et al., 2018). In Saccharomyces cerevisiae, cells overexpressing the wild-type Spc98p/GCP3 or carrying the temperature-sensitive allele spc98-1 arrest in mitosis with a defective spindle (Geissler et al., 1996). The duplication and separation of spindle pole body (SPB; yeast centrosome) are not affected in these cells. Disruption of gcpC/GCP3 in Aspergillus nidulans results in absent functional spindles and defective mitosis (Xiong and Oakley, 2009). In Drosophila mutants for disks-degenerate 4 (dd4, which encodes GCP3), cells exhibit reduced density of spindle microtubules and delayed cell cycle progression from mitosis (Barbosa et al., 2000). Centriole duplication and separation are defective in some of the dd4 mutant cells. In addition, γ-tubulin is missing from the spindle poles and becomes dispersed throughout the cell. Mitotic arrest has been observed in Hela, T98, and U87MG cell lines after depletion of GCP3 using siRNA (Draberova et al., 2015; Farache et al., 2016; Cota et al., 2017). However, Mikule et al. (2007) found that cells harboring wild-type p53 (RPE-1, BJ-1, HME-1, and HCT-116) arrest in G1 phase in a p53-dependent manner after being transfected with siRNA against GCP3. Given that U87MG cells expressing wild-type p53 show mitotic arrest, it remains unclear which types of cell cycle defects will happen in the GCP3-deleted cells with wild-type p53 gene. These different cell cycle defects may occur in a cell type-specific manner as these studies were carried out using different cell lines. Moreover, there have been no functional studies of GCP3 in vivo in a vertebrate system. (Oakley et al., 1990; Geissler et al., 1996; Knop et al., 1997; Yuba-Kubo et al., 2005; Xiong and Oakley, 2009; Pouchucq et al., 2018). Immunofluorescence and TUNEL Assay Immunofluorescence and TUNEL Assay Embryos were fixed in 4% paraformaldehyde for 2 h at room temperature (RT) except for anti-γ-tubulin staining fixed in 4% formalin. Cryosections were prepared as described in the previous ISH section. Cryosections were boiled in 0.01 M citric acid (pH 6) for 30 min. After being washed three times in PBST (0.1% Triton X-100 and 0.1% Tween 20 in PBS), the sections were incubated in blocking solution (2% horse serum, 10% FBS, 0.1% Triton X-100, 0.1% Tween 20, 10% DMSO in PBS) for 60 min. The sections were then incubated with primary antibodies at 4◦C overnight. Primary antibodies used in this study include rabbit anti-phosphohistone-H3 (Ser-10) (06-570, Millipore; 1:400), mouse anti-BrdU (11170376001, Roche; 1:300), rabbit anti-γH2AX (Ser-139) antibody (GTX127342, GeneTex; 1:300), mouse anti-PCNA (P8825, Sigma-Aldrich; 1:200), mouse anti-γ-Tubulin antibody (T5326, Sigma-Aldrich; 1:1000), mouse anti-α-Tubulin antibody (T9026, Sigma-Aldrich; 1:1000), mouse monoclonal anti-acetylated tubulin (T6793, Sigma-Aldrich; 1:1000), rabbit polyclonal anti-opsin (AB5404, Millipore; 1:1000), mouse monoclonal ZPR-1 (ab174435, Abcam; 1:500) and mouse monoclonal anti-phodopsin 4D2 (ab183359, Abcam; 1:1000). The sections were washed three times in PBST and incubated with secondary antibodies at RT for 2 h. Secondary antibodies were goat anti-mouse Alexa-Fluor-488 (A-11001, Invitrogen; 1:1000), goat anti-mouse Alexa-Fluor-594 (A-21135, Invitrogen; 1:1000), goat anti-mouse Alexa-Fluor-555 (A-21422, Invitrogen; 1:1000), goat anti-rabbit Alexa-Fluor-488 (A-11034, Invitrogen; 1:1000) and goat anti-rabbit Alexa-Fluor-594 (A-11037, Invitrogen; 1:1000). Sections were counterstained with 4′,6-diamidino-2-phenylindole (DAPI) (D3571, Invitrogen) when needed. The filamentous actin (F-actin) was stained with Alexa Fluor 488 phalloidin (A12379, Thermo Fisher; 1:100). For BrdU staining, sections were treated with 2M HCl for 1 h at RT before being incubated in blocking solution. For whole-mount immunostaining, the 4% paraformaldehyde fixed embryos were permeabilized Generation of tubgcp3 Mutants by the CRISPR/Cas9 System and Phenotypic Analysis Disruption of tubgcp3 transcript variant X1 (GenBank accession number XM_005170995) was performed using CRISPR/Cas9 technology. Cas9 nuclease target sites were designed using the ZiFiT Targeter online software. The target site in the exon 4 was selected and the corresponding sequence was 5′-GGTCCTCACAGAGGCTGAGCAGG-3′. Cas9 mRNA and guide RNA (gRNA) were synthesized using the mMESSAGE mMACHINE T7 Transcription Kit (AM1344, Invitrogen, United States) and MAXIscript T7 Transcription Kit (AM1322, Invitrogen, United States), respectively. Then, 300 pg Cas9 mRNA and 30 pg gRNA were co-injected into the one-cell stage zebrafish embryos to knockout the tubgcp3 gene. The PCR primers for genotyping were as follows: forward (5′-ATTACGCAGAGGACCAAGA-3′) and reverse (5′-AAAATAGGATTTCATACAGGAACCCG-3′). The tubgcp3 mutants were identified at 3 dpf by the developmental defects of the head and the arch. Heterozygous animals were incrossed to generate embryos for experimental analyses. Homozygous mutants were used as the experimental group and siblings as the control in this study. For morphological measurements, embryos were anesthetized with 0.16 mg/mL Tricaine (A5040, Sigma-Aldrich) and embedded in 3% methylcellulose (M0387, Sigma-Aldrich). Body May 2019 | Volume 12 | Article 126 Frontiers in Molecular Neuroscience | www.frontiersin.org Frontiers in Molecular Neuroscience | www.frontiersin.org 2 Tubgcp3 in Zebrafish Retinal Development Li et al. BrdU Incorporation length was measured laterally in the rostral-caudal axis. Eye size was measured laterally along the longest diameter of the eye. Brain size was measured by calculating the dorsal area of the brain using the transgenic line Tg(HuC:GFP) (Park et al., 2000). length was measured laterally in the rostral-caudal axis. Eye size was measured laterally along the longest diameter of the eye. Brain size was measured by calculating the dorsal area of the brain using the transgenic line Tg(HuC:GFP) (Park et al., 2000). To examine RPC proliferation, 66 hpf embryos were incubated in the thymidine analog 5-bromo-2-deoxyuridine (BrdU) (B5002, Sigma-Aldrich) at 10 mM/1% dimethyl sulfoxide (276855, Sigma-Aldrich) in embryo medium for 6 h at 28.5◦C. Then, the embryos were rinsed twice with PBS before being fixed at 72 hpf. To examine RSC proliferation, 4 dpf embryos were incubated with 3 mM BrdU/1% dimethyl sulfoxide in embryo medium for 24 h before being fixed at 5 dpf. For cartilage staining, 5 dpf embryos were fixed in Bouin’s solution overnight. The fixed embryos were washed three times in 70% ethanol/0.1% ammonia, then washed two more times in 95% ethanol. The embryos were transferred into Alcian blue solution (80% ethanol/20% glacial acetic acid, 0.1% Alcian blue) and stained overnight. After staining, the embryos were gradually rehydrated in a decreasing ethanol series (60%, 40%, and 20%) and washed twice in phosphate-buffered saline (PBS). The embryos were incubated in 3% hydrogen peroxide/1% potassium hydroxide until the pigmentation was removed. After that, the samples were incubated in 0.05% trypsin in 30% sodium tetraborate until cleared. Then, the embryos were transferred into 70% glycerol for imaging. Semi-Quantitative RT-PCR and Plasmids Semi-Quantitative RT-PCR and Plasmids Total RNA was extracted from whole embryos at the indicated developmental stages using a TRIZOL reagent. cDNA synthesis was carried out using a TOYOBO RT-PCR kit (FSQ-301, TOYOBO, Japan) according to the manufacturer’s instructions. The expression profile of tubgcp3 was analyzed using the following primers: tubgcp3 forward (5′-AGAAGAGATGGCCGAGTGGG-3′) and reverse (5′-CGCCAGACGAGTTCTGAGTA-3′); β-actin forward (5′-CAGCCTTCCTTCCTGGGTAT-3′) and reverse (5′-GCCATACAGAGCAGAAGCCA-3′). cDNA encoding full-length γ-tubulin was amplified by PCR and inserted into pEGFP-N2 (Clontech, United States) using EcoR I and Xho I. cDNA encoding Full-length, N-terminal (Tubgcp3 1–551 aa) and C-terminal (Tubgcp3 552–906 aa) Tubgcp3 were amplified by PCR and cloned into pCMV-Myc (Clontech, United States) using EcoRI and BamHI. HE Staining For Hematoxylin and Eosin (HE) staining, embryos were dehydrated using a graded ethanol series (50, 70, 90, 95, and 100%) before being transferred to xylene. Then, the embryos were embedded in paraffin wax and sectioned at 5 µm using a Leica Cryostat (Leica RM2235, Leica). HE staining was performed according to standard protocols. RESULTS For immunoprecipitation, HEK293T cells were co-transfected with GFP-tagged zebrafish γ-tubulin and Myc-tagged zebrafish Tubgcp3 constructs using Lipofectamine 2000 Transfection Reagent (Invitrogen). After 48 h, transfected cells were lysed with lysis buffer (50 mM HEPES, pH 7.5, 150 mM NaCl, 1 mM MgCl2, 1 mM EGTA, 0.5% NP-40, protease inhibitor cocktail (04693132001, Roche)) and incubated on ice for 10 min. The lysate was obtained by centrifugation at 16,000 × g for 15 min at 4◦C. The supernatants were incubated with anti-Myc antibody and protein A-Sepharose (GE Healthcare) at 4◦C for 4 h. Then the precipitants were washed three times with lysis buffer before being boiled in SDS loading buffer for immunoblot. Zebrafish embryos (5 dpf) were collected, washed and homogenized in RIPA lysis buffer (P0013B, Beyotime Biotechnology, China) containing protease inhibitor cocktail (04693132001, Roche). The following primary antibodies were used: rabbit anti-Myc (A5598, Sigma-Aldrich; 1:1000), rabbit anti-GFP (50430-2-AP, ProteinTech; 1:2000), rabbit anti-TUBGCP3 (15719-1-AP, ProteinTech; 1:1000), mouse anti-β-Actin (CW0264M, CWBIO; 1:2000) and rabbit anti-β-Actin (GTX124388, GeneTex; 1:5000). The Expression Pattern of Zebrafish tubgcp3 During Early Development To analyze the roles of tubgcp3 during zebrafish early development, we first examined the expression pattern of tubgcp3 by RT-PCR (Figure 1A) and whole-mount in situ hybridization (WISH) (Figures 1B–J). The RT-PCR analyses showed tubgcp3 transcripts were maternally deposited and continually expressed from 2-cell stage to 5 days post fertilization (dpf) during early embryonic development (Figure 1A). The expression of tubgcp3 mRNA first decreased and then increased from 2-cell stage to 24 hpf, indicating the degradation of maternally deposited tubgcp3 transcripts and the activation of zygotic transcripts during the maternal-to-zygotic transition (MZT). Consistent with RT-PCR results, WISH analyses showed that tubgcp3 mRNA was detected at all developmental stages from cleavage stage to 3 dpf compared with the control group (Figures 1B–J,N,O). Furthermore, we found that the expression of tubgcp3 was enriched in the head and eye as well as weak expression in other tissues of the embryos from 1 to 3 dpf (Figures 1B–J). To further characterize its expression in zebrafish retina, in situ hybridization (ISH) was performed on cryosections of the embryo eyes. In comparison with the sense probe as the control (Figure 1P), tubgcp3 was expressed throughout the retina with a gradual enrichment at CMZ (Figures 1K–M). We also detected the expression of tubgcp2 and γ-tubulin, which encodes another two subunits of γTuSC. Their expression was similar to that of tubgcp3 (Supplementary Figures S1A–H). In situ Hybridization Analyses In situ hybridization was performed on 10 µm cryosections of zebrafish eyes. Briefly, zebrafish embryos were fixed in 4% paraformaldehyde overnight at 4◦C. The next day, the fixed embryos were washed three times with PBS and dehydrated in 30% sucrose. Then, the embryos were embedded in OCT (Invitrogen) before being sectioned at 10 µm with a Leica cryostat (Leica CM1860, Leica Microsystems, Germany). For whole-mount in situ hybridization, the steps were performed as previously described (Thisse and Thisse, 2008). To generate in situ probes, PCR products of γ-tubulin, tubgcp2, tubgcp3, pcna, vsx2, col15a1b, ccnd1, atoh7, and cdkn1c were amplified from cDNA and subcloned into pGEM-T Easy vector (A1360, Promega). Probe plasmids were digested with restriction enzyme to make DNA templates. Digoxigenin-labeled RNA probes were generated by in vitro transcription using the MAXIscript SP6/T7 Transcription Kit (AM1322, Invitrogen). In situ hybridization signals were detected by using NBT/BCIP (11681451001, Roche) for sections and BM-Purple (11442074001, Roche) for whole-mount embryos. May 2019 | Volume 12 | Article 126 Frontiers in Molecular Neuroscience | www.frontiersin.org 3 Tubgcp3 in Zebrafish Retinal Development Li et al. Li et al. by proteinase K digestion before being incubated in blocking solution. region including ∼400 µm of the tails. Statistical analyses were performed with unpaired Student’s t-test using GraphPad Prism software. A P-value < 0.05 was considered statistically significant (∗P < 0.05, ∗∗P < 0.01). Data are expressed as mean + SEM. To detect cell death, a TUNEL assay was performed on sections using the In Situ Cell Death Detection Kit (Roche) according to the manufactures’ instruction. RESULTS In addition, the expression of pcna, a proliferation marker, was confined in the CMZ from 3 to 5 dpf (Supplementary Figures S1I–L). These data indicate that tubgcp3 may have a role in cell proliferation during zebrafish retinal development. Generation of Zebrafish tubgcp3 Mutants and Morphological Analysis The images of in situ hybridization, HE staining and SA-β-gal assay were captured using a Nikon ECLIPSE Ni microscope (Nikon) or Olympus microscope (IX83, Olympus). Immunostaining images were acquired using a Zeiss Axio Observer.Z1 microscope (Zeiss) or Nikon A1 confocal microscope (Nikon). Bright-field images of whole mount zebrafish embryos were taken using a Leica microscope (Leica M205FA, Leica). p g y To investigate the roles of tubgcp3 during zebrafish embryonic development, we established tubgcp3 knockout zebrafish lines using the CRISPR/Cas9 system. The CRISPR/Cas9 target site was designed in the exon 4 of the tubgcp3 gene. Finally, two mutant alleles with 5-base pair (bp) deletion and 11-bp insertion were identified (Figure 2A and data not shown). Since the two mutant lines exhibited the same phenotypes, we used the 5-bp deletion line for further research. The 5-bp deletion was predicted to lead to a premature termination in Tubgcp3 protein translation and yield a 99-amino acid (aa)-truncated Tubgcp3 protein absent of the two conversed GRIP domains (Figure 2B). tubgcp3 transcripts were detected in the tubgcp3 mutant retina (Supplementary Figure S2A), which suggested that the mutated tubgcp3 mRNA escaped non-sense-mediated mRNA decay Senescence-Associated β-Galactosidase (SA-β-gal) Assay To detect cellular senescence, β-galactosidase assay was performed using the Senescence Cells Histochemical Staining Kit (CS0030, Sigma-Aldrich). Zebrafish embryos (5 dpf) were fixed in 0.2% glutaraldehyde at RT for 2 h. The fixed embryos were washed three times in PBS before being embedded in OCT (Invitrogen). Then, the embryos were sectioned at 10 µm for the assay. Statistical Analyses To calculate cell proliferation and cell death in zebrafish retina, sections of the most central portion of the retina were selected for the analysis. The cell number was manually counted using ImageJ software within a defined region in the nasal part of the retina including the nasal CMZ (140 µm × 100 µm). Proliferating cells in embryo tails was counted within a defined May 2019 | Volume 12 | Article 126 Frontiers in Molecular Neuroscience | www.frontiersin.org 4 Tubgcp3 in Zebrafish Retinal Development Li et al. FIGURE 1 | Expression of tubgcp3 during zebrafish early development. (A) Semi-quantitative RT-PCR analyses showing the expression of zebrafish tubgcp3 from 2-cell stage to 5 days post-fertilization (dpf). β-actin was used as the internal control. (B–D) Whole-mount in situ hybridization (WISH) displaying ubiquitous expression of tubgcp3 at the two-cell stage (B), 50%-epiboly (C) and 8-somite stage (8 s) (D). (E–J) From 1 to 3 dpf, the expression of tubgcp3 becomes concentrated at the head. (K–M) In situ hybridization (ISH) of zebrafish retinal cryosections exhibit the expression of tubgcp3 throughout the whole retina at 1 dpf (K). From 3 dpf, its expression is enriched at the ciliary marginal zone (CMZ) (L,M). (N–P) No positive staining is detected with the sense probe. Arrows indicate the CMZ of the retina. Scale bars: 200 µm (B–J,N,O); 50 µm (K–M,P). FIGURE 1 | Expression of tubgcp3 during zebrafish early development. (A) Semi-quantitative RT-PCR analyses showing the expression of zebrafish tubgcp3 from 2-cell stage to 5 days post-fertilization (dpf). β-actin was used as the internal control. (B–D) Whole-mount in situ hybridization (WISH) displaying ubiquitous expression of tubgcp3 at the two-cell stage (B), 50%-epiboly (C) and 8-somite stage (8 s) (D). (E–J) From 1 to 3 dpf, the expression of tubgcp3 becomes concentrated at the head. (K–M) In situ hybridization (ISH) of zebrafish retinal cryosections exhibit the expression of tubgcp3 throughout the whole retina at 1 dpf (K). From 3 dpf, its expression is enriched at the ciliary marginal zone (CMZ) (L,M). (N–P) No positive staining is detected with the sense probe. Arrows indicate the CMZ of the retina. Scale bars: 200 µm (B–J,N,O); 50 µm (K–M,P). phenotype with reduced brain and eye size (Figures 2D,F). We determined the small brain phenotype using transgenic Tg(HuC:GFP), in which GFP expression is controlled by the promoter of neuronal gene HuC (Park et al., 2000). The tubgcp3 Mutants Exhibit Abnormal CMZ In order to investigate the eye defects in tubgcp3 mutants in detail, we performed Hematoxylin and Eosin (HE) staining on transverse eye paraffin sections. The tubgcp3 mutant retina showed defective CMZ with disorderly cells when compared to wild-type siblings at 3 dpf (Figures 3A,B,E,F). Notably, these abnormal cells disappeared from the CMZ at 5 dpf (Figures 3C,D,G,H). However, the laminar structure of central retina appeared normal in tubgcp3 mutants at 3 dpf and 5 dpf (Figures 3I–L), including the ganglion cell layer (GCL), inner plexiform layer (IPL), inner nuclear layer (INL), outer plexiform layer (OPL), outer nuclear layer (ONL) and retinal pigment epithelium (RPE). p Ciliary marginal zone is responsible for adding new neurons to the continuously growing retina in zebrafish larvae, which consists of retinal stem cells (RSCs) and retinal progenitor cells (RPCs) (Wehman et al., 2005; Cerveny et al., 2010; Valdivia et al., 2016; Wan et al., 2016). vsx2 encodes a homeodomain transcription factor, which is expressed in CMZ cells, Müller glia and a subpopulation of bipolar cells (Vitorino et al., 2009). The expression region of vsx2 was reduced in tubgcp3 mutant CMZ from 3 to 5 dpf (Figures 4A–D), which was consistent with the development defects detected by HE staining (Figures 3E–H). col15a1b expressed at the most periphery of CMZ, where it was considered to be a stem-cell niche (the location of RSCs) (Pujic et al., 2006; Cerveny et al., 2010; Gonzalez-Nunez et al., 2010; Valdivia et al., 2016). Its expression seems to be unaffected in the tubgcp3 mutants (Supplementary Figure S4A). ccnd1, a marker for proliferating cells, encodes Cyclin D1 (CCND1) which is required for G1-S transition (Cerveny et al., 2010; Valdivia et al., 2016). The expression of ccnd1 was significantly reduced in tubgcp3 mutant CMZ (Figures 4E–H). atoh7 encodes ATH5, a member of bHLH transcription factor, and is involved in the differentiation of ganglion cells (Masai et al., 2000; Cerveny et al., 2010; Valdivia et al., 2016). cdkn1c encodes the p57cip/kip, a cyclin-dependent kinase inhibitor, which is required for many retinal cells to exit from the cell cycle before their FIGURE 1 | Expression of tubgcp3 during zebrafish early development. (A) Semi-quantitative RT-PCR analyses showing the expression of zebrafish tubgcp3 from 2-cell stage to 5 days post-fertilization (dpf). β-actin was used as the internal control. Frontiers in Molecular Neuroscience | www.frontiersin.org Statistical Analyses We found that the brain size was reduced about 10% in the tubgcp3 mutants compared to the wild-type siblings at 3 dpf (Figure 2G). The brain size reduction in tubgcp3 mutants became more significant (about 24% reduction) when measured at 5 dpf (Figure 2G). Notably, the eyes became smaller in the tubgcp3 mutants when compared with wild-type siblings from 3 dpf to 5 dpf (Figures 2E,F). Other defects including dorsal tail curvature (Figure 2D), uninflated swim bladder (Figure 2D), body length reduction (Supplementary Figure S3A) and jaw malformation (Supplementary Figure S3B) were also visible in tubgcp3 mutants. The developmental defects were gradually more serious, and the mutants died around 10–14 dpf. The tubgcp3 Mutants Exhibit Abnormal CMZ (B–D) Whole-mount in situ hybridization (WISH) displaying ubiquitous expression of tubgcp3 at the two-cell stage (B), 50%-epiboly (C) and 8-somite stage (8 s) (D). (E–J) From 1 to 3 dpf, the expression of tubgcp3 becomes concentrated at the head. (K–M) In situ hybridization (ISH) of zebrafish retinal cryosections exhibit the expression of tubgcp3 throughout the whole retina at 1 dpf (K). From 3 dpf, its expression is enriched at the ciliary marginal zone (CMZ) (L,M). (N–P) No positive staining is detected with the sense probe. Arrows indicate the CMZ of the retina. Scale bars: 200 µm (B–J,N,O); 50 µm (K–M,P). FIGURE 1 | Expression of tubgcp3 during zebrafish early development. (A) Semi-quantitative RT-PCR analyses showing the expression of zebrafish tubgcp3 from 2-cell stage to 5 days post-fertilization (dpf). β-actin was used as the internal control. (B–D) Whole-mount in situ hybridization (WISH) displaying ubiquitous expression of tubgcp3 at the two-cell stage (B), 50%-epiboly (C) and 8-somite stage (8 s) (D). (E–J) From 1 to 3 dpf, the expression of tubgcp3 becomes concentrated at the head. (K–M) In situ hybridization (ISH) of zebrafish retinal cryosections exhibit the expression of tubgcp3 throughout the whole retina at 1 dpf (K). From 3 dpf, its expression is enriched at the ciliary marginal zone (CMZ) (L,M). (N–P) No positive staining is detected with the sense probe. Arrows indicate the CMZ of the retina. Scale bars: 200 µm (B–J,N,O); 50 µm (K–M,P). (NMD). In addition, sequencing analyses confirmed that the 5-bp deletion transcripts existed in tubgcp3 mutants (Supplementary Figure S2B). Furthermore, the full-length Tubgcp3 protein was significantly decreased in mutant embryos (Figure 2C). The residual full-length Tubgcp3 in tubgcp3 mutants maybe attributed to the maternal supplied Tubgcp3 that was unusually stable in its associated complexes or depleted at a very low rate in embryos. All these results indicate a loss-of-function mutation in tubgcp3 gene. The tubgcp3 mutant embryos were indistinguishable from their wild-type siblings before 2 dpf. From 3 to 5 dpf, the mutants exhibited a progressed MCPH (microcephaly)-like May 2019 | Volume 12 | Article 126 Frontiers in Molecular Neuroscience | www.frontiersin.org 5 Li et al. Tubgcp3 in Zebrafish Retinal Development FIGURE 2 | CRISPR/Cas9-mediated tubgcp3 knockout results in zebrafish developmental defects. (A) Sanger sequencing displaying a 5-base pair (bp) deletion in tubgcp3 gene in the zebrafish mutants. The black box indicates the deletion. The tubgcp3 Mutants Exhibit Abnormal CMZ The expression of atoh7 and cdkn1c was significantly reduced in tubgcp3 mutant CMZ at 3 dpf and almost disappeared at 5 dpf (Figures 4I–P). These results reveal that the tubgcp3 mutants suffer from a significant reduction in proliferating and differentiating in CMZ cells. The tubgcp3 Mutants Exhibit Abnormal CMZ (B) Predicted structure and amino acid sequence of the wild-type and the mutant alleles of Tubgcp3. The 5-bp deletion in tubgcp3 gene was predicted to generate a 99 amino acid (aa)-truncated Tubgcp3 protein without the GRIP1 domain (green box) and GRIP2 domain (purple box). (C) Western blotting analysis showing Tubgcp3 protein decreased in tubgcp3 mutant embryos at 5 dpf. (D) Whole-mount lateral views of the tubgcp3 mutant and sibling embryos at the indicated developmental stages. (E) Higher magnification of the lateral and dorsal views of zebrafish heads from siblings and tubgcp3 mutants at 3 and 5 dpf. The brain size is measured based on the fluorescent area in the head of Tg(HuC:GFP). Red dotted lines indicate the brain area of the embryos used for analysis. (F,G) Scatter plot of eye and head size from wild-type siblings and tubgcp3 mutants at 3 and 5 dpf. Data are from 29 embryos for each group. Student’s t-test: ∗∗P < 0.01. Scale bars: 1 mm (D); 200 µm (E). FIGURE 2 | CRISPR/Cas9-mediated tubgcp3 knockout results in zebrafish developmental defects. (A) Sanger sequencing displaying a 5-base pair (bp) deletion in tubgcp3 gene in the zebrafish mutants. The black box indicates the deletion. (B) Predicted structure and amino acid sequence of the wild-type and the mutant alleles of Tubgcp3. The 5-bp deletion in tubgcp3 gene was predicted to generate a 99 amino acid (aa)-truncated Tubgcp3 protein without the GRIP1 domain (green box) and GRIP2 domain (purple box). (C) Western blotting analysis showing Tubgcp3 protein decreased in tubgcp3 mutant embryos at 5 dpf. (D) Whole-mount lateral views of the tubgcp3 mutant and sibling embryos at the indicated developmental stages. (E) Higher magnification of the lateral and dorsal views of zebrafish heads from siblings and tubgcp3 mutants at 3 and 5 dpf. The brain size is measured based on the fluorescent area in the head of Tg(HuC:GFP). Red dotted lines indicate the brain area of the embryos used for analysis. (F,G) Scatter plot of eye and head size from wild-type siblings and tubgcp3 mutants at 3 and 5 dpf. Data are from 29 embryos for each group. Student’s t-test: ∗∗P < 0.01. Scale bars: 1 mm (D); 200 µm (E). and structures are unaffected in the central reitna of the tubgcp3 mutants. further differentiation (Ohnuma et al., 1999; Shkumatava and Neumann, 2005; Cerveny et al., 2010; Valdivia et al., 2016). Loss of Tubgcp3 in CMZ Cells Causes M-Phase Arrest However, these cells were still PH3+ after the 6 h BrdU treatment, which indicates that they were still in the mitotic (M) phase. Since G2 and M phase are shorter than 6 h, the results suggest that these RPCs were arrested in M-phase. Moreover, there were also more BrdU+ PH3+ cells in the tubgcp3 mutants than in wild-type siblings (Figures 5E,F,G), suggesting that some of the cycling RPCs were arrested in M-phase after they passed the S phase. When whole-mount immunostaining was carried out under the same BrdU treatment condition, we observed similar results that a large number of PH3+ BrdU- cells existed in the tubgcp3 mutant tails while they absent in wild-type siblings (Supplementary Figures S5A,B). These results suggest that Tubgcp3 is required for RPCs to go through mitosis. Given the mitotic arrested cells detected in the tubgcp3 mutant retinae, we analyzed the spindle formation by immunostaining using anti-α-tubulin and anti-PH3 antibodies. In wild-type siblings, bipolar mitotic spindles were formed in mitotic cells (Figures 5J,L). In contrast, abnormal monopolar spindles were observed in the mitotic arrested cells in tubgcp3 mutant retina (Figures 5K,M,N). The microtubules arrayed radially in the center and the condensed chromosomes located at the periphery in these cells (Figures 5I,K,M). These results suggest that depletion of Tubgcp3 causes a defect in mitotic spindle formation in RPCs, resulting in mitotic arrest in these cells. Loss of Tubgcp3 in CMZ Cells Causes M-Phase Arrest Given the reduction of cell proliferation and differentiation in the tubgcp3 mutant CMZ (Figures 4E–P), we first examined whether cell cycle progression was defective in mutant retinae using BrdU incorporation as an S phase marker and Phospho-Histone H3 (PH3) as a mitotic marker. Considering the length of the cell cycle in the CMZ at early larval stages is about 6 to 8 h (Li et al., 2000; Wehman et al., 2007), zebrafish embryos were incubated with BrdU from 66 to 72 hpf and then subjected to section and cell cycle analysis. Cycling RPCs would be labeled by BrdU except those that had passed S phase and would exit cell cycle and undergo differentiation. In addition, different retinal cell types, including Müller glia cells (expressing vsx2) (Figures 4A–D), a subset of bipolar cells (expressing vsx2) (Figures 4A–D), cones (labeled with anti-ZPR1 for double cone photoreceptors and anti-M-opsin for cone outer segments) (Figures 4Q–T and Supplementary Figure S4B) and rods (labeled with anti-4D2 for rod outer segments) (Supplementary Figure S4B), appeared normal in the tubgcp3 mutants. Moreover, cilia in photoreceptor cells (labeled with anti-acetylated α-tubulin) and retinal laminar structures, including the inner segment, inter plexiform layer (IPL), the outer limiting membrane (OLM) and the outer plexiform layer (OPL) (labeled with phalloidin) (Supplementary Figure S4B and data not shown), were also normal in tubgcp3 mutants. These results suggest that these differentiated cells We compared expression patterns of BrdU and PH3 between the tubgcp3 mutants and wild-type siblings. In wild-type siblings, the entire CMZ was labeled with BrdU with about three PH3+ cells scattered along the CMZ (Figures 5A,C,E,G). In the tubgcp3 May 2019 | Volume 12 | Article 126 Frontiers in Molecular Neuroscience | www.frontiersin.org 6 Li et al. Tubgcp3 in Zebrafish Retinal Development FIGURE 3 | The tubgcp3 mutants exhibit developmental defects in the CMZ of the retina. (A–D) Hematoxylin and Eosin (HE) staining displaying significant defects in the CMZ of the tubgcp3 mutant retinae at 3 dpf and 5 dpf. (E–H) Higher-magnification images of the CMZ in blue dotted rectangles in (A–D). (I–L) Higher-magnification image of the orange dotted rectangles in (A–D). The tubgcp3 mutants exhibit normal retinal laminar structures in the central retina. GCL, ganglion cell layer; IPL, inner plexiform layer; INL, inner nuclear layer; OPL, outer plexiform layer; ONL, outer nuclear layer; RPE, retinal pigment epithelium. Scale bars: 100 µm (A–D); 20 µm (E–L). Loss of Tubgcp3 in CMZ Cells Causes M-Phase Arrest FIGURE 3 | The tubgcp3 mutants exhibit developmental defects in the CMZ of the retina. (A–D) Hematoxylin and Eosin (HE) staining displaying significant defects in the CMZ of the tubgcp3 mutant retinae at 3 dpf and 5 dpf. (E–H) Higher-magnification images of the CMZ in blue dotted rectangles in (A–D). (I–L) Higher-magnification image of the orange dotted rectangles in (A–D). The tubgcp3 mutants exhibit normal retinal laminar structures in the central retina. GCL, ganglion cell layer; IPL, inner plexiform layer; INL, inner nuclear layer; OPL, outer plexiform layer; ONL, outer nuclear layer; RPE, retinal pigment epithelium. Scale bars: 100 µm (A–D); 20 µm (E–L). mutants, there was a significantly increased number of PH3+ cells in CMZ and its adjacent regions (Figures 5B,F,G). We noticed that a portion of these PH3+ cells were BrdU negative (Figure 5F). In contrast, there were no PH3+ BrdU- cells in wild-type siblings (Figure 5E). In addition, BrdU+ cells were significantly reduced in mutant CMZ (Figures 5D,F,G). The PH3+ BrdU- cells in tubgcp3 mutants had passed S phase when we performed BrdU treatment, and they then went into mitosis as they were stained by PH3. However, these cells were still PH3+ after the 6 h BrdU treatment, which indicates that they were still in the mitotic (M) phase. Since G2 and M phase are shorter than 6 h, the results suggest that these RPCs were arrested in M-phase. Moreover, there were also more BrdU+ PH3+ cells in the tubgcp3 mutants than in wild-type siblings (Figures 5E,F,G), suggesting that some of the cycling RPCs were arrested in M-phase after they passed the S phase. When whole-mount immunostaining was carried out under the same BrdU treatment condition, we observed similar results that a large number of PH3+ BrdU- cells existed in the tubgcp3 mutant tails while they absent in wild-type siblings (Supplementary mutants, there was a significantly increased number of PH3+ cells in CMZ and its adjacent regions (Figures 5B,F,G). We noticed that a portion of these PH3+ cells were BrdU negative (Figure 5F). In contrast, there were no PH3+ BrdU- cells in wild-type siblings (Figure 5E). In addition, BrdU+ cells were significantly reduced in mutant CMZ (Figures 5D,F,G). The PH3+ BrdU- cells in tubgcp3 mutants had passed S phase when we performed BrdU treatment, and they then went into mitosis as they were stained by PH3. Frontiers in Molecular Neuroscience | www.frontiersin.org Tubgcp3 Deficiency Impairs Centrioles Distribution Since centriole duplication and segregation are essential for bipolar spindle formation during mitosis, we examined whether these processes were affected in the tubgcp3 mutant retinal cells May 2019 | Volume 12 | Article 126 Frontiers in Molecular Neuroscience | www.frontiersin.org Frontiers in Molecular Neuroscience | www.frontiersin.org 7 Li et al. Tubgcp3 in Zebrafish Retinal Development FIGURE 4 | The tubgcp3 mutant embryos exhibit decreased expression of proliferation and differentiation markers in CMZ cells. (A–D) ISH analyses show that the expression of vsx2 is normal in the central retina but significantly reduced in the CMZ in tubgcp3 mutant retinae at 3 dpf and 5 dpf. (E–H) ISH analyses exhibit that ccnd1 is highly expressed in wild-type sibling CMZ (M,O) but clearly reduced in tubgcp3 mutant CMZ (N,P) at 3 dpf and 5 dpf. (I–P) atoh7 and cdkn1c (associated with retinal cell differentiation) are expressed in the central CMZ of wild-type sibling retina but significantly reduced in tubgcp3 mutant CMZ at 3 dpf and almost disappeared at 5 dpf. (Q–T) Immunostaining analyses displaying normal ZPR-1 staining (green/red double cone photoreceptors marker) in the central area of the tubgcp3 mutant retina. Arrows indicate the CMZ of the retina. Scale bars: 100 µm (A–T). FIGURE 4 | The tubgcp3 mutant embryos exhibit decreased expression of proliferation and differentiation markers in CMZ cells. (A–D) ISH analyses show that the expression of vsx2 is normal in the central retina but significantly reduced in the CMZ in tubgcp3 mutant retinae at 3 dpf and 5 dpf. (E–H) ISH analyses exhibit that ccnd1 is highly expressed in wild-type sibling CMZ (M,O) but clearly reduced in tubgcp3 mutant CMZ (N,P) at 3 dpf and 5 dpf. (I–P) atoh7 and cdkn1c (associated with retinal cell differentiation) are expressed in the central CMZ of wild-type sibling retina but significantly reduced in tubgcp3 mutant CMZ at 3 dpf and almost disappeared at 5 dpf. (Q–T) Immunostaining analyses displaying normal ZPR-1 staining (green/red double cone photoreceptors marker) in the central area of the tubgcp3 mutant retina. Arrows indicate the CMZ of the retina. Scale bars: 100 µm (A–T). distribution of γ-tubulin was affected after Tubgcp3 depletion. Our immunostaining results showed that γ-tubulin located at each spindle pole during mitosis in wild-type siblings (Figure 5R). In contrast, the distribution of γ-tubulin was abnormal in the mitotic arrested RPCs in tubgcp3 mutants. Frontiers in Molecular Neuroscience | www.frontiersin.org Tubgcp3 Deficiency Impairs Centrioles Distribution Most of the arrested cells that displayed γ-tubulin focus in the center of the cells (Figure 5S). Others showed scattered γ-tubulin staining patterns (Figure 5T). In order to test whether the interaction between Tubgcp3 and γ-tubulin is conserved in zebrafish, we performed co-Immunoprecipitation (co-IP) assays using HEK293 cells by co-transfecting Myc-tagged zebrafish Tubgcp3 and GFP-tagged zebrafish γ-tubulin. Co-IP assays showed that Tubgcp3 binds to γ-tubulin through its C-terminal domain, which is consistent with previous studies (Figure 5V). using anti-centrin (a marker for centriole) and anti-PH3. In wild-type siblings, the mitotic cells had a pair of centrioles (two centrioles per centrosome) at each spindle pole (Figure 5O). In the tubgcp3 mutants, the M-phase arrested cells had four centriole dots like the wild-type siblings (Figures 5P,Q). However, the distribution of centrioles was abnormal. They were located at the center of the cell (Figure 5P) or randomly scattered in the cell (Figure 5Q). These data suggest that the centrioles duplicate normally but fail to separate correctly in mitotic arrested RPCs in the tubgcp3 mutants. Previous work has reported that Tubgcp3 interacts with γ-tubulin to form γ-TuRC complexes, which are located at the centrosome during mitosis (Pereira et al., 1998; Kollman et al., 2010; Figure 5U). We next detected whether the May 2019 | Volume 12 | Article 126 Frontiers in Molecular Neuroscience | www.frontiersin.org 8 Li et al. Tubgcp3 in Zebrafish Retinal Development FIGURE 5 | The tubgcp3 mutant CMZ cells arrest in M-phase showing monopolar spindles and abnormal distributed centrioles and γ-tubulin. (A–F) Immunostaining nalysis of cell proliferation in zebrafish retina at 3 dpf using DNA replication marker (BrdU, red) and mitotic marker (PH3, green). Embryos are incubated with BrdU or 6 h before being collected at 72 hpf for the analysis. Almost all cells in wild-type sibling CMZ are BrdU+ with several PH3+ cells among them (A,C,E). In the (Continued IGURE 5 | The tubgcp3 mutant CMZ cells arrest in M-phase showing monopolar spindles and abnormal distributed centrioles and γ-tubulin. (A–F) Immunostaining nalysis of cell proliferation in zebrafish retina at 3 dpf using DNA replication marker (BrdU, red) and mitotic marker (PH3, green). Embryos are incubated with BrdU or 6 h before being collected at 72 hpf for the analysis. Almost all cells in wild-type sibling CMZ are BrdU+ with several PH3+ cells among them (A,C,E). DISCUSSION In this study, we generated the zebrafish tubgcp3 mutant and investigated the function of tubgcp3 in eye development. Our data reveal that Tubgcp3 plays important roles in cell cycle progression in the CMZ of the retina. Depletion of Tubgcp3 in RPCs results in monopolar spindle formation and impairs the distribution of centrioles and γ-tubulin, causing M-phase arrest and further apoptosis. In addition, depletion of Tubgcp3 results in cell proliferation defects and senescence at the peripheral CMZ. These defects led to the small eye phenotype in the tubgcp3 mutants. To our knowledge, this is the first in vivo model for the functional study of Tubgcp3. Our findings also provide some clues for studying the roles of its associated complexes, γ-TuSC and γ-TuRC, in vertebrate development. In this study, we generated the zebrafish tubgcp3 mutant and investigated the function of tubgcp3 in eye development. Our data reveal that Tubgcp3 plays important roles in cell cycle progression in the CMZ of the retina. Depletion of Tubgcp3 in RPCs results in monopolar spindle formation and impairs the distribution of centrioles and γ-tubulin, causing M-phase arrest and further apoptosis. In addition, depletion of Tubgcp3 results in cell proliferation defects and senescence at the peripheral CMZ. These defects led to the small eye phenotype in the tubgcp3 mutants. To our knowledge, this is the first in vivo model for the functional study of Tubgcp3. Our findings also provide some clues for studying the roles of its associated complexes, γ-TuSC and γ-TuRC, in vertebrate development. g In addition, RSCs [marked by col15a1b (Pujic et al., 2006; Cerveny et al., 2010; Gonzalez-Nunez et al., 2010; Valdivia et al., 2016)] still could be detected at the most peripheral CMZ (close to the lens) in the tubgcp3 mutant retina at 5 dpf (Supplementary Figure S4A). Apoptosis signal was also absent in this region at 3 dpf (Figures 6H,Q) and 5 dpf (Supplementary Figure S6). We next want to detect cell proliferation at the peripheral CMZ. Embryos were incubated with BrdU for 24 h before being fixed at 5 dpf for the assay. In this region, BrdU+ cells were significantly decreased in the tubgcp3 mutants compared to wild-type siblings (Figures 6S–T”,Y). As the proliferation of RSCs occurs at the peripheral CMZ, we speculated that RSC proliferation might be affected in the tubgcp3 mutant CMZ. Tubgcp3 Deficiency Impairs Centrioles Distribution In the (Continued) FIGURE 5 | The tubgcp3 mutant CMZ cells arrest in M-phase showing monopolar spindles and abnormal distributed centrioles and γ-tubulin. (A–F) Immunostaining analysis of cell proliferation in zebrafish retina at 3 dpf using DNA replication marker (BrdU, red) and mitotic marker (PH3, green). Embryos are incubated with BrdU for 6 h before being collected at 72 hpf for the analysis. Almost all cells in wild-type sibling CMZ are BrdU+ with several PH3+ cells among them (A,C,E). In the (Continued) May 2019 | Volume 12 | Article 126 Frontiers in Molecular Neuroscience | www.frontiersin.org 9 Li et al. Li et al. Tubgcp3 in Zebrafish Retinal Development FIGURE 5 | Continued tubgcp3 mutant retina, PH3+ cells are significantly increased (B,F), but BrdU+ cells are markedly decreased (D,F). Note that PH3+ BrdU- cells are detected in the tubgcp3 mutant retina (F) but absent in the wild-type sibling (E). (G) Bar chart analyses depicting quantification of BrdU- and PH3-labeled cells in wild-type sibling and tubgcp3 mutant retinae. Data are mean + SEM from 50 retinal sections for each group. Student’s t-test: ∗∗P < 0.01. (H–M) Immunostaining of 3 dpf retinal cryosections with anti-α-tubulin (red) and anti-PH3 (green) displaying bipolar spindles formed in mitotic cells in wild-type siblings (H,J,L). In the tubgcp3 mutant retina, many mitotic RPCs exhibit monopolar spindles (I,K,M). Insets indicate high-magnification images of mitotic RPCs in rectangles in (H–M). (N) Bar charts depicting quantification of mitotic cells with monopolar spindles in wild-type sibling (0.12 per section, n = 43 sections) and the tubgcp3 mutant retinae (8.14 per section, n = 36 sections). (O–Q) Immunostaining analyses displaying a pair of centrioles at each pole of the bipolar spindle in mitotic cells in wild-type sibling CMZ (O). In the tubgcp3 mutant retinae, centrioles are distributed at the center of the M-phase arrested cells (57.6%, n = 59 M-phase arrested cells) (P) or randomly scatter in these cells (42.4%, n = 59 M-phase arrested cells) (Q). (R–T) Immunostaining analyses exhibiting γ-tubulin at the spindle poles in mitotic cells in wild-type sibling (R). In tubgcp3 mutant retinae, γ-tubulin localizes at the center of the M-phase arrested cells, showing a single focus (62.5%, n = 80 M-phase arrested cells) (S) or scattered foci (37.5%, n = 80 M-phase arrested cells) (T). (U) Schematic representation of the structure of γ-TuSC and γ-TuRC. Tubgcp3 Deficiency Impairs Centrioles Distribution (V) Co-immunoprecipitation (IP) assays showing Tubgcp3 interacts with γ-tubulin through its C terminal domain. HEK293T cells were transfected with plasmids to express GFP-tagged zebrafish γ-tubulin and Myc-tagged zebrafish Tubgcp3 fragments, including full length (1–906 aa) Tubgcp3, N terminal (1–551 aa) Tubgcp3 and C terminal (552–906 aa) Tubgcp3. Then the cell samples were performed by immunoprecipitation with anti-Myc antibody and analyzed by immunoblotting (IB) with anti-Myc and anti-GFP antibodies. β-Actin was used as the loading control. Arrowheads indicate the IgG heavy chain (∼50 kDa) and IgG light chain (∼25 kDa). Scale bars: 20 µm (A–F); 20 µm (H–M); 2 µm (O–T). Kumar, 2010; Schmidt et al., 2010; Hossain and Tsang, 2013). Consistent with these reports, we found that the expression of senescence-associated β-galactosidase (SA-β-gal), a widely used senescent marker (Dimri et al., 1995), was significantly increased at the peripheral CMZ in the tubgcp3 mutant CMZ compared to the wild-type siblings (Figures 6U–X). These results indicate that depletion of Tubgcp3 caused cellular senescence at the peripheral CMZ that contains RSCs. Taken together, our data suggest that depletion of Tubgcp3 does not affect centriole duplication, but results in abnormal distribution of centrioles and γ-tubulin. Taken together, our data suggest that depletion of Tubgcp3 does not affect centriole duplication, but results in abnormal distribution of centrioles and γ-tubulin. Tupgcp3-Deficient Cells Undergo Apoptosis and Senescence Given our HE staining results showed disappearance of cells in the tubgcp3 mutant CMZ from 3 to 5 dpf (Figures 3A–H), we next investigated whether the mitotic arrest RPCs underwent apoptosis using TUNEL assay. There were almost no TUNEL+ cells in wild-type siblings (Figures 6C,E,G,I). In contrast, TUNEL+ cells were significantly increased in tubgcp3 mutant CMZ and the adjacent regions (Figures 6D,F,H,I) at 3 dpf. However, the TUNEL+ cells and PH3+ cells did not co-localize in the mutants (Figures 6F,H). This may be due to the fact that PH3 expression was absent in late-stage apoptotic cells (Huang et al., 2006). Next, we performed immunostaining using γ-H2AX, an early stage apoptotic marker (Rogakou et al., 2000), together with PH3. There was a significant increase in the number of γ-H2AX + cells in the tubgcp3 mutant retina at 3 dpf (Figures 6M,O,Q,R), compared to wild-type siblings (Figures 6L,N,P,R). Moreover, some of the γ-H2AX+ cells overlapped with PH3+ cells (Figures 6O,Q). These results suggest that the M-phase arrested RPCs undergo apoptosis in the tubgcp3 mutants. Frontiers in Molecular Neuroscience | www.frontiersin.org DISCUSSION Previous studies have reported that centrosome dysfunction caused by centrosomal protein depletion could induce cellular senescence (Manning and γ-TuSC, composed of Tubgcp3, Tubgcp2, and γ-tubulin, is an essential complex for microtubule nucleation and spindle assembly during mitosis. Each component of γ-TuSC is likely essential for all cell proliferation in the developing zebrafish. Recently, Pouchucq et al. (2018) reported that morpholino (MO)-mediated tubg1/γ-tubulin knockdown caused zebrafish embryo development arrest at the mid-gastrula stage. The early developmental defects are most probably attributable to the fact that MO was designed against the translation start site of tubg1 mRNA, which blocks the translation of both the maternal and zygotic tubg1 mRNA (Pouchucq et al., 2018). Although cell cycle defects and increased apoptosis were observed after depletion of γ-tubulin (Pouchucq et al., 2018), study on the function of γ-tubulin in later stages of development has been limited. In contrast, the tubgcp3 mutants can survive longer than May 2019 | Volume 12 | Article 126 Frontiers in Molecular Neuroscience | www.frontiersin.org Frontiers in Molecular Neuroscience | www.frontiersin.org 10 Li et al. Tubgcp3 in Zebrafish Retinal Development Li et al. Tubgcp3 in Zebrafish Retinal Development FIGURE 6 | Tupgcp3 deficient cells undergo apoptosis and senescence. (A–H) Immunostaining analyses displaying significantly increased TUNEL+ cells in the tubgcp3 mutant retina (D,F,H) at 3 dpf compared to wild-type sibling (C,E,G). Note the increased PH3+ cells in the tubgcp3 mutant retina do not co-localize with the TUNEL+ cells (F,H). (I) Bar chart analyses depicting quantification of TUNEL+ cells in wild-type sibling and the tubgcp3 mutant retinae. (J–Q) Immunostaining analyses exhibiting markedly increased γ-H2AX+ cells in the tubgcp3 mutant retina (M,O,Q) at 3 dpf compared to wild-type sibling (L,N,P). Note that some of the (Continued) Frontiers in Molecular Neuroscience | www frontiersin org 11 May 2019 | Volume 12 | Article 126 FIGURE 6 | Tupgcp3 deficient cells undergo apoptosis and senescence. (A–H) Immunostaining analyses displaying significantly increased TUNEL+ cells in the tubgcp3 mutant retina (D,F,H) at 3 dpf compared to wild-type sibling (C,E,G). Note the increased PH3+ cells in the tubgcp3 mutant retina do not co-localize with the TUNEL+ cells (F,H). (I) Bar chart analyses depicting quantification of TUNEL+ cells in wild-type sibling and the tubgcp3 mutant retinae. (J–Q) Immunostaining analyses exhibiting markedly increased γ-H2AX+ cells in the tubgcp3 mutant retina (M,O,Q) at 3 dpf compared to wild-type sibling (L,N,P). DISCUSSION In CMZ, new neurons are produced for the continuous growth of zebrafish eyes after the embryogenesis of retina completed at 60 hpf. The tissue-specific defects in CMZ are in accordance with the rapid depletion of the maternal store in the regions of high proliferation. This also correlates with the function of γ-TuSC in cell proliferation. 10 days due to the maternal deposition of tubgcp3 gene products. The maternal effect provides a possibility to study its function at relatively late developmental stages. In the tubgcp3 mutant, the differentiated cells seem to be unaffected (Figures 3I–L). However, the CMZ exhibits obvious defects from 3 to 5 dpf (Figures 3E–H). This is associated with the relatively higher expression of tubgcp3 in CMZ compared to other retinal regions (Figures 1L,M). In CMZ, new neurons are produced for the continuous growth of zebrafish eyes after the embryogenesis of retina completed at 60 hpf. The tissue-specific defects in CMZ are in accordance with the rapid depletion of the maternal store in the regions of high proliferation. This also correlates with the function of γ-TuSC in cell proliferation. g p Autosomal recessive primary microcephaly (MCPH) is a neurodevelopmental disorder characterized by markedly reduced brain size. The patients exhibited significantly reduced number of neural progenitor cells caused by cell proliferation defects, increased cell death and the disruption of the balance between symmetric and asymmetric division (Barbelanne and Tsang, 2014; Buchwalter et al., 2016; O’Neill et al., 2018). Currently, at least nine centrosome-related genes have been genetically linked to microcephaly disorders (Megraw et al., 2011; Novorol et al., 2013; Chavali et al., 2014; Morris-Rosendahl and Kaindl, 2015; Buchwalter et al., 2016). Mutations in tubgcp4 and tubgcp6 have been reported to be associated with MCPH (Buchwalter et al., 2016). They encode TUBGCP4 and TUBGCP6, respectively, two components of γ-TuRC (Zheng et al., 1995). In addition, the MCPH models have been established using zebrafish retinal neuroepithelium by depletion of centrosomal proteins, including STIL, ASPM, WDR62, and ODF2 (Novorol et al., 2013). STIL localizes to the procentriolar cartwheel region and plays important roles in centriole duplication (Arquint and Nigg, 2014). ASPM localizes at the spindle poles and is involved in the organization of spindle poles (Tungadi et al., 2017). WDR62, which also localizes to the spindle poles, is required for mitotic entry of neural stem cells (Ramdas Nair et al., 2016). DISCUSSION ODF2, a mother centriole subdistal appendage protein, is indispensable for the assembly of the mother centriole (Ishikawa et al., 2005). In these models, zebrafish embryos display the MCPH phenotype with significantly reduced head and eye size (Novorol et al., 2013). After knockout of tubgcp3 gene, the zebrafish embryos exhibit the similar MCPH phenotype (Figures 2E–G). M-phase cell cycle arrest (Figures 5A–G) and increased apoptosis are also observed (Figures 6A–R) in tubgcp3 mutant retinae, which is consistent with these MCPH models (Novorol et al., 2013). Moreover, cell proliferation defect and senescence were also observed at the peripheral CMZ (stem cell niche) (Figures 6S–V,Y). Senescent cells were also observed in the brain of the tubgcp3 mutants (Supplementary Figure S8). Given the MCPH phenotype observed in tubgcp3 mutants (Figures 2E–G) and the requirement of Tubgcp3 in γ-TuRC Despite the fact that many studies have been carried out among different organisms to understand the function of Tubgcp3 in γ-TuRC assembly and centrosome function (Geissler et al., 1996; Barbosa et al., 2000; Mikule et al., 2007; Xiong and Oakley, 2009; Farache et al., 2016; Cota et al., 2017), its roles in vertebrate development remain unclear. In vitro studies using human cell lines show that GCP3/Tubgcp3 is required for cell cycle progression (Mikule et al., 2007; Draberova et al., 2015; Cota et al., 2017). However, the cell cycle defects caused by GCP3 depletion are conflicting. Draberova et al. (2015) reported that the wild-type p53 U87MG cells and mutant p53 T98 cells arrested in M-phase after depletion of GCP3 using siRNA. GCP3-depleted HeLa cells also arrested in the M-phase (Cota et al., 2017). In the tubgcp3 mutants, we found that RPCs arrested in M-phase in the CMZ of the retina (Figures 5B,D,F,G), which is consistent with previous studies. Moreover, the mitotic arrest RPCs underwent apoptosis (Figures 6A–R). However, Mikule et al. (2007) found that some GCP3-depleted cell lines, such as RPE-1, BJ-1, HME- 1, and HCT-116, did not arrest in M-phase, but arrested in G1 phase in a p53-dependent manner. In our study, we found that cell proliferation was affected at the peripheral CMZ in the tubgcp3 mutant retina. These cells might be RSCs, which failed to progress into S phase (Figures 6S–T”,Y). They did not arrest in M-phase as PH3+ cells did not accumulate in the mutant peripheral CMZ at 5 dpf (Supplementary Figure S7). DISCUSSION Note that some of the (Continued Frontiers in Molecular Neuroscience | www.frontiersin.org May 2019 | Volume 12 | Article 126 11 Li et al. Li et al. Tubgcp3 in Zebrafish Retinal Development FIGURE 6 | Continued increased PH3+ cells overlap with the γ-H2AX+ cells in the tubgcp3 mutant (O,Q). Arrows mark the PH3 and γ-H2AX double positive cells in the tubgcp3 mutant retina. Arrowheads indicate the location of RSCs in the CMZ of the retina. (R) Bar chart analyses depicting quantification of γ-H2AX+ and PH3+ cells in wild-type sibling and the tubgcp3 mutant retinae. Data are mean + SEM from 30 sections for each group. Student’s t-test: ∗∗P < 0.01. (S–T”) ISH and immunostaining analysis of cell proliferation at the extreme periphery of CMZ at 5 dpf. Zebrafish embryos were incubated in BrdU for 24 h before collected at 5 dpf for the double staining assay. In the wild-type sibling, there are many BrdU+ cells in col15a1b-labeled region (S,S’,S”). In contrast, BrdU+ cells are significantly decreased in this region in the tubgcp3 mutant CMZ (T,T’,T”). (U–X) Senescence-associated β-galactosidase (SA-β-gal) staining exhibiting increased β-galactosidase activity at the CMZ in the tubgcp3 mutant (V) compared to the wild-type sibling (U). Nuclei are stained with DAPI (W,X). Insets indicate high-magnification images of the peripheral edge of CMZ in rectangles in (U–X). (Y) Bar chart analyses depicting quantification of BrdU+ cells in the col15a1b-labeled region in wild-type sibling and the tubgcp3 mutant CMZ. Data are mean + SEM from 36 sections for each group. Student’s t-test: ∗∗P < 0.01. Scale bars: 20 µm (A–H); 20 µm (J–Q); 20 µm (S–T”); 50 µm (U–X). could induce cellular senescence (Manning and Kumar, 2010; Schmidt et al., 2010; Hossain and Tsang, 2013). Consistent with these reports, we observed that some cells underwent senescence at the extreme periphery of CMZ in tubgcp3 mutants. Since CMZ cells are involved in the growth of zebrafish eye, these defects together caused the small eye phenotype in the tubgcp3 mutants. 10 days due to the maternal deposition of tubgcp3 gene products. The maternal effect provides a possibility to study its function at relatively late developmental stages. In the tubgcp3 mutant, the differentiated cells seem to be unaffected (Figures 3I–L). However, the CMZ exhibits obvious defects from 3 to 5 dpf (Figures 3E–H). This is associated with the relatively higher expression of tubgcp3 in CMZ compared to other retinal regions (Figures 1L,M). Frontiers in Molecular Neuroscience | www.frontiersin.org REFERENCES glioblastoma. J. Neuropathol. Exp. Neurol. 74, 723–742. doi: 10.1097/NEN. 0000000000000212 glioblastoma. J. Neuropathol. Exp. Neurol. 74, 723–742. doi: 10.1097/NEN. 0000000000000212 Arquint, C., and Nigg, E. A. (2014). STIL microcephaly mutations interfere with APC/C-mediated degradation and cause centriole amplification. Curr. Biol. 24, 351–360. doi: 10.1016/j.cub.2013.12.016 Farache, D., Jauneau, A., Chemin, C., Chartrain, M., Remy, M. H., Merdes, A., et al. (2016). Functional analysis of gamma-tubulin complex proteins indicates specific lateral association via their N-terminal domains. J. Biol. Chem. 291, 23112–23125. doi: 10.1074/jbc.M116.744862 Barbelanne, M., and Tsang, W. Y. (2014). Molecular and cellular basis of autosomal recessive primary microcephaly. Biomed. Res. Int. 2014:547986. doi: 10.1155/ 2014/547986 Geissler, S., Pereira, G., Spang, A., Knop, M., Soues, S., Kilmartin, J., et al. (1996). The spindle pole body component Spc98p interacts with the gamma-tubulin- like Tub4p of Saccharomyces cerevisiae at the sites of microtubule attachment. EMBO J. 15, 3899–3911. doi: 10.1002/j.1460-2075.1996.tb00764.x Barbosa, V., Yamamoto, R. R., Henderson, D. S., and Glover, D. M. (2000). Mutation of a drosophila gamma tubulin ring complex subunit encoded by discs degenerate-4 differentially disrupts centrosomal protein localization. Genes Dev. 14, 3126–3139. doi: 10.1101/gad.182800 like Tub4p of Saccharomyces cerevisiae at the sites of microtubule attachment. EMBO J. 15, 3899–3911. doi: 10.1002/j.1460-2075.1996.tb00764.x y EMBO J. 15, 3899–3911. doi: 10.1002/j.1460-2075.1996.tb00764.x Gonzalez-Nunez, V., Nocco, V., and Budd, A. (2010). Characterization of drCol 15a1b: a novel component of the stem cell niche in the zebrafish retina. Stem Cells 28, 1399–1411. doi: 10.1002/stem.461 Bornens, M. (2002). Centrosome composition and microtubule anchoring mechanisms. Curr. Opin. Cell Biol. 14, 25–34. doi: 10.1016/S0955-0674(01) 00290-3 Hossain, D., and Tsang, W. Y. (2013). Centrosome dysfunction and senescence: coincidence or causality? J. Aging Sci. 1:3. doi: 10.4172/2329-8847.1000113 Buchwalter, R. A., Chen, J. V., Zheng, Y., and Megraw, T. L. (2016). Centrosome in cell division, development and disease. eLS 30, 1–2. Huang, X., Kurose, A., Tanaka, T., Traganos, F., Dai, W., and Darzynkiewicz, Z. (2006). Sequential phosphorylation of Ser-10 on histone H3 and ser-139 on histone H2AX and ATM activation during premature chromosome condensation: relationship to cell-cycle phase and apoptosis. Cytometry A 69, 222–229. doi: 10.1002/cyto.a.20257 Cerveny, K. L., Cavodeassi, F., Turner, K. J., de Jong-Curtain, T. A., Heath, J. K., and Wilson, S. W. (2010). The zebrafish flotte lotte mutant reveals that the local retinal environment promotes the differentiation of proliferating precursors emerging from their stem cell niche. Development 137, 2107–2115. ETHICS STATEMENT This study was carried out according to the Guide for the Care and Use of Laboratory Animals from the National Institutes of Health. The experimental protocol was approved by the Animal Care and Use Committee of Fudan University. ACKNOWLEDGMENTS We acknowledge Haitao Zhou for excellent fish care. The transgenic line Tg(HuC:GFP) was kindly provided by Su Guo (University of California). We are grateful to laboratory members Ruilin Zhang (Fudan University), Su Guo (University of California), Jie He (Chinese Academy of Sciences), and Ying Cao (Tongji University) for technical advice. We thank members of our laboratory for helpful discussions. We also thank the China Zebrafish Resource Center (CZRC) and the Zebrafish All Genes Knockout Consortium (ZAKOC) for important cooperation and assistance. FUNDING assembly and centrosome function (Geissler et al., 1996; Barbosa et al., 2000; Mikule et al., 2007; Xiong and Oakley, 2009; Farache et al., 2016; Cota et al., 2017), we speculate that premature senescence may provide a possible new view to explain the mechanism of MCPH. Further studies to characterize the function of other centrosomal proteins will be necessary to fully understand the relationship between centrosome and microcephaly disorders. assembly and centrosome function (Geissler et al., 1996; Barbosa et al., 2000; Mikule et al., 2007; Xiong and Oakley, 2009; Farache et al., 2016; Cota et al., 2017), we speculate that premature senescence may provide a possible new view to explain the mechanism of MCPH. Further studies to characterize the function of other centrosomal proteins will be necessary to fully understand the relationship between centrosome and microcephaly disorders. This work was supported by grants from the National Science Foundation of China (31530044, 31671514, and 31471357). SUPPLEMENTARY MATERIAL TZ conceived and directed the project. GL carried out the experiments and discovered the roles of Tubgcp3 in cell cycle progression during zebrafish retinal development. TZ, DJ, and GL prepared the figures and wrote the manuscript. The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fnmol. 2019.00126/full#supplementary-material DISCUSSION It is not feasible for us to isolate RSCs for fluorescence-activated cell sorter analysis (FACS) due to the absence of available transgenic zebrafish lines expressing RSC-specific reporters in our lab. Whether depletion of Tubgcp3 in RSCs causes G1 arrest still needs further study. To study whether p53 is involved in these processes will be an important extension to the functional study of Tubgcp3. It has been reported that centrosome dysfunction May 2019 | Volume 12 | Article 126 Frontiers in Molecular Neuroscience | www.frontiersin.org Frontiers in Molecular Neuroscience | www.frontiersin.org 12 Li et al. Li et al. Tubgcp3 in Zebrafish Retinal Development REFERENCES S. Jr. (1999). Neurogenesis in the visual system of embryonic and adult zebrafish (Danio rerio). Vis. Neurosci. 16, 417–424. doi: 10.1017/s095252389916303x Masai, I., Stemple, D. L., Okamoto, H., and Wilson, S. W. (2000). Midline signals regulate retinal neurogenesis in zebrafish. Neuron 27, 251–263. doi: 10.1016/ S0896-6273(00)00034-9 Shkumatava, A., and Neumann, C. J. (2005). Shh directs cell-cycle exit by activating p57Kip2 in the zebrafish retina. EMBO Rep. 6, 563–569. doi: 10.1038/sj.embor. 7400416 Megraw, T. L., Sharkey, J. T., and Nowakowski, R. S. (2011). Cdk5rap2 exposes the centrosomal root of microcephaly syndromes. Trends Cell Biol. 21, 470–480. doi: 10.1016/j.tcb.2011.04.007 Thisse, C., and Thisse, B. (2008). High-resolution in situ hybridization to whole-mount zebrafish embryos. Nat. Protoc. 3, 59–69. doi: 10.1038/nprot.200 7.514 Mikule, K., Delaval, B., Kaldis, P., Jurcyzk, A., Hergert, P., and Doxsey, S. (2007). Loss of centrosome integrity induces p38-p53-p21-dependent G1-S arrest. Nat. Cell Biol. 9, 160–170. Tungadi, E. A., Ito, A., Kiyomitsu, T., and Goshima, G. (2017). Human microcephaly ASPM protein is a spindle pole-focusing factor that functions redundantly with CDK5RAP2. J. Cell. Sci. 130, 3676–3684. doi: 10.1242/jcs. 203703 Morris-Rosendahl, D. J., and Kaindl, A. M. (2015). What next-generation sequencing (NGS) technology has enabled us to learn about primary autosomal recessive microcephaly (MCPH). Mol. Cell. Probes 29, 271–281. doi: 10.1016/j. mcp.2015.05.015 Valdivia, L. E., Lamb, D. B., Horner, W., Wierzbicki, C., Tafessu, A., Williams, A. M., et al. (2016). Antagonism between Gdf6a and retinoic acid pathways controls timing of retinal neurogenesis and growth of the eye in zebrafish. Development 143, 1087–1098. doi: 10.1242/dev.130922 Novorol, C., Burkhardt, J., Wood, K. J., Iqbal, A., Roque, C., Coutts, N., et al. (2013). Microcephaly models in the developing zebrafish retinal neuroepithelium point to an underlying defect in metaphase progression. Open Biol. 3:130065. doi: 10.1098/rsob.130065 Vitorino, M., Jusuf, P. R., Maurus, D., Kimura, Y., Higashijima, S., and Harris, W. A. (2009). Vsx2 in the zebrafish retina: restricted lineages through derepression. Neural Dev. 4:14. doi: 10.1186/1749-8104-4-14 Oakley, B. R., Oakley, C. E., Yoon, Y. S., and Jung, M. K. (1990). Gamma-tubulin is a component of the spindle pole body that is essential for microtubule function in aspergillus-nidulans. Cell 61, 1289–1301. doi: 10.1016/0092-8674(90)90 693-9 Wan, Y., Almeida, A. D., Rulands, S., Chalour, N., Muresan, L., Wu, Y., et al. (2016). The ciliary marginal zone of the zebrafish retina: clonal and time- lapse analysis of a continuously growing tissue. Development 143, 1099–1107. REFERENCES doi: 10.1242/ dev.047753 Ishikawa, H., Kubo, A., Tsukita, S., and Tsukita, S. (2005). Odf2-deficient mother centrioles lack distal/subdistal appendages and the ability to generate primary cilia. Nat. Cell Biol. 7, 517–524. doi: 10.1038/ncb1251 Chavali, P. L., Putz, M., and Gergely, F. (2014). Small organelle, big responsibility: the role of centrosomes in development and disease. Philos. Trans. R. Soc. Lond. B Biol. Sci. 369:20130468. doi: 10.1098/rstb.2013.0468 Kellogg, D. R., Moritz, M., and Alberts, B. M. (1994). The centrosome and cellular organization. Annu. Rev. Biochem. 63, 639–674. doi: 10.1146/annurev.bi.63. 070194.003231 Cota, R. R., Teixido-Travesa, N., Ezquerra, A., Eibes, S., Lacasa, C., Roig, J., et al. (2017). MZT1 regulates microtubule nucleation by linking gammaTuRC assembly to adapter-mediated targeting and activation. J. Cell Sci. 130, 406–419. doi: 10.1242/jcs.195321 Knop, M., Pereira, G., Geissler, S., Grein, K., and Schiebel, E. (1997). The spindle pole body component Spc97p interacts with the gamma-tubulin of Saccharomyces cerevisiae and functions in microtubule organization and spindle pole body duplication. EMBO J. 16, 1550–1564. doi: 10.1093/emboj/16. 7.1550 Dimri, G. P., Lee, X. H., Basile, G., Acosta, M., Scott, C., Roskelley, C., et al. (1995). A biomarker that identifies senescent human-cells in culture and in aging skin In-Vivo. Proc. Natl. Acad. Sci. U.S.A. 92, 9363–9367. doi: 10.1073/pnas.92.20. 9363 Kollman, J. M., Polka, J. K., Zelter, A., Davis, T. N., and Agard, D. A. (2010). Microtubule nucleating gamma-TuSC assembles structures with 13-fold microtubule-like symmetry. Nature 466, 879–882. doi: 10.1038/nature09207 Draberova, E., D’Agostino, L., Caracciolo, V., Sladkova, V., Sulimenko, T., Sulimenko, V., et al. (2015). Overexpression and nucleolar localization of gamma-tubulin small complex proteins GCP2 and GCP3 in Li, Z., Joseph, N. M., and Easter, S. S. Jr. (2000). The morphogenesis of the zebrafish eye, including a fate map of the optic vesicle. Dev. Dyn. 218, 175–188. May 2019 | Volume 12 | Article 126 Frontiers in Molecular Neuroscience | www.frontiersin.org 13 Li et al. Tubgcp3 in Zebrafish Retinal Development Manning, J. A., and Kumar, S. (2010). A potential role for NEDD1 and the centrosome in senescence of mouse embryonic fibroblasts. Cell Death Dis. 1:e35. doi: 10.1038/cddis.2010.12 phosphorylation of H2AX histone at serine 139. J. Biol. Chem. 275, 9390–9395. doi: 10.1074/jbc.275.13.9390 Schmidt, S., Schneider, L., Essmann, F., Cirstea, I. C., Kuck, F., Kletke, A., et al. (2010). The centrosomal protein TACC3 controls paclitaxel sensitivity by modulating a premature senescence program. Oncogene 29, 6184–6192. doi: 10.1038/onc.2010.354 Marcus, R. C., Delaney, C. L., and Easter, S. REFERENCES doi: 10.1242/dev.133314 Ohnuma, S., Philpott, A., Wang, K., Holt, C. E., and Harris, W. A. (1999). p27Xic1, a Cdk inhibitor, promotes the determination of glial cells in xenopus retina. Cell 99, 499–510. doi: 10.1016/S0092-8674(00)81538-X Wehman, A. M., Staub, W., and Baier, H. (2007). The anaphase-promoting complex is required in both dividing and quiescent cells during zebrafish development. Dev. Biol. 303, 144–156. doi: 10.1016/j.ydbio.2006. 10.043 O’Neill, R. S., Schoborg, T. A., and Rusan, N. M. (2018). Same but different: pleiotropy in centrosome-related microcephaly. Mol. Biol. Cell 29, 241–246. doi: 10.1091/mbc.E17-03-0192 Wehman, A. M., Staub, W., Meyers, J. R., Raymond, P. A., and Baier, H. (2005). Genetic dissection of the zebrafish retinal stem-cell compartment. Dev. Biol. 281, 53–65. doi: 10.1016/j.ydbio.2005.02.010 Park, H. C., Kim, C. H., Bae, Y. K., Yeo, S. Y., Kim, S. H., Hong, S. K., et al. (2000). Analysis of upstream elements in the HuC promoter leads to the establishment of transgenic zebrafish with fluorescent neurons. Dev. Biol. 227, 279–293. doi: 10.1006/dbio.2000.9898 Westerfield, M. (2000). The Zebrafish Book. A Guide for the Laboratory Use of Zebrafish (Danio rerio). Eugene, OR: University of Oregon Press. Xiong, Y., and Oakley, B. R. (2009). In vivo analysis of the functions of gamma- tubulin-complex proteins. J. Cell. Sci. 122(Pt 22), 4218–4227. doi: 10.1242/jcs. 059196 Pelegri, F. (2003). Maternal factors in zebrafish development. Dev. Dyn. 228, 535–554. doi: 10.1002/dvdy.10390 Yuba-Kubo, A., Kubo, A., Hata, M., and Tsukita, S. (2005). Gene knockout analysis of two gamma-tubulin isoforms in mice. Dev. Biol. 282, 361–373. doi: 10.1016/ j.ydbio.2005.03.031 Pereira, G., Knop, M., and Schiebel, E. (1998). Spc98p directs the yeast gamma- tubulin complex into the nucleus and is subject to cell cycle-dependent phosphorylation on the nuclear side of the spindle pole body. Mol. Biol. Cell 9, 775–793. doi: 10.1091/mbc.9.4.775 Zheng, Y., Wong, M. L., Alberts, B., and Mitchison, T. (1995). Nucleation of microtubule assembly by a gamma-tubulin-containing ring complex. Nature 378, 578–583. doi: 10.1038/378578a0 Pouchucq, L., Undurraga, C. A., Fuentes, R., Cornejo, M., Allende, M. L., and Monasterio, O. (2018). γ-Tubulin small complex formation is essential for early zebrafish embryogenesis. Mechan. Dev. 154, 145–152. doi: 10.1016/j.mod.2018. 06.006 Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Pujic, Z., Omori, Y., Tsujikawa, M., Thisse, B., Thisse, C., and Malicki, J. (2006). REFERENCES Reverse genetic analysis of neurogenesis in the zebrafish retina. Dev. Biol. 293, 330–347. doi: 10.1016/j.ydbio.2005.12.056 Copyright © 2019 Li, Jin and Zhong. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Copyright © 2019 Li, Jin and Zhong. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Ramdas Nair, A., Singh, P., Salvador Garcia, D., Rodriguez-Crespo, D., Egger, B., and Cabernard, C. (2016). The microcephaly-associated protein Wdr62/CG7337 is required to maintain centrosome asymmetry in drosophila neuroblasts. Cell Rep. 14, 1100–1113. doi: 10.1016/j.celrep.2015.12.097 Rogakou, E. P., Nieves-Neira, W., Boon, C., Pommier, Y., and Bonner, W. M. (2000). Initiation of DNA fragmentation during apoptosis induces May 2019 | Volume 12 | Article 126 Frontiers in Molecular Neuroscience | www.frontiersin.org 14
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Mechanochemical Synthesis and Biological Evaluation of Novel Isoniazid Derivatives with Potent Antitubercular Activity
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Article Mechanochemical Synthesis and Biological Evaluation of Novel Isoniazid Derivatives with Potent Antitubercular Activity Paulo F. M. Oliveira 1,2,3,† ID , Brigitte Guidetti 2,3, Alain Chamayou 1, Christiane André-Barrès 2,3, Jan Madacki 4, Jana Korduláková 4,*, Giorgia Mori 5, Beatrice Silvia Orena 5, Laurent Roberto Chiarelli 5 ID , Maria Rosalia Pasca 5,* ID , Christian Lherbet 2,3, Chantal Carayon 2,3, Stéphane Massou 2, Michel Baron 1 and Michel Baltas 2,3,* 1 Department of Process Engineering, Université de Toulouse, Mines-Albi, CNRS UMR 5302, Centre RAPSODEE, Campus Jarlard, 81013 Albi, France; paul_marqs@hotmail.com (P.F.M.O.); alain.chamayou@mines-albi.fr (A.C.); baron@mines-albi.fr (M.B.) 2 Department of Chemistry, Université de Toulouse, UPS, CNRS UMR 5068, LSPCMIB, 118 Route de Narbonne, 31062 Toulouse, France; guidetti@chimie.ups-tlse.fr (B.G.); candre@chimie.ups-tlse.fr (C.A.-B.) christian.lherbet@itav.fr (C.L.); andre@chimie.ups-tlse.fr (C.C.); massou@chimie.ups-tlse.fr (S.M.) 3 Narbonne, 31062 Toulouse, France; guidetti@chimie.ups-tlse.fr (B.G.); candre@chimie.ups-tlse.fr (C.A.-B.); christian.lherbet@itav.fr (C.L.); andre@chimie.ups-tlse.fr (C.C.); massou@chimie.ups-tlse.fr (S.M.) 3 CNRS, Laboratoire de Synthèse et Physico-Chimie de Molécules d’Intérêt Biologique, LSPCMIB, UMR-5068, 118 Route de Narbonne, 31062 Toulouse, France p p 3 CNRS, Laboratoire de Synthèse et Physico-Chimie de Molécules d’Intérêt Biologique, LSPCMIB, UMR-5 118 Route de Narbonne, 31062 Toulouse, France 4 Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Science Mlynská Dolina, Ilkoviˇcova 6, 84215 Bratislava, Slovakia; jan.madacki@gmail.com 5 Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia; via Ferrata 1, 27100 Pavia, Italy; giorgia.mori@unipv.it (G.M.); beatricesilvia.orena01@universitadipavia.it (B.S.O.); laurent.chiarelli@unipv.it (L.R.C.) * Correspondence: kordulakova@fns.uniba.sk (J.K.); mariarosalia.pasca@unipv.it (M.R.P.); baltas@chimie.ups-tlse.fr (M.B.); Tel.: +421-(0)260296547 (J.K.); +39-0382-985576 (M.R.P.); +33-(0)561556289 (M.B.) † Current address: Université de Lille, UMET, Unité Matériaux et Transformations, CNRS UMR 8207, F-59000 Lille, France. Received: 2 July 2017; Accepted: 24 July 2017; Published: 1 September 2017 Received: 2 July 2017; Accepted: 24 July 2017; Published: 1 September 2017 Abstract: A series of isoniazid derivatives bearing a phenolic or heteroaromatic coupled frame were obtained by mechanochemical means. Their pH stability and their structural (conformer/isomer) analysis were checked. The activity of prepared derivatives against Mycobacterium tuberculosis cell growth was evaluated. Some compounds such as phenolic hydrazine 1a and almost all heteroaromatic ones, especially 2, 5 and 7, are more active than isoniazid, and their activity against some M. tuberculosis MDR clinical isolates was determined. Compounds 1a and 7 present a selectivity index >1400 evaluated on MRC5 human fibroblast cells. The mechanism of action of selected hydrazones was demonstrated to block mycolic acid synthesis due to InhA inhibition inside the mycobacterial cell. Keywords: Mycobacterium tuberculosis; mechanochemistry; hydrazone Molecules 2017, 22, 1457; doi:10.3390/molecules22091457 molecules molecules molecules 1. Introduction Tuberculosis (TB), caused by Mycobacterium tuberculosis (M.tb), represents an enduring, deadly infectious disease worldwide. According to the World Health Organization (WHO), one third of the global population is infected with M.tb. In comparison with other diseases caused by a single infectious agent, TB is the second leading cause of mortality. It is estimated that in 2015 TB killed 1.8 million people, mainly in underdeveloped countries [1]. New effective drugs for the treatment www.mdpi.com/journal/molecules Molecules 2017, 22, 1457; doi:10.3390/molecules22091457 2 of 27 Molecules 2017, 22, 1457 of TB are necessary firstly to reduce the duration of TB treatment and, secondly, for the treatment of M.tb multidrug-resistant (MDR) [2,3], extensively-drug resistant (XDR) [4], and totally-drug resistant (TDR) strains [5]. In the recent years, two molecules bedaquiline and delamanid (Figure 1) have been approved for the treatment of MDR-TB when an effective treatment regimen is not otherwise available [6,7]. Molecules 2017, 22, 1457 2 of 27 (TDR) strains [5]. In the recent years, two molecules bedaquiline and delamanid (Figure 1) have been approved for the treatment of MDR-TB when an effective treatment regimen is not otherwise available [6,7]. Figure 1. Antitubercular drug Isoniazid (1952), and Bedaquiline and Delamanid, two new compounds approved for the treatment of MDR-TB. Figure 1. Antitubercular drug Isoniazid (1952), and Bedaquiline and Delamanid, two new compounds approved for the treatment of MDR-TB. Figure 1. Antitubercular drug Isoniazid (1952), and Bedaquiline and Delamanid, two new compounds approved for the treatment of MDR-TB. Figure 1. Antitubercular drug Isoniazid (1952), and Bedaquiline and Delamanid, two new compounds approved for the treatment of MDR-TB. One of the main known drug targets to fight M.tb growth is the enoyl-ACP reductase or InhA. This well-known enzyme is already the indirect target of Isoniazid (INH), a front-line prodrug used clinically to treat TB. INH remains a key component in all multiple drug treatment regiments recommended by the WHO even if M.tb resistant isolates have been rapidly generated during monotherapy or inappropriate treatment. Hence, improvement of INH molecule by introducing chemical modifications in its core structure in order to enhance biological response (prodrug, increase of bioavailability, and membrane permeability) continues to be an interesting scientific challenge. Recently, for example, compounds containing isonicotinoyl moiety with potential dual inhibition targeting FabG4 and HtdX, were successfully characterized [8]. 1. Introduction Hydrazide-hydrazone derivatives have long attracted attention because of their wide range of applications in medicinal chemistry [9–12] Hydrazide and hydrazone derivatives showed strong One of the main known drug targets to fight M.tb growth is the enoyl-ACP reductase or InhA. This well-known enzyme is already the indirect target of Isoniazid (INH), a front-line prodrug used clinically to treat TB. INH remains a key component in all multiple drug treatment regiments recommended by the WHO even if M.tb resistant isolates have been rapidly generated during monotherapy or inappropriate treatment. Hence, improvement of INH molecule by introducing chemical modifications in its core structure in order to enhance biological response (prodrug, increase of bioavailability, and membrane permeability) continues to be an interesting scientific challenge. Recently, for example, compounds containing isonicotinoyl moiety with potential dual inhibition targeting FabG4 and HtdX, were successfully characterized [8]. applications in medicinal chemistry [9–12]. Hydrazide and hydrazone derivatives showed strong antioxidant and radical scavenging properties, while others ones displayed potent anticancer, antimicrobial, anticonvulsant or anti-inflammatory activities in vitro [9]. Recently, interesting anti- mycobacterial activities were reported about the following derivatives: guanylhydrazones [13], trans- cinnamic acid hydrazides derivatives [14], fluorine containing hydrazones [15], sulfonyl-hydrazones [16], and L-proline derived hydrazones [17]. Moreover, isoniazid-related hydrazones showed similar or better efficiency than the INH [18]. Isonicotinoylhydrazone derivatives were also synthesized and evaluated as anti-mycobacterial agents [19 20] Interestingly vanillic acylhydrazones were reported as potential β keto acyl carrier g g y Hydrazide-hydrazone derivatives have long attracted attention because of their wide range of applications in medicinal chemistry [9–12]. Hydrazide and hydrazone derivatives showed strong antioxidant and radical scavenging properties, while others ones displayed potent anticancer, antimicrobial, anticonvulsant or anti-inflammatory activities in vitro [9]. Recently, interesting anti-mycobacterial activities were reported about the following derivatives: guanylhydrazones [13], trans-cinnamic acid hydrazides derivatives [14], fluorine containing hydrazones [15], sulfonyl-hydrazones [16], and L-proline derived hydrazones [17]. agents [19,20]. Interestingly, vanillic acylhydrazones were reported as potential β-keto acyl carrier protein synthase III (FabH) inhibitors [21]. Schiff bases of isoniazid, considered as chemical modification that can block N-acetylation of INH, showed good activity in vitro and in vivo and in some cases low toxicity [22,23]. In 2008, an extended study reported a quantitative structure activity relationships (QSAR) of a large hydrazide family for the developing of antitubercular compounds [24]. Finally, some researchers focused on establishing a predictive QSAR model for different INH derivatives including isonicotinoylhydrazones [25]. 1. Introduction Our group is involved both in synthesizing new antitubercular compounds, including cinnamic acid derivatives [26–29], triazoles [30–33], pyrrolidines [34–36], semicarbazones and hydrazine/hydrazones Moreover, isoniazid-related hydrazones showed similar or better efficiency than the INH [18]. Isonicotinoylhydrazone derivatives were also synthesized and evaluated as anti-mycobacterial agents [19,20]. Interestingly, vanillic acylhydrazones were reported as potential β-keto acyl carrier protein synthase III (FabH) inhibitors [21]. Schiff bases of isoniazid, considered as chemical modification that can block N-acetylation of INH, showed good activity in vitro and in vivo and in some cases low toxicity [22,23]. In 2008, an extended study reported a quantitative structure activity relationships (QSAR) of a large hydrazide family for the developing of antitubercular compounds [24]. Finally, some researchers focused on establishing a predictive QSAR model for different INH derivatives including isonicotinoylhydrazones [25]. Molecules 2017, 22, 1457 3 of 27 Our group is involved both in synthesizing new antitubercular compounds, including cinnamic acid derivatives [26–29], triazoles [30–33], pyrrolidines [34–36], semicarbazones and hydrazine/hydrazones [37], and in searching for new and innovative synthetic reactions. We have recently reported the solvent-free mechanosynthesis of a series of hydrazones [38,39]. Mechanochemistry has been used for a long time for the chemical and physicochemical transformations of inorganic materials to generate all states of aggregation produced by the effect of mechanical energy [40]. More recently, the mechanical energy has been used to synthesize organic molecules in milling devices [41–52]. Molecules 2017, 22, 1457 3 of 27 [37], and in searching for new and innovative synthetic reactions. We have recently reported the solvent- free mechanosynthesis of a series of hydrazones [38,39]. Mechanochemistry has been used for a long time for the chemical and physicochemical transformations of inorganic materials to generate all states of Considering the pharmaceutical area [53], the mechanical action was used in particular to develop nitrogen-containing heterocycles, well represented in many therapeutic classes. For example, phthalazoles [54], phenazines [55], pyrazoles, pyridazinones [56], and pyrroles [57] were obtained by mechanosynthesis. Non-heterocyclic nitrogen-containing molecules were also synthesized under mechanical solid-state and solvent-free conditions, including imines, azomethines [58,59], azines [56], enamines and hydrazones [60–62]. for the chemical and physicochemical transformations of inorganic materials to generate all states of aggregation produced by the effect of mechanical energy [40]. More recently, the mechanical energy has been used to synthesize organic molecules in milling devices [41–52]. 1. Introduction Considering the pharmaceutical area [53], the mechanical action was used in particular to develop nitrogen-containing heterocycles, well represented in many therapeutic classes. For example, phthalazoles [54], phenazines [55], pyrazoles, pyridazinones [56], and pyrroles [57] were obtained by mechanosynthesis. Non-heterocyclic nitrogen-containing molecules were also synthesized under h i l lid t t d l t f diti i l di i i thi [58 59] i [56] In this work, this methodology was used in order to synthesize hydrazones under solvent-free conditions, in particular the isonicotinoyl ones. Thus, herein we report the synthesis of a series of phenol and hetero aryl isonicotinoylhydrazones through mechanochemistry and the evaluation of their anti-tuberculosis activities. mechanical solid-state and solvent-free conditions, including imines, azomethines [58,59], azines [56], enamines and hydrazones [60–62]. In this work, this methodology was used in order to synthesize hydrazones under solvent-free conditions, in particular the isonicotinoyl ones. Thus, herein we report the synthesis of a series of phenol and hetero aryl isonicotinoylhydrazones through mechanochemistry and the evaluation of 2. Results and Discussion their anti tuberculosis ac 2.1. Chemistry 2. Results 2 1 Ch i Mechanosynthesis of Isonicotinoyl Hydrazones 2.1. Chemistry Mechanosynthesis of Isonicotinoyl Hydra ones Table 1 Hydra ones 2 11 produced mechanochemically by reacting INH and imida olic inda olic y g g g times of 2 h. Table 1 Hydra ones 2 11 produced mechanochemically by reacting INH and imida olic inda olic The hydrazones listed in Table 1 were thus obtained with a high transformation ratio in grinding times of 2 h. The hydrazones listed in Table 1 were thus obtained with a high transformation ratio in grinding times of 2 h. The hydrazones listed in Table 1 were thus obtained with a high transformation ratio in grinding times of 2 h. The hydrazones listed in Table 1 were thus obtained with a high transformation ratio in grinding times of 2 h. Aldehydes Heterocyclic Hydrazones (6) Derived From Isoniazid Imidazole derivatives or indolic aldehydes. The reaction was catalyzed by p TSA. Aldehydes Heterocyclic Hydrazones (6) Derived From Isoniazid Imidazole derivatives 2 (80%) [a] 3 (98%) [a] Indazole derivatives 4 (98%) [a] 5 (99%) [a] Indole derivatives 6 (99%) [a] 7 (94%) [a] 8 (99%) [a] 9 (99%) [a] 10 (91%) [a] 11 (99%) [a] [a] Yields after washing with NaHCO3 aqueous solution to eliminate p-TSA. According to TLC, 1H- NMR and MS, the conversions were quantitative. It is still important to mention that, differently from the phenolic hydrazones, a melting was or indolic aldehydes. The reaction was catalyzed by p TSA. Aldehydes Heterocyclic Hydrazones (6) Derived From Isoniazid Imidazole derivatives 2 (80%) [a] 3 (98%) [a] Indazole derivatives 4 (98%) [a] 5 (99%) [a] Indole derivatives 6 (99%) [a] 7 (94%) [a] 8 (99%) [a] 9 (99%) [a] 10 (91%) [a] 11 (99%) [a] [a] Yields after washing with NaHCO3 aqueous solution to eliminate p-TSA. According to TLC, 1H- NMR and MS, the conversions were quantitative. It is still important to mention that, differently from the phenolic hydrazones, a melting was Indazole derivatives or indolic aldehydes. The reaction was catalyzed by p-TSA. Aldehydes Heterocyclic Hydrazones (6) Derived From Isoniazid Imidazole derivatives 2 (80%) [a] 3 (98%) [a] Indazole derivatives 4 (98%) [a] 5 (99%) [a] Indole derivatives 6 (99%) [a] 7 (94%) [a] 8 (99%) [a] 9 (99%) [a] 10 (91%) [a] 11 (99%) [a] [a] Yields after washing with NaHCO3 aqueous solution to eliminate p-TSA. According to TLC, 1H- NMR and MS, the conversions were quantitative. Mechanosynthesis of Isonicotinoyl Hydrazones 2.1. Chemistry Mechanosynthesis of Isonicotinoyl Hydra ones It is still important to mention that, differently from the phenolic hydrazones, a melting was or indolic aldehydes. The reaction was catalyzed by p-TSA. Aldehydes Heterocyclic Hydrazones (6) Derived From Isoniazid Imidazole derivatives 2 (80%) [a] 3 (98%) [a] Indazole derivatives 4 (98%) [a] 5 (99%) [a] Indole derivatives 6 (99%) [a] 7 (94%) [a] 8 (99%) [a] 9 (99%) [a] 10 (91%) [a] 11 (99%) [a] [a] Yields after washing with NaHCO3 aqueous solution to eliminate p-TSA. According to TLC, 1H- NMR and MS, the conversions were quantitative. It is still important to mention that, differently from the phenolic hydrazones, a melting was Indole derivatives Table 1. Hydrazones 2 11 produced mechanochemically by reacting INH and imidazolic, indazolic or indolic aldehydes. The reaction was catalyzed by p-TSA. Aldehydes Heterocyclic Hydrazones (6) Derived From Isoniazid Imidazole derivatives 2 (80%) [a] 3 (98%) [a] Indazole derivatives 4 (98%) [a] 5 (99%) [a] Indole derivatives 6 (99%) [a] 7 (94%) [a] 8 (99%) [a] 9 (99%) [a] 10 (91%) [a] 11 (99%) [a] [a] Yields after washing with NaHCO3 aqueous solution to eliminate p-TSA. According to TLC, 1H- NMR and MS, the conversions were quantitative. I i ill i i h diff l f h h li h d l i Table 1. Hydrazones 2 11 produced mechanochemically by reacting INH and imidazolic, indazolic or indolic aldehydes. The reaction was catalyzed by p-TSA. Aldehydes Heterocyclic Hydrazones (6) Derived From Isoniazid Imidazole derivatives 2 (80%) [a] 3 (98%) [a] Indazole derivatives 4 (98%) [a] 5 (99%) [a] Indole derivatives 6 (99%) [a] 7 (94%) [a] 8 (99%) [a] 9 (99%) [a] 10 (91%) [a] 11 (99%) [a] [a] Yields after washing with NaHCO3 aqueous solution to eliminate p-TSA. According to TLC, 1H- NMR and MS, the conversions were quantitative. I i ill i i h diff l f h h li h d l i Table 1. Hydrazones 2–11 produced mechanochemically by reacting INH and imidazolic, indazolic or indolic aldehydes. The reaction was catalyzed by p-TSA. Aldehydes Heterocyclic Hydrazones (6) Derived From Isoniazid Imidazole derivatives 2 (80%) [a] 3 (98%) [a] Indazole derivatives 4 (98%) [a] 5 (99%) [a] Indole derivatives 6 (99%) [a] 7 (94%) [a] 8 (99%) [a] 9 (99%) [a] 10 (91%) [a] 11 (99%) [a] [a] Yields after washing with NaHCO3 aqueous solution to eliminate p-TSA. According to TLC, 1H- NMR and MS, the conversions were quantitative. Table 1. Mechanosynthesis of Isonicotinoyl Hydrazones 2.1. Chemistry Mechanosynthesis of Isonicotinoyl Hydra ones Hydrazones 2–11 produced mechanochemically by reacting INH and imidazolic, indazolic or indolic aldehydes. The reaction was catalyzed by p-TSA. Aldehydes Heterocyclic Hydrazones (6) Derived From Isoniazid Imidazole derivatives 2 (80%) [a] 3 (98%) [a] Indazole derivatives 4 (98%) [a] 5 (99%) [a] Indole derivatives 6 (99%) [a] 7 (94%) [a] 8 (99%) [a] 9 (99%) [a] 10 (91%) [a] 11 (99%) [a] [a] Yields after washing with NaHCO3 aqueous solution to eliminate p-TSA. According to TLC, 1H- NMR and MS, the conversions were quantitative. Table 1. Hydrazones 2–11 produced mechanochemically by reacting INH and imidazolic, indazolic or indolic aldehydes. The reaction was catalyzed by p-TSA. Aldehydes Heterocyclic Hydrazones (6) Derived From Isoniazid Imidazole derivatives 2 (80%) [a] 3 (98%) [a] Indazole derivatives 4 (98%) [a] 5 (99%) [a] Indole derivatives 6 (99%) [a] 7 (94%) [a] 8 (99%) [a] 9 (99%) [a] 10 (91%) [a] 11 (99%) [a] [a] Yields after washing with NaHCO3 aqueous solution to eliminate p-TSA. According to TLC, 1H- NMR and MS, the conversions were quantitative. Table 1. Hydrazones 2–11 produced mechanochemically by reacting INH and imidazolic, indazolic or indolic aldehydes. The reaction was catalyzed by p-TSA. Aldehydes Heterocyclic Hydrazones (6) Derived From Isoniazid Imidazole derivatives 2 (80%) [a] 3 (98%) [a] Indazole derivatives 4 (98%) [a] 5 (99%) [a] Indole derivatives 6 (99%) [a] 7 (94%) [a] 8 (99%) [a] 9 (99%) [a] 10 (91%) [a] 11 (99%) [a] [a] Yields after washing with NaHCO3 aqueous solution to eliminate p-TSA. According to TLC, 1H- NMR and MS, the conversions were quantitative. [a] Yields after washing with NaHCO3 aqueous solution to eliminate p-TSA. According to TLC, 1H-NMR and MS, the conversions were quantitative. Heterocyclic Hydrazones (6) Derived From Isoniazid Heterocyclic Hydrazones (6) Derived From Isoniazid Heterocyclic Hydrazones (6) Derived From Isoniazi y y p Heterocyclic Hydrazones (6) Derived From Isoniazid y y p Heterocyclic Hydrazones (6) Derived From Isoniazi was catalyzed by p-TSA. n was catalyzed by p-TSA. y y g was catalyzed by p-TSA. n was catalyzed by p-TSA. ed mechanochemically by reacting INH and imidazolic, was catalyzed by p-TSA. ced mechanochemically by reacting INH and imidazoli n was catalyzed by p-TSA. Mechanosynthesis of Isonicotinoyl Hydrazones 2.1. Chemistry Mechanosynthesis of Isonicotinoyl Hydra ones Mechanosynthesis of Isonicotinoyl Hydrazones 2.1. Chemistry Mechanosynthesis of Isonicotinoyl Hydrazones The classical methods to synthesize hydrazones are generally carried out at low concentration, and require times from 3 to 24 h or even 48 h under reflux of toluene or ethanol in order to obtain good yields. We previously employed the vibratory mill Pulverisette 0 (P0) (Fritsch, Germany) to synthesize phenolic hydrazones mechanochemically [38]. A comparative study has been therein reported with various hydrazides, among them the isoniazid and phenolic aldehydes leading to compounds already described 1a–d (Figure 2). Mechanosynthesis of Isonicotinoyl Hydrazones The classical methods to synthesize hydrazones are generally carried out at low concentration, and require times from 3 to 24 h or even 48 h under reflux of toluene or ethanol in order to obtain good yields. We previously employed the vibratory mill Pulverisette 0 (P0) (Fritsch, Germany) to synthesize phenolic hydrazones mechanochemically [38]. A comparative study has been therein reported with various hydrazides, among them the isoniazid and phenolic aldehydes leading to compounds already described 1a–d (Figure 2). Figure 2. Isonicotinoyl hydrazones synthesized by co-grinding of isoniazide and an aldehyde. Figure 2. Isonicotinoyl hydrazones synthesized by co-grinding of isoniazide and an aldehyde. Figure 2. Isonicotinoyl hydrazones synthesized by co-grinding of isoniazide and an aldehyde. Figure 2. Isonicotinoyl hydrazones synthesized by co-grinding of isoniazide and an aldehyde. We decided to synthesize a series of isonicotinoylhydrazones derivatives bearing various N- heterocyclic indole, indazole or imidazole moieties using the mechanochemical approach. The corresponding aldehydes were selected because of the importance of these N-heterocyclic fragments in a large number of natural or synthetic biologically active molecules. Indeed, compounds bearing We decided to synthesize a series of isonicotinoylhydrazones derivatives bearing various N-heterocyclic indole, indazole or imidazole moieties using the mechanochemical approach. The corresponding aldehydes were selected because of the importance of these N-heterocyclic 4 of 27 Molecules 2017, 22, 1457 fragments in a large number of natural or synthetic biologically active molecules. Indeed, compounds bearing these frames may exhibit various activities, i.e., antibacterial, anticancer, antioxidant, anti-inflammatory, anti-diabetic, antiviral, anti-proliferative, antituberculosis, antispermatogenic or antipsychotic activities [63–67]. Mechanosynthesis of Isonicotinoyl Hydrazones 2.1. Chemistry Mechanosynthesis of Isonicotinoyl Hydra ones Molecules 2017, 22, 1457 4 of 27 these frames may exhibit various activities, i.e., antibacterial, anticancer, antioxidant, anti- Molecules 2017, 22, 1457 4 of 27 these frames may exhibit various activities, i.e., antibacterial, anticancer, antioxidant, anti- Molecules 2017, 22, 1457 4 of 27 these frames may exhibit various activities i e antibacterial anticancer antioxidant anti- Molecules 2017, 22, 1457 4 of 27 these frames may exhibit various activities i e antibacterial anticancer antioxidant anti- Molecules 2017, 22, 1457 4 of 27 Molecules 2017, 22, 1457 4 of 27 Molecules 2017, 22, 1457 4 of 27 Molecules 2017, 22, 1457 4 of 27 Molecules 2017, 22, 1457 4 of 27 Molecules 2017, 22, 1457 4 of 27 The reaction described for phenolic compounds was firstly used with the 4-methyl-5-imidazolecarboxaldehyde as model of heterocyclic aldehyde. However, in spite of the milling was carried out by up to eight hours, TLC and NMR analysis showed incomplete conversion. In that respect, we evaluated the efficiency of the reaction in acidic media. inflammatory, anti-diabetic, antiviral, anti-proliferative, antituberculosis, antispermatogenic or antipsychotic activities [63–67]. The reaction described for phenolic compounds was firstly used with the 4-methyl-5- imidazolecarboxaldehyde as model of heterocyclic aldehyde. However, in spite of the milling was carried out by up to eight hours TLC and NMR analysis showed incomplete conversion In that inflammatory, anti-diabetic, antiviral, anti-proliferative, antituberculosis, antispermatogenic or antipsychotic activities [63–67]. The reaction described for phenolic compounds was firstly used with the 4-methyl-5- imidazolecarboxaldehyde as model of heterocyclic aldehyde. However, in spite of the milling was carried out by up to eight hours TLC and NMR analysis showed incomplete conversion In that these frames may exhibit various activities, i.e., antibacterial, anticancer, antioxidant, anti inflammatory, anti-diabetic, antiviral, anti-proliferative, antituberculosis, antispermatogenic or antipsychotic activities [63–67]. The reaction described for phenolic compounds was firstly used with the 4-methyl-5- imidazolecarboxaldehyde as model of heterocyclic aldehyde. However, in spite of the milling was ese a es ay e ibi a ious ac i i ies, i e , a ibac e ia , a ica ce , a io ida , a i inflammatory, anti-diabetic, antiviral, anti-proliferative, antituberculosis, antispermatogenic or antipsychotic activities [63–67]. The reaction described for phenolic compounds was firstly used with the 4-methyl-5- imidazolecarboxaldehyde as model of heterocyclic aldehyde. Mechanosynthesis of Isonicotinoyl Hydrazones 2.1. Chemistry Mechanosynthesis of Isonicotinoyl Hydra ones However, in spite of the milling was these frames may exhibit various activities, i.e., antibacterial, anticancer, antioxidant, anti- inflammatory, anti-diabetic, antiviral, anti-proliferative, antituberculosis, antispermatogenic or antipsychotic activities [63–67]. The reaction described for phenolic compounds was firstly used with the 4-methyl-5- imidazolecarboxaldehyde as model of heterocyclic aldehyde. However, in spite of the milling was these frames may exhibit various activities, i.e., antibacterial, anticancer, antioxidant, anti- inflammatory, anti-diabetic, antiviral, anti-proliferative, antituberculosis, antispermatogenic or antipsychotic activities [63–67]. The reaction described for phenolic compounds was firstly used with the 4-methyl-5- imidazolecarboxaldehyde as model of heterocyclic aldehyde. However, in spite of the milling was these frames may exhibit various activities, i.e., antibacterial, anticancer, antioxidant, anti- inflammatory, anti-diabetic, antiviral, anti-proliferative, antituberculosis, antispermatogenic or antipsychotic activities [63–67]. The reaction described for phenolic compounds was firstly used with the 4-methyl-5- i id l b ld h d d l f h t li ld h d H i it f th illi these frames may exhibit various activities, i.e., antibacterial, anticancer, antioxidant, anti- inflammatory, anti-diabetic, antiviral, anti-proliferative, antituberculosis, antispermatogenic or antipsychotic activities [63–67]. The reaction described for phenolic compounds was firstly used with the 4-methyl-5- i id l b ld h d d l f h t li ld h d H i it f th illi these frames may exhibit various activities, i.e., antibacterial, anticancer, antioxidant, anti- inflammatory, anti-diabetic, antiviral, anti-proliferative, antituberculosis, antispermatogenic or antipsychotic activities [63–67]. The reaction described for phenolic compounds was firstly used with the 4-methyl-5- these frames may exhibit various activities, i.e., antibacterial, anticancer, antioxidant, anti- inflammatory, anti-diabetic, antiviral, anti-proliferative, antituberculosis, antispermatogenic or antipsychotic activities [63–67]. The reaction described for phenolic compounds was firstly used with the 4-methyl-5- The reaction was thus carried out in the presence of AlCl3 or of p-toluenesulfonic acid (p-TSA); the latter one showed the best result when using 50% mol of p-TSA. TLC showed the consumption of the reagents and the consequent appearance of the hydrazone, which was confirmed by 1H- and 13C-NMR analysis. carried out by up to eight hours, TLC and NMR analysis showed incomplete conversion. In that respect, we evaluated the efficiency of the reaction in acidic media. The reaction was thus carried out in the presence of AlCl3 or of p-toluenesulfonic acid (p-TSA); the latter one showed the best result when using 50% mol of p-TSA. Mechanosynthesis of Isonicotinoyl Hydrazones 2.1. Chemistry Mechanosynthesis of Isonicotinoyl Hydra ones TLC showed the consumption of the reagents and the consequent appearance of the hydrazone, which was confirmed by 1H- and 13C- carried out by up to eight hours, TLC and NMR analysis showed incomplete conversion. In that respect, we evaluated the efficiency of the reaction in acidic media. The reaction was thus carried out in the presence of AlCl3 or of p-toluenesulfonic acid (p-TSA); the latter one showed the best result when using 50% mol of p-TSA. TLC showed the consumption of the reagents and the consequent appearance of the hydrazone, which was confirmed by 1H- and 13C- carried out by up to eight hours, TLC and NMR analysis showed incomplete conversion. In that respect, we evaluated the efficiency of the reaction in acidic media. The reaction was thus carried out in the presence of AlCl3 or of p-toluenesulfonic acid (p-TSA); the latter one showed the best result when using 50% mol of p-TSA. TLC showed the consumption of the reagents and the consequent appearance of the hydrazone which was confirmed by 1H- and 13C- carried out by up to eight hours, TLC and NMR analysis showed incomplete conversion. In that respect, we evaluated the efficiency of the reaction in acidic media. The reaction was thus carried out in the presence of AlCl3 or of p-toluenesulfonic acid (p-TSA); the latter one showed the best result when using 50% mol of p-TSA. TLC showed the consumption of the reagents and the consequent appearance of the hydrazone which was confirmed by 1H- and 13C- imidazolecarboxaldehyde as model of heterocyclic aldehyde. However, in spite of the milling was carried out by up to eight hours, TLC and NMR analysis showed incomplete conversion. In that respect, we evaluated the efficiency of the reaction in acidic media. The reaction was thus carried out in the presence of AlCl3 or of p-toluenesulfonic acid (p-TSA); the latter one showed the best result when using 50% mol of p-TSA. TLC showed the consumption of imidazolecarboxaldehyde as model of heterocyclic aldehyde. However, in spite of the milling was carried out by up to eight hours, TLC and NMR analysis showed incomplete conversion. In that respect, we evaluated the efficiency of the reaction in acidic media. The reaction was thus carried out in the presence of AlCl3 or of p-toluenesulfonic acid (p-TSA); the latter one showed the best result when using 50% mol of p-TSA. Mechanosynthesis of Isonicotinoyl Hydrazones 2.1. Chemistry Mechanosynthesis of Isonicotinoyl Hydra ones 3 (98%) [a] 3 (98%) [a] 3 (98%) [a] 3 (98%) [a] ) Derived From Isoniazid 6) Derived From Isoniazid ) Derived From Isoniazid 6) Derived From Isoniazid ) Derived From Isoniazid 6) Derived From Isoniazid 2 (80%) [a] 2 (80%) [a] y y 2 (80%) [a] y y 2 (80%) [a] Heterocyclic Hydrazone (80%) [ ] Heterocyclic Hydrazon (80%) [ ] Heterocyclic Hydrazone Heterocyclic Hydrazon Heterocyclic Hydrazone Heterocyclic Hydrazon 2 (80%) [a] 2 (80%) [a] 2 (80%) [a] 2 (80%) [a (98%) [a] 3 (98%) [a] (98%) [a] 3 (98%) [a] 5 (99%) [a] 5 (99%) [a] 5 (99%) [a] 5 (99%) [a] 3 (98%) [a] 5 (99%) [a] 3 (98%) [a] 5 (99%) [a] 3 (98%) [a] (99%) [ ] 3 (98%) [a] 5 (99%) [ ] 3 (98%) [a] 3 (98%) [a] Indazole derivatives 4 (98%) [a] Indazole derivatives 4 (98%) [a] Indazole derivatives Indazole derivatives 4 (98%) [a] Indazole derivatives 4 (98%) [a] ( ) Indazole derivatives 4 (98%) [a] ( ) Indazole derivatives 4 (98%) [a] 2 (80%) [a] Indazole derivatives 2 (80%) [a] Indazole derivatives 2 (80%) [a] Indazole derivatives 2 (80%) [a] Indazole derivatives tives 4 (98%) [a] vatives 4 (98%) [a] stives 4 (98%) [a] vatives 4 (98%) [a] ( ) tives 4 (98%) [a] ( ) vatives 4 (98%) [a] 2 (80%) [a] tives 2 (80%) [a] vatives 2 (80%) [a] tives 2 (80%) [a] vatives Indazole derivativ Indazole derivat Indazole derivatives Indazole derivativ Indazole deriva Indazole derivativ Indazole derivat Indazole derivativ Indazole derivat 5 (99%) [a] 5 (99%) [a] 5 (99%) [a] 5 (99%) [a] 5 (99%) [a] 5 (99%) [a] 4 (98%) [a] 4 (98%) [a] 4 (98%) [a] 4 (98%) [a] 4 (98%) [a] 4 (98%) [a] 7 (94%) [a] 7 (94%) [a] 7 (94%) [a] 7 (94%) [a] 7 (94%) [a] 7 (94%) [a] 7 (94%) [a] 7 (94%) [a] 5 (99%) [ ] 7 (94%) [ ] 5 (99%) 7 (94%) [a] 6 (99%) [a] 6 (99%) [a] 6 (99%) [a] 6 (99%) [a] 6 (99%) [a] 6 (99%) [a] ( ) 6 (99%) [a] ( ) 6 (99%) [a] 4 (98%) [a] 6 (99%) [ ] 4 (98%) [a] 6 (99%) [a] Indole derivatives 7 (94%) 7 (94%) 7 (94%) [a] 7 (94%) [a] 7 (94%) [a] 7 (94%) [a] 7 (94%) [a] 7 (94%) [a] 7 (94%) [a] 7 (94%) [a] 6 (99%) 6 (99%) 6 (99%) [a] 6 (99%) [a 6 (99%) [a] 6 (99%) [a] 6 (99%) [a] 6 (99%) [a] 6 (99%) [ ] 6 (99%) [a] 9 (99%) [a] 9 (99%) [a] 9 (99%) [a] 9 (99%) [a] 9 (99%) [a] 9 (99%) [a] 7 (94%) (9 %) 7 (94%) [a] 7 (94%) [a] 8 (99%) [a] 8 (99%) [a] 8 (99%) [a] 8 (99%) [a] 8 (99%) [a] 8 (99%) [a] 8 (99%) [a] 8 (99%) [a] 6 (99%) [ ] 8 (99%) [a] 6 (99%) 8 (99%) [a] 8 (99%) [ ] 8 (99%) 8 (99%) [a] 8 (99%) [a] 8 (99%) [a] 8 (99%) [a] 8 (99%) [a] 8 (99%) [a] 11 (99%) [a] nate p-TSA. Mechanosynthesis of Isonicotinoyl Hydrazones 2.1. Chemistry Mechanosynthesis of Isonicotinoyl Hydra ones TLC showed the consumption of imidazolecarboxaldehyde as model of heterocyclic aldehyde. However, in spite of the milling was carried out by up to eight hours, TLC and NMR analysis showed incomplete conversion. In that respect, we evaluated the efficiency of the reaction in acidic media. The reaction was thus carried out in the presence of AlCl3 or of p-toluenesulfonic acid (p-TSA); the latter one showed the best result when using 50% mol of p-TSA. TLC showed the consumption of imidazolecarboxaldehyde as model of heterocyclic aldehyde. However, in spite of the milling was carried out by up to eight hours, TLC and NMR analysis showed incomplete conversion. In that respect, we evaluated the efficiency of the reaction in acidic media. The reaction was thus carried out in the presence of AlCl3 or of p-toluenesulfonic acid (p-TSA); the latter one showed the best result when using 50% mol of p-TSA. TLC showed the consumption of imidazolecarboxaldehyde as model of heterocyclic aldehyde. However, in spite of the milling was carried out by up to eight hours, TLC and NMR analysis showed incomplete conversion. In that respect, we evaluated the efficiency of the reaction in acidic media. The reaction was thus carried out in the presence of AlCl3 or of p-toluenesulfonic acid (p-TSA); the latter one showed the best result when using 50% mol of p TSA TLC showed the consumption of imidazolecarboxaldehyde as model of heterocyclic aldehyde. However, in spite of the milling was carried out by up to eight hours, TLC and NMR analysis showed incomplete conversion. In that respect, we evaluated the efficiency of the reaction in acidic media. The reaction was thus carried out in the presence of AlCl3 or of p-toluenesulfonic acid (p-TSA); the latter one showed the best result when using 50% mol of p TSA TLC showed the consumption of The hydrazones listed in Table 1 were thus obtained with a high transformation ratio in grinding times of 2 h. NMR analysis. The hydrazones listed in Table 1 were thus obtained with a high transformation ratio in grinding i f 2 h NMR analysis. The hydrazones listed in Table 1 were thus obtained with a high transformation ratio in grinding i f 2 h the reagents and the consequent appearance of the hydrazone, which was confirmed by 1H- and 13C- NMR analysis. Mechanosynthesis of Isonicotinoyl Hydrazones 2.1. Chemistry Mechanosynthesis of Isonicotinoyl Hydra ones The hydrazones listed in Table 1 were thus obtained with a high transformation ratio in grinding the reagents and the consequent appearance of the hydrazone, which was confirmed by H and C NMR analysis. The hydrazones listed in Table 1 were thus obtained with a high transformation ratio in grinding the reagents and the consequent appearance of the hydrazone, which was confirmed by 1H- and 13C- NMR analysis. Th h d li t d i T bl 1 th bt i d ith hi h t f ti ti i i di the reagents and the consequent appearance of the hydrazone, which was confirmed by 1H- and 13C- NMR analysis. Th h d li t d i T bl 1 th bt i d ith hi h t f ti ti i i di the latter one showed the best result when using 50% mol of p TSA. TLC showed the consumption of the reagents and the consequent appearance of the hydrazone, which was confirmed by 1H- and 13C- NMR analysis. the latter one showed the best result when using 50% mol of p TSA. TLC showed the consumption of the reagents and the consequent appearance of the hydrazone, which was confirmed by 1H- and 13C- NMR analysis. the latter one showed the best result when using 50% mol of p-TSA. TLC showed the consumption of the reagents and the consequent appearance of the hydrazone, which was confirmed by 1H- and 13C- NMR analysis. the latter one showed the best result when using 50% mol of p-TSA. TLC showed the consumption of the reagents and the consequent appearance of the hydrazone, which was confirmed by 1H- and 13C- NMR analysis. Table 1. Hydrazones 2–11 produced mechanochemically by reacting INH and imidazolic, indazolic or indolic aldehydes. The reaction was catalyzed by p-TSA. Table 1. Hydrazones 2–11 produced mechanochemically by reacting INH and imidazolic, indazolic i d li ld h d Th ti t l d b TSA Table 1. Hydrazones 2–11 produced mechanochemically by reacting INH and imidazolic, indazolic i d li ld h d Th ti t l d b TSA times of 2 h. Table 1. Hydrazones 2–11 produced mechanochemically by reacting INH and imidazolic, indazolic times of 2 h. Table 1. Hydrazones 2–11 produced mechanochemically by reacting INH and imidazolic, indazolic y g g g times of 2 h. Mechanosynthesis of Isonicotinoyl Hydrazones 2.1. Chemistry Mechanosynthesis of Isonicotinoyl Hydra ones According to TLC, 1H- 11 (99%) [a] minate p-TSA. According to TLC, 1H- 9 (99%) 11 (99%) [a] nate p-TSA. According to TLC, 1H- 9 (99%) 11 (99%) [a] minate p-TSA. According to TLC, 1H- 9 (99%) [a] 11 (99%) [a] nate p TSA According to TLC 1H 9 (99%) [a] 11 (99%) [a] minate p TSA According to TLC 1H 9 (99%) [a] 11 (99%) [a] 9 (99%) [a] 11 (99%) [a] 9 (99%) [a] 11 (99%) [a] 9 (99%) [a] 11 (99%) [a] 9 (99%) 9 (99%) 9 (99%) [a] 9 (99%) [a] 9 (99%) [a] 9 (99%) [a] 9 (99%) [a] 9 (99%) [a] 10 (91%) [a] ing with NaHCO3 aqueous solution to el onversions were quantitative 10 (91%) [a] shing with NaHCO3 aqueous solution to conversions were quantitative 10 (91%) [a] ing with NaHCO3 aqueous solution to el 10 (91%) [a] shing with NaHCO3 aqueous solution to 10 (91%) [a] ing with NaHCO3 aqueous solution to el 10 (91%) [a] shing with NaHCO3 aqueous solution to 8 (99%) [ ] 10 (91%) [a] h O l l 8 (99%) 10 (91%) [a] h h CO l 8 (99%) [a] 10 (91%) [a] 8 (99%) [a] 10 (91%) [a] According to According t According to . According t 11 (99%) [a] According to 11 (99%) [a] According to 11 (99%) [a] 11 (99%) [a] 11 (99%) [a] 11 (99%) [a] CO3 aqueous re quantitativ HCO3 aqueou were quantitat CO3 aqueous HCO3 aqueou 10 (91%) [a] CO3 aqueous 10 (91%) [a] HCO3 aqueou 10 (91%) [a] 10 (91%) [a] 10 (91%) [a] 10 (91%) [a] NM a MS, e co e sio s e e qua i a i e It is still important to mention that, differently from the phenolic hydrazones, a melting was a , e o e io e e qua i a i e It is still important to mention that, differently from the phenolic hydrazones, a melting wa NMR and MS, the conversions were quantitative. It is still important to mention that differently from the phenolic hydrazones a melting was NMR and MS, the conversions were quantitative. It is still important to mention that differently from the phenolic hydrazones a melting w g q p g , NMR and MS, the conversions were quantitative. g q p g , NMR and MS, the conversions were quantitative. Molecules 2017, 22, 1457 5 of 27 Molecules 2017, 22, 1457 It is still important to mention that, differently from the phenolic hydrazones, a melting was produced when the p-TSA was added, and, therefore, the reaction was not fully in solid-state. The formation of a fluid phase is vastly found for solid mixtures (eutectic melting) [68] and surely contributed to reach high conversions in short times of grinding for these hydrazones. Molecules 2017, 22, 1457 5 of 27 formation of a fluid phase is vastly found for solid mixtures (eutectic melting) [68] and surely contributed to reach high conversions in short times of grinding for these hydrazones. 2.2. Structural Analysis of Isonicotinoyl Hydrazones by DFT and NMR: Determination of the Free Activation Energy (∆G̸=) between Conformers of Selected Compounds 1a and 5 2.2. Structural Analysis of Isonicotinoyl Hydrazones by DFT and NMR: Determination of the Free Activation Energy (G≠) between Conformers of Selected Compounds 1a and 5 The structures of all the hydrazones were identified and fully characterized by 1H- and 13C-NMR, MS and HRMS, FTIR and UV-vis (see Supplementary Materials). The structures of all the hydrazones were identified and fully characterized by 1H- and 13C-NMR, MS and HRMS, FTIR and UV-vis (see Supplementary Materials). C h d ll l h d h d h f f Concerning the NMR data, all isonicotinoyl hydrazones showed the presence of conformers in dimethylsulfoxide (DMSO) solution. NMR spectral and theoretical studies previously demonstrated that acylhydrazones generally exist predominantly or solely as a mixture of isomers [69–71]. In theory, N-acylhydrazones may exist with four possible arrangements in respect to (E/Z)-configurational isomers relative to the C=N bond and (E’/Z’)-rotamers caused by inversion of the amide bonds C(O)NH, here named cis/trans amide conformers (Figure 3) [69,72]. Concerning the NMR data, all isonicotinoyl hydrazones showed the presence of conformers in dimethylsulfoxide (DMSO) solution. NMR spectral and theoretical studies previously demonstrated that acylhydrazones generally exist predominantly or solely as a mixture of isomers [69–71]. In theory, N-acylhydrazones may exist with four possible arrangements in respect to (E/Z)- configurational isomers relative to the C=N bond and (E’/Z’)-rotamers caused by inversion of the amide bonds C(O)NH, here named cis/trans amide conformers (Figure 3) [69,72]. Figure 3. E/Z-configurational isomers and cis/trans amide conformers for N-acylhydrazones. Figure 3. E/Z-configurational isomers and cis/trans amide conformers for N-acylhydrazones. Figure 3. E/Z-configurational isomers and cis/trans amide conformers for N-acylhydrazones. Figure 3. E/Z-configurational isomers and cis/trans amide conformers for N-acylhydrazones. Molecules 2017, 22, 1457 Although the four forms were considered, E/Z isomerization is generally not observed and the Z geometric isomers are absent or present only in poor part. An exception is for R’ = 2-pyridyl, in which strong intramolecular hydrogen bonds are present in the (Z)-form [70] mainly in less polar Although the four forms were considered, E/Z isomerization is generally not observed and the Z geometric isomers are absent or present only in poor part. An exception is for R’ = 2-pyridyl, in which strong intramolecular hydrogen bonds are present in the (Z)-form [70] mainly in less polar solvents. solvents. While all isonicotinoyl hydrazones showed the presence of conformers in DMSO solution, for study purposes, two derivatives were chosen to be further investigated: phenolic hydrazone (1a) and indazole derivative (5). Both of them showed two sets of signals indicating the possibility of equilibrium between rotamers in solution. Theoretical assessment of the existence of the isomers was While all isonicotinoyl hydrazones showed the presence of conformers in DMSO solution, for study purposes, two derivatives were chosen to be further investigated: phenolic hydrazone (1a) and indazole derivative (5). Both of them showed two sets of signals indicating the possibility of equilibrium between rotamers in solution. Theoretical assessment of the existence of the isomers was carried out. carried out. The four structures of Z/E geometrical isomers and cis/trans amide conformers of 1a were modeled by Density Functional theory (DFT), using Gaussian 09, firstly at HF/STO-3G level. The Z conformers were found higher in energy than the E ones, around 6 kcal/mol (see Table S1 in the Supplementary Materials). Thus, only the cisE and transE-isomers were then modeled at the B3LYP/6- 31+G(d,p) level and the frequencies calculations were performed on the optimized geometries at 298 The four structures of Z/E geometrical isomers and cis/trans amide conformers of 1a were modeled by Density Functional theory (DFT), using Gaussian 09, firstly at HF/STO-3G level. The Z conformers were found higher in energy than the E ones, around 6 kcal/mol (see Table S1 in the Supplementary Materials). Thus, only the cisE and transE-isomers were then modeled at the B3LYP/6-31+G(d,p) level and the frequencies calculations were performed on the optimized geometries at 298 K, showing all positive frequencies and allowing evaluation of the Gibbs free energy. K, showing all positive frequencies and allowing evaluation of the Gibbs free energy. Mechanosynthesis of Isonicotinoyl Hydrazones 2.1. Chemistry Mechanosynthesis of Isonicotinoyl Hydra ones [a] Yields after washing with NaHCO3 aqueous solution to eliminate p-TSA. According to TLC, 1H- NMR and MS, the conversions were quantitative. [a] Yields after washing with NaHCO3 aqueous solution to eliminate p-TSA. According to TLC, 1H- NMR and MS, the conversions were quantitative. [a] Yields after washing with NaHCO3 aqueous solution to eliminate p-TSA. According to TLC, 1H- NMR and MS, the conversions were quantitative. [a] Yields after washing with NaHCO3 aqueous solution to eliminate p-TSA. According to TLC, 1H- NMR and MS, the conversions were quantitative. [a] Yields after washing with NaHCO3 aqueous solution to eliminate p-TSA. According to TLC, 1H-NMR and MS, the conversions were quantitative. Molecules 2017, 22, 1457 p At the coalescence temperature Tc At the coalescence temperature Tc kexch = π/√2 = 2.22· (Hz) kexch = (kB·Tc/h)exp(−G≠/RTc) (Eyringss equation G≠ = −RTcLn(kexch·h/kB·Tc) with kB = 1.38 × 10−23 kJ/K, h = 6.626 × 10−34 J·s, and R kexch = π∆ν/√2 = 2.22·∆ν (Hz) kexch = (kB·Tc/h)exp(−∆G̸=/RTc) (Eyringss equation) ∆G̸= = −RTcLn(kexch·h/kB·Tc) J J J The 1H-NMR study at increasing temperatures (from 298 K to 388 K) allo with kB = 1.38 × 10−23 kJ/K, h = 6.626 × 10−34 J·s, and R = 8.314 J·mol−1·K−1. The 1H-NMR study at increasing temperatures (from 298 K to 388 K) allo with kB = 1.38 × 10−23 kJ/K, h = 6.626 × 10−34 J·s, and R = 8.314 J·mol−1·K−1. of coalescence temperatures of the same signals of each isomer (Figure S1). Correlation of the coalescence temperatures Tc with the difference in chemical shift of the signals led to G≠ following the precedent equation described (Supplementary Materials, Table S3). The mean value obtained on several signals led to G≠ = 17.58 kcal·mol−1. This experimental value is in agreement with the calculated one of 17.63 kcal·mol−1 at the B3LYP/6-31+G(d,p) level. The same study was performed on compound 5, which possesses eight isomers. As previously d b d h f h h h h / O h d h h The 1H-NMR study at increasing temperatures (from 298 K to 388 K) allowed the determination of coalescence temperatures of the same signals of each isomer (Figure S1). Correlation of the coalescence temperatures Tc with the difference in chemical shift of the signals led to ∆G̸= following the precedent equation described (Supplementary Materials, Table S3). The mean value obtained on several signals led to ∆G̸= = 17.58 kcal·mol−1. This experimental value is in agreement with the calculated one of 17.63 kcal·mol−1 at the B3LYP/6-31+G(d,p) level. described, the optimization of geometries on the height isomers at the HF/STO-3G showed that the Z isomers are higher in energy (6–7.5 kcal/mol) (Supplementary Materials, Table S4). Tsshus, the calculations were carried out at the B3LYP/6-31+G(d,p) level on the four isomers: cis and trans E- isomers and the two rotamers, in the gas phase and in the DMSO modeled by the SMD polarizable continuum model. Boltzmann analysis was used to determine the relative distribution of each conformer both in the gas phase and in the DMSO continuum model. Molecules 2017, 22, 1457 Following Boltzmann distribution, (Pi/Pj = exp((Gj − Gi)/kBT), cisE-isomer was present at 92% and transE at 8% in the gas phase, whereas in DMSO, using the polarizable solvent continuum model (SMD) th ti i t d i /t 6/94 (T bl 2) Following Boltzmann distribution, (Pi/Pj = exp((Gj −Gi)/kBT), cisE-isomer was present at 92% and transE at 8% in the gas phase, whereas in DMSO, using the polarizable solvent continuum model (SMD), the ratio was inverted: cis/trans: 6/94 (Table 2). 6 of 27 6 of 27 6 of 27 6 of 27 Molecules 2017, 22, 1457 Molecules 2017, 22, 1457 Table 2. Geometries and energies of minima and transition state for cis and trans E-isomers of 1a obtained at B3LYP/6-31+G(d,p) level in the gas phase and using the DMSO polarizable continuum model (SMD). Table 2. Geometries and energies of minima and transition state for cis and trans E-isomers of 1a obtained at B3LYP/6-31+G(d,p) level in the gas phase and using the DMSO polarizable continuum model (SMD). Table 2. Geometries and energies of minima and transition state for cis and trans E-isomers of 1a obtained at B3LYP/6-31+G(d,p) level in the gas phase and using the DMSO polarizable continuum model (SMD). Table 2. Geometries and energies of minima and transition state for cis and trans E-isomers of 1a obtained at B3LYP/6-31+G(d,p) level in the gas phase and using the DMSO polarizable continuum model (SMD). transE-1a cisE-1a TS-E-1a In the Gas Phase E (ua) G (ua) G (kcal/mol) % transE_1a −816.730569 −816.553707 1.47 8 cisE_1a −816.733307 −816.55605 0 92 In DMSO E (ua) G (ua) G (kcal/mol) % transE_1a −816.763427 −816.585816 −1.68 94 cisE_1a −816.761415 −816.583145 0 6 TS_1a −816.765271 −816.557724 17.63 - In the Gas Phase E (ua) G (ua) ∆G (kcal/mol) % transE_1a −816.730569 −816.553707 1.47 8 cisE_1a −816.733307 −816.55605 0 92 In DMSO E (ua) G (ua) ∆G (kcal/mol) % transE_1a −816.763427 −816.585816 −1.68 94 cisE_1a −816.761415 −816.583145 0 6 TS_1a −816.765271 −816.557724 17.63 - A transition state (TS-1a) was found between transE and cisE, characterized by its imaginary frequency at −115.79 cm−1. The difference between Gibbs free energy of the transition state and the energy of the cis-E-isomer (G≠) was equal to 17.63 kcal·mol−1. A transition state (TS-1a) was found between transE and cisE, characterized by its imaginary frequency at −115.79 cm−1. Molecules 2017, 22, 1457 The difference between Gibbs free energy of the transition state and the energy of the cis-E-isomer (∆G̸=) was equal to 17.63 kcal·mol−1. e e gy o e cis E iso e ( G ) as equa o 63 a o The NMR chemical shift calculations were then performed at B3LYP/6-311+ (2d,p) level, using the DMSO polarizable continuum model (PCM). Isotropic shielding constants () for 1H and 13C nuclei were transformed in chemical shift (δ) using linear regression procedure proposed by Lodewyk [73]. Calculated values are presented in the Supplementary Materials (Table S2). By comparing calculated values and experimental ones, we unambiguously concluded that the transE- isomer is the major one. This result is also in agreement with the calculated Gibbs free energy values in DMSO, at 298 K, as transE-isomer is −1.68 kcal/mol lower than the cis (ratio cis/trans around 6/94). gy q The NMR chemical shift calculations were then performed at B3LYP/6-311+ (2d,p) level, using the DMSO polarizable continuum model (PCM). Isotropic shielding constants (σ) for 1H and 13C nuclei were transformed in chemical shift (δ) using linear regression procedure proposed by Lodewyk [73]. Calculated values are presented in the Supplementary Materials (Table S2). By comparing calculated values and experimental ones, we unambiguously concluded that the transE-isomer is the major one. This result is also in agreement with the calculated Gibbs free energy values in DMSO, at 298 K, as transE-isomer is −1.68 kcal/mol lower than the cis (ratio cis/trans around 6/94). gy ( ) q The NMR chemical shift calculations were then performed at B3LYP/6-311+ (2d,p) level, using the DMSO polarizable continuum model (PCM). Isotropic shielding constants () for 1H and 13C nuclei were transformed in chemical shift (δ) using linear regression procedure proposed by The NMR chemical shift calculations were then performed at B3LYP/6-311+ (2d,p) level, using the DMSO polarizable continuum model (PCM). Isotropic shielding constants (σ) for 1H and 13C nuclei were transformed in chemical shift (δ) using linear regression procedure proposed by Lodewyk [73]. , , / ( / / ) This activation energy can also be measured by 1H-NMR analysis, by determining the coalescence temperature Tc. This activation energy can also be measured by 1H-NMR analysis, by determining the coalescence temperature Tc. 2.3.1. Hydrolytic Stability 2.3.1. Hydrolytic Stability 2.3.1. Hydrolytic Stability 2.3.1. Hydrolytic Stability 2.3.1. Hydrolytic Stability Stability studies were carried out in order to confirm that biological activities evidenced for isonicotinoyl hydrazones arise from the tested compounds, and not from the hydrolysis of the imine bond. UV-vis spectrophotometry at the λmax of absorbance of the related molecule was used to monitor the stability of the most prominent synthesized compounds. The study was carried out for all compounds; here, we present the results for some of them while all other data are in the Supplementary Materials. Table 4 summarizes the conditions used and the stability results observed for 1a–1d, 5 and 7 compounds. Stability studies were carried out in order to confirm that biological activities evidenced for isonicotinoyl hydrazones arise from the tested compounds, and not from the hydrolysis of the imine bond. UV-vis spectrophotometry at the λmax of absorbance of the related molecule was used to monitor the stability of the most prominent synthesized compounds. The study was carried out for all compounds; here, we present the results for some of them while all other data are in the Supplementary Materials. Table 4 summarizes the conditions used and the stability results observed for 1a–1d, 5 and 7 compounds. Stability studies were carried out in order to confirm that biological activities evidenced for isonicotinoyl hydrazones arise from the tested compounds, and not from the hydrolysis of the imine bond. UV-vis spectrophotometry at the λmax of absorbance of the related molecule was used to monitor the stability of the most prominent synthesized compounds. The study was carried out for all compounds; here, we present the results for some of them while all other data are in the Supplementary Materials. Table 4 summarizes the conditions used and the stability results observed for 1a–1d, 5 and 7 compounds. Stability studies were carried out in order to confirm that biological activities evidenced for isonicotinoyl hydrazones arise from the tested compounds, and not from the hydrolysis of the imine bond. UV-vis spectrophotometry at the λmax of absorbance of the related molecule was used to monitor the stability of the most prominent synthesized compounds. The study was carried out for all compounds; here, we present the results for some of them while all other data are in the Supplementary Materials. Table 4 summarizes the conditions used and the stability results observed for 1a–1d, 5 and 7 compounds. Molecules 2017, 22, 1457 Isomer Geometry (In Gas Phase) G (In Gas Phase) % G (In DMSO) % transE_5_1 −888.90736 0.34 −888.94471 28.22 transE_5_2 −888.909926 5.09 −888.94528 51.50 cisE_5_1 −888.910465 9.0 −888.941968 1.54 cisE_5_2 −888.912591 85.6 −888.944326 18.72 −888.90736 0.34 −888.94471 28.22 transE_5_2 ( ,p) g p ( ) Isomer Geometry (In Gas Phase) G (In Gas Phase) % G (In DMSO) % transE_5_1 −888.90736 0.34 −888.94471 28.22 transE_5_2 −888.909926 5.09 −888.94528 51.50 cisE_5_1 −888.910465 9.0 −888.941968 1.54 cisE_5_2 −888.912591 85.6 −888.944326 18.72 −888.909926 5.09 −888.94528 51.50 cisE_5_1 5 at the B3LYP/6 31 G(d,p) in the gas phase and in the DMSO continuum solvent model (SMD). Isomer Geometry (In Gas Phase) G (In Gas Phase) % G (In DMSO) % transE_5_1 −888.90736 0.34 −888.94471 28.22 transE_5_2 −888.909926 5.09 −888.94528 51.50 cisE_5_1 −888.910465 9.0 −888.941968 1.54 cisE_5_2 −888.912591 85.6 −888.944326 18.72 −888.910465 9.0 −888.941968 1.54 cisE_5_2 5 at the B3LYP/6 31 G(d,p) in the gas phase and in the DMSO continuum solvent model (SMD). Isomer Geometry (In Gas Phase) G (In Gas Phase) % G (In DMSO) % transE_5_1 −888.90736 0.34 −888.94471 28.22 transE_5_2 −888.909926 5.09 −888.94528 51.50 cisE_5_1 −888.910465 9.0 −888.941968 1.54 cisE_5_2 −888.912591 85.6 −888.944326 18.72 −888.912591 85.6 −888.944326 18.72 1H- and 13C-NMR chemical shifts were calculated as previously described at the B3LYP/6- 311+G(2d,p) using DMSO continuum model (PCM) and taking into account the Boltzmann distribution of the two conformers for each isomer, which means transE-1/transE-2: 35%/65%, and cisE-1/cisE-2: 8%/92%. The comparison of calculated chemical shifts and experimental ones of both 1H and 13C (Supplementary Materials, Figure S2 and Table S5), showed that trans isomer is the major compound in DMSO. 1H- and 13C-NMR chemical shifts were calculated as previously described at the B3LYP/6- 311+G(2d,p) using DMSO continuum model (PCM) and taking into account the Boltzmann distribution of the two conformers for each isomer, which means transE-1/transE-2: 35%/65%, and cisE-1/cisE-2: 8%/92%. The comparison of calculated chemical shifts and experimental ones of both 1H and 13C (Supplementary Materials, Figure S2 and Table S5), showed that trans isomer is the major compound in DMSO. Molecules 2017, 22, 1457 The a ti atio e e y a e aluated by 1H NMR a aly i at i ea i te e atu e (f o 298 1H- and 13C-NMR chemical shifts were calculated as previously described at the B3LYP/6- 311+G(2d,p) using DMSO continuum model (PCM) and taking into account the Boltzmann distribution of the two conformers for each isomer, which means transE-1/transE-2: 35%/65%, and cisE-1/cisE-2: 8%/92%. The comparison of calculated chemical shifts and experimental ones of both 1H and 13C (Supplementary Materials, Figure S2 and Table S5), showed that trans isomer is the major compound in DMSO. Th i i l d b 1H NMR l i i i (f 298 1H- and 13C-NMR chemical shifts were calculated as previously described at the B3LYP/6- 311+G(2d,p) using DMSO continuum model (PCM) and taking into account the Boltzmann distribution of the two conformers for each isomer, which means transE-1/transE-2: 35%/65%, and cisE-1/cisE-2: 8%/92%. The comparison of calculated chemical shifts and experimental ones of both 1H and 13C (Supplementary Materials, Figure S2 and Table S5), showed that trans isomer is the major compound in DMSO. Th i i l d b 1H NMR l i i i (f 298 1H- and 13C-NMR chemical shifts were calculated as previously described at the B3LYP/6-311+G(2d,p) using DMSO continuum model (PCM) and taking into account the Boltzmann distribution of the two conformers for each isomer, which means transE-1/transE-2: 35%/65%, and cisE-1/cisE-2: 8%/92%. The comparison of calculated chemical shifts and experimental ones of both 1H and 13C (Supplementary Materials, Figure S2 and Table S5), showed that trans isomer is the major compound in DMSO. The activation energy was evaluated by 1H-NMR analysis at increasing temperatures (from 298 K to 388 K) and was evaluated at 17.8 kcal/mol (Supplementary Materials, Table S6) in the same order as for compound 1a. The activation energy was evaluated by 1H-NMR analysis at increasing temperatures (from 298 K to 388 K) and was evaluated at 17.8 kcal/mol (Supplementary Materials, Table S6) in the same order as for compound 1a. Th b ti i t t t i t d t ti i ht h i t The activation energy was evaluated by 1H-NMR analysis at increasing temperatures (from 298 K to 388 K) and was evaluated at 17.8 kcal/mol (Supplementary Materials, Table S6) in the same order as for compound 1a. Molecules 2017, 22, 1457 Th b i i i d i i h h i The activation energy was evaluated by 1H-NMR analysis at increasing temperatures (from 298 K to 388 K) and was evaluated at 17.8 kcal/mol (Supplementary Materials, Table S6) in the same order as for compound 1a. Th b i i i d i i h h i The activation energy was evaluated by 1H-NMR analysis at increasing temperatures (from 298 K to 388 K) and was evaluated at 17.8 kcal/mol (Supplementary Materials, Table S6) in the same order as for compound 1a. These observations are important as restricted rotations might have an impact on pharmacological properties. These observations are important as restricted rotations might have an impact on pharmacological properties. These observations are important as restricted rotations might have an impact on pharmacological properties. These observations are important as restricted rotations might have an impact on pharmacological properties. p These observations are important as restricted rotations might have an impact on pharmacological properties. 2.3. Physicochemical Studies of Some Isonicotinoyl Hydrazones 2.3. Physicochemical Studies of Some Isonicotinoyl Hydrazones 2.3. Physicochemical Studies of Some Isonicotinoyl Hydrazones 2.3. Physicochemical Studies of Some Isonicotinoyl Hydrazones 2.3. Physicochemical Studies of Some Isonicotinoyl Hydrazones Molecules 2017, 22, 1457 Geometries, Gibbs free energies and Boltzmann distribution of the four major conformers of 5 at the B3LYP/6 31+G(d p) in the gas phase and in the DMSO continuum solvent model (SMD) Table 3. Geometries, Gibbs free energies and Boltzmann distribution of the four major conformers of 5 at the B3LYP/6-31+G(d,p) in the gas phase and in the DMSO continuum solvent model (SMD). Table 3. Geometries, Gibbs free energies and Boltzmann distribution of the four major conformers of 5 at the B3LYP/6-31+G(d p) in the gas phase and in the DMSO continuum solvent model (SMD) Table 3. Geometries, Gibbs free energies and Boltzmann distribution of the four major conformers of 5 at the B3LYP/6-31+G(d p) in the gas phase and in the DMSO continuum solvent model (SMD) at the B3LYP/6-31+G(d,p) in the gas phase and in the DMSO continuum solvent model (SMD). Table 3. Geometries, Gibbs free energies and Boltzmann distribution of the four major conformers o 5 at the B3LYP/6 31+G(d p) in the gas phase and in the DMSO continuum solvent model (SMD) Table 3. Geometries, Gibbs free energies and Boltzmann distribution of the four major conformers o 5 at the B3LYP/6-31+G(d,p) in the gas phase and in the DMSO continuum solvent model (SMD). Table 3. Geometries, Gibbs free energies and Boltzmann distribution of the four major conformers o 5 at the B3LYP/6-31+G(d p) in the gas phase and in the DMSO continuum solvent model (SMD) Table 3. Geometries, Gibbs free energies and Boltzmann distribution of the four major conformers o 5 at the B3LYP/6-31+G(d p) in the gas phase and in the DMSO continuum solvent model (SMD) Isomer Geometry (In Gas Phase) G (In Gas Phase) % G (In DMSO) % transE_5_1 5 at the B3LYP/6 31+G(d,p) in the gas phase and in the DMSO continuum solvent model (SMD). Molecules 2017, 22, 1457 In the gas phase, cis compounds are the major ones, although, in the DMSO continuum, trans h E % i E % ( bl ) The same study was performed on compound 5, which possesses eight isomers. As previously described, the optimization of geometries on the height isomers at the HF/STO-3G showed that the Z isomers are higher in energy (6–7.5 kcal/mol) (Supplementary Materials, Table S4). Tsshus, the calculations were carried out at the B3LYP/6-31+G(d,p) level on the four isomers: cis and trans E-isomers and the two rotamers, in the gas phase and in the DMSO modeled by the SMD polarizable continuum model. Boltzmann analysis was used to determine the relative distribution of each conformer both in the gas phase and in the DMSO continuum model. 7 of 27 Molecules 2017, 22, 1457 In the gas phase, cis compounds are the major ones, although, in the DMSO continuum, trans isomers are the major ones: transE: 80%, cisE: 20% (Table 3). Molecules 2017, 22, 1457 7 of 27 Molecules 2017, 22, 1457 7 of 27 Molecules 2017, 22, 1457 7 of 27 Molecules 2017, 22, 1457 7 of 27 Table 3. Geometries, Gibbs free energies and Boltzmann distribution of the four major conformers of 5 Table 3 Geo et ies Gibbs f ee e e gies a d Bolt a dist ibutio of the fou ajo co fo e s of Table 3 Geometries Gibbs free energies and Boltzmann distribution of the four major conformers o Table 3 Geometries Gibbs free energies and Boltzmann distribution of the four major conformers o Table 3 Geometries Gibbs free energies and Boltzmann distribution of the four major conformers of Table 3. Geometries, Gibbs free energies and Boltzmann distribution of the four major conformers of 5 at the B3LYP/6-31+G(d p) in the gas phase and in the DMSO continuum solvent model (SMD) Table 3. Geometries, Gibbs free energies and Boltzmann distribution of the four major conformers of Table 3. Geometries, Gibbs free energies and Boltzmann distribution of the four major conformers of Table 3. Geometries, Gibbs free energies and Boltzmann distribution of the four major conformers of Table 3. Geometries, Gibbs free energies and Boltzmann distribution of the four major conformers of Table 3. Geometries, Gibbs free energies and Boltzmann distribution of the four major conformers of 5 at the B3LYP/6-31+G(d,p) in the gas phase and in the DMSO continuum solvent model (SMD). Table 3. 2.3.1. Hydrolytic Stability 2.3.1. Hydrolytic Stability 2.3.1. Hydrolytic Stability 2.3.1. Hydrolytic Stability 2.3.1. Hydrolytic Stability Stability studies were carried out in order to confirm that biological activities evidenced for isonicotinoyl hydrazones arise from the tested compounds, and not from the hydrolysis of the imine bond. UV-vis spectrophotometry at the λmax of absorbance of the related molecule was used to monitor the stability of the most prominent synthesized compounds. The study was carried out for all compounds; here, we present the results for some of them while all other data are in the Supplementary Materials. Table 4 summarizes the conditions used and the stability results observed for 1a–1d, 5 and 7 compounds. p As expected, UV-vis spectroscopy demonstrated that all the tested compounds are stable for a prolonged time (up to 22 h–7 days) and no significant decomposition was observed. Only 5 showed a very small reduction (3%) of the absorbance after 20 h. It is known that hydrazones possess greater 8 of 27 8 of 27 Molecules 2017, 22, 1457 Molecules 2017, 22, 1457 intrinsic hydrolytic stability than that of imines. In addition to the contribution of the NH-N=C in electron delocalization, the resonance forms in acylhydrazones increase the negative-charge on the C=N and thus, reduce its electrophilicity and the affinity to the nucleophile attack from water [74]. Furthermore, the repulsion of the lone pairs of the NH-N can be relieved in the conjugates [75]. Table 4. Stability study of hydrazones. Compound Medium Conc. (mol/L) pH Time Stability 1a 28% EtOH/H2O 6.0 × 10−5 6.1 22 h stable 1b 6.3 × 10−5 6.5 22 h stable 1c 6.9 × 10−5 6.3 15 h stable Table 4. Stability study of hydrazones. Compound Medium Conc. (mol/L) pH Time Stability 1a 28% EtOH/H2O 6.0 × 10−5 6.1 22 h stable 1b 6.3 × 10−5 6.5 22 h stable 1c 6.9 × 10−5 6.3 15 h stable 1d 5.9 × 10−5 6.2 21 h stable 5 5% EtOH/PIPES buffer (50 mM) 4.1 × 10−5 6.8 20 h 3% Abs. reduction 7 3.1 × 10−5 6.8 20 h stable 7 days 5% Abs. reduction 1d 5.9 × 10−5 6.2 21 h stable 5 5% EtOH/PIPES buffer (50 mM) 4.1 × 10−5 6.8 20 h 3% Abs. reduction 7 3.1 × 10−5 6.8 20 h stable 7 days 5% Abs. reduction As expected, UV-vis spectroscopy demonstrated that all the tested compounds are stable for a prolonged time (up to 22 h–7 days) and no significant decomposition was observed. 2.3.2. pKa Determination 2.3.2. pKa Determination The acid dissociation constant (Ka, or more commonly expressed by pKa) is a very important physicochemical parameter in a wide range of research areas, including the development of active molecules due to solubility issues. The pKa of the molecules studied for stability could also be determined by using UV-vis spectrometry based on the variation of the absorbance as function of the pH due to the presence of chromophores close to the ionization site of the molecules. The molar absorptivity varies according to the conjugation forms that dynamically change when and where the molecule is charged by the effect of pH and protonation/dissociation. As an example, the different protonation states for the hydrazone 1d are shown in Figure 4. The acid dissociation constant (Ka, or more commonly expressed by pKa) is a very important physicochemical parameter in a wide range of research areas, including the development of active molecules due to solubility issues. The pKa of the molecules studied for stability could also be determined by using UV-vis spectrometry based on the variation of the absorbance as function of the pH due to the presence of chromophores close to the ionization site of the molecules. The molar absorptivity varies according to the conjugation forms that dynamically change when and where the molecule is charged by the effect of pH and protonation/dissociation. As an example, the different protonation states for the hydrazone 1d are shown in Figure 4. Figure 4. Protonation states of the hydrazone 1d as function of pH. Figure 4. Protonation states of the hydrazone 1d as function of pH. Figure 4. Protonation states of the hydrazone 1d as function of pH. Figure 4. Protonation states of the hydrazone 1d as function of pH. For experimental pKa determination, the molecules were solubilized in hydroalcoholic solutions at ethanol 28% and the ionic strength was maintained by the addition of KCl (0.1 M). The pH was adjusted with concentrated solutions of KOH and HCl. The UV spectra were recorded at each pH value and, at least three wavelengths were monitored. The absorbance variation was plotted as function of the pH. As an example, the variations on the UV-vis spectra for compound 1d and the resulting plot for six wavelength values are shown in Figure 5a,b, respectively (all other spectra are present in Figures S4–S8). 2.3.1. Hydrolytic Stability 2.3.1. Hydrolytic Stability 2.3.1. Hydrolytic Stability 2.3.1. Hydrolytic Stability 2.3.1. Hydrolytic Stability Only 5 showed a very small reduction (3%) of the absorbance after 20 h. It is known that hydrazones possess greater intrinsic hydrolytic stability than that of imines. In addition to the contribution of the NH-N=C in electron delocalization, the resonance forms in acylhydrazones increase the negative-charge on the C=N and thus, reduce its electrophilicity and the affinity to the nucleophile attack from water [74]. Furthermore the repulsion of the lone pairs of the NH N can be relieved in the conjugates [75] Table 4. Stability study of hydrazones. 5.9 × 10 5 6.2 4.1 × 10−5 6.8 Moreover, the stability of compound 1d was further assessed upon incubation in DMSO, the solvent used for biological assays, by mass spectrometry analysis; in addition, no relevant peaks corresponding to possibly released INH have been detected (Figure S3). , p p j g [ ] Moreover, the stability of compound 1d was further assessed upon incubation in DMSO, the solvent used for biological assays, by mass spectrometry analysis; in addition, no relevant peaks corresponding to possibly released INH have been detected (Figure S3). Moreover, the stability of compound 1d was further assessed upon incubation in DMSO, the solvent used for biological assays, by mass spectrometry analysis; in addition, no relevant peaks corresponding to possibly released INH have been detected (Figure S3). p p j g [ ] Moreover, the stability of compound 1d was further assessed upon incubation in DMSO, the solvent used for biological assays, by mass spectrometry analysis; in addition, no relevant peaks corresponding to possibly released INH have been detected (Figure S3). 2.3.2. pKa Determination 2.3.2. pKa Determination The protonation/dissociation of the molecule is accompanied by a variation For experimental pKa determination, the molecules were solubilized in hydroalcoholic solutions at ethanol 28% and the ionic strength was maintained by the addition of KCl (0.1 M). The pH was adjusted with concentrated solutions of KOH and HCl. The UV spectra were recorded at each pH value and, at least three wavelengths were monitored. The absorbance variation was plotted as function of the pH. As an example, the variations on the UV-vis spectra for compound 1d and the resulting plot for six wavelength values are shown in Figure 5a,b, respectively (all other spectra are present in Figures S4–S8). The protonation/dissociation of the molecule is accompanied by a variation in the 9 of 27 7 Molecules 2017, 22, 1457 absorbance (Figure 5a) and is graphically represented for six wavelength values as function of pH in Figure 5b. in the absorbance (Figure 5a) and is graphically represented for six wavelength values as function of pH in Figure 5b. (a) (b) Figure 5. The variations on the UV-vis spectra for compound 1d and the resulting plot for six wavelength values. (a) UV-vis spectra obtained for compound 1d as function of pH variation; (b) Plots of absorbance for six wavelength values (λ/nm) as function of pH for compound 1d. Th i fl ti i t d t th h i th t t t d/di i t d t t f th Wavelength (nm) 250 300 350 400 450 500 Absorbance (AU) 0 0.2 0.4 0.6 0.8 1 1.2 1.4 221 334 Figure 5. The variations on the UV-vis spectra for compound 1d and the resulting plot for six wavelength values. (a) UV-vis spectra obtained for compound 1d as function of pH variation; (b) Plots of absorbance for six wavelength values (λ/nm) as function of pH for compound 1d. (a) Wavelength (nm) 250 300 350 400 450 500 Absorbance (AU) 0 0.2 0.4 0.6 0.8 1 1.2 1.4 221 334 (a) (a) (a) (b) (b) Figure 5. The variations on the UV-vis spectra for compound 1d and the resulting plot for six wavelength values. (a) UV-vis spectra obtained for compound 1d as function of pH variation; (b) Plots of absorbance for six wavelength values (λ/nm) as function of pH for compound 1d. Figure 5. The variations on the UV-vis spectra for compound 1d and the resulting plot for six wavelength values. 2.3.2. pKa Determination 2.3.2. pKa Determination (a) UV-vis spectra obtained for compound 1d as function of pH variation; (b) Plots of absorbance for six wavelength values (λ/nm) as function of pH for compound 1d. molecule, and, therefore, the pH at that point amounts to the pKa. Thus, by using this method, the pKa values of 1d were determined [76]. The same protocol was applied for the other molecules and the resulted pKa are presented in Table 5, as an average value from three different λ. Table 5. pKa values determined for the isonicotinoylhydrazones. The inflection points correspond to the change in that protonated/dissociated state of the molecule, and, therefore, the pH at that point amounts to the pKa. Thus, by using this method, the pKa values of 1d were determined [76]. The same protocol was applied for the other molecules and the resulted pKa are presented in Table 5, as an average value from three different λ. Compound 1a 1b 1c 1d 5 7 pKa1 nd a nd a 3.4 3.0 3.4 3.6 pKa2 9.2 ± 0.1 7.4 ± 0.1 9.1 ± 0.1 9.5 ± 0.1 10.4 ± 0.1 11 pKa3 - 8.9 ± 0.1 - >11 - - a nd for not determined. Table 5. pKa values determined for the isonicotinoylhydrazones. Compound 1a 1b 1c 1d 5 7 pKa1 nd a nd a 3.4 3.0 3.4 3.6 pKa2 9.2 ± 0.1 7.4 ± 0.1 9.1 ± 0.1 9.5 ± 0.1 10.4 ± 0.1 11 pKa3 - 8.9 ± 0.1 - >11 - - a nd for not determined. 1a 1b 1c 1d d d 3 4 3 0 3 Table 5. pKa values determined for the isonicotinoylhydrazones. a nd for not determined. An inflection point was always observed close to pH 3, which is related with the protonation of 4-pyridinic nitrogen of isoniazid moiety (pKa2 of isoniazid = 3.5), and corresponds to pKa1 of the 10 of 27 Molecules 2017, 22, 1457 hydrazones. The pKa2 of the molecules ranges from 7.7 to 11. It means that they are in dissociated form from milder (1b) to stronger (7) basic conditions. hydrazones. The pKa2 of the molecules ranges from 7.7 to 11. It means that they are in dissociated form from milder (1b) to stronger (7) basic conditions. 2.4. Biology of Mechanochemically Synthesized Hydrazones 2.4. Biology of Mechanochemically Synthesized Hydrazones 2.4.1. InhA Inhibition Assay InhA, the NADH-dependent fatty acid biosynthesis (FAS-II) enoylreductase from M. tuberculosis, has emerged as a promising drug target due to its vital role in synthesis of mycolic acids. InhA is the main target of Isoniazid [77–80]. Recombinant M.tb InhA was expressed in E. coli and subsequently purified. The selected synthetic compounds, corresponding to the phenolic isonicotinoyl hydrazones 1a–d and the corresponding heterocyclic ones 2–11 series, were evaluated in vitro for the inhibition of M.tb InhA activity at 50 µM by applying a previously described method [81] (Table 6). Table 6. Enzyme inhibition values for the INH derivatives. Results are expressed as a percentage of InhA inhibition. Compound % Inhibition at 50 µM (Inhibitor) Compound % Inhibition at 50 µM (Inhibitor) 1a 45 5 19 1b 54 6 43 1c 48 7 39 1d 64 8 42 2 54 9 32 3 3 10 79 4 33 11 not soluble TCL >99 Considering the four phenolic derivatives 1a–d, the tri-substituted one (1d) presents the better InhA inhibition activity with 64% value at 50 µM. Derivatives 1a–c are less potent with 45–54% InhA inhibition range at 50 µM. Under these conditions, 99% inhibition is obtained for Triclosan (TCL). Concerning the heterocyclic isonicotinoyl hydrazones, compounds 2, 3 and 11 were difficult to evaluate due to solubility issues at high concentrations. Compound 5 is a very poor inhibitor (19% InhA inhibition), while compounds 4, 6 and 7 may be considered as poor inhibitors with 32%, 43% and 39% values, respectively. Compound 10 is the derivative exhibiting the highest inhibition of InhA enzyme with 79% at 50 µM. In comparing isonicotinoyl derivatives derived from indoles (compounds 6–10), we can notice that those possessing an indol-3-yl frame have the same activities with inhibition values between 32% and 43%. Compounds 6 and 8 differing by one methyl group (position 2 of the indol-3-yl frame) have the same inhibition values. On the contrary, compound 10 possessing an indole-2-yl frame is two-fold more active (79% of inhibition). Concerning the imidazole and indazole derivatives, we might hypothesize that the striking differences in activities could arise by a better positioning of the compounds 2 and 4 guided by their nitrogen atoms on their heterocyclic parts. Molecules 2017, 22, 1457 Molecules 2017, 22, 1457 11 of 27 It is noteworthy that a series of phenolic hydrazones bearing the four phenolic frames (a–d), previously synthetized by mechanochemical means were already tested against M.tb. cell growth [38]. Among the different hydrazines (isoniazid, hydralazine, 2-hydrazino-benzothiazole, 3-aminorhodanine, benzyl carbazate and benzhydrazide), used to form the corresponding hydrazones, only the isonicotinoyl derivatives were active against M.tb growth, whilst the other compounds were not effective (MIC > 30 µM; data not shown, but reported in Reference [39]). p Isonicotinoyl derivatives 1a–d showed good anti-mycobacterial activity with 0.0125 or 0.125 µg/mL MIC values. Among these four, those bearing two or more substituents ortho to the phenolic function presented potent activities with a MIC value of 0.125 µg/mL, which is five times higher than that of INH. Compound 1a, synthesized from p-hydroxybenzaldehyde and INH, is the most potent derivative with a MIC value of 0.0125 µg/mL (0.05 µM), which is 2–4 times lower than that of INH (0.025 µg/mL, 0.18 µM). 2.4.3. M.tb H37Rv Growth Inhibition Assays of Nitrogen Heterocyclic Hydrazones (2–11) 2.4.3. M.tb H37Rv Growth Inhibition Assays of Nitrogen Heterocyclic Hydrazones (2–11) The MIC values of the series of hydrazones, bearing the INH moiety coupled with different N-heterocyclic aldehydes, were also determined (Table 8). The MIC values of the series of hydrazones, bearing the INH moiety coupled with different N-heterocyclic aldehydes, were also determined (Table 8). Table 8. MICs of Isoniazid-Nitrogen heterocyclic hydrazones against M.tb H37Rv. Table 8. MICs of Isoniazid-Nitrogen heterocyclic hydrazones against M.tb H37Rv. Compound MW (g/mol) MIC (µg/mL)/(µM) LogP Cpd MW (g/mol) MIC (µg/mL)/(µM) LogP 2 215.21 0.03/0.14 −1.00 7 265.27 0.015/0.056 0.24 3 229.24 0.03/0.13 −1.37 8 264.28 0.06/0.23 0.86 4 265.27 0.06/0.23 1.38 9 343.18 0.125/0.36 1.69 5 265.27 0.03/0.11 −0.52 10 264.28 0.06/0.23 0.52 6 278.31 0.25/0.90 0.49 11 309.28 0.25/0.81 1.39 INH 137.14 0.05/0.36 −0.64 All four imidazole and indazole derivatives (2–5) were 1.5–3 times more effective than isoniazid, while their InhA inhibition activities were much lower to inexistent with activities against M.tb growth, in the range of 0.11–0.23 µM. For indole derivatives, nitro substitution on the aromatic ring (compound 11) or methyl substitution on the indole ring (compound 6), compromised the anti-TB activity. While the bromo derivative 9 had the same activity as INH (0.36 µM), compounds 7, 8 and 10 presented better MIC values than INH. 2.4.2. Activity of Phenolic Isonicotinoyl Hydrazones (1a–d) against M.tb Cell Growth 2.4.2. Activity of Phenolic Isonicotinoyl Hydrazones (1a–d) against M.tb Cell Growth The determination of the minimal inhibitory concentration (MIC) was performed using M.tb H37Rv strain and INH as control (Table 7). Table 7. Phenolic isonicotinoyl hydrazones tested as inhibitory agents against M.tb growth (H37Rv strain). Compound MW (g/mol) MIC (µg/mL)/(µM) LogP Cpd MW (g/mol) MIC (µg/mL)/(µM) LogP 1a 241.25 0.0125/0.05 1.64 1c 271.27 0.125/0.46 1.51 1b 257.24 0.125/0.49 1.25 1d 301.30 0.125/0.41 1.38 INH 137.14 0.025/0.18 −0.64 Table 7. Phenolic isonicotinoyl hydrazones tested as inhibitory agents against M.tb growth (H37Rv strain). Molecules 2017, 22, 1457 Interestingly, the azaindole derivative 7 showed the highest anti-TB activity in this series and was found as active as the phenolic compound 1a (MIC = 0.015 µg/mL/0.056 µM). Finally, we can notice that all active compounds here presented, can show different lipophilic values as given by their LogP values, probably supporting the inference that there is no clear relationship between lipophilicity and in vitro activity as pointed also by others [25]. The resistance to the current tested drugs (first- and second-line) remains a very serious problem, mostly resulting from inhA and katG mutations [82] and culminates in the occurrence of M.tb multidrug-resistant (MDR) strains. Owing the good results obtained for the herein studied INH-derived hydrazones, we tested them against a M.tb multidrug-resistant clinical isolate (IC2; resistant to streptomycin, INH, rifampicin, ethambutol, pyrazinamide, ethionamide, and capreomicin) (Table 9). The indazole and indole derivatives were not active against IC2 isolate (MICs > 10 µg/mL), except for the nitro derivative 11. The imidazole containing derivatives 2 and 3 were poor active (MIC = 5–10 µg/mL). By comparing results for compounds 10 and 11, it appears that the nitro substituent improves the activity against IC2 clinical isolate. Interestingly, the phenolic derivatives 1a and 1b presented the best activities against the MDR isolate, with MIC of 2.5 µg/mL (10.36 µM) and 1 µg/mL (3.89 µM), respectively. 12 of 27 Molecules 2017, 22, 1457 Table 9. MIC of isoniazid derivatives against M.tb MDR isolate IC2. Table 9. MIC of isoniazid derivatives against M.tb MDR isolate IC2. Table 9. MIC of isoniazid derivatives against M.tb MDR isolate IC2. Compound MIC (µg/mL)/(µM) H37Rv IC2 1a 0.0125/0.05 2.5/10.36 1b 0.125/0.49 1/3.89 1c 0.125/0.46 >2.5/>9.22 1d 0.125/0.41 >2.5/>8.30 2 0.03/0.14 5/23.2 3 0.03/0.13 5–10/21.8–43.6 4 0.06/0.23 >10 5 0.03/0.11 >10 6 0.25/0.90 >10 7 0.015/0.056 >10 8 0.06/0.23 >10 9 0.125/0.36 >10 10 0.06/0.23 >10 11 0.25/0.81 5–10/18.9–37.8 INH 0.025/0.18 >2/>14.58 2.4.4. Cytotoxicity and Selectivity Index Determination 2.4.4. Cytotoxicity and Selectivity Index Determination Cytotoxicities of all compounds bearing the INH moiety were also evaluated on MRC5 human fibroblast cells. Almost all compounds tested presented LD50 values above 80 µM (Table 10), with the exception of 1b (LD50 = 36.3 µM). The LD50 evaluation is essential to determine the selectivity index (SI), which indicates the best candidates in terms of high biological activity against the target and low cytotoxicity. The SI presented in Table 10 are the ratio between LD50 and the in vitro MIC value against M.tb H37Rv previously obtained. Table 10. Cytotoxicity (LD50) and selectivity index (SI) for the most active hydrazones against H37Rv M.tb. Compound LD50 (µM) SI Compound LD50 (µM) SI 1a >80 >1600 5 >80 >727 1b 36.3 74 6 129 143 1c >80 >173 7 >80 >1429 1d >80 >195 8 >80 >364 2 >80 >571 9 >80 >222 3 >80 >615 10 71.4 310 4 >80 >364 11 156 193 INH - - Apart from compound 1b, due to its high toxicity, the phenolic hydrazones presented good selectivities higher than 170. A great result was obtained for 1a which has the lowest MIC value (0.0125 µg/mL), LD50 > 80 µM and the highest SI (>1600). The N-heterocyclic INH derivatives 2–11 presented good SI values, with the exception of 6 and 11, which possessed the highest MIC values. Compounds 4, 8, 9 and 10 conducted to comparable SI. Compound 10 must be considered (MIC = 0.06 µg/mL, LD50 = 71.4 µM and SI = 310), mainly due to its InhA inhibition of 78%. Great SI values closer to 600 are found for 2 and 3 but, nonetheless, some reservation must be taken due to the poor solubility of these molecules. Finally, the SI of compound 5 is higher than 727 and 7 is highlighted with MIC = 0.015 µg/mL and an SI higher than 1469. 2.4.5. In Search for the Molecular Target of Prepared Hydrazones in Mycobacteria 2.4.5. In Search for the Molecular Target of Prepared Hydrazones in Mycobacteria In order to confirm the enoylreductase InhA as a target of synthesized hydrazones, we analyzed the effect of selected compounds with the best MIC values and cytotoxicity scores on synthesis of 13 of 27 13 f 27 Molecules 2017, 22, 1457 mycolic acids in avirulent strain M.tb H37Ra. Tested hydrazones, specifically 1a, 3, 5, 7 and 10, as well as INH as control InhA inhibitor, were added to M.tb H37Ra culture when it reached early mid-log phase of growth and, after subsequent 24 h cultivation, 14C acetate was added as a metabolic tracer. TLC analysis of lipid fractions extracted from harvested 14C labeled cells revealed that, similar to INH, all of the tested hydrazones abolish the synthesis of trehalose monomycolates and trehalose dimycolates (Figure 6). mycolic acids in avirulent strain M.tb H37Ra. Tested hydrazones, specifically 1a, 3, 5, 7 and 10, as well as INH as control InhA inhibitor, were added to M.tb H37Ra culture when it reached early mid-log phase of growth and, after subsequent 24 h cultivation, 14C acetate was added as a metabolic tracer. TLC analysis of lipid fractions extracted from harvested 14C labeled cells revealed that, similar to INH, all of the tested hydrazones abolish the synthesis of trehalose monomycolates and trehalose dimycolates (Figure 6). mycolic acids in avirulent strain M.tb H37Ra. Tested hydrazones, specifically 1a, 3, 5, 7 and 10, as well as INH as control InhA inhibitor, were added to M.tb H37Ra culture when it reached early mid-log phase of growth and, after subsequent 24 h cultivation, 14C acetate was added as a metabolic tracer. TLC analysis of lipid fractions extracted from harvested 14C labeled cells revealed that, similar to INH, all of the tested hydrazones abolish the synthesis of trehalose monomycolates and trehalose dimycolates (Figure 6). Figure 6. TLC analysis of lipids extracted from 14C acetate labeled M.tb H37Ra cells treated with compounds 1a, 3, 5, 7 and 10, INH and DMSO as a control. Lipids were separated in chloroform:methanol:water (20:4:0.5) and detected by autoradiography (TDM: trehalose dimycolates; TMM: trehalose monomycolates; PE: phosphatidylethanolamine; CL: cardiolipin). Figure 6. TLC analysis of lipids extracted from 14C acetate labeled M.tb H37Ra cells treated with compounds 1a, 3, 5, 7 and 10, INH and DMSO as a control. 2.4.5. In Search for the Molecular Target of Prepared Hydrazones in Mycobacteria Lipids were separated in chloroform:methanol:water (20:4:0.5) and detected by autoradiography (TDM: trehalose dimycolates; TMM: trehalose monomycolates; PE: phosphatidylethanolamine; CL: cardiolipin). Figure 6. TLC analysis of lipids extracted from 14C acetate labeled M.tb H37Ra cells treated with compounds 1a, 3, 5, 7 and 10, INH and DMSO as a control. Lipids were separated in chloroform:methanol:water (20:4:0.5) and detected by autoradiography (TDM: trehalose dimycolates; TMM: trehalose monomycolates; PE: phosphatidylethanolamine; CL: cardiolipin). Figure 6. TLC analysis of lipids extracted from 14C acetate labeled M.tb H37Ra cells treated with compounds 1a, 3, 5, 7 and 10, INH and DMSO as a control. Lipids were separated in chloroform:methanol:water (20:4:0.5) and detected by autoradiography (TDM: trehalose dimycolates; TMM: trehalose monomycolates; PE: phosphatidylethanolamine; CL: cardiolipin). Figure 6. TLC analysis of lipids extracted from 14C acetate labeled M.tb H37Ra cells treated with compounds 1a, 3, 5, 7 and 10, INH and DMSO as a control. Lipids were separated in chloroform:methanol:water (20:4:0.5) and detected by autoradiography (TDM: trehalose dimycolates; TMM: trehalose monomycolates; PE: phosphatidylethanolamine; CL: cardiolipin). Figure 6. TLC analysis of lipids extracted from 14C acetate labeled M.tb H37Ra cells treated with compounds 1a, 3, 5, 7 and 10, INH and DMSO as a control. Lipids were separated in chloroform:methanol:water (20:4:0.5) and detected by autoradiography (TDM: trehalose dimycolates; TMM: trehalose monomycolates; PE: phosphatidylethanolamine; CL: cardiolipin) Analysis of fatty/mycolic acids isolated from whole 14C labeled cells proved that these compounds specifically inhibit synthesis of mycolic acids (Figure 7). Analysis of fatty/mycolic acids isolated from whole 14C labeled cells proved that these compounds specifically inhibit synthesis of mycolic acids (Figure 7). Analysis of fatty/mycolic acids isolated from whole 14C labeled cells proved that these compounds specifically inhibit synthesis of mycolic acids (Figure 7). Analysis of fatty/mycolic acids isolated from whole 14C labeled cells proved that these compounds specifically inhibit synthesis of mycolic acids (Figure 7). Analysis of fatty/mycolic acids isolated from whole 14C labeled cells proved that these compounds specifically inhibit synthesis of mycolic acids (Figure 7). Analysis of fatty/mycolic acids isolated from whole 14C labeled cells proved that these compounds specifically inhibit synthesis of mycolic acids (Figure 7). Figure 7. TLC analysis of methyl esters of fatty (FAME) and mycolic (MAME) acids isolated from 14C acetate labeled M.tb H37Ra cells treated with compounds 1a, 3, 5, 7 and 10, INH and DMSO as a control. 2.4.5. In Search for the Molecular Target of Prepared Hydrazones in Mycobacteria Different forms of methyl esters were separated in n-hexane:ethyl acetate (95:5; 3×) and detected by autoradiography. (, methoxy, and keto refer to forms of MAMEs). 0.1 0.5 0 5 0.1 0.5 0.1 0.5 0.1 0.5 0.1 0.5 g/mL 1a INH 3 5 7 10 FAME methoxy keto M A M E y y y ( g ) compounds specifically inhibit synthesis of mycolic acids (Figure 7). Figure 7. TLC analysis of methyl esters of fatty (FAME) and mycolic (MAME) acids isolated from 14C acetate labeled M.tb H37Ra cells treated with compounds 1a, 3, 5, 7 and 10, INH and DMSO as a control. Different forms of methyl esters were separated in n-hexane:ethyl acetate (95:5; 3×) and detected by autoradiography. (, methoxy, and keto refer to forms of MAMEs). 0.1 0.5 0 5 0.1 0.5 0.1 0.5 0.1 0.5 0.1 0.5 g/mL 1a INH 3 5 7 10 FAME methoxy keto M A M E Figure 7. TLC analysis of methyl esters of fatty (FAME) and mycolic (MAME) acids isolated from 14C acetate labeled M.tb H37Ra cells treated with compounds 1a, 3, 5, 7 and 10, INH and DMSO as a control. Different forms of methyl esters were separated in n-hexane:ethyl acetate (95:5; 3×) and detected by autoradiography. (α, methoxy, and keto refer to forms of MAMEs). Figure 7. TLC analysis of methyl esters of fatty (FAME) and mycolic (MAME) acids isolated from 14C acetate labeled M.tb H37Ra cells treated with compounds 1a, 3, 5, 7 and 10, INH and DMSO as a control. Different forms of methyl esters were separated in n-hexane:ethyl acetate (95:5; 3×) and detected by autoradiography. (, methoxy, and keto refer to forms of MAMEs). Figure 7. TLC analysis of methyl esters of fatty (FAME) and mycolic (MAME) acids isolated from 14C acetate labeled M.tb H37Ra cells treated with compounds 1a, 3, 5, 7 and 10, INH and DMSO as a control. Different forms of methyl esters were separated in n-hexane:ethyl acetate (95:5; 3×) and detected by autoradiography. (, methoxy, and keto refer to forms of MAMEs). Figure 7. TLC analysis of methyl esters of fatty (FAME) and mycolic (MAME) acids isolated from 14C acetate labeled M.tb H37Ra cells treated with compounds 1a, 3, 5, 7 and 10, INH and DMSO as a control. Different forms of methyl esters were separated in n-hexane:ethyl acetate (95:5; 3×) and detected by autoradiography. A series 3.1. Material ability to inhibit M.tb H37Rv strain growth, the most active being 1a and 7. Imidazole derivative 5 and indazole one 10 are also active against H37Rv with their nitro substituent. Compounds 1a and 1b were the most effective against both M.tb H37Rv strain and drug-resistant IC2 isolate. The mechanism of anti-mycobacterial activities of selected hydrazones with the best scores regarding the MICs and toxicities was confirmed to be through the cessation of mycolic acid synthesis due to InhA inhibition inside the mycobacterial cell. 4. Materials and Methods 4.1. Material All chemicals were obtained from Maybridge, TCI, Aldrich or Alfa Aesar, 97–99% and used without further purification. Nuclear magnetic resonance spectra (1H- and 13C-NMR) were recorded on Bruker AC 300, Avance-400 MHz and Avance-500 spectrometers with DMSO-d6 as solvent. Chemical shifts δ were expressed in parts per million (ppm) relative to TMS. Solvent residue signals were used for calibration of spectral data. Mass spectrometry (MS) data were obtained from the “Service Commun de Spectrométrie de masse” of the Plateforme Technique, Institut de Chimie de Toulouse (Toulouse France) MS were performed using a Waters Quadrupole Time of flight mass All chemicals were obtained from Maybridge, TCI, Aldrich or Alfa Aesar, 97–99% and used without further purification. Nuclear magnetic resonance spectra (1H- and 13C-NMR) were recorded on Bruker AC 300, Avance-400 MHz and Avance-500 spectrometers with DMSO-d6 as solvent. Chemical shifts δ were expressed in parts per million (ppm) relative to TMS. Solvent residue signals were used for calibration of spectral data. Mass spectrometry (MS) data were obtained from the “Service Commun de Spectrométrie de masse” of the Plateforme Technique, Institut de Chimie de Toulouse (Toulouse, France). MS were performed using a Waters Quadrupole Time-of-flight mass spectrometer XEVO G2-S QTof. The samples were dissolved in methanol and Electrospray ionization method was used. High-resolution mass spectra (HRMS) were recorded on a ThermoFinnigan MAT 95 XL spectrometer using electrospray ionization (ESI) methods. Melting points were measured using a Kofler heating bench system Heizbank Type WME (Wagner &Munz GmbH, Munich, Germany), with measuring accuracy of ±1 ◦C in the range of 50–260 ◦C. If the melting point was higher than 260 ◦C or if it could not be exactly determined because of an apparent degradation, the DSC analysis was employed. The analysis was performed in a ATG-DSC 111 (Sertaram). Molecules 2017, 22, 1457 Molecules 2017, 22, 1457 Molecules 2017, 22, 1457 Molecules 2017, 22, 1457 Next, we overproduced InhA protein in M.tb H37Ra and tested sensitivity of overproducer, as well as control strain carrying empty vector against synthesized hydrazones by drop dilution method. Clearly, this testing showed, that MICs of all of tested compounds against M.tb H37Ra pMV261-InhA are 5–10× higher comparing to control strain confirming InhA as molecular target of these inhibitors inside mycobacterial cells (Figure 8). e , e o e p o u e I A p o ei i a a e e e i i i y o o e p o u e , a well as control strain carrying empty vector against synthesized hydrazones by drop dilution method. Clearly, this testing showed, that MICs of all of tested compounds against M.tb H37Ra pMV261-InhA are 5–10× higher comparing to control strain confirming InhA as molecular target of these inhibitors inside mycobacterial cells (Figure 8). Figure 8. Determination of sensitivity of M.tb H37Ra pMV261 and M.tb H37Ra pMV261-InhA against 1a (Left panel) and 3, 5, 7 and 10 (Right panel) by drop dilution method. Figure 8. Determination of sensitivity of M.tb H37Ra pMV261 and M.tb H37Ra pMV261-InhA against 1a (Left panel) and 3, 5, 7 and 10 (Right panel) by drop dilution method. Figure 8. Determination of sensitivity of M.tb H37Ra pMV261 and M.tb H37Ra pMV261-InhA against 1a (Left panel) and 3, 5, 7 and 10 (Right panel) by drop dilution method. Figure 8. Determination of sensitivity of M.tb H37Ra pMV261 and M.tb H37Ra pMV261-InhA against 1a (Left panel) and 3, 5, 7 and 10 (Right panel) by drop dilution method. 3. Conclusions 3. Materials and Methods A series 3.1. Material 2.4.5. In Search for the Molecular Target of Prepared Hydrazones in Mycobacteria (α, methoxy, and keto refer to forms of MAMEs). 14 of 27 14 of 27 3.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis 4.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis The derivatives 1a–d were synthesized as previously described by us [38]. Compounds 1a–1d have also a CAS number: 1a (840-81-3); 1b (13838-18-1); 1c (149-17-7); 1d (315230-80-9). The derivatives 1a–d were synthesized as previously described by us [38]. Compounds 1a–1d have also a CAS number: 1a (840-81-3); 1b (13838-18-1); 1c (149-17-7); 1d (315230-80-9). The derivatives 1a–d were synthesized as previously described by us [38]. Compounds 1a–1d have also a CAS number: 1a (840-81-3); 1b (13838-18-1); 1c (149-17-7); 1d (315230-80-9). The derivatives 1a–d were synthesized as previously described by us [38]. Compounds 1a–1d have also a CAS number: 1a (840-81-3); 1b (13838-18-1); 1c (149-17-7); 1d (315230-80-9). 3.2.2. General Procedure for Isoniazid Nitrogen-Containing Heterocycles Derivatives 2–11 4.2.2. General Procedure for Isoniazid Nitrogen-Containing Heterocycles Derivatives 2–11 A mixture the solid reactants, INH (1 equivalent), the aldehyde (1 equivalent) and the catalyst (p-TSA, 0.5 equivalent) were placed in milling device and the reaction proceeded between 1 h–2 h, depending on the aldehyde. The Cryomill (Restch) was used for the screening of catalysts (milling started at the room temperature) at 25 Hz during 1 h. After the choice of the catalyst (p-TSA), all the reactions were carried out in the vibratory ball-mill Pulverisette 0 (Fritsch, Germany) equipped with a single stainless steel ball of 50 mm of diameter and 500 g, in a semi-spherical vessel of 9.5 cm of diameter. The plate vibrates with a frequency of 50 Hz and amplitude of 2.0 mm. The amounts of reactant powder were stoichiometric conditions for reactants totalizing 1 g + the amount of catalyst. The transformation was monitored by TLC. After the reaction time, the powder mixture was washed with a NaHCO3 solution to eliminate the catalyst and the powder was dried under vacuum. 1H-, 13C-NMR spectra and Mass Spectra for all new compounds are included in Supplementary Materials; NMR data show both conformers). NMR data reported below correspond to the major conformer. A mixture the solid reactants, INH (1 equivalent), the aldehyde (1 equivalent) and the catalyst (p-TSA, 0.5 equivalent) were placed in milling device and the reaction proceeded between 1 h–2 h, depending on the aldehyde. The Cryomill (Restch) was used for the screening of catalysts (milling started at the room temperature) at 25 Hz during 1 h. A series 3.1. Material The temperature programming was from 20 ◦C to 200 or 260 ◦C according to the sample with a constant rate of 5 ◦C/min under nitrogen atmosphere. Fourier Transformed Infrared Spectroscopy (FTIR) analysis for identification was performed using KB ll t Th Ni l t 5700 t t (Th Ni l t M di WI USA) Th i “Service Commun de Spectrométrie de masse” of the Plateforme Technique, Institut de Chimie de Toulouse (Toulouse, France). MS were performed using a Waters Quadrupole Time-of-flight mass spectrometer XEVO G2-S QTof. The samples were dissolved in methanol and Electrospray ionization Fourier Transformed Infrared Spectroscopy (FTIR) analysis for identification was performed using KBr pellets on a Thermo Nicolet 5700 spectrometer (Thermo-Nicolet, Madison, WI, USA). The main peaks/bands were identified, especially the –C=N– that is attributed to the hydrazone. FTIR studies “Service Commun de Spectrométrie de masse” of the Plateforme Technique, Institut de Chimie de Toulouse (Toulouse, France). MS were performed using a Waters Quadrupole Time-of-flight mass spectrometer XEVO G2-S QTof. The samples were dissolved in methanol and Electrospray ionization Fourier Transformed Infrared Spectroscopy (FTIR) analysis for identification was performed using KBr pellets on a Thermo Nicolet 5700 spectrometer (Thermo-Nicolet, Madison, WI, USA). The main peaks/bands were identified, especially the –C=N– that is attributed to the hydrazone. FTIR studies 15 of 27 formed A). The 15 of 27 formed A). The Molecules 2017, 22, 1457 Fourier Transfo using KBr pellets on 22, 1457 with the solid hydrazines as function of temperature were recorded in IN10MX Thermo Scientific FTIR microscope equipped with THMS600 (Linkam Scientific Instruments, Tadworth, Surrey, UK) heating and freezing stage. studies with the solid hydrazines as function of temperature were recorded in IN10MX Thermo Scientific FTIR microscope equipped with THMS600 (Linkam Scientific Instruments, Tadworth, Surrey, UK) heating and freezing stage. 2C, C2,6), 134,36 (1C, C5′), 143.08 (2C, C3,5). KBr) ν cm−1: 3193.59 (N-H), 3038.08 (C-Har), 1648.96 (C=O), 1626.02 (C=N-N), 1596.86 1551.04 (Car N), 1506.46 (C=N). OH 182 μM 25 °C): λ = 309 nm ε = 5495 05 dm3·mol−1·cm−1 (very poorly soluble) g g UV-vis spectroscopy was performed using a HP (Hewlett Packard, Palo Alto, CA, USA) 8452A diode array spectrophotometer from 200 to 400 nm, with ethanol as a solvent at 20 ◦C and using quartz cells. A series 3.1. Material The molar absorptivity was determined for the wavelength with the highest absorbance through Lambert–Beer’s law with the molar absorptivity ε in (dm3·mol−1·cm−1) expressed for the λmax of the molecule. UV-vis spectroscopy was performed using a HP (Hewlett Packard, Palo Alto, CA, USA) 8452A diode array spectrophotometer from 200 to 400 nm, with ethanol as a solvent at 20 °C and using quartz cells. The molar absorptivity was determined for the wavelength with the highest absorbance through Lambert–Beer’s law with the molar absorptivity ε in (dm3·mol−1·cm−1) expressed for the λmax of the molecule. OH, 182 μM, 25 C): λ = 309 nm, ε = 5495.05 dm3·mol 1·cm 1 (very poorly soluble). , TOF, MeOH) m/z: 238.0708 [M + Na+]; 216.0887 [M + H+]. (ES, TOF) m/z: M + H+ calc. for C10H10N5O: 216.0885. Found: 216.0887. ethyl-1H-imidazol-5-yl)methylene)isonicotinohydrazide (3) 3.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis 4.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis After the choice of the catalyst (p-TSA), all the reactions were carried out in the vibratory ball-mill Pulverisette 0 (Fritsch, Germany) equipped with a single stainless steel ball of 50 mm of diameter and 500 g, in a semi-spherical vessel of 9.5 cm of diameter. The plate vibrates with a frequency of 50 Hz and amplitude of 2.0 mm. The amounts of reactant powder were stoichiometric conditions for reactants totalizing 1 g + the amount of catalyst. The transformation was monitored by TLC. After the reaction time, the powder mixture was washed with a NaHCO3 solution to eliminate the catalyst and the powder was dried under vacuum. 1H-, 13C-NMR spectra and Mass Spectra for all new compounds are included in Supplementary Materials; NMR data show both conformers). NMR data reported below correspond to the major conformer. 9 °C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). R (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.53 H-C=N), 9.11 (s, 1H, H3′), 9.14 (dd, J = 5.5, 1.8 Hz, 2H, H3,5), 15.98 (br, 2H, N-H). R (75 MHz, DMSO) δ ppm: 9.38 (1C, CH3), 123.60 (1C, C1′) 125.38 (2C, C2,6), 131.78 (1C, C5′), C, C=N), 142.84 (1C, C3′), 144.03 (2C, C3,5), 147.78 (1C, C1), 159.52 (1C, C=O). KBr) ν cm−1: 3194.75 (N-H), 3097.19 (Car-H), 1660.58 (C=O), 1621.45 (C=N-N), 1602.24 , 1551.49 (Car N). OH, 161.58 μM, 25 °C): λ = 316 nm, ε = 5551.73 dm3·mol−1·cm−1 (very poorly soluble). TOF, MeOH) m/z: 252.0866 [M + Na+]; 230.1049 [M + H+]. ES, TOF) m/z: [M + H+] calc. for C11H12N5O: 230.1042. Found: 230.1049. -dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) (E)-N′-((1H-imidazol-4-yl)methylene)isonicotinohydrazide (2) (E)-N′-((1H-imidazol-4-yl)methylene)isonicotinohydrazide (2) (E)-N′-((1H-imidazol-4-yl)methylene)isonicotinohydrazide (2) (E) N′ ((1H imidazol 4 yl)methylene)isonicotinohydrazide (2) m.p.: 296.7 °C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). 1H NMR (300 MH DMSO d ) δ 8 15 (d J 1 4 H 1H H ) 8 36 (dd J 6 6 1 5 H 2H H ) .: 296.7 ◦C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 0 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H, m.p.: 296.7 °C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v H NMR ( MH DMSO d ) δ 8 1 (d J 1 m.p.: 296.7 ◦C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). 2.5 C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 3.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis 4.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis R (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H 1H-NMR (300 MHz, DMSO-d6) δ ppm: 8.15 (d, J = 1.4 Hz, 1H, H5′), 8.36 (dd, J = 6.6, 1.5 Hz, 2H, H2,6), 8.52 (s, 1H, H-C=N), 9.10 (dd, J = 6.6, 1.5 Hz, 2H, H3,5), 9.21 (d, J = 1.3 Hz, 1H, H3′), 15.67 (s, 2H, N-H). 13C-NMR (75 MHz, DMSO) δ ppm: 122.02 (1C, C5′), 125.10 (2C, C2,6), 128.25 (1C, C1′), 138.37 (1C, C=N), 136,80 (1C, C3′), 144.77 (2C, C3,5), 146.91 (1C, C1), 160.14 (1C, C=O). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 8.15 (d, J = 1.4 Hz, 1H, H5′), 8.36 (dd, J = 6.6, 1.5 Hz, 2H, H2,6), 8.52 (s, 1H, H-C=N), 9.10 (dd, J = 6.6, 1.5 Hz, 2H, H3,5), 9.21 (d, J = 1.3 Hz, 1H, H3′), 15.67 (s, 2H, N-H). 13C-NMR (75 MHz, DMSO) δ ppm: 122.02 (1C, C5′), 125.10 (2C, C2,6), 128.25 (1C, C1′), 138.37 (1C, C=N), 136,80 (1C, C3′), 144.77 (2C, C3,5), 146.91 (1C, C1), 160.14 (1C, C=O). 126.78 (2C, C2,6), 134,36 (1C, C5′), 143.08 (2C, C3,5). R (300 MHz, DMSO d6) δ ppm: 7.63 (d, J 8.7 Hz, 1H, H3), 7.84 (dd, J 4.4, 1.6 Hz, 2H, 0 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, =N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). R (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, 19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, 50.76 (2C, C3,5), 161.87 (1C, C=O). FTIR (KBr) ν cm−1: 3193.59 (N-H), 3038.08 (C-Har), 1648.96 (C=O), 1626.02 (C=N-N), 1596.86 (C=Car), 1551.04 (Car KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.84 1549.40 (Car N). N), 1506.46 (C=N). ( ) ( ) OH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. TOF MeOH) m/z: 266 1046 [M + H+] ) ( ) UV (EtOH, 182 µM, 25 ◦C): λ = 309 nm, ε = 5495.05 dm3·mol−1·cm−1 (very poorly soluble). MS (ES TOF M OH) / 238 0708 [M N +] 216 0887 [M H+] (( ) OH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. TOF, MeOH) m/z: 266.1046 [M + H+]. 3.2. Chemistry 4.2. Chemistry 3.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis 4.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) FTIR (KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.84 13C-NMR (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, C9′), 124.19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). FTIR (KB ) 1 3188 96 (N H) 3027 37 (C H) 1652 (C O) 1622 47 (C N N) 1607 84 ) ( 3,5) ( ) ( ind) 13C-NMR (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, C9′), 124.19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N H), 13.31 (s, 1H, N Hind). R (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, 19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, 50.76 (2C, C3,5), 161.87 (1C, C=O). C9′), 124.19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). FTIR (KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.84 13C-NMR (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, C9′), 124.19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). FTIR (KB ) 1 3188 96 (N H) 3027 37 (C H) 1652 (C O) 1622 47 (C N N) 1607 84 , 13C-NMR (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, C9′), 124.19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). ), ( , , , ), ( , , ), ( , , ) R (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, 19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, 50.76 (2C, C3,5), 161.87 (1C, C=O). 3.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis 4.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis 13C-NMR (75 MHz, DMSO) δ ppm: 9.38 (1C, CH3), 123.60 (1C, C1′) 125.38 (2C, C2,6), 131.78 (1C, C5′), 138.44 (1C, C=N), 142.84 (1C, C3′), 144.03 (2C, C3,5), 147.78 (1C, C1), 159.52 (1C, C=O). FTIR (KBr) ν cm−1: 3194.75 (N-H), 3097.19 (Car-H), 1660.58 (C=O), 1621.45 (C=N-N), 1602.24 9 °C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). R (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.53 H-C=N), 9.11 (s, 1H, H3′), 9.14 (dd, J = 5.5, 1.8 Hz, 2H, H3,5), 15.98 (br, 2H, N-H). R (75 MHz, DMSO) δ ppm: 9.38 (1C, CH3), 123.60 (1C, C1′) 125.38 (2C, C2,6), 131.78 (1C, C5′), 1C, C=N), 142.84 (1C, C3′), 144.03 (2C, C3,5), 147.78 (1C, C1), 159.52 (1C, C=O). KBr) ν cm−1: 3194.75 (N-H), 3097.19 (Car-H), 1660.58 (C=O), 1621.45 (C=N-N), 1602.24 13C-NMR (75 MHz, DMSO) δ ppm: 9.38 (1C, CH3), 123.60 (1C, C1′) 125.38 (2C, C2,6), 131.78 (1C, C5′), 138.44 (1C, C=N), 142.84 (1C, C3′), 144.03 (2C, C3,5), 147.78 (1C, C1), 159.52 (1C, C=O). FTIR (KB ) 3194 75 (N H) 3097 19 (C H) 1660 58 (C O) 1621 45 (C N N) 1602 24 13C-NMR (75 MHz, DMSO) δ ppm: 9.38 (1C, CH3), 123.60 (1C, C1′) 125.38 (2C, C2,6), 131.78 (1C, C5′), 138.44 (1C, C=N), 142.84 (1C, C3′), 144.03 (2C, C3,5), 147.78 (1C, C1), 159.52 (1C, C=O). pp ( ) ( ) ( ) ( 19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, 50.76 (2C, C3,5), 161.87 (1C, C=O). (s, 1H, H-C=N), 9.11 (s, 1H, H3′), 9.14 (dd, J = 5.5, 1.8 Hz, 2H, H3,5), 15.98 (br, 2H, N-H). 13C-NMR (75 MHz, DMSO) δ ppm: 9.38 (1C, CH3), 123.60 (1C, C1′) 125.38 (2C, C2,6), 131.78 (1C, C5′), 138 44 (1C C N) 142 84 (1C C ) 144 03 (2C C ) 147 78 (1C C ) 159 52 (1C C O) pp ( ) ( J ) H-C=N), 9.11 (s, 1H, H3′), 9.14 (dd, J = 5.5, 1.8 Hz, 2H, H3,5), 15.98 (br, 2H, N-H). R (75 MHz, DMSO) δ ppm: 9.38 (1C, CH3), 123.60 (1C, C1′) 125.38 (2C, C2,6), 131.78 (1C, C5′), FTIR (KBr) ν cm−1: 3194.75 (N-H), 3097.19 (Car-H), 1660.58 (C=O), 1621.45 (C=N-N), 1602.24 (Car=Car), 1551.49 (Car N). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) y ) y ) y ( ) yl)methylene)isonicotinohydrazide (4) p ( ) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H m.p.: 302.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H NMR (300 MH DMSO d ) δ 7 63 (d J 8 7 H 1H H ) 7 84 (dd J 4 4 1 6 H 2H .: 302.5 ◦C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). p ( ) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′) m.p.: 302.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H NMR (300 MH DMSO d ) δ 7 63 (d J 8 7 H 1H H ) m.p.: 302.5 ◦C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). .5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). p 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8. m.p.: 302.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). H NMR (300 MH DMSO d ) δ 7 63 (d J 8 m.p.: 302.5 ◦C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 2.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). H2,6), 7.90 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, 1H, H-C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). 13C-NMR (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H, H2,6), 7.90 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, 1H, H-C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). 13C NMR (75 MH DMSO) δ 111 39 (1C C ) 121 98 (2C C ) 122 73 (1C C ) 123 35 (1C 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H, H2,6), 7.90 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, 1H, H-C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). 3.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis 4.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis 3 , FTIR (KBr) ν cm−1: 3194.75 (N-H), 3097.19 (Car-H), 1660.58 (C=O), 1621.45 (C=N-N), 1602.24 (Car=Car), 1551.49 (Car ( , ), ( , ) KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.84 , 1549.40 (Car N). N). 138.44 (1C, C=N), 142.84 (1C, C3′), 144.03 (2C, C3,5), 147.78 (1C, C1), 159.52 (1C, C=O). FTIR (KBr) ν cm−1: 3194.75 (N-H), 3097.19 (Car-H), 1660.58 (C=O), 1621.45 (C=N-N), 1602.24 (C C ) 1551 49 (C N) , pp ( ) ( ) ( ) ( ) 1C, C=N), 142.84 (1C, C3′), 144.03 (2C, C3,5), 147.78 (1C, C1), 159.52 (1C, C=O). KBr) ν cm−1: 3194.75 (N-H), 3097.19 (Car-H), 1660.58 (C=O), 1621.45 (C=N-N), 1602.24 UV (EtOH, 161.58 μM, 25 °C): λ = 316 nm, ε = 5551.73 dm3·mol−1·cm−1 (very poorly soluble). MS (ES, TOF, MeOH) m/z: 252.0866 [M + Na+]; 230.1049 [M + H+]. HRMS (ES TOF) m/z: [M + H+] calc for C11H12N5O: 230 1042 Found: 230 1049 OH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. , TOF, MeOH) m/z: 266.1046 [M + H+]. UV (EtOH, 161.58 µM, 25 ◦C): λ = 316 nm, ε = 5551.73 dm3·mol−1·cm−1 (very poorly soluble). MS (ES, TOF, MeOH) m/z: 252.0866 [M + Na+]; 230.1049 [M + H+]. (Car=Car), 1551.49 (Car N). UV (EtOH, 161.58 μM, 25 °C): λ = 316 nm, ε = 5551.73 dm3·mol−1·cm−1 (very poorly soluble). MS (ES, TOF, MeOH) m/z: 252 0866 [M + Na+]; 230 1049 [M + H+] , 1551.49 (Car N). OH, 161.58 μM, 25 °C): λ = 316 nm, ε = 5551.73 dm3·mol−1·cm−1 (very poorly soluble). HRMS (ES, TOF) m/z: [M + H+] calc. for C11H12N5O: 230.1042. Found: 230.1049. ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1046. HRMS (ES, TOF) m/z: [M + H+] calc. for C11H12N5O: 230.1042. Found: 230.1049. MS (ES, TOF, MeOH) m/z: 252.0866 [M + Na+]; 230.1049 [M + H+]. HRMS (ES, TOF) m/z: [M + H+] calc. for C11H12N5O: 230.1042. Found: 230.1049. TOF, MeOH) m/z: 252.0866 [M + Na+]; 230.1049 [M + H+]. 3.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis 4.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis ES TOF) / [M + H+] al fo C H N O 230 1042 Fou d 230 1049 (E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) (E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) (E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) , [ ] dih d 1H i d l 5 l) th l )i i ti h d id (4) (E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) (E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) (E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) 3.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis 4.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis R (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, m.p.: 299 °C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.53 ( 1H H C N) 11 ( 1H H ) 14 (dd J 1 H H H ) 1 (b H N H) 9 °C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). R (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.53 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.53 (s, 1H, H-C=N), 9.11 (s, 1H, H3′), 9.14 (dd, J = 5.5, 1.8 Hz, 2H, H3,5), 15.98 (br, 2H, N-H). 13C-NMR (75 MHz, DMSO) δ ppm: 9.38 (1C, CH3), 123.60 (1C, C1′) 125.38 (2C, C2,6), 131.78 (1C, C5′), 138.44 (1C, C=N), 142.84 (1C, C3′), 144.03 (2C, C3,5), 147.78 (1C, C1), 159.52 (1C, C=O). FTIR (KBr) ν cm−1: 3194.75 (N-H), 3097.19 (Car-H), 1660.58 (C=O), 1621.45 (C=N-N), 1602.24 (Car=Car), 1551.49 (Car N). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.53 (s, 1H, H-C=N), 9.11 (s, 1H, H3′), 9.14 (dd, J = 5.5, 1.8 Hz, 2H, H3,5), 15.98 (br, 2H, N-H). 13C-NMR (75 MHz, DMSO) δ ppm: 9.38 (1C, CH3), 123.60 (1C, C1′) 125.38 (2C, C2,6), 131.78 (1C, C5′), 138.44 (1C, C=N), 142.84 (1C, C3′), 144.03 (2C, C3,5), 147.78 (1C, C1), 159.52 (1C, C=O). FTIR (KBr) ν cm−1: 3194.75 (N-H), 3097.19 (Car-H), 1660.58 (C=O), 1621.45 (C=N-N), 1602.24 (Car=Car), 1551.49 (Car C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). R (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, .19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, 50.76 (2C, C3,5), 161.87 (1C, C=O). KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.84 , 1549.40 (Car N). N). m.p.: 299 C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.53 (s, 1H, H-C=N), 9.11 (s, 1H, H3′), 9.14 (dd, J = 5.5, 1.8 Hz, 2H, H3,5), 15.98 (br, 2H, N-H). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) / / ( / / ) R (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H, 0 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, =N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). H2,6), 7.90 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, 1H, H-C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). 13C-NMR (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H, H2,6), 7.90 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, 1H, H-C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). C NMR ( MH DMSO) δ 111 3 (1C C ) 1 1 ( C C ) 1 3 (1C C ) 1 3 3 (1C 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H, H2,6), 7.90 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, 1H, H-C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). ( ) R (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H, 0 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, =N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). C9′), 124.19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) C9′), 124.19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). FTIR (KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.84 13C-NMR (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, C9′), 124.19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). FTIR (KB ) 1 3188 96 (N H) 3027 37 (C H) 1652 (C O) 1622 47 (C N N) 1607 84 , 13C-NMR (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, C9′), 124.19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). ), ( , , , ), ( , , ), ( , , ) R (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, 19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, 50.76 (2C, C3,5), 161.87 (1C, C=O). (Car=Car), 1549.40 (Car N). UV (EtOH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. MS (ES TOF M OH) / 266 1046 [M H ] FTIR (KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.84 (Car=Car), 1549.40 (Car N). UV (EtOH 38 37 μM 25 °C): λ = 234 nm ε = 22 666 92 dm3·mol−1·cm−1 , FTIR (KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.84 (Car=Car), 1549.40 (Car ( , ), ( , ) KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.84 , 1549.40 (Car N). N). MS (ES, TOF, MeOH) m/z: 266.1046 [M + H+]. HRMS (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1046. UV (EtOH, 38.37 μM, 25 C): λ = 234 nm, ε = 22,666.92 dm3·mol 1·cm 1. MS (ES, TOF, MeOH) m/z: 266.1046 [M + H+]. HRMS (ES TOF) m/z: [M + H+] calc for C14H12N5O: 266 1042 Found: 266 1046 OH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. , TOF, MeOH) m/z: 266.1046 [M + H+]. UV (EtOH, 38.37 µM, 25 ◦C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. 3.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis 4.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis R (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H 0 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), / / m.p.: 299 °C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v m.p.: 299 ◦C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). R (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H 0 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 299 °C (d ) R 0 1 E OA /M OH (4 1 / 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.53 (s, 1H, H-C=N), 9.11 (s, 1H, H3′), 9.14 (dd, J = 5.5, 1.8 Hz, 2H, H3,5), 15.98 (br, 2H, N-H). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.53 (s, 1H, H-C=N), 9.11 (s, 1H, H3′), 9.14 (dd, J = 5.5, 1.8 Hz, 2H, H3,5), 15.98 (br, 2H, N-H). ( , J , , , ), ( , , ), ( , J , , ), ( , =N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). R (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, m.p.: 299 °C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.53 dd b 9 °C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). R (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.53 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.53 (s, 1H, H-C=N), 9.11 (s, 1H, H3′), 9.14 (dd, J = 5.5, 1.8 Hz, 2H, H3,5), 15.98 (br, 2H, N-H). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.53 (s, 1H, H-C=N), 9.11 (s, 1H, H3′), 9.14 (dd, J = 5.5, 1.8 Hz, 2H, H3,5), 15.98 (br, 2H, N-H). ( , J , , , ), ( , , ), ( , J , , ), ( , =N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). 3.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis 4.2.1. General Procedure for Phenolic Isonicotinoyl Hydrazones Synthesis ) ( ) UV (EtOH, 182 µM, 25 ◦C): λ = 309 nm, ε = 5495.05 dm3·mol−1·cm−1 ( MS (ES, TOF, MeOH) m/z: 238.0708 [M + Na+]; 216.0887 [M + H+]. OH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. TOF, MeOH) m/z: 266.1046 [M + H+]. (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1046. UV (EtOH, 182 µM, 25 ◦C): λ = 309 nm, ε = 5495.05 dm3·mol−1·cm−1 (very poorly so MS (ES, TOF, MeOH) m/z: 238.0708 [M + Na+]; 216.0887 [M + H+]. HRMS (ES, TOF) m/z: M + H+ calc. for C10H10N5O: 216.0885. Found: 216.0887. (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1046. HRMS (ES, TOF) m/z: M + H+ calc. for C10H10N5O: 216.0885. Found: 216.0887. 16 of 27 16 of 27 Molecules 2017, 22, 1457 MS (ES, TOF, (ES, TOF) m/z: [M + H UV (EtOH, 182 MS (ES TOF M , 1551.04 (Car N), OH, 182 μM, 25 °C): λ (E)-N′-((4-methyl-1H-imidazol-5-yl)methylene)isonicotinohydrazide (3) (E)-N′-((4-methyl-1H-imidazol-5-yl)methylene)isonicotinohydrazide (3) y y y y HRMS (ES, TOF) m/z: M + H+ calc. for C10H10N5O: 216.0885. Found: 2 , , [ ]; [ ] (ES, TOF) m/z: M + H+ calc. for C10H10N5O: 216.0885. Found: 216.0887. (E)-N′-((4-methyl-1H-imidazol-5-yl)methylene)isonicotinohydrazide (3) (E)-N′-((4-methyl-1H-imidazol-5-yl)methylene)isonicotinohydrazide (3) HRMS (ES, TOF) m/z: M + H+ calc. for C10H10N5O: 216.0885. Found: 2 , , [ ] [ ] (ES, TOF) m/z: M + H+ calc. for C10H10N5O: 216.0885. Found: 216.0887. E)-N′-((4-methyl-1H-imidazol-5-yl)methylene)isonicotinohydrazide (3) E)-N′-((4-methyl-1H-imidazol-5-yl)methylene)isonicotinohydrazide (3) HRMS (ES, TOF) m/z: M + H+ calc. for C10H10N5O: 216.0885. Found: 2 [ ] [ ] S, TOF) m/z: M + H+ calc. for C10H10N5O: 216.0885. Found: 216.0887. eOH (5:5:3 v/v/v). y y y hylene)isonicotinohydrazide (3) 5:5:3 m.p.: 299 °C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). m.p.: 299 ◦C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). R (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H, 0 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, 299 °C (d ) R 0 1 E OA /M OH (4 1 / ) m.p.: 299 °C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v m.p.: 299 ◦C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) Rf: 0.55 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H-NMR (300 MHz DMSO-d6) δ ppm: 2 54 (s 3H CH3) 7 12 (ddt J = 24 4 9 3 1 9 1 9 Hz 2H m.p.: 281.1 ◦C. Rf: 0.55 PE/EtOAc/MeOH (5:5:3 v/v/v). 1 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.54 (s, 3H, C H5′, H6′), 7.35 (tt, J = 2.4, 1.7, 0.9, 0.8 Hz, 1H, H4′), 7.85 m.p.: 281.1 °C. Rf: 0.55 PE/EtOAc/MeOH (5:5:3 v/v/v) 1H NMR (300 MH DMSO d ) δ 2 54 ( 3H C m.p.: 281.1 ◦C. Rf: 0.55 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.54 (s, 3H, C H5′, H6′), 7.35 (tt, J = 2.4, 1.7, 0.9, 0.8 Hz, 1H, H4′), 7.85 m.p.: 281.1 °C. Rf: 0.55 PE/EtOAc/MeOH (5:5:3 v/v/v) 1H NMR (300 MH DMSO d ) δ 2 54 ( 3H C m.p.: 281.1 ◦C. Rf: 0.55 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.54 (s, 3H, C H5′ H6′) 7 35 (tt J = 2 4 1 7 0 9 0 8 Hz 1H H4′) 7 85 m.p.: 281.1 °C. Rf: 0.55 PE/EtOAc/MeOH (5:5:3 v/v/v) 1H NMR (300 MH DMSO d ) δ 2 54 ( 3H C m.p.: 281.1 ◦C. Rf: 0.55 PE/EtOAc/MeOH (5:5:3 v/v/v). H5, H6), 7.35 (tt, J 2.4, 1.7, 0.9, 0.8 Hz, 1H, H4), 7.85 (dd, J 4.5, 1.8 Hz, 2H, H2,6), 8.16 8.32 (m, 1H, H7′), 8.71 (s, 1H, H-C=N), 8.78 (dd, J = 4.4, 1.6 Hz, 2H, H3,5), 11.55 (d, J = 7.4 Hz, 1H, N-H), 11.67 (s, 1H, N-Hind). 13C-NMR (75 MHz, DMSO) δ ppm: 11.97 (1C, CH3), 107.84 (1C, C1′), 111.34 (1C, C4′), 120.82 (1C, C7′), 121 63(1C C5′) 121 87 (2C C2 6) 122 34 (1C C6′) 125 85 (1C C9′) 136 19 (1C C8′) 141 05 (1C C2′) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.54 (s, 3H, CH3), 7.12 (ddt, J = 24.4, 9.3, 1.9, 1.9 Hz, 2H, H5′, H6′), 7.35 (tt, J = 2.4, 1.7, 0.9, 0.8 Hz, 1H, H4′), 7.85 (dd, J = 4.5, 1.8 Hz, 2H, H2,6), 8.16–8.32 (m, 1H, H7′), 8.71 (s, 1H, H-C=N), 8.78 (dd, J = 4.4, 1.6 Hz, 2H, H3,5), 11.55 (d, J = 7.4 Hz, 1H, N-H), 11.67 (s, 1H, N-Hind). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) 13C NMR (75 MH DMSO) δ 110 75 (1C C ) 119 03 (1C C ) 121 51 (2C C ) 122 01 (1C C ) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.61 (dd, J = 8.5, 1.3 Hz, 1H, H7′), 7.84 (m, 4H, H2,6, H2′, H6′), 8.13 (d, J = 1.3 Hz, 1H, H5′), 8.60 (s, 1H, H-C=N), 8.80 (br, 2H, H3,5), 12.12 (s, 1H, N-H), 13.28 (s, 1H, N-Hind). / / ( / / ) R (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H, 90 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). m.p.: 295.2 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.61 (dd, J = 8.5, 1.3 Hz, 1H, H7′), 7.84 (m, 4H, H2,6, H2′, H6′), 8.13 (d, J = 1.3 Hz, 1H, H5′), 8.60 (s, 1H, H-C=N), 8.80 (br, 2H, H3,5), 12.12 (s, 1H, N-H), 13.28 13C-NMR (75 MHz, DMSO) δ ppm: 110.75 (1C, C2′), 119.03 (1C, C7′), 121.51 (2C, C2,6), 122.01 (1C, C6′), 124.39 (1C, C8′), 132.43 (1C, C1′), 134.21 (1C, C5′), 140.33 (1C, C1), 140.95 (1C, C9′), 150.03 (1C, C=N), 150.79 (2C, C3,5), 162.08 (1C, C=O). FTIR (KB ) 1 3193 59 (N H) 3038 08 (C H ) 1648 96 (C O) 1626 02 (C N N) 1596 86 13C-NMR (75 MHz, DMSO) δ ppm: 110.75 (1C, C2′), 119.03 (1C, C7′), 121.51 (2C, C2,6), 122.01 (1C, C6′), 124.39 (1C, C8′), 132.43 (1C, C1′), 134.21 (1C, C5′), 140.33 (1C, C1), 140.95 (1C, C9′), 150.03 (1C, C=N), 150.79 (2C, C3,5), 162.08 (1C, C=O). ), ( , , ), ( , , ), ( , , ) R (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, 19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, 50.76 (2C, C3,5), 161.87 (1C, C=O). (s, 1H, N-Hind). 13C-NMR (75 MHz, DMSO) δ ppm: 110.75 (1C, C2′), 119.03 (1C, C7′), 121.51 (2C, C2,6), 122.01 (1C, C6′), 124.39 (1C, C8′), 132.43 (1C, C1′), 134.21 (1C, C5′), 140.33 (1C, C1), 140.95 (1C, C9′), 150.03 (1C, C=N), m.p.: 299 °C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) FTIR (KBr) ν cm−1: 3385.07 (N-H), 3209.03 (N-H), 3049.08 (Car-H), 1655.09 (C=O), 1626.02 (C=N- N), 1599.50 (C=Car), 1550.60 (Car N), 1506.46 (C=N). UV (EtOH, 57.29 μM, 25 °C): λ = 224 nm, ε = 21,909.58 dm3·mol−1·cm−1. 141.56 (1C, C1), 146.10 (1C, C=N), 150.69 (2C, C3,5), 161.00 (1C, C=O). FTIR (KBr) ν cm−1: 3385.07 (N-H), 3209.03 (N-H), 3049.08 (Car-H), 1655.09 (C=O), 1626.02 (C=N-N), 1599.50 (C=Car), 1550.60 (Car C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). FTIR (KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.8 (Car=Car), 1549.40 (Car N). UV (EtOH 38 37 M 25 °C) λ 234 22 666 92 d 3 ol 1 1 N), 1506.46 (C=N). UV (EtOH 57 29 M 25 ◦C) λ 224 21 909 58 d 3 l 1 1 N), 1599.50 (C Car), 1550.60 (Car N), 1506.46 (C N). UV (EtOH, 57.29 μM, 25 °C): λ = 224 nm, ε = 21,909.58 dm3·mol−1·cm−1. MS (ES, TOF, MeOH) m/z: 279.1246 [M + H+]. FTIR (KBr) ν cm−1: 3385.07 (N-H), 3209.03 (N-H), 3049.08 (Car-H), 1655.09 (C=O), 1626.02 (C=N- N), 1599.50 (C=Car), 1550.60 (Car N), 1506.46 (C=N). UV (EtOH 57 29 μM 25 °C): λ = 224 nm ε = 21 909 58 dm3 mol−1 cm−1 , FTIR (KBr) ν cm−1: 3385.07 (N-H), 3209.03 (N-H), 3049.08 (Car-H), 1655.09 (C=O), 1626.02 (C=N-N), 1599.50 (C=Car), 1550.60 (Car ) ( ) ( ) FTIR (KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.8 (Car=Car), 1549.40 (Car N). N), 1506.46 (C=N). ( , , ) [ ] HRMS (ES, TOF) m/z: [M + H+] calc. for C16H15N4O: 279.1246. Found: UV (EtOH, 57.29 μM, 25 C): λ = 224 nm, ε = 21,909.58 dm3·mol 1·cm 1 MS (ES TOF MeOH) m/z: 279 1246 [M + H+] ( ) ( ) UV (EtOH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm UV (EtOH, 57.29 µM, 25 ◦C): λ = 224 nm, ε = 21,909.58 dm3·mol−1·cm−1. , , [ ] HRMS (ES, TOF) m/z: [M + H+] calc. for C16H15N4O: 279.1246. Found: 279.12 UV (EtOH, 57.29 μM, 25 C): λ = 224 nm, ε = 21,909.58 dm mol cm . MS (ES TOF MeOH) m/z: 279 1246 [M + H+] UV (EtOH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. UV (EtOH, 57.29 µM, 25 ◦C): λ = 224 nm, ε = 21,909.58 dm3·mol−1·cm−1. E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.54 (s, 3H, CH3), 7.12 (ddt, J = 24.4, 9.3, 1.9, 1.9 Hz, 2H, H5′, H6′), 7.35 (tt, J = 2.4, 1.7, 0.9, 0.8 Hz, 1H, H4′), 7.85 (dd, J = 4.5, 1.8 Hz, 2H, H2,6), 8.16–8.32 (m, 1H, H7′), 8.71 (s, 1H, H-C=N), 8.78 (dd, J = 4.4, 1.6 Hz, 2H, H3,5), 11.55 (d, J = 7.4 Hz, 1H, N-H), 11.67 (s, 1H, N-Hind). 13C-NMR (75 MHz, DMSO) δ ppm: 11.97 (1C, CH3), 107.84 (1C, C1′), 111.34 (1C, C4′), 120.82 (1C, C7′), m.p.: 281.1 ◦C. Rf: 0.55 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.54 (s, 3H, CH3), 7.12 (ddt, J = 24.4, 9.3, 1.9, 1.9 Hz, 2H, H5′, H6′), 7.35 (tt, J = 2.4, 1.7, 0.9, 0.8 Hz, 1H, H4′), 7.85 (dd, J = 4.5, 1.8 Hz, 2H, H2,6), 8.16–8.32 (m, 1H, H7′), 8.71 (s, 1H, H-C=N), 8.78 (dd, J = 4.4, 1.6 Hz, 2H, H3,5), 11.55 (d, J = 7.4 Hz, 1H, N-H), 11.67 (s, 1H, N-Hind). 13C-NMR (75 MHz, DMSO) δ ppm: 11.97 (1C, CH3), 107.84 (1C, C1′), 111.34 (1C, C4′), 120.82 (1C, C7′), MS (ES, TOF, MeOH) m/z: 252.0866 [M + Na ]; 230.1049 [M + H ]. HRMS (ES, TOF) m/z: [M + H+] calc. for C11H12N5O: 230.1042. Found: 230.1049. (E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) m.p.: 302.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H H2,6), 7.90 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 ( 1H, H-C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). 13C-NMR (75 MHz DMSO) δ ppm: 111 39 (1C C3′) 121 98 (2C C2 6) 122 73 (1C C7′) 123 35 (1 (E) N ((2 methyl 1H indol 3 yl)methylene)isonicotinohydrazide (6) (E)-N′-((2-methyl-1H-indol-3-yl)methylene)isonicotinohydrazide (6) (E)-N′-((2-methyl-1H-indol-3-yl)methylene)isonicotinohydrazide (6) MS (ES, TOF, MeOH) m/z: 252.0866 [M + Na ]; 230.1049 [M + HRMS (ES, TOF) m/z: [M + H+] calc. for C11H12N5O: 230.1042. 55 PE/EtOAc/MeOH (5:5:3 v/v/v). o-1H-indazol-5-yl)methylene)isonicotinohydrazide ( EtO 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.54 (s, 3H, CH3), 7.12 (ddt, J = 24.4, 9.3, 1.9, 1.9 Hz, 2H, H5′, H6′), 7.35 (tt, J = 2.4, 1.7, 0.9, 0.8 Hz, 1H, H4′), 7.85 (dd, J = 4.5, 1.8 Hz, 2H, H2,6), 8.16–8.32 (m, m.p.: 281.1 °C. E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.54 (s, 3H, CH3), 7.12 (ddt, J = 24.4, H5′, H6′), 7.35 (tt, J = 2.4, 1.7, 0.9, 0.8 Hz, 1H, H4′), 7.85 (dd, J = 4.5, 1.8 Hz, 2H 1H, H7′), 8.71 (s, 1H, H-C=N), 8.78 (dd, J = 4.4, 1.6 Hz, 2H, H3,5), 11.55 (d, J (E)-N′-((2-methyl-1H-indol-3-yl)methylene)isonicotinohydrazide (6) (E)-N′-((2-methyl-1H-indol-3-yl)methylene)isonicotinohydrazide (6) m.p.: 281.1 °C. Rf: 0.55 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.54 (s, 3H, CH3), 7.12 (ddt, J = 24.4, H5′, H6′), 7.35 (tt, J = 2.4, 1.7, 0.9, 0.8 Hz, 1H, H4′), 7.85 (dd, J = 4.5, 1.8 Hz, 2H m.p.: 281.1 ◦C. Rf: 0.55 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.54 (s, 3H, CH3), 7.12 (ddt, J = 24.4, 9.3, H ) 7 35 (tt J 2 4 1 7 0 9 0 8 H 1H H ) 7 85 (dd J 4 5 1 8 H 2H H ) 8 MS (ES, TOF, MeOH) m/z: 252.0866 [M + Na ]; 230.1049 [M + H ]. HRMS (ES, TOF) m/z: [M + H+] calc. for C11H12N5O: 230.1042. Found: 230 (E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) m.p.: 302.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). d (E) N ((2 methyl 1H indol 3 yl)methylene)isonicotinohydrazide (6) (E)-N′-((2-methyl-1H-indol-3-yl)methylene)isonicotinohydrazide (6) (E)-N′-((2-methyl-1H-indol-3-yl)methylene)isonicotinohydrazide (6) MS (ES, TOF, MeOH) m/z: 252.0866 [M + Na ]; 230.1049 [M + HRMS (ES, TOF) m/z: [M + H+] calc. for C11H12N5O: 230.1042. (E) N ((2 methyl 1H indol 3 yl)methylene)isonicotinohydrazide (6) m.p.: 281.1 °C. Rf: 0.55 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.54 (s, 3H, CH3), 7.12 (ddt, J = 24.4, 9.3, 1.9, 1.9 Hz, 2H, H5′, H6′), 7.35 (tt, J = 2.4, 1.7, 0.9, 0.8 Hz, 1H, H4′), 7.85 (dd, J = 4.5, 1.8 Hz, 2H, H2,6), 8.16–8.32 (m, 1H, H7′), 8.71 (s, 1H, H-C=N), 8.78 (dd, J = 4.4, 1.6 Hz, 2H, H3,5), 11.55 (d, J = 7.4 Hz, 1H, N-H), 11.67 (s, 1H, N-Hind). 13C-NMR (75 MHz, DMSO) δ ppm: 11.97 (1C, CH3), 107.84 (1C, C1′), 111.34 (1C, C4′), 120.82 (1C, C7′), 121.63(1C, C5′), 121.87 (2C, C2,6), 122.34 (1C, C6′), 125.85 (1C, C9′), 136.19 (1C, C8′), 141.05 (1C, C2′), 141 56 (1C C1) 146 10 (1C C=N) 150 69 (2C C3 5) 161 00 (1C C=O) (E)-N′-((2-methyl-1H-indol-3-yl)methylene)isonicotinohydrazide (6) (E)-N′-((2-methyl-1H-indol-3-yl)methylene)isonicotinohydrazide (6) m.p.: 281.1 °C. Rf: 0.55 PE/EtOAc/MeOH (5:5:3 v/v/v). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) MS (ES, TOF, MeOH) m/z: 266.1046 [M + H+]. MS (ES, TOF, MeOH) m/z: 266.1046 [M + H+]. HRMS (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.104 UV (EtOH, 38.37 μM, 25 C): λ = 234 nm, ε = 22,666.92 dm3·mol 1·cm 1. MS (ES, TOF, MeOH) m/z: 266.1046 [M + H+]. OH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. TOF MeOH) m/z: 266 1046 [M + H+] UV (EtOH, 38.37 µM, 25 ◦C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. MS (ES TOF M OH) / 266 1046 [M H+] HRMS (ES, TOF) m/z: [M + H ] calc. for C14H12N5O: 266.1042. Found: 266.1046 ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1046. HRMS (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1046. HRMS (ES, TOF) m/z: [M + H ] calc. for C14H12N5O: 266.1042. Found: 266.1046 (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1046. HRMS (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1046. 17 of 27 16 of 2 17 of 27 16 of 2 Molecules 2017, 22, 1457 OH, 161.58 μM, 25 °C ) / Molecules 2017, 22, 14 (E)-N′-((2H-indazol-6-yl)methylene)isonicotinohydrazide (5) , , (E)-N′-((2H-indazol-6-yl)methylene)isonicotinohydrazide (5) ES, TOF) m/z: [M + H+] calc. for C11H12N5O: 230.1042. Found: 23 Molecules 2017, 22, 1457 FTIR (KBr) ν cm−1: 3193.59 (N-H), 3038.08 (C-Har), 1 (C=Car), 1551.04 (Car N), 1506.46 (C=N). (E)-N′-((2H-indazol-6-yl)methylene)isonicotinohydrazide (5) (E)-N′-((2H-indazol-6-yl)methylene)isonicotinohydrazide (5) (ES, TOF) m/z: [M + H+] calc. for C11H12N5O: 230.1042. Found: 23 Molecules 2017, 22, 1457 FTIR (KBr) ν cm−1: 3193.59 (N-H), 3038.08 (C-Har), 1 (C=Car), 1551 04 (Car N), 1506 46 (C=N) y ) y ) y ( ) zol-6-yl)methylene)isonicotinohydrazide (5) H, 182 μM, 25 C): λ = 309 nm, ε = 5495.05 dm3·mol 1·cm 1 (very poorly soluble). TOF, MeOH) m/z: 238.0708 [M + Na+]; 216.0887 [M + H+]. S, TOF) m/z: M + H+ calc. for C10H10N5O: 216.0885. Found: 216.0887. hyl-1H-imidazol-5-yl)methylene)isonicotinohydrazide (3) m.p.: 295.2 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H NMR (300 MH DMSO d ) δ 7 61 (dd J 8 5 1 3 H 1H H ) 7 84 ( 4H H H .: 295.2 ◦C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). m.p.: 295.2 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) 1H NMR (300 MH DMSO d ) δ 7 61 (dd J m.p.: 295.2 ◦C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 2.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). m.p.: 295.2 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H NMR (300 MH DMSO d ) δ 7 61 (dd J m.p.: 295.2 ◦C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 2.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.61 (dd, J = 8.5, 1.3 Hz, 1H, H7′), 7.84 (m, 4H, H2,6, H2′, H6′), 8.13 (d, J = 1.3 Hz, 1H, H5′), 8.60 (s, 1H, H-C=N), 8.80 (br, 2H, H3,5), 12.12 (s, 1H, N-H), 13.28 (s, 1H, N-Hind). 13C NMR (75 MH DMSO) δ 110 75 (1C C ) 119 03 (1C C ) 121 51 (2C C ) 122 01 (1C C ) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.61 (dd, J = 8.5, 1.3 Hz, 1H, H7′), 7.84 (m, 4H, H2,6, H2′, H6′), 8.13 (d, J = 1.3 Hz, 1H, H5′), 8.60 (s, 1H, H-C=N), 8.80 (br, 2H, H3,5), 12.12 (s, 1H, N-H), 13.28 (s, 1H, N-Hind). / / ( / / ) R (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H, 90 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). m.p.: 295.2 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.61 (dd, J = 8.5, 1.3 Hz, 1H, H7′), 7.84 (m, 4H, H2,6, H2′, H6′), 8.13 (d, J = 1.3 Hz, 1H, H5′), 8.60 (s, 1H, H-C=N), 8.80 (br, 2H, H3,5), 12.12 (s, 1H, N-H), 13.28 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.61 (dd, J = 8.5, 1.3 Hz, 1H, H7′), 7.84 (m, 4H, H2,6, H2′, H6′), 8.13 (d, J = 1.3 Hz, 1H, H5′), 8.60 (s, 1H, H-C=N), 8.80 (br, 2H, H3,5), 12.12 (s, 1H, N-H), 13.28 (s, 1H, N-Hind). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.5 (s 1H H C=N) 9 11 (s 1H H3′) 9 14 (dd J = 5 5 1 8 Hz 2H H3 5) 15 98 (br 2H N H) FTIR (KBr) ν cm−1: 3193.59 (N-H), 3038.08 (C-Har), 1648.96 (C=O), 1626.02 (C=N-N), 1596.86 (C=Car), 1551.04 (Car N), 1506.46 (C=N). UV (EtOH 37 39 μM 25 °C): λ 313 nm ε 25 055 1 dm3 mol−1 cm−1 ( , 3,5), ( , ) FTIR (KBr) ν cm−1: 3193.59 (N-H), 3038.08 (C-Har), 1648.96 (C=O), 1626.02 (C=N-N), 1596.86 (C=Car), 1551.04 (Car 50.76 (2C, C3,5), 161.87 (1C, C O). KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.84 , 1549.40 (Car N). N), 1506.46 (C=N). 150.79 (2C, C3,5), 162.08 (1C, C=O). FTIR (KBr) ν cm−1: 3193.59 (N-H), 3038.08 (C-Har), 1648.96 (C=O), 1626.02 (C=N-N), 1596.86 (s, 1H, H-C=N), 9.11 (s, 1H, H3′), 9.14 (dd, J = 5.5, 1.8 Hz, 2H, H3,5), 15.98 (br, 2H, N-H). 13C-NMR (75 MHz, DMSO) δ ppm: 9.38 (1C, CH3), 123.60 (1C, C1′) 125.38 (2C, C2,6), 131.78 (1C, C5′ 138 44 (1C C=N) 142 84 (1C C3′) 144 03 (2C C3 5) 147 78 (1C C1) 159 52 (1C C=O) UV (EtOH, 37.39 μM, 25 °C): λ = 313 nm, ε = 25,055.1 dm3·mol−1·cm−1 MS (ES, TOF, MeOH) m/z: 266.1047 [M + H+]. HRMS (ES TOF) m/z: [M + H+] calc for C14H12N5O: 266 1042 Found 1551.04 (Car , 1549.40 (Car N). OH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. TOF, MeOH) m/z: 266.1046 [M + H+]. N), 1506.46 (C N). UV (EtOH, 37.39 µM, 25 ◦C): λ = 313 nm, ε = 25,055.1 dm3·mol−1·cm−1. MS (ES, TOF, MeOH) m/z: 266.1047 [M + H+]. (C=Car), 1551.04 (Car N), 1506.46 (C=N). UV (EtOH, 37.39 μM, 25 °C): λ = 313 nm, ε = 25,055.1 dm3·mol−1·cm−1 MS (ES TOF M OH) / 266 1047 [M H ] 138.44 (1C, C=N), 142.84 (1C, C3′), 144.03 (2C, C3,5), 147.78 (1C, C1), FTIR (KBr) ν cm−1: 3194.75 (N-H), 3097.19 (Car-H), 1660.58 (C= (Car=Car), 1551.49 (Car N). UV (EtOH, 37.39 μM, 25 °C): λ = 313 nm, ε = 25,055.1 dm3·mol−1·cm−1. MS (ES, TOF, MeOH) m/z: 266.1047 [M + H+]. E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) FTIR (KBr) ν cm−1: 3385.07 (N-H), 3209.03 (N-H), 3049.08 (Car-H), 1655.09 (C=O), 1626.02 (C=N-N), 1599 50 (C=C ) 1550 60 (C , ), ( , , ), ( , , ), ( , , ) 13C-NMR (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C C9′), 124.19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). FTIR (KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.84 (C =C ) 1549 40 (C N) N) 1506 46 (C=N) 121.63(1C, C5), 121.87 (2C, C2,6), 122.34 (1C, C6), 125.85 (1C, C9), 136.19 (1C, C8), 141.05 (1C, C2), 141.56 (1C, C1), 146.10 (1C, C=N), 150.69 (2C, C3,5), 161.00 (1C, C=O). FTIR (KBr) ν cm−1: 3385.07 (N-H), 3209.03 (N-H), 3049.08 (Car-H), 1655.09 (C=O), 1626.02 (C=N- N), 1599.50 (C=Car), 1550.60 (Car N), 1506.46 (C=N). 13C-NMR (75 MHz, DMSO) δ ppm: 11.97 (1C, CH3), 107.84 (1C, C1′), 111.34 (1C, C4′), 120.82 (1C, C7′), 121.63(1C, C5′), 121.87 (2C, C2,6), 122.34 (1C, C6′), 125.85 (1C, C9′), 136.19 (1C, C8′), 141.05 (1C, C2′), 141.56 (1C, C1), 146.10 (1C, C=N), 150.69 (2C, C3,5), 161.00 (1C, C=O). FTIR (KBr) ν cm−1: 3385 07 (N H) 3209 03 (N H) 3049 08 (C H) 1655 09 (C=O) 1626 02 (C=N 13C-NMR (75 MHz, DMSO) δ ppm: 11.97 (1C, CH3), 107.84 (1C, C1′), 111.34 (1C, C4′), 120.82 (1C, C7′), 121.63(1C, C5′), 121.87 (2C, C2,6), 122.34 (1C, C6′), 125.85 (1C, C9′), 136.19 (1C, C8′), 141.05 (1C, C2′), 141.56 (1C, C1), 146.10 (1C, C=N), 150.69 (2C, C3,5), 161.00 (1C, C=O). ) ( ) ( ) ( ) 13C-NMR (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C C9′), 124.19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). N), 1599.50 (C=Car), 1550.60 (Car N), 1506.46 (C=N). UV (EtOH, 57.29 μM, 25 °C): λ = 224 nm, ε = 21,909.58 dm3·mol−1·cm−1. MS (ES, TOF, MeOH) m/z: 279.1246 [M + H+]. HRMS (ES TOF) / [M H ] l f C H N O 279 1246 F d 279 1246 141.56 (1C, C1), 146.10 (1C, C N), 150.69 (2C, C3,5), 161.00 (1C, C O). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) HRMS (ES TOF) m/z: [M + H+] calc for C14H12N5O: 266 1042 Found: 26 ( ar , ( ) OH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. TOF, MeOH) m/z: 266.1046 [M + H+]. ), ( ) UV (EtOH, 37.39 µM, 25 ◦C): λ = 313 nm, ε = 25,055.1 dm3·mol−1·cm−1. MS (ES, TOF, MeOH) m/z: 266.1047 [M + H+]. (C=Car), 1551.04 (Car N), 1506.46 (C=N). UV (EtOH, 37.39 μM, 25 °C): λ = 313 nm, ε = 25,055.1 dm3·mol−1·cm−1. (E O O ) / 138.44 (1C, C=N), 142.84 (1C, C3′), 144.03 (2C, C3,5), 147.78 (1C, C1), 159 FTIR (KBr) ν cm−1: 3194.75 (N-H), 3097.19 (Car-H), 1660.58 (C=O), (Car=Car) 1551 49 (Car N) UV (EtOH, 37.39 μM, 25 °C): λ = 313 nm, ε = 25,055.1 dm3·mol−1·cm−1. MS (ES, TOF, MeOH) m/z: 266.1047 [M + H+]. HRMS (ES TOF) m/z: [M + H+] calc for C14H12N5O: 266 1042 Found: 266 1047 ( ar , ( ) OH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. TOF, MeOH) m/z: 266.1046 [M + H+]. ), ( ) UV (EtOH, 37.39 µM, 25 ◦C): λ = 313 nm, ε = 25,055.1 dm3·mol−1·cm−1. MS (ES, TOF, MeOH) m/z: 266.1047 [M + H+]. (C=Car), 1551.04 (Car N), 1506.46 (C=N). UV (EtOH, 37.39 μM, 25 °C): λ = 313 nm, ε = 25,055.1 dm3·mol−1·cm−1. MS (ES TOF M OH) / 266 1047 [M H+] 138.44 (1C, C=N), 142.84 (1C, C3′), 144.03 (2C, C3,5), 147.78 (1C, C1), 159.52 (1C, C=O). FTIR (KBr) ν cm−1: 3194.75 (N-H), 3097.19 (Car-H), 1660.58 (C=O), 1621.45 (C=N-N), 1602.2 (Car=Car), 1551.49 (Car N). HRMS (ES, TOF) m/z: [M + H ] calc. for C14H12N5O: 266.1042. Found: 266.1047 ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1046. HRMS (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1047. MS (ES, TOF, MeOH) m/z: 266.1047 [M + H+]. HRMS (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1047 ( ), ( ) UV (EtOH, 161.58 μM, 25 °C): λ = 316 nm, ε = 5551.73 dm3·mol−1·cm−1 (very (E)-N -((2-methyl-1H-indol-3-yl)methylene)isonicotinohydrazide (6) m.p.: 281.1 °C. Rf: 0.55 PE/EtOAc/MeOH (5:5:3 v/v/v). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) 13C NMR (75 MH DMSO) δ 11 97 (1C CH ) 107 84 (1C C ) 111 34 (1C C ) 120 82 (1C C ) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.54 (s, 3H, CH3), 7.12 (ddt, J = 24.4, 9.3, 1.9, 1.9 Hz, 2H, H5′, H6′), 7.35 (tt, J = 2.4, 1.7, 0.9, 0.8 Hz, 1H, H4′), 7.85 (dd, J = 4.5, 1.8 Hz, 2H, H2,6), 8.16–8.32 (m, 1H, H7′), 8.71 (s, 1H, H-C=N), 8.78 (dd, J = 4.4, 1.6 Hz, 2H, H3,5), 11.55 (d, J = 7.4 Hz, 1H, N-H), 11.67 (s, 1H, N-Hind). m.p.: 302.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H H2,6), 7.90 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s 1H, H-C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). 121.63(1C, C5), 121.87 (2C, C2,6), 122.34 (1C, C6), 125.85 (1C, C9), 136.19 (1C, C8), 141.05 (1C, C2), 141.56 (1C, C1), 146.10 (1C, C=N), 150.69 (2C, C3,5), 161.00 (1C, C=O). FTIR (KBr) ν cm−1: 3385.07 (N-H), 3209.03 (N-H), 3049.08 (Car-H), 1655.09 (C=O), 1626.02 (C=N- N), 1599.50 (C=Car), 1550.60 (Car N), 1506.46 (C=N). UV (EtOH, 57.29 μM, 25 °C): λ = 224 nm, ε = 21,909.58 dm3·mol−1·cm−1. MS (ES TOF M OH) / 279 1246 [M H+] 13C-NMR (75 MHz, DMSO) δ ppm: 11.97 (1C, CH3), 107.84 (1C, C1′), 111.34 (1C, C4′), 120.82 (1C, C7′), 121.63(1C, C5′), 121.87 (2C, C2,6), 122.34 (1C, C6′), 125.85 (1C, C9′), 136.19 (1C, C8′), 141.05 (1C, C2′), 141.56 (1C, C1), 146.10 (1C, C=N), 150.69 (2C, C3,5), 161.00 (1C, C=O). FTIR (KBr) ν cm−1: 3385.07 (N-H), 3209.03 (N-H), 3049.08 (Car-H), 1655.09 (C=O), 1626.02 (C=N- N), 1599.50 (C=Car), 1550.60 (Car N), 1506.46 (C=N). 13C-NMR (75 MHz, DMSO) δ ppm: 11.97 (1C, CH3), 107.84 (1C, C1′), 111.34 (1C, C4′), 120.82 (1C, C7′), 121.63(1C, C5′), 121.87 (2C, C2,6), 122.34 (1C, C6′), 125.85 (1C, C9′), 136.19 (1C, C8′), 141.05 (1C, C2′), 141.56 (1C, C1), 146.10 (1C, C=N), 150.69 (2C, C3,5), 161.00 (1C, C=O). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) HRMS (ES, TOF) m/z: [M H ] calc. for C16H15N4O: 279.1246. Found: 279.1246 Compound 6 can also be found (commercial source; CAS No.: 113143-57-0). HRMS (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.10 HRMS (ES, TOF) m/z: [M + H+] calc. for C16H15N4O: 279.1246. Found: 279.1246. p ( Compound 6 can also be found (commercial source; CAS No.: 113143-57-0). 18 of 27 N), 1596.8 18 of 27 N), 1596.8 Molecules 2017, 22, 1457 MS (ES, TO HRMS (ES FTIR (KBr) (C=Car), 155 (E)-N′-((1H-pyrrolo[2,3-b]pyridin-3-yl)methylene)isonicotinohydrazide (7) , , (E)-N′-((1H-pyrrolo[2 3-b]pyridin-3-yl)methylene)isonicotinohydrazide (7) (E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide ( Molecules 2017, 22, 1457 μ ( MS (ES, TOF, MeOH) m/z: 238.0708 [M + Na+]; 216.0887 [M + H+]. HRMS (ES TOF) m/z: M + H+ calc for C10H10N5O: 216 0885 Found: 2 (E)-N′-((1H-pyrrolo[2,3-b]pyridin-3-yl)methylene)isonicotinohydrazide (7) (E)-N′-((1H-pyrrolo[2 3-b]pyridin-3-yl)methylene)isonicotinohydrazide (7) (E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide ( Molecules 2017, 22, 1457 μ ( MS (ES, TOF, MeOH) m/z: 238.0708 [M + Na+]; 216.0887 [M + H+]. HRMS (ES TOF) m/z: M + H+ calc for C10H10N5O: 216 0885 Found: 2 ]pyridin-3-yl)methylene)isonicotinohydrazide (7) midazol-5-yl)methylene)isonicotinohydrazide (3) 323.2 °C (dec.). Rf: 0.34 PE/EtAc/MeOH (5:5:3 v/v). 2 ◦C (dec.). Rf: 0.34 PE/EtAc/MeOH (5:5:3 v/v). p.: 302.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). m.p.: 323.2 °C (dec.). Rf: 0.34 PE/EtAc/MeOH (5:5:3 v/v m.p.: 323.2 ◦C (dec.). Rf: 0.34 PE/EtAc/MeOH (5:5:3 v/v). m.p.: 302.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v 1H-NMR (300 MHz, DMSO-d6) δ ppm: 77.24 (tt, J = 7.8, 4.7, 4.7 Hz, 1H, H6′), 7.84 (dd, J = 4.2, 1.7 Hz, 2H, H2,6), 8.03 (d, J = 2.3 Hz, 1H, H2′), 8.33 (dd, J = 4.7, 1.7 Hz, 1H, H7′), 8.58 (d, J = 1.6 Hz, 1H, H5′), 8.62 (s, 1H, H-C=N), 8.78 (dd, J = 4.4, 1.7 Hz, 2H, H3,5), 11.86 (s, 1H, N-H), 12.17 (s, 1H, N-Hind). 13C-NMR (75 MHz, DMSO)δ ppm: 110.85 (1C, C1), 117,13 (1C, C9′), 117.44 (1C, C6′), 121.95 (2C, C2,6), 130.56 (1C, C5′), 131.51 (1C, C2′), 141.39 (1C, C1), 144.56 (1C, C7′), 146.09 (1C, C=N), 149.84 (1C, C8′), 150.71 (2C, C3,5), 161.49 (1C, C=O). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) ( ) O p ( ) f ( ) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 77.24 (tt, J = 7.8, 4.7, 4.7 Hz, 1H, H6′), 7.84 (dd, J = 4.2, 1.7 Hz, 2H, H2,6), 8.03 (d, J = 2.3 Hz, 1H, H2′), 8.33 (dd, J = 4.7, 1.7 Hz, 1H, H7′), 8.58 (d, J = 1.6 Hz, 1H, H5′), 8.62 (s, 1H, H-C=N), 8.78 (dd, J = 4.4, 1.7 Hz, 2H, H3,5), 11.86 (s, 1H, N-H), 12.17 (s, 1H, N-Hind). 13C-NMR (75 MHz, DMSO)δ ppm: 110.85 (1C, C1), 117,13 (1C, C9′), 117.44 (1C, C6′), 121.95 (2C, C2,6), 130.56 (1C, C5′), 131.51 (1C, C2′), 141.39 (1C, C1), 144.56 (1C, C7′), 146.09 (1C, C=N), 149.84 (1C, C8′), 150.71 (2C, C3,5), 161.49 (1C, C=O). m.p.: 302.5 C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H H2,6), 7.90 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s 1H, H-C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). 13C-NMR (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C C9′), 124.19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). m.p.: 323.2 °C (dec.). Rf: 0.34 PE/EtAc/MeOH (5:5:3 v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 77.24 (tt, J = 7.8, 4.7, 4.7 Hz, 1H, H6′), 7.84 (dd, J = 4.2, 1.7 Hz, 2H, H2,6), 8.03 (d, J = 2.3 Hz, 1H, H2′), 8.33 (dd, J = 4.7, 1.7 Hz, 1H, H7′), 8.58 (d, J = 1.6 Hz, 1H, H5′), 8.62 (s, 1H, H-C=N), 8.78 (dd, J = 4.4, 1.7 Hz, 2H, H3,5), 11.86 (s, 1H, N-H), 12.17 (s, 1H, N-Hind). 13C-NMR (75 MHz, DMSO)δ ppm: 110.85 (1C, C1), 117,13 (1C, C9′), 117.44 (1C, C6′), 121.95 (2C, C2,6), 130.56 (1C, C5′), 131.51 (1C, C2′), 141.39 (1C, C1), 144.56 (1C, C7′), 146.09 (1C, C=N), 149.84 m.p.: 299 °C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.53 (s, 1H, H-C=N), 9.11 (s, 1H, H3′), 9.14 (dd, J = 5.5, 1.8 Hz, 2H, H3,5), 15.98 (br, 2H, N-H). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) Hz, 2H, H2,6), 8.03 (d, J = 2.3 Hz, 1H, H2′), 8.33 (dd, J = 4.7, 1.7 Hz, 1H, H7′), 8.58 (d, J = 1.6 Hz, 1H, H5′), 8.62 (s, 1H, H-C=N), 8.78 (dd, J = 4.4, 1.7 Hz, 2H, H3,5), 11.86 (s, 1H, N-H), 12.17 (s, 1H, N-Hind). 13C-NMR (75 MHz, DMSO)δ ppm: 110.85 (1C, C1), 117,13 (1C, C9′), 117.44 (1C, C6′), 121.95 (2C, C2,6), 130.56 (1C, C5′), 131.51 (1C, C2′), 141.39 (1C, C1), 144.56 (1C, C7′), 146.09 (1C, C=N), 149.84 m.p.: 299 °C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.5 (s, 1H, H-C=N), 9.11 (s, 1H, H3′), 9.14 (dd, J = 5.5, 1.8 Hz, 2H, H3,5), 15.98 (br, 2H, N-H). 13C-NMR (75 MHz, DMSO) δ ppm: 9.38 (1C, CH3), 123.60 (1C, C1′) 125.38 (2C, C2,6), 131.78 (1C, C5′) FTIR (KBr) ν cm−1: 3454.03 (N-H), 3199.51 (N-H), 3031.09 (Car-H), 1662.68 (C=O), 1611.72 (C=N- N), 1600.48 (C=Car), 1551.26 (Car N), 1284.78 (C-N). UV (EtOH 58 08 M 25 °C) λ 200 18 839 92 d 3 l 1 1 λ 218 17 446 62 FTIR (KBr) ν cm−1: 3454.03 (N-H), 3199.51 (N-H), 3031.09 (Car-H), 1662.68 (C=O), 1611.72 (C=N-N), 1600.48 (C=Car), 1551.26 (Car ) ( ) ( ) FTIR (KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.8 (Car=Car), 1549.40 (Car N). N), 1284.78 (C-N). (1C, C8′), 150.71 (2C, C3,5), 161.49 (1C, C=O). FTIR (KBr) ν cm−1: 3454.03 (N-H), 3199.51 (N-H), 3031.09 (Car-H), 1662.68 (C=O), 1611.72 (C=N- N) 1600 48 (C C ) 1551 26 (C N) 1284 78 (C N) 138.44 (1C, C=N), 142.84 (1C, C3′), 144.03 (2C, C3,5), 147.78 (1C, C1), 159.52 (1C, C=O). FTIR (KBr) ν cm−1: 3194.75 (N-H), 3097.19 (Car-H), 1660.58 (C=O), 1621.45 (C=N-N), 1602.2 UV (EtOH, 58.08 μM, 25 °C): λ = 200 nm, ε = 18,839.92 dm3·mol−1·cm−1, λ = 218 nm, ε = 17,446.62 dm3·mol−1·cm−1, λ = 322 nm, ε = 17,193.69 dm3·mol−1·cm−1. MS (ES TOF MeOH) / 266 1045 [M + H+] ( ) ( ) UV (EtOH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. MS (ES, TOF, MeOH) m/z: 266.1046 [M + H+]. UV (EtOH, 58.08 µM, 25 ◦C): λ = 200 nm, ε = 18,839.92 dm3·mol−1·cm−1, λ = 218 nm, ε = 17,446.62 dm3·mol−1·cm−1, λ = 322 nm, ε = 17,193.69 dm3·mol−1·cm−1. E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) 13C-NMR (75 MHz, DMSO) δ ppm: 9.38 (1C, CH3), 123.60 (1C, C1′) 125.38 (2C, C2,6), 131.78 (1C, C5′) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 77.24 (tt, J = 7.8, 4.7, 4.7 Hz, 1H, H6′), 7.84 (dd, J = Hz, 2H, H2,6), 8.03 (d, J = 2.3 Hz, 1H, H2′), 8.33 (dd, J = 4.7, 1.7 Hz, 1H, H7′), 8.58 (d, J = 1.6 H dd 1H-NMR (300 MHz, DMSO-d6) δ ppm: 77.24 (tt, J = 7.8, 4.7, 4.7 Hz, 1H, H6′), 7.84 (dd, J = 4.2, 2H, H2,6), 8.03 (d, J = 2.3 Hz, 1H, H2′), 8.33 (dd, J = 4.7, 1.7 Hz, 1H, H7′), 8.58 (d, J = 1.6 Hz, 1H p / / ( / / ) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1. H2,6), 7.90 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H m.p.: 323.2 °C (dec.). Rf: 0.34 PE/EtAc/MeOH (5:5:3 v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 77.24 (tt, J = 7.8, 4.7, 4.7 Hz, 1H, H6′), 7.84 (dd, J = H5′), 8.62 (s, 1H, H-C=N), 8.78 (dd, J = 4.4, 1.7 Hz, 2H, H3,5), 11.86 (s, 1H, N-H), 12.17 (s, 1H, N-Hind). 13C-NMR (75 MHz, DMSO)δ ppm: 110.85 (1C, C1), 117,13 (1C, C9′), 117.44 (1C, C6′), 121.95 (2C, C2,6), 130.56 (1C, C5′), 131.51 (1C, C2′), 141.39 (1C, C1), 144.56 (1C, C7′), 146.09 (1C, C=N), 149.84 (1C, C8′), 150.71 (2C, C3,5), 161.49 (1C, C=O). 8.62 (s, 1H, H-C=N), 8.78 (dd, J = 4.4, 1.7 Hz, 2H, H3,5), 11.86 (s, 1H, N-H), 12.17 (s, 1H, N-Hind). 13C-NMR (75 MHz, DMSO)δ ppm: 110.85 (1C, C1), 117,13 (1C, C9′), 117.44 (1C, C6′), 121.95 (2C, C2,6), 130.56 (1C, C5′), 131.51 (1C, C2′), 141.39 (1C, C1), 144.56 (1C, C7′), 146.09 (1C, C=N), 149.84 (1C, C8′), 150.71 (2C, C3,5), 161.49 (1C, C=O). 1H, H-C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). 13C-NMR (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C C9′), 124.19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) Rf: 0.45 PE/EtOAc/MeOH (5:5:3 1H-NMR (300 MHz, DMSO-d6) δ ppm: δ 7.11–7.28 (m, 2H, H5′,6′), 7.47 (dt, J = 7.9, 0.9 Hz, 1H, H4′), 7 85 (dd J 4 4 1 6 H 2H H ) 7 88 (d J 2 8 H 1H H ) 8 31 (dd J 6 8 1 5 H 1H H ) m.p.: 242 °C. Rf: 0.55 PE/EtAc/MeOH (5:5:3 v/v/v). ( O d ) d m.p.: 242 ◦C. Rf: 0.55 PE/EtAc/MeOH (5:5:3 v/v/v). m.p.: 302.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 7.85 (dd, J = 4.4, 1.6 Hz, 2H, H2,6), 7.88 (d, J = 2.8 Hz, 1H, H2′), 8.31 (dd, J = 6.8, 1.5 Hz, 1H, H9′), 8.65 (s, 1H, H-C=N), 8.78 (dd, J = 4.4, 1.6 Hz, 2H, H3, 5), 11.65 (s, 1H, N-H), 11.76 (s, 1H, N-Hind). 13C-NMR (75 MHz, DMSO) δ ppm: 111.96 (1C, C1′), 112.34 (1C, C4′), 121.00 (1C, C5′), 121.95 (2C, 1H-NMR (300 MHz, DMSO-d6) δ ppm: δ 7.11–7.28 (m, 2H, H5′,6′), 7.47 (dt, J = 7.9, 0.9 Hz, 1H, H4′), 7.85 (dd, J = 4.4, 1.6 Hz, 2H, H2,6), 7.88 (d, J = 2.8 Hz, 1H, H2′), 8.31 (dd, J = 6.8, 1.5 Hz, 1H, H9′), 8.65 (s, 1H, H-C=N), 8.78 (dd, J = 4.4, 1.6 Hz, 2H, H3, 5), 11.65 (s, 1H, N-H), 11.76 (s, 1H, N-Hind). 1H-NMR (300 MHz, DMSO-d6) δ ppm: δ 7.11–7.28 (m, 2H, H5′,6′), 7.47 (dt, J = 7.9, 0.9 Hz, 1H, H4′), 7.85 (dd, J = 4.4, 1.6 Hz, 2H, H2,6), 7.88 (d, J = 2.8 Hz, 1H, H2′), 8.31 (dd, J = 6.8, 1.5 Hz, 1H, H9′), 8.65 (s, 1H, H-C=N), 8.78 (dd, J = 4.4, 1.6 Hz, 2H, H3, 5), 11.65 (s, 1H, N-H), 11.76 (s, 1H, N-Hind). p / / ( / / ) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H H2,6), 7.90 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s 1H, H-C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). C2,6), 122.44 (1C, C7′), 123.17 (1C, C6′), 123.35 (1C, C7′), 124.77 (1C, C9′), 131.36 (1C, C2′), 137.53 (1C, C8′), 141.54 (1C, C1), 146.63 (1C, C=N), 150.69 (2C, C3,5), 161.33 (1C, C=O). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) N), 1600.48 (C=Car), 1551.26 (Car N), 1284.78 (C-N). UV (EtOH, 58.08 μM, 25 °C): λ = 200 nm, ε = 18,839.92 dm3·mol−1·cm−1, λ = 218 nm, ε = 17,446.62 d 3 l 1 1 λ 322 17 193 69 d 3 l 1 1 (Car=Car), 1551.49 (Car N). UV (EtOH, 161.58 μM, 25 °C): λ = 316 nm, ε = 5551.73 dm3·mol−1·cm−1 (very poorly soluble). MS (ES, TOF, MeOH) m/z: 266.1045 [M + H HRMS (ES TOF) m/z: [M + H+] calc for C14 HRMS (ES, TOF) m/z: [M + H+] calc. for C MS (ES, TOF, MeOH) m/z: 266.1045 [M + H+]. dm3·mol−1·cm−1, λ = 322 nm, ε = 17,193.69 dm MS (ES TOF MeOH) m/z: 266 1045 [M + H MS (ES, TOF, MeOH) m/z: 252.0866 [M + HRMS (ES TOF) / [M H ] l f C MS (ES, TOF, MeOH) m/z: 266.1045 [M + H+]. HRMS (ES TOF) m/z: [M + H+] calc for C14H12N5O: 266 1042 Found: 266 1045 HRMS (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1046. MS (ES, TOF, MeOH) m/z: 266.1045 [M + H+]. dm3·mol−1·cm−1, λ = 322 nm, ε = 17,193.69 dm3·mol−1·cm−1. MS (ES TOF MeOH) m/z: 266 1045 [M + H+] MS (ES, TOF, MeOH) m/z: 252.0866 [M + Na+]; 230.1049 [M + H+]. HRMS (ES TOF) / [M H+] l f C H N O 230 1042 F d 230 1049 HRMS (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1045 HRMS (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1045. MS (ES, TOF, MeOH) m/z: 266.1045 [M + H+]. HRMS (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1045 HRMS (ES, TOF) m/z: [M + H+] calc. for C11H12N5O: 230.1042. Found: 230.10 (E)-N′-((1H-indol-3-yl)methylene)isonicotinohydrazide (8) m p : 242 °C Rf: 0 55 PE/EtAc/MeOH (5:5:3 v/v/v) (E)-N′-((1H-indol-3-yl)methylene)isonicotinohydrazide (8) (E)-N′-((1H-indol-3-yl)methylene)isonicotinohydrazide (8) (E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) (E)-N′-((1H-indol-3-yl)methylene)isonicotinohydrazide (8) (E)-N′-((1H-indol-3-yl)methylene)isonicotinohydrazide (8) (E)-N′-((1H-indol-3-yl)methylene)isonicotinohydrazide (8) (E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonico (E)-N′-((1H-indol-3-yl)methylene)isonicotinohydrazide (8) (E)-N′-((1H-indol-3-yl)methylene)isonicotinohydrazide (8) (E)-N′-((1H-indol-3-yl)methylene)isonicotinohydrazide (8) (E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonic 5 PE/EtAc/MeOH (5:5:3 v/v/v) A / p ( ) 1H-NMR (300 MHz, DMSO-d6) δ ppm: δ 7.11–7.2 m.p.: 242 °C. Rf: 0.55 PE/EtAc/MeOH (5:5:3 v/v/v) m.p.: 242 ◦C. Rf: 0.55 PE/EtAc/MeOH (5:5:3 v/v/v). m.p.: 302.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 1H-NMR (300 MHz, DMSO-d6) δ ppm: δ 7.11–7.2 m.p.: 242 °C. Rf: 0.55 PE/EtAc/MeOH (5:5:3 v/v/v) m.p.: 242 ◦C. Rf: 0.55 PE/EtAc/MeOH (5:5:3 v/v/v). m.p.: 302.5 °C. E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) FTIR (KBr) ν cm−1: 3543.66 (N-H), 3395.82 (N-H), 2886.55 (C-Har), 1656.52 (C=O), 1626.02 (C=N- N) 1598 83 (C C ) 1550 54 (C N) 1496 83 (C N) 13C-NMR (75 MHz, DMSO) δ ppm: 111.96 (1C, C1′), 112.34 (1C, C4′), 121.00 (1C, C5′), 121.95 (2C, C2,6), 122.44 (1C, C7′), 123.17 (1C, C6′), 123.35 (1C, C7′), 124.77 (1C, C9′), 131.36 (1C, C2′), 137.53 (1C, C8′), 141.54 (1C, C1), 146.63 (1C, C=N), 150.69 (2C, C3,5), 161.33 (1C, C=O). TIR ( B ) 4 66 ( H) ( H) 6 (C H ) 16 6 (C O) 16 6 (C 13C-NMR (75 MHz, DMSO) δ ppm: 111.96 (1C, C1′), 112.34 (1C, C4′), 121.00 (1C, C5′), 121.95 (2C, C2,6), 122.44 (1C, C7′), 123.17 (1C, C6′), 123.35 (1C, C7′), 124.77 (1C, C9′), 131.36 (1C, C2′), 137.53 (1C, C8′), 141.54 (1C, C1), 146.63 (1C, C=N), 150.69 (2C, C3,5), 161.33 (1C, C=O). , ), ( , , ), ( , , ), ( , , ) 13C-NMR (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C C9′), 124.19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). C2,6), 122.44 (1C, C7′), 123.17 (1C, C6′), 123.35 (1C, C7′), 124.77 (1C, C9′), 131.36 (1C, C2′), 137.53 (1C, C8′), 141.54 (1C, C1), 146.63 (1C, C=N), 150.69 (2C, C3,5), 161.33 (1C, C=O). FTIR (KBr) ν cm−1: 3543.66 (N-H), 3395.82 (N-H), 2886.55 (C-Har), 1656.52 (C=O), 1626.02 (C=N- ) (C C ) (C ) (C ) 13C-NMR (75 MHz, DMSO) δ ppm: 111.96 (1C, C1′), 112.34 (1C, C4′), 121.00 (1C, C5′), 121.95 (2C, C2,6), 122.44 (1C, C7′), 123.17 (1C, C6′), 123.35 (1C, C7′), 124.77 (1C, C9′), 131.36 (1C, C2′), 137.53 (1C, C8′), 141.54 (1C, C1), 146.63 (1C, C=N), 150.69 (2C, C3,5), 161.33 (1C, C=O). 13C-NMR (75 MHz, DMSO) δ ppm: 111.96 (1C, C1′), 112.34 (1C, C4′), 121.00 (1C, C5′), 121.95 (2C, C2,6), 122.44 (1C, C7′), 123.17 (1C, C6′), 123.35 (1C, C7′), 124.77 (1C, C9′), 131.36 (1C, C2′), 137.53 (1C, C8′), 141.54 (1C, C1), 146.63 (1C, C=N), 150.69 (2C, C3,5), 161.33 (1C, C=O). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) , ), ( , , ), ( , , ), ( , , ) 13C-NMR (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C C9′), 124.19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). N), 1598.83 (C=Car), 1550.54 (Car N), 1496.83 (C=N). UV (EtOH, 40.01 μM, 25 °C): λ = 221 nm, ε = 22,519 dm3·mol−1·cm−1. MS (ES TOF M OH) / 265 1092 [M H+] FTIR (KBr) ν cm−1: 3543.66 (N-H), 3395.82 (N-H), 2886.55 (C-Har), 1656.52 (C=O), 1626.02 (C=N- N), 1598.83 (C=Car), 1550.54 (Car N), 1496.83 (C=N). UV (EtOH 40 01 M 25 °C) λ 221 22 519 d 3 l 1 1 , FTIR (KBr) ν cm−1: 3543.66 (N-H), 3395.82 (N-H), 2886.55 (C-Har), 1656.52 (C=O), 1626.02 (C=N-N), 1598.83 (C=Car), 1550.54 (Car ), ( , ), ( , ) FTIR (KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.8 (Car=Car), 1549.40 (Car N). N), 1496.83 (C=N). N), 1598.83 (C=Car), 1550.54 (Car N), 1496.83 (C=N). UV (EtOH, 40.01 μM, 25 °C): λ = 221 nm, ε = 22,519 dm3·mol−1·cm−1. MS (ES TOF M OH) / 265 1092 [M H+] FTIR (KBr) ν cm−1: 3543.66 (N-H), 3395.82 (N-H), 2886.55 (C-Har), 1656.52 (C=O), 1626.02 (C=N- N), 1598.83 (C=Car), 1550.54 (Car N), 1496.83 (C=N). UV (EtOH 40 01 M 25 °C) λ 221 22 519 d 3 l 1 1 , FTIR (KBr) ν cm−1: 3543.66 (N-H), 3395.82 (N-H), 2886.55 (C-Har), 1656.52 (C=O), 1626.02 (C=N-N), 1598.83 (C=Car), 1550.54 (Car ) ( ) ( ) FTIR (KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.8 (Car=Car), 1549.40 (Car N). N), 1496.83 (C=N). MS (ES, TOF, MeOH) m/z: 265.1092 [M + H+]. HRMS (ES TOF) m/z: [M + H+] calc for C H N O: 265 1089 Found UV (EtOH, 40.01 μM, 25 °C): λ = 221 nm, ε = 22,519 dm3·mol−1·cm−1. MS (ES TOF MeOH) m/z 265 1092 [M + H+] ( ) ( ( ) ( ) UV (EtOH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·c ) ( ) UV (EtOH, 40.01 µM, 25 ◦C): λ = 221 nm, ε = 22,519 dm3·mol−1·cm−1. Compound 8 can also be found (commercial source; CAS No.: 10245-44-0). HRMS (ES, TOF) m/z: [M + H+] calc. for C15H13N4O: 265.1089. Found: 265.1092. E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.35 (dd, J = 8.7, 2.1 Hz, 1H5′), 7.44 (d, J = 8.5 Hz, 1H, H4′), 7.84 (dd, J = 4.5, 1.9 Hz, 2H, H2,6), 7.95 (d, J = 2.7 Hz, 1H, H9′), 8.48 (s, 1H, H2′), 8.62 (s, 1H, H-C=N), 8.73–8.89 (m, 2H, H3,5), 11.83 (d, J = 6.0 Hz, 2H, N-H). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.35 (dd, J = 8.7, 2.1 Hz, 1H5′), 7.44 (d, J = 8.5 Hz, 1H, H4′), 7.84 (dd, J = 4.5, 1.9 Hz, 2H, H2,6), 7.95 (d, J = 2.7 Hz, 1H, H9′), 8.48 (s, 1H, H2′), 8.62 (s, 1H, H-C=N), 8.73–8.89 (m, 2H, H3,5), 11.83 (d, J = 6.0 Hz, 2H, N-H). / / ( / / ) R (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H, 90 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). m.p.: 309.3 °C (dec.). Rf: 0.61 PE/EtAc/MeOH (5:5:3 v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.35 (dd, J = 8.7, 2.1 Hz, 1H5′), 7.44 (d, J = 8.5 Hz, 1H, H4′), 7.84 (dd, J = 4.5, 1.9 Hz, 2H, H2,6), 7.95 (d, J = 2.7 Hz, 1H, H9′), 8.48 (s, 1H, H2′), 8.62 (s, 1H, H-C=N), 13C-NMR (75 MHz, DMSO) δ ppm: 111.59 (1C, C1′), 113,70 (1C, C6′), 114.42 (1C, C4′), 121.93 (2C, C2,6), 124.60 (1C, C2′), 125.71 (1C, C5′), 126.42 (1C, C9′), 132.71 (1C, C7′), 136.27 (1C, C8′), 141.38 (1C, C1), 146.13 (1C, C=N), 150.72 (2C, C3,5), 161.40 (1C, C=O). FTIR (KB ) 31 (N H ) 1 3 (C H ) 166 6 (C O) 161 34 (C N N) 1 3 13C-NMR (75 MHz, DMSO) δ ppm: 111.59 (1C, C1′), 113,70 (1C, C6′), 114.42 (1C, C4′), 121.93 (2C, C2,6), 124.60 (1C, C2′), 125.71 (1C, C5′), 126.42 (1C, C9′), 132.71 (1C, C7′), 136.27 (1C, C8′), 141.38 (1C, C1), 146.13 (1C, C=N), 150.72 (2C, C3,5), 161.40 (1C, C=O). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) Compound 8 can also be found (commercial source; CAS No.: 10245-44-0). HRMS (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1046. [ ] HRMS (ES, TOF) m/z: [M + H+] calc. for C15H13N4O: 265.1089. Found: 265.1092. Compound 8 can also be found (commercial source; CAS No.: 10245-44-0). Compound 8 can also be found (commercial source; CAS No.: 10245-44-0). HRMS (ES, TOF) m/z: [M + H+] calc. for C15H13N4O: 265.1089. Found: 265.1092 Compound 8 can also be found (commercial source; CAS No.: 10245-44-0). HRMS (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.10 HRMS (ES, TOF) m/z: [M + H+] calc. for C15H13N4O: 265.1089. Found: 265.1092. Compound 8 can also be found (commercial source; CAS No.: 10245-44-0). HRMS (ES, TOF) m/z: [M + H+] calc. for C15H13N4O: 265.1089. Found: 265.1092. Compound 8 can also be found (commercial source; CAS No.: 10245-44-0). HRMS (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.104 HRMS (ES, TOF) m/z: [M + H+] calc. for C15H13N4O: 265.1089. Found: 265.1092. Compound 8 can also be found (commercial source; CAS No.: 10245-44-0). Compound 8 can also be found (commercial source; CAS No.: 10245 44 Compound 8 can also be found (commercial source; CAS No.: 10245-44-0). 19 of 27 Molecules 2017, 22, 1457 , ) (ES, TOF) m/z: [M + H 2C, C2,6), 134,36 (1C, (E)-N′-((5-bromo-1H-indol-3-yl)methylene)isonicotinohydrazide (9) (E)-N′-((5-bromo-1H-indol-3-yl)methylene)isonicotinohydrazide (9) a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) Molecules 2017, 22, 1457 , 1551.04 (Car N), 1506.46 (C=N). OH 182 μM 25 °C): λ = 309 nm ε = 5495 05 dm3·mol−1·cm−1 (very poorly (E)-N′-((5-bromo-1H-indol-3-yl)methylene)isonicotinohydrazide (9) (E)-N′-((5-bromo-1H-indol-3-yl)methylene)isonicotinohydrazide (9) -dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) Molecules 2017, 22, 1457 1551.04 (Car N), 1506.46 (C=N). OH, 182 μM, 25 °C): λ = 309 nm ε = 5495 05 dm3·mol−1·cm−1 (very poorly 3 yl)methylene)isonicotinohydrazide (9) 8 [M + Na+]; 216.0887 [M + H+]. for C10H10N5O: 216.0885. Found: 216.0887. hylene)isonicotinohydrazide (3) p.: 309.3 °C (dec.). Rf: 0.61 PE/EtAc/MeOH (5:5:3 v/v). NMR (300 MH DMSO d ) δ 7 35 (dd J 8 7 2 1 H 1H ) 7 44 (d J 8 5 H 1H H ) 09.3 ◦C (dec.). Rf: 0.61 PE/EtAc/MeOH (5:5:3 v/v). f: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). m.p.: 309.3 °C (dec.). Rf: 0.61 PE/EtAc/MeOH (5:5:3 v/v m.p.: 309.3 ◦C (dec.). Rf: 0.61 PE/EtAc/MeOH (5:5:3 v/v). 2.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). (E)-N -((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) -dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4 13C-NMR (75 MHz, DMSO) δ ppm: 107.98 (1C, C2′), 112.57 (1C, C3′), 120.06 (1C, C4′), 121.31 (1C, C6′), 122.01 (2C, C2,6), 128.05 (1C, C9′), 133.28 (1C, C1′), 138.47 (1C, C8′), 142.16 (1C, C=N), 150.79 (2C, C3, 5), 161.84 (1C, C=O). FTIR (KBr) ν cm−1: 3250.19 (N-H), 3032.16 (C-Har), 1689.09 (C=O), 1621.50 (C=N-N), 1599.80 (C C ) 1548 50 (C N) Hz, 1H), 7.18 (ddd, J 8.3, 7.0, 1.2 Hz, 1H), 7.47 (dq, J 8.2, 0.9 Hz, 1H), 7.58 (dd, J 7.9, 1.1 Hz, 1H), 7.86 (dd, J = 4.4, 1.6 Hz, 2H), 8.51 (s, 1H), 8.81 (dd, J = 4.4, 1.7 Hz, 2H), 11.65 (s, 1H), 12.05 (s, 1H). 13C-NMR (75 MHz, DMSO) δ ppm: 107.98 (1C, C2′), 112.57 (1C, C3′), 120.06 (1C, C4′), 121.31 (1C, C6′), 122.01 (2C, C2,6), 128.05 (1C, C9′), 133.28 (1C, C1′), 138.47 (1C, C8′), 142.16 (1C, C=N), 150.79 (2C, C3, 5), 161.84 (1C, C=O). 1H), 7.18 (ddd, J = 8.3, 7.0, 1.2 Hz, 1H), 7.47 (dq, J = 8.2, 0.9 Hz, 1H), 7.58 (dd, J = 7.9, 1.1 Hz, 1H), 7.86 (dd, J = 4.4, 1.6 Hz, 2H), 8.51 (s, 1H), 8.81 (dd, J = 4.4, 1.7 Hz, 2H), 11.65 (s, 1H), 12.05 (s, 1H). 13C-NMR (75 MHz, DMSO) δ ppm: 107.98 (1C, C2′), 112.57 (1C, C3′), 120.06 (1C, C4′), 121.31 (1C, C6′), 122.01 (2C, C2,6), 128.05 (1C, C9′), 133.28 (1C, C1′), 138.47 (1C, C8′), 142.16 (1C, C=N), 150.79 (2C, C3, 5), 161.84 (1C, C=O). 0 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). R (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, .19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, 50.76 (2C, C3,5), 161.87 (1C, C=O). C6′), 122.01 (2C, C2,6), 128.05 (1C, C9′), 133.28 (1C, C1′), 138.47 (1C, C8′), 142.16 (1C, C=N), 150.79 (2C, C3, 5), 161.84 (1C, C=O). FTIR (KBr) ν cm−1: 3250.19 (N-H), 3032.16 (C-Har), 1689.09 (C=O), 1621.50 (C=N-N), 1599.80 (C C ) (C ) 13C-NMR (75 MHz, DMSO) δ ppm: 107.98 (1C, C2′), 112.57 (1C, C3′), 120.06 (1C, C4′), 121.31 (1C, C6′), 122.01 (2C, C2,6), 128.05 (1C, C9′), 133.28 (1C, C1′), 138.47 (1C, C8′), 142.16 (1C, C=N), 150.79 (2C, C3, 5), 161.84 (1C, C=O). (E)-N -((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) -dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4 / / ( / / ) R (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H, 0 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, =N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). Hz, 1H), 7.18 (ddd, J = 8.3, 7.0, 1.2 Hz, 1H), 7.47 (dq, J = 8.2, 0.9 Hz, 1H), 7.58 (dd, J = 7.9, 1.1 Hz, 1H), 7.86 (dd, J = 4.4, 1.6 Hz, 2H), 8.51 (s, 1H), 8.81 (dd, J = 4.4, 1.7 Hz, 2H), 11.65 (s, 1H), 12.05 (s, 1H). 13C-NMR (75 MHz, DMSO) δ ppm: 107.98 (1C, C2′), 112.57 (1C, C3′), 120.06 (1C, C4′), 121.31 (1C, 1H-NMR (300 MHz, DMSO-d6) δ ppm: 76.90 (dd, J = 2.1, 0.9 Hz, 1H), 7.02 (ddd, J = 8.0, 7.0, 1.1 Hz, 1H), 7.18 (ddd, J = 8.3, 7.0, 1.2 Hz, 1H), 7.47 (dq, J = 8.2, 0.9 Hz, 1H), 7.58 (dd, J = 7.9, 1.1 Hz, 1H), 7.86 (dd, J = 4.4, 1.6 Hz, 2H), 8.51 (s, 1H), 8.81 (dd, J = 4.4, 1.7 Hz, 2H), 11.65 (s, 1H), 12.05 (s, 1H). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 76.90 (dd, J = 2.1, 0.9 Hz, 1H), 7.02 (ddd, J = 8.0, 7.0, 1.1 Hz, 1H), 7.18 (ddd, J = 8.3, 7.0, 1.2 Hz, 1H), 7.47 (dq, J = 8.2, 0.9 Hz, 1H), 7.58 (dd, J = 7.9, 1.1 Hz, 1H), 7.86 (dd, J = 4.4, 1.6 Hz, 2H), 8.51 (s, 1H), 8.81 (dd, J = 4.4, 1.7 Hz, 2H), 11.65 (s, 1H), 12.05 (s, 1H). ( ) R (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H, 0 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, =N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). 7.86 (dd, J 4.4, 1.6 Hz, 2H), 8.51 (s, 1H), 8.81 (dd, J 4.4, 1.7 Hz, 2H), 11.65 (s, 1H), 12.05 (s, 1H). (E)-N -((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) -dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4 13C-NMR (75 MHz, DMSO) δ ppm: 107.98 (1C, C2′), 112.57 (1C, C3′), 120.06 (1C, C4′), 121.31 (1C, C6′), 122.01 (2C, C2 6), 128.05 (1C, C9′), 133.28 (1C, C1′), 138.47 (1C, C8′), 142.16 (1C, C=N), 150.79 (2C, C3 5), 2.5 C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). R (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H, 0 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 (s, C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). R (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, .19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, Hz, 1H), 7.18 (ddd, J = 8.3, 7.0, 1.2 Hz, 1H), 7.47 (dq, J = 8.2, 0.9 Hz, 1H), 7.58 (dd, J = 7.9, 1.1 Hz, 1H), 7.86 (dd, J = 4.4, 1.6 Hz, 2H), 8.51 (s, 1H), 8.81 (dd, J = 4.4, 1.7 Hz, 2H), 11.65 (s, 1H), 12.05 (s, 1H). 13C-NMR (75 MHz, DMSO) δ ppm: 107.98 (1C, C2′), 112.57 (1C, C3′), 120.06 (1C, C4′), 121.31 (1C, 1H-NMR (300 MHz, DMSO-d6) δ ppm: 76.90 (dd, J = 2.1, 0.9 Hz, 1H), 7.02 (ddd, J = 8.0, 7.0, 1.1 Hz, 1H), 7.18 (ddd, J = 8.3, 7.0, 1.2 Hz, 1H), 7.47 (dq, J = 8.2, 0.9 Hz, 1H), 7.58 (dd, J = 7.9, 1.1 Hz, 1H), 7.86 (dd, J = 4.4, 1.6 Hz, 2H), 8.51 (s, 1H), 8.81 (dd, J = 4.4, 1.7 Hz, 2H), 11.65 (s, 1H), 12.05 (s, 1H). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 76.90 (dd, J = 2.1, 0.9 Hz, 1H), 7.02 (ddd, J = 8.0, 7.0, 1.1 Hz, 1H), 7.18 (ddd, J = 8.3, 7.0, 1.2 Hz, 1H), 7.47 (dq, J = 8.2, 0.9 Hz, 1H), 7.58 (dd, J = 7.9, 1.1 Hz, 1H), 7.86 (dd, J = 4.4, 1.6 Hz, 2H), 8.51 (s, 1H), 8.81 (dd, J = 4.4, 1.7 Hz, 2H), 11.65 (s, 1H), 12.05 (s, 1H). (E)-N -((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) -dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4 13C-NMR (75 MHz, DMSO) δ ppm: 107.98 (1C, C2′), 112.57 (1C, C3′), 120.06 (1C, C4′), 121.31 (1C, C6′), 122.01 (2C, C2,6), 128.05 (1C, C9′), 133.28 (1C, C1′), 138.47 (1C, C8′), 142.16 (1C, C=N), 150.79 (2C, C3, 5), 161.84 (1C, C=O). ), ( , , , ), ( , , ), ( , , ) R (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, .19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, 50.76 (2C, C3,5), 161.87 (1C, C=O). (C=Car), 1548.50 (Car N). UV (EtOH, 52.65 μM, 25 °C): λ = 206 nm, ε = 27,480 dm3·mol−1·cm−1, λ = 350 nm, ε = 33,825 d 3 l 1 1 FTIR (KBr) ν cm−1: 3250.19 (N-H), 3032.16 (C-Har), 1689.09 (C=O), 1621.50 (C=N-N), 1599.80 (C=Car), 1548.50 (Car N). U (E O °C) 6 d l FTIR (KBr) ν cm−1: 3250.19 (N-H), 3032.16 (C-Har), 1689.09 (C=O), 1621.50 (C=N-N), 1599.80 (C=Car), 1548.50 (Car ( ) ( ) KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.84 , 1549.40 (Car N). N). (C=Car), 1548.50 (Car N). UV (EtOH, 52.65 μM, 25 °C): λ = 206 nm, ε = 27,480 dm3·mol−1·cm−1, λ = 350 nm, ε = 33,825 d l FTIR (KBr) ν cm−1: 3250.19 (N-H), 3032.16 (C-Har), 1689.09 (C=O), 1621.50 (C=N-N), 1599.80 (C=Car), 1548.50 (Car N). FTIR (KBr) ν cm−1: 3250.19 (N-H), 3032.16 (C-Har), 1689.09 (C=O), 1621.50 (C=N-N), 1599.80 (C=Car), 1548.50 (Car KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.84 , 1549.40 (Car N). N). dm3·mol−1·cm−1. MS (ES, TOF, MeOH) m/z: 265.1090 [M + H+]. HRMS (ES TOF) / [M H ] l f C H N O 265 1089 F d 265 1090 UV (EtOH, 52.65 μM, 25 °C): λ = 206 nm, ε = 27,480 dm3·mol−1·cm−1, λ = 350 nm, ε = 33,825 dm3·mol−1·cm−1. S (ES O O ) / OH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. TOF, MeOH) m/z: 266.1046 [M + H+]. UV (EtOH, 52.65 µM, 25 ◦C): λ = 206 nm, ε = 27,480 dm3·mol−1·cm−1, λ = 350 nm, ε = 33,825 dm3·mol−1·cm−1. dm3·mol−1·cm−1. MS (ES, TOF, MeOH) m/z: 265.1090 [M + H+]. (E)-N -((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) -dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4 HRMS (ES TOF) / [M H+] l f C H N O 265 1089 F d 265 1090 UV (EtOH, 52.65 μM, 25 °C): λ = 206 nm, ε = 27,480 dm3·mol−1·cm−1, λ = 350 nm, ε = 33,825 dm3·mol−1·cm−1. MS (ES TOF M OH) / 265 1090 [M H ] OH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. TOF, MeOH) m/z: 266.1046 [M + H+]. UV (EtOH, 52.65 µM, 25 ◦C): λ = 206 nm, ε = 27,480 dm3·mol−1·cm−1, λ = 350 nm, ε = 33,825 dm3·mol−1·cm−1. HRMS (ES, TOF) m/z: [M + H+] calc. for C1 X Ray structure of this compound has been MS (ES, TOF, MeOH) m/z: 265.1090 [M + H HRMS (ES TOF) m/z: [M + H+] calc for C15 ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1 MS (ES, TOF, MeOH) m/z: 265.1090 [M + H+]. HRMS (ES, TOF) m/z: [M + H+] calc. for C1 X Ray structure of this compound has been MS (ES, TOF, MeOH) m/z: 265.1090 [M + H HRMS (ES TOF) m/z: [M + H+] calc for C ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1 MS (ES, TOF, MeOH) m/z: 265.1090 [M + H+]. HRMS (ES, TOF) m/z: [M + H+] calc. for C15H13N4O: 265.1089. Found: 265.1090. X-Ray structure of this compound has been recently reported [83]. MS (ES, TOF, MeOH) m/z: 265.1090 [M + H+]. HRMS (ES, TOF) m/z: [M + H+] calc. for C15H13N4O: 265.1089. Found: 265.1090. X-Ray structure of this compound has been recently reported [83]. (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1046. MS (ES, TOF, MeOH) m/z: 265.1090 [M + H+]. HRMS (ES, TOF) m/z: [M + H+] calc. for C15H13N4O: 265.1089. Found: 265.1090. X Ray structure of this compound has been recently reported [83] , [ ] X-Ray structure of this compound has been recently reported [83]. ( , , ) [ ] HRMS (ES, TOF) m/z: [M + H+] calc. for C15H13N4O: 265.1089. Found: 265.1090. X-Ray structure of this compound has been recently reported [83]. (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. Found: 266.1046. MS (ES, TOF, MeOH) m/z: 265.1090 [M + H+]. HRMS (ES, TOF) m/z: [M + H+] calc. for C15H13N4O: 265.1089. Found: 265.1090. X-Ray structure of this compound has been recently reported [83]. HRMS (ES, TOF) m/z: [M + H+] calc. (E)-N -((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) -dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4 0 82 PE/EtA /M OH (5 5 3 / / ) p ( ) / / ( / / ) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 76.90 (dd, J = 2.1, 0.9 Hz, 1H), 7.02 (ddd, J = 8.0, 7.0, 1.1 m.p.: 231 °C (dec.). Rf: 0.82 PE/EtAc/MeOH (5:5:3 v/v/v). m.p.: 231 ◦C (dec.). Rf: 0.82 PE/EtAc/MeOH (5:5:3 v/v/v). 2.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). p ( ) ( ) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 76.90 (dd, J = 2 m.p.: 231 °C (dec.). Rf: 0.82 PE/EtAc/MeOH (5:5:3 v/v/v) m.p.: 231 ◦C (dec.). Rf: 0.82 PE/EtAc/MeOH (5:5:3 v/v/v). .5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). Hz, 1H), 7.18 (ddd, J = 8.3, 7.0, 1.2 Hz, 1H), 7.47 (dq, J = 8.2, 0.9 Hz, 1H), 7.58 (dd, J = 7.9, 1.1 Hz, 1H), 7.86 (dd, J = 4.4, 1.6 Hz, 2H), 8.51 (s, 1H), 8.81 (dd, J = 4.4, 1.7 Hz, 2H), 11.65 (s, 1H), 12.05 (s, 1H). 13C-NMR (75 MHz, DMSO) δ ppm: 107.98 (1C, C2′), 112.57 (1C, C3′), 120.06 (1C, C4′), 121.31 (1C, C6′), 122.01 (2C, C2,6), 128.05 (1C, C9′), 133.28 (1C, C1′), 138.47 (1C, C8′), 142.16 (1C, C=N), 150.79 (2C, C3, 5), 161.84 (1C, C=O). p ( ) ( ) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 76.90 (dd, J = 2.1, 0.9 Hz, 1H), 7.02 (ddd, J = 8.0, 7.0, 1.1 Hz, 1H), 7.18 (ddd, J = 8.3, 7.0, 1.2 Hz, 1H), 7.47 (dq, J = 8.2, 0.9 Hz, 1H), 7.58 (dd, J = 7.9, 1.1 Hz, 1H), 7.86 (dd, J = 4.4, 1.6 Hz, 2H), 8.51 (s, 1H), 8.81 (dd, J = 4.4, 1.7 Hz, 2H), 11.65 (s, 1H), 12.05 (s, 1H). 13C-NMR (75 MHz, DMSO) δ ppm: 107.98 (1C, C2′), 112.57 (1C, C3′), 120.06 (1C, C4′), 121.31 (1C, C6′), 122.01 (2C, C2,6), 128.05 (1C, C9′), 133.28 (1C, C1′), 138.47 (1C, C8′), 142.16 (1C, C=N), 150.79 p ( ) f ( ) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 76.90 (dd, J = 2.1, 0.9 Hz, 1H), 7.02 (ddd, J = 8.0, 7.0, 1.1 Hz, 1H), 7.18 (ddd, J = 8.3, 7.0, 1.2 Hz, 1H), 7.47 (dq, J = 8.2, 0.9 Hz, 1H), 7.58 (dd, J = 7.9, 1.1 Hz, 1H), 7.86 (dd, J = 4.4, 1.6 Hz, 2H), 8.51 (s, 1H), 8.81 (dd, J = 4.4, 1.7 Hz, 2H), 11.65 (s, 1H), 12.05 (s, 1H). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) ), ( , , ), ( , , ), ( , , ) R (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C, 19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C, 50.76 (2C, C3,5), 161.87 (1C, C=O). 8.73–8.89 (m, 2H, H3,5), 11.83 (d, J = 6.0 Hz, 2H, N-H). 13C-NMR (75 MHz, DMSO) δ ppm: 111.59 (1C, C1′), 113,70 (1C, C6′), 114.42 (1C, C4′), 121.93 (2C, C2,6), 124.60 (1C, C2′), 125.71 (1C, C5′), 126.42 (1C, C9′), 132.71 (1C, C7′), 136.27 (1C, C8′), 141.38 (1C, C1), 9 °C (dec.). Rf: 0.1 EtOAc/MeOH (4:1 v/v). R (300 MHz, DMSO-d6) δ ppm: 2.43 (s, 3H, CH3), 8.42 (dd, J = 5.5, 1.8 Hz, 2H, H2,6), 8.53 FTIR (KBr) ν cm−1: 3127.58 (N-Hind), 2891.39 (C-Har), 1662.69 (C=O), 1618.34 (C=N-N), 1538 (C=Car), 1552.13 (Car N), 1041.12 (Car-Br). UV (EtOH 52 65 M 25 °C) λ 201 29 890 d 3 l 1 1 λ 226 25 981 , FTIR (KBr) ν cm−1: 3127.58 (N-Hind), 2891.39 (C-Har), 1662.69 (C=O), 1618.34 (C=N-N), 1538 (C=Car), 1552.13 (Car ( , ), ( , ) KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.84 , 1549.40 (Car N). N), 1041.12 (Car-Br). 146.13 (1C, C=N), 150.72 (2C, C3,5), 161.40 (1C, C=O). FTIR (KBr) ν cm−1: 3127.58 (N-Hind), 2891.39 (C-Har), 1662.69 (C=O), 1618.34 (C=N-N), 1538 (C C ) 1552 13 (C N) 1041 12 (C B ) pp ( ) ( J ) H-C=N), 9.11 (s, 1H, H3′), 9.14 (dd, J = 5.5, 1.8 Hz, 2H, H3,5), 15.98 (br, 2H, N-H). R (75 MHz, DMSO) δ ppm: 9.38 (1C, CH3), 123.60 (1C, C1′) 125.38 (2C, C2,6), 131.78 (1C, C5′), UV (EtOH, 52.65 μM, 25 °C): λ = 201 nm, ε = 29,890 dm3·mol−1·cm−1, λ = 226 nm, ε = 25,981 dm3·mol−1·cm−1, λ = 330 nm, ε = 18,196 dm3·mol−1·cm−1. MS (ES TOF MeOH) m/z: 343 0194 [M + H+] ( ) OH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. TOF, MeOH) m/z: 266.1046 [M + H+]. UV (EtOH, 52.65 µM, 25 ◦C): λ = 201 nm, ε = 29,890 dm3·mol−1·cm−1, λ = 226 nm, ε = 25,981 dm3·mol−1·cm−1, λ = 330 nm, ε = 18,196 dm3·mol−1·cm−1. (C=Car), 1552.13 (Car N), 1041.12 (Car-Br). E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) Compound 9 can also be found (CAS No.: 113143-44-5). HRMS (ES, TOF) m/z: [M + H+] calc. for C15H12BrN4O: 343.0193. Found: 343.0194. Compound 9 can also be found (CAS No.: 113143-44-5). OH, 161.58 μM, 25 C): λ 316 nm, ε 5551.73 dm mol cm (very poorly soluble). TOF, MeOH) m/z: 252.0866 [M + Na+]; 230.1049 [M + H+]. (ES TOF) m/z: [M + H+] calc for C11H12N5O: 230 1042 Found: 230 1049 Compound 9 can also be found (CAS No.: 113143-44-5). Compound 9 can also be found (CAS No.: 113143-44-5). HRMS (ES, TOF) m/z: [M + H+] calc. for C15H12BrN4O: 343.0193. Found: 343.0194. Compound 9 can also be found (CAS No.: 113143-44-5). TOF, MeOH) m/z: 252.0866 [M + Na+]; 230.1049 [M + H+]. ES TOF) m/z: [M + H+] calc for C11H12N5O: 230 1042 Found: 230 1049 (E)-N -((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) UV (EtOH, 52.65 μM, 25 °C): λ = 201 nm, ε = 29,890 dm3·mol−1·cm−1, λ = 226 nm, ε = 25,981 dm3 mol 1 cm 1 λ 330 nm ε 18 196 dm3 mol 1 cm 1 1C, C=N), 142.84 (1C, C3′), 144.03 (2C, C3,5), 147.78 (1C, C1), 159.52 (1C, C=O). KBr) ν cm−1: 3194.75 (N-H), 3097.19 (Car-H), 1660.58 (C=O), 1621.45 (C=N-N), 1602.24 UV (EtOH, 52.65 μM, 25 °C): λ = 201 nm, ε = 29,890 dm3·mol−1·cm−1, λ = 226 nm, ε = 25,981 dm3·mol−1·cm−1, λ = 330 nm, ε = 18,196 dm3·mol−1·cm−1. MS (ES TOF MeOH) m/z: 343 0194 [M + H+] OH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. TOF, MeOH) m/z: 266.1046 [M + H+]. UV (EtOH, 52.65 µM, 25 ◦C): λ = 201 nm, ε = 29,890 dm3·mol−1·cm−1, λ = 226 nm, ε = 25,981 dm3·mol−1·cm−1, λ = 330 nm, ε = 18,196 dm3·mol−1·cm−1. (C=Car), 1552.13 (Car N), 1041.12 (Car-Br). UV (EtOH, 52.65 μM, 25 °C): λ = 201 nm, ε = 29,890 dm3·mol−1·cm−1, λ = 226 nm, ε = 25,981 d 3 ol 1 1 λ 330 18 196 d 3 ol 1 1 1C, C=N), 142.84 (1C, C3′), 144.03 (2C, C3,5), 147.78 (1C, C1), 159.52 (1C, C=O). KBr) ν cm−1: 3194.75 (N-H), 3097.19 (Car-H), 1660.58 (C=O), 1621.45 (C=N-N), 1602.24 MS (ES, TOF, MeOH) m/z: 343.0194 [M + H HRMS (ES TOF) m/z: [M + H+] calc for C1 OF) m/z: [M + H+] calc. for C14H12N5O: 266.1 ES, TOF, MeOH) m/z: 343.0194 [M + H+]. dm3·mol−1·cm−1, λ = 330 nm, ε = 18,196 dm3·m MS (ES TOF MeOH) m/z: 343 0194 [M + H 49 (Car N). MS (ES, TOF, MeOH) m/z: 343.0194 [M + H HRMS (ES TOF) m/z: [M + H+] calc for C15 ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1 MS (ES, TOF, MeOH) m/z: 343.0194 [M + H+]. dm3·mol−1·cm−1, λ = 330 nm, ε = 18,196 dm3·m MS (ES TOF MeOH) m/z: 343 0194 [M + H 1551.49 (Car N). H 161 8 M 2 °C) λ 316 5551 73 d MS (ES, TOF, MeOH) m/z: 343.0194 [M + H HRMS (ES TOF) m/z: [M + H+] calc for C1 ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1 MS (ES, TOF, MeOH) m/z: 343.0194 [M + H+]. E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4) dih d 1H i d l 5 l) th l )i i ti h d id (4) dm3·mol−1·cm−1, λ = 330 nm, ε = 18,196 dm3· MS (ES TOF MeOH) m/z: 343 0194 [M + H 1551.49 (Car N). H 161 58 M 25 °C) λ 316 5551 73 d HRMS (ES, TOF) m/z: [M + H+] calc. for C15H12BrN4O: 343.0193. Found: 343.0194. Compound 9 can also be found (CAS No.: 113143-44-5). ( , , ) [ ] HRMS (ES, TOF) m/z: [M + H+] calc. for C15H12BrN4O: 343.0193. Found: 343.0194. Compound 9 can also be found (CAS No.: 113143-44-5). MS (ES, TOF, MeOH) m/z: 343.0194 [M + H+]. HRMS (ES, TOF) m/z: [M + H+] calc. for C15H12BrN4O: 343.0193. Found: 343.0194. Compound 9 can also be found (CAS No.: 113143-44-5). OH, 161.58 μM, 25 °C): λ = 316 nm, ε = 5551.73 dm3·mol−1·cm−1 (very poorly soluble). TOF, MeOH) m/z: 252.0866 [M + Na+]; 230.1049 [M + H+]. (ES TOF) m/z: [M + H+] calc for C11H12N5O: 230 1042 Found: 230 1049 HRMS (ES, TOF) m/z: [M + H+] calc. for C15H12BrN4O: 343.0193. Found: 343.0194. Compound 9 can also be found (CAS No.: 113143-44-5). HRMS (ES, TOF) m/z: [M + H+] calc. for C15H12BrN4O: 343.0193. Found: 343.0194. Compound 9 can also be found (CAS No.: 113143-44-5). MS (ES, TOF, MeOH) m/z: 343.0194 [M + H+]. HRMS (ES, TOF) m/z: [M + H+] calc. for C15H12BrN4O: 343.0193. Found: 343.0194. Compound 9 can also be found (CAS No : 113143-44-5) OH, 161.58 μM, 25 °C): λ = 316 nm, ε = 5551.73 dm3·mol−1·cm−1 (very poorly soluble). TOF, MeOH) m/z: 252.0866 [M + Na+]; 230.1049 [M + H+]. ES TOF) / [M H ] l f C H N O 230 1042 F d 230 1049 HRMS (ES, TOF) m/z: [M + H+] calc. for C15H12BrN4O: 343.0193. Found: 343.0194. Compound 9 can also be found (CAS No.: 113143-44-5). HRMS (ES, TOF) m/z: [M + H+] calc. for C15H12BrN4O: 343.0193. Found: 343.0194. Compound 9 can also be found (CAS No : 113143 44 5) MS (ES, TOF, MeOH) m/z: 343.0194 [M + H+]. HRMS (ES, TOF) m/z: [M + H+] calc. for C15H12BrN4O: 343.0193. Found: 343.0194. OH, 161.58 μM, 25 °C): λ = 316 nm, ε = 5551.73 dm3·mol−1·cm−1 (very poorly soluble). , TOF, MeOH) m/z: 252.0866 [M + Na+]; 230.1049 [M + H+]. Compound 9 can also be found (CAS No.: 113143-44-5). HRMS (ES, TOF) m/z: [M + H+] calc. for C15H12BrN4O: 343.0193. Found: 343.0194. (E)-N -((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) -dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4 for C15H13N4O: 265.1089. Found: 265.1090. X Ray structure of this compound has been recently reported [83] HRMS (ES, TOF) m/z: [M + H+] calc. for C15H13N4O: 265.1089. Found: 265.1090. X-Ray structure of this compound has been recently reported [83]. HRMS (ES, TOF) m/z: [M + H+] calc. for C15H13N4O: 265.1089. Found: 265.1090 X Ray structure of this compound has been recently reported [83] HRMS (ES, TOF) m/z: [M + H+] calc. for C15H13N4O: 265.1089. Found: 265.1090. X-Ray structure of this compound has been recently reported [8 X-Ray structure of this compound has been recently reported [83]. X-Ray structure of this compound has been recently reported [8 X-Ray structure of this compound has been recently reported [83]. 20 of 27 20 of 27 Molecules 2017, 22, 1457 HRMS (ES, (E)-N′-((4-nitro-1H-indol-3-yl)methylene)isonicotinohydrazide (11) (E)-N′-((4-nitro-1H-indol-3-yl)methylene)isonicotinohydrazide (11) (E)-N′-((3a,7a-dihydro-1H-indazol-5-yl)methylene)isonicotinohyd m.p.: 317.1 °C (dec.). Rf: 0.70 PE/EtOAc/MeOH (5:5:3 v/v/v) m.p.: 317.1 ◦C (dec.). Rf: 0.70 PE/EtOAc/MeOH (5:5:3 v/v/v). m.p.: 302.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). m.p.: 317.1 °C (dec.). Rf: 0.70 PE/EtOAc/MeOH (5:5:3 v/v/v). m.p.: 317.1 ◦C (dec.). Rf: 0.70 PE/EtOAc/MeOH (5:5:3 v/v/v). m.p.: 302.5 °C. Rf: 0.45 PE/EtOAc/MeOH (5:5:3 v/v/v). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.36 (t, J = 8.0 Hz, 1H, H5′), 7.84 (dd, J = 4.4, 1.7 Hz, 2H, H2,6), 7.94 (dd, J = 11.8, 7.9 Hz, 2H, H4′,6′), 8.28 (d, J = 2.9 Hz, 1H, H2′), 8.78 (dd, J = 4.4, 1.7 Hz, 2H, H3,5), 8.91 (s, 1H, H-C=N), 12.00 (s, 1H, N-H), 12.55 (s, 1H, N-H). 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.36 (t, J = 8.0 Hz, 1H, H5′), 7.84 (dd, J = 4.4, 1.7 Hz, 2H, H2,6), 7.94 (dd, J = 11.8, 7.9 Hz, 2H, H4′,6′), 8.28 (d, J = 2.9 Hz, 1H, H2′), 8.78 (dd, J = 4.4, 1.7 Hz, 2H, H3,5), 8.91 (s, 1H, H-C=N), 12.00 (s, 1H, N-H), 12.55 (s, 1H, N-H). p ( ) 1H-NMR (300 MHz, DMSO-d6) δ ppm: 7.63 (d, J = 8.7 Hz, 1H, H3′), 7.84 (dd, J = 4.4, 1.6 Hz, 2H H2,6), 7.90 (dd, J = 8.8, 1.5 Hz, 1H, H2′), 8.03–8.10 (m, 1H, H7′), 8.17 (t, J = 1.2 Hz, 1H, H6′), 8.57 ( 1H, H-C=N), 8.79 (s, 2H, H3,5), 12.01 (s, 1H, N-H), 13.31 (s, 1H, N-Hind). Physicochemical studies: hydrolytic stability and pKa determination: UV spectra were recorded with HP8453 (Agilent) temperature controll Physicochemical studies: hydrolytic stability and pKa determination: The pHs of the solutions were measured at room temperature (temperature probe) with a combined pH electrode with Seven Multi (Mettler Toledo) pHmeter. The pHs of the solutions were measured at room temperature (temperature probe) with a combined pH electrode with Seven Multi (Mettler Toledo) pHmeter. The pHs of the solutions were measured at room temperature (temperature probe) with a combined pH electrode with Seven Multi (Mettler Toledo) pHmeter. The pHs of the solutions were measured at room temperature (temperature probe) with a combined pH electrode with Seven Multi (Mettler Toledo) pHmeter. 4.3.1. Hydrolytic Stability 3.3.1. Hydrolytic Stability In the case of compounds 1a, 1b, 1c and 1d, a small quantity (respectively, 1.45 mg, 1.63 mg, 1.87 mg, and 1.79 mg) of each product was weighted and dissolved in 1 mL of EtOH. The aliquots were then placed in 100 mL standard flask with a concentration of 28% EtOH/H2O. Final concentrations of compounds were respectively 1a: 6.0 × 10−5 mol/L, 1b: 6.3 × 10−5 mol/L, 1c: 6.0 × 10−5 mol/L and 1d: 5.9 × 10−5 mol/L. In the case of compounds 5 and 7, a small quantity (respectively, 1.65 mg and 1.20 mg) of each d h d d d l d 4 L f E OH A f f h l ( l 1 30 In the case of compounds 1a, 1b, 1c and 1d, a small quantity (respectively, 1.45 mg, 1.63 mg, 1.87 mg, and 1.79 mg) of each product was weighted and dissolved in 1 mL of EtOH. The aliquots were then placed in 100 mL standard flask with a concentration of 28% EtOH/H2O. Final concentrations of compounds were respectively 1a: 6.0 × 10−5 mol/L, 1b: 6.3 × 10−5 mol/L, 1c: 6.0 × 10−5 mol/L and 1d: 5.9 × 10−5 mol/L. product was weighted and dissolved in 4 mL of EtOH. A fraction of this solution (respectively 1.30 mL and 1.36 mL) were placed in 50 mL standard flask and mixed with PIPES buffer (50 mM) with a final concentration of 5% EtOH/PIPES. The solution was stirred at room temperature; pH values and λ max of absorbance of the related d d f l h 15 h In the case of compounds 5 and 7, a small quantity (respectively, 1.65 mg and 1.20 mg) of each product was weighted and dissolved in 4 mL of EtOH. A fraction of this solution (respectively 1.30 mL and 1.36 mL) were placed in 50 mL standard flask and mixed with PIPES buffer (50 mM) with a final concentration of 5% EtOH/PIPES. compounds were measured for longer than 15 h. 4 3 2 pKa Determination [84] The solution was stirred at room temperature; pH values and λ max of absorbance of the related compounds were measured for longer than 15 h. (E)-N -((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) -dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4 Found: 266.10 MS (ES, TOF, MeOH) m/z: 332.0760 [M + Na+]; 310.0940 [M + H+]. HRMS (ES, TOF) m/z: [M + H+] calc. for C15H12N5O3: 310.0937. Found: 310.0940. HRMS (ES, TOF) m/z: [M + H+] calc. for C15H12N5O3: 310.0937. Found: 310.0940 HRMS (ES, TOF) m/z: [M + H+] calc. for C15H12N5O3: 310.0937. Found: 310.0940. (E)-N -((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) (E)-N′-((1H-indol-2-yl)methylene)isonicotinohydrazide (10) -dihydro-1H-indazol-5-yl)methylene)isonicotinohydrazide (4 13C-NMR (75 MHz, DMSO) δ ppm: 110.29 (1C, C9′), 117.59 (1C, C1′), 118.94 (1C, C4′), 119.92 (1C, C6′), 121.50 (1C, C5′), 122.01 (2C, C2, 6), 131.31 (1C, C2′), 139.55 (1C, C8′), 141.22 (1C, C1), 141.90 (1C, C-NO2), 146.43 (1C, C=N), 150.66 (2C, C3,5), 161.56 (1C, C=O). 13C-NMR (75 MHz, DMSO) δ ppm: 110.29 (1C, C9′), 117.59 (1C, C1′), 118.94 (1C, C4′), 119.92 (1C, C6′), 121.50 (1C, C5′), 122.01 (2C, C2, 6), 131.31 (1C, C2′), 139.55 (1C, C8′), 141.22 (1C, C1), 141.90 (1C, C-NO2), 146.43 (1C, C=N), 150.66 (2C, C3,5), 161.56 (1C, C=O). , ), ( , , , ), ( , , ), ( , , ) 13C-NMR (75 MHz, DMSO) δ ppm: 111.39 (1C, C3′), 121.98 (2C, C2,6), 122.73 (1C, C7′), 123.35 (1C C9′), 124.19 (1C, C2′), 127.23 (1C, C1′), 134.99 (1C, C6′), 141.07 (1C, C1), 141.14 (1C, C8′), 150.31 (1C C=N), 150.76 (2C, C3,5), 161.87 (1C, C=O). FTIR (KBr) ν cm−1: 3156.34 (N-H), 3137.68 (N-H), 3053.25 (C-Har), 1664.06 (C=O), 1628.34 (C=N-N), 1590.99 (C=Car), 1554.10 (Car N), 1513.15 (C=N-NO2). UV (EtOH 52 64 M 25 °C) λ 214 26 971 88 d 3 l 1 1 λ 331 17 046 35 , FTIR (KBr) ν cm−1: 3156.34 (N-H), 3137.68 (N-H), 3053.25 (C-Har), 1664.06 (C=O), 1628.34 (C=N-N), 1590.99 (C=Car), 1554.10 (Car ), ( , ), ( , ) FTIR (KBr) ν cm−1: 3188.96 (N-H), 3027.37 (Car-H), 1652 (C=O), 1622.47 (C=N-N), 1607.8 (Car=Car), 1549.40 (Car N). N), 1513.15 (C=N-NO2). UV (EtOH, 52.64 μM, 25 °C): λ = 214 nm, ε = 26,971.88 dm3·mol−1·cm−1, λ = 331 nm, ε = 17,046.35 dm3·mol−1·cm−1. UV (EtOH, 38.37 μM, 25 °C): λ = 234 nm, ε = 22,666.92 dm3·mol−1·cm−1. MS (ES, TOF, MeOH) m/z: 266.1046 [M + H+]. UV (EtOH, 52.64 µM, 25 ◦C): λ = 214 nm, ε = 26,971.88 dm3·mol−1·cm−1, λ = 331 nm, ε = 17,046.35 dm3·mol−1·cm−1. MS (ES, TOF, MeOH) m/z: 332.0760 [M + Na+]; 310.0940 [M + H HRMS (ES TOF) m/z: [M + H+] calc for C15H12N5O3: 310 0937 F HRMS (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042 MS (ES, TOF, MeOH) m/z: 332.0760 [M + Na+]; 310.0940 [M + H+]. MS (ES, TOF, MeOH) m/z: 332.0760 [M + Na+]; 310.0940 [M + H+]. HRMS (ES, TOF) m/z: [M + H+] calc. for C15H12N5O3: 310.0937. Found: 310.0940 HRMS (ES, TOF) m/z: [M + H+] calc. for C14H12N5O: 266.1042. 4.3. Physicochemical Studies: Hydrolytic Stability and pKa Determination 3.3. Physicochemical Studies: Hydrolytic Stability and pKa Determination 4.3. Physicochemical Studies: Hydrolytic Stability and pKa Determination 3.3. Physicochemical Studies: Hydrolytic Stability and pKa Determination Physicochemical studies: hydrolytic stability and pKa determination: UV spectra were recorded with HP8453 (Agilent) temperature controll Physicochemical studies: hydrolytic stability and pKa determination: A small quantity (1–2 3.3.2. pKa Determination aliquots were then placed in 100 mL standard flask with a final concentration of 28% EtOH/H2O. The ionic strength was fixed at 0.1 M with potassium chloride. The pH was adjusted to the required value by adding concentrated 0.1 M KOH or 0.1 M HCl. The solution was stirred at room temperature. The absorbance at three different wavelengths was measured. Absorbance vs. pH curves were plotted and the pKa values were evaluated graphically by geometric method. A small quantity (1–2 mg) of each product was weighted and dissolved in a 1 mL of EtOH. The aliquots were then placed in 100 mL standard flask with a final concentration of 28% EtOH/H2O. The ionic strength was fixed at 0.1 M with potassium chloride. The pH was adjusted to the required value by adding concentrated 0.1 M KOH or 0.1 M HCl. The solution was stirred at room temperature. The absorbance at three different wavelengths was measured. Absorbance vs. pH curves were plotted and the pKa values were evaluated graphically by geometric method [84]. 21 of 27 21 of 27 Molecules 2017, 22, 1457 3.4.2. MIC Determination in M.tb H37Rv strain was used as the reference strain. M.tb H37Rv and IC2 clinical isolate [31] were grown at 37 ◦C in Middlebrook 7H9 broth (Difco), supplemented with 0.05% Tween 80, or on solid Middlebrook 7H11 medium (Difco) supplemented with oleic acid-albumin-dextrose-catalase (OADC). MICs for the compounds were determined by means of the micro-broth dilution method. Dilutions of M.tb wild-type or mutant strain (about 105–106 cfu/mL) were streaked onto 7H11 solid medium containing a range of drug concentrations (0.125 µg/mL to 40 µg/mL). Plates were incubated at 37 ◦C for about 21 days and the growth was visually evaluated. The lowest drug dilution at which visible growth failed to occur was taken as the MIC value. Results were expressed as the average of at least three independent determinations. 3.4.3. Determination of LC50 Human primary fibroblast (MRC5 ATCC CCL171) were seeded at 5 k/well in a corning Cell bind 96-well plate and treated with growing concentration of compounds. Seventy-two hours post-treatment, cells were directly stained with Hoechst 33342 and imaged under a Cellomics Array scan HCS microscope using the cell cycle algorithm. Total number of cells were assessed in each condition and normalized over untreated wells. LC50 were determined as concentration inducing 50% reduction in cell number. 3.3.3. DMSO stability of Compound 1d The stability of compound 1a in DMSO was assessed at 25 ◦C. To this purpose, the compound was dissolved in DMSO, at a final concentration of 10 mM, and incubated for 16 h at 25 ◦C. The compound was then diluted in methanol, and analysed. The mass spectra were recorded in negative ESI resolution mode with a Thermo LTQ-XL mass spectrometer, and compared with those of compound 1a and of INH freshly dissolved in DMSO (10 mM) and diluted in methanol. 3.4. Biological Assays 3.4. Biological Assays 3.4.1. Inhibition Kinetics in the Presence of InhA Inhibition kinetic was performed as described [81,85]. Inhibition kinetic was performed as described [81,85]. Supplementary Materials: Supplementary Materials are available online. Acknowledgments: We thank the CNRS and University Paul Sabatier for financial support. We thank the Minister of Industry for Ph.D. grant (P.F.M.O.); William R. Jacobs for pMV261-InhA construct and grant VEGA 1/0284/15. We thank F. Gaillardo (NeoVirTech, ITAV, Centre P. Potier, Toulouse) for the cytotoxicity evaluation of the hydrazone compounds. Author Contributions: P.F.M.O.: Ph.D. student synthetic experiments; B.G., A.C. and M.Baron (co-director of P.F.M.O. thesis): supervised the synthetic part; C.A.B.: NMR and DFT studies; G.M. and B.S.O. performed the MIC experiments; L.R.C. performed MS; M.R.P. directed this part; J.M., J.K.: analysis on lipids and mycolic acids, J.K. directed this part; C.L.: InhA inhibition experiments; C.C.: hydrolytic stability and pKa determination; S.M.: NMR experiments; M.Baltas: conceive and direct the project, co-direct the P.F.M.O. thesis. All authors contributed in writing the manuscript. Conflicts of Interest: The authors declare no conflict of interest. 3.4.5. Determination of Sensitivity of M.tb H37Ra Strain Overproducing InhA to Hydrazones InhA protein was overproduced in M.tb H37Ra using pMV261-InhA construct as already described [88]. Sensitivity of InhA overproducing strain, as well as control strain carrying empty vector to compounds 1a, 3, 5, 7 and 10 was analysed by drop dilution methods. Both cultures grown in 7H9 broth supplemented with albumin-dextrose-catalase and 0.05% Tween 80 were adjusted to OD600 0.5 and 4 µL aliquots of 100, 10−1, 10−2 and 10−3 dilutions were dropped on 7H11 agar supplemented with oleic acid-albumin-dextrose-catalase and incubated 25 days at 37 ◦C. 4. Conclusions A series of hydrazones were synthesized through mechanochemistry and evaluated for their ability to inhibit M.tb H37Rv strain growth, the most active being 1a and 7. Imidazole derivative 5 and indazole one 10 are also active against H37Rv with their nitro substituent. Compounds 1a and 1b were the most effective against both M.tb H37Rv strain and drug-resistant IC2 isolate. The mechanism of anti-mycobacterial activities of selected hydrazones with the best scores regarding the MICs and toxicities was confirmed to be through the cessation of mycolic acid synthesis due to InhA inhibition inside the mycobacterial cell. 3.4.4. Analysis of the Effect of Hydrazones on Lipids and Mycolic Acids of M.tb H37Ra The modes of actions of selected hydrazones were analyzed by metabolic labeling of M.tb H37Ra strain with 14C acetate as already described [34]. Briefly, M.tb H37Ra culture was grown in Middlebrook 7H9 broth (Difco) supplemented with albumin-dextrose-catalase (Difco) and 0.05% Tween 80 (MP Biomedicals) at 37 ◦C till OD600 reached 0.24. The culture was then divided into 20 mL aliquots and tested compounds dissolved in DMSO were added in 0.41 µM (0.1 µg/mL) and 2.05 µM (0.5 µg/mL) final concentrations for 1a, 0.44 µM (0.1 µg/mL) and 2.2 µM (0.5 µg/mL) for 3, 0.38 µM (0.1 µg/mL) and 1.9 µM (0.5 µg/mL) for 5, 0.38 µM (0.1 µg/mL) and 1.9 µM (0.5 µg/mL) for 7, 0.38 µM (0.1 µg/mL) and 1.9 µM (0.5 µg/mL) for 10 and 36.5 µM (5 µg/mL) for INH. The final concentration of DMSO was kept at 1% in each experiment. 14C acetate (specific activity 106 mCi/mmol, ARC) in the final concentration of 0.5 µCi/mL was added to each of the cultures after 24 h of cultivation with shaking (120 rpm) and the cells were cultivated for next 24 h. Lipids were extracted from whole cells harvested from 10 mL culture aliquots as described earlier [34,86], dissolved in chloroform:methanol (2:1)—350 µL per 1 unit of OD600 of harvested cells. Five microliters were loaded on thin-layer chromatography (TLC) silica gel plates F254 (Merck) and the lipids were separated in chloroform:methanol:water (20:4:0.5) and detected by autoradiography. Fatty acid methyl esters (FAME) and mycolic acids methyl esters (MAME) were prepared from whole cells harvested from 10 mL culture aliquots as previously described [34,87]. Dried extracts were dissolved 22 of 27 Molecules 2017, 22, 1457 in chloroform:methanol (2:1) and loaded on TLC plates as described for lipid extracts. Different forms of methyl esters were separated by running three times in n-hexane: ethyl acetate (95:5) and detected by autoradiography. References Molecules 2007, 12, 1910–1939. [CrossRef] [PubMed] 10. Rasras, A.J.M.; Al-Tel, T.H.; Al-Aboudi, A.F.; Al-Qawasmeh, R.A. Synthesis and antimicrobial activity of cholic acid hydrazone analogues. Eur. J. Med. Chem. 2010, 45, 2307–2313. [CrossRef] [PubMed] 11. Mohareb, R.M.; Fleita, D.H.; Sakka, O.K. Novel Synthesis of Hydrazide-Hydrazone Derivatives and Their Utilization in the Synthesis of Coumarin, Pyridine, Thiazole and Thiophene Derivatives with Antitumor Activity. Molecules 2011, 16, 16–27. [CrossRef] [PubMed] 12. Asif, M. Pharmacologically potentials of hydrazonone containing compounds: A promising scaffold. Int. J. Adv. Chem. 2014, 2, 85–103. [CrossRef] 13. Bairwa, R.; Kakwani, M.; Tawari, N.R.; Lalchandani, J.; Ray, M.K.; Rajan, M.G.R.; Degani, M.S. Novel molecular hybrids of cinnamic acids and guanylhydrazones as potential antitubercular agents. Bioorg. Med. Chem. Lett. 2010, 20, 1623–1625. [CrossRef] [PubMed] 14. Carvalho, S.A.; da Silva, E.F.; de Souza, M.V.N.; Lourenço, M.C.S.; Vicente, F.R. Synthesis and antimycobacterial evaluation of new trans-cinnamic acid hydrazide derivatives. Bioorg. Med. Chem. Lett. 2008, 18, 538–541. [CrossRef] [PubMed] 15. Vavˇríková, E.; Polanc, S.; Koˇcevar, M.; Horváti, K.; B˝osze, S.; Stolaˇríková, J.; Vávrová, K.; Vinšová, J. New fluorine-containing hydrazones active against MDR-tuberculosis. Eur. J. Med. Chem. 2011, 46, 4937–4945. [CrossRef] [PubMed] 16. Oliveira, K.N.; Chiaradia, L.D.; Martins, P.G.A.; Mascarello, A.; Cordeiro, M.N.S.; Guido, R.V.C.; Andricopulo, A.D.; Yunes, R.A.; Nunes, R.J.; Terenzi, J.H. Sulfonyl-hydrazones of cyclic imides derivatives as potent inhibitors of the Mycobacterium tuberculosis protein tyrosine phosphatase B (PtpB). Med. Chem. Comm. 2011, 2, 500–504. [CrossRef] 17. Reddy, K.S.; Ramesh, M.; Srimai, V.; Chandra, K.S.; Satyender, A. Synthesis, antimycobacterial activity and docking studies of L-proline derived hydrazones. Der Pharma Chemica 2014, 6, 267–271. 18. Maccari, R.; Ottanà, R.; Vigorita, M.G. In vitro advanced antimycobacterial screening of isoniazid-related hydrazones, hydrazides and cyanoboranes: Part 14. Bioorg. Med. Chem. Lett. 2005, 15, 2509–2513. [CrossRef] [PubMed] 19. Naveen Kumar, H.S.; Parumasivam, T.; Jumaat, F.; Ibrahim, P.; Asmawi, M.Z.; Sadikun, A. Synthesis and evaluation of isonicotinoyl hydrazone derivatives as antimycobacterial and anticancer agents. Med. Chem. Res. 2014, 23, 269–279. [CrossRef] 20. Vavˇríková, E.; Polanc, S.; Koˇcevar, M.; Košmrlj, J.; Horváti, K.; B˝osze, S.; Stolaˇríková, J.; Imramovský, A.; Vinšová, J. New series of isoniazid hydrazones linked with electron-withdrawing substituents. Eur. J. Med. Chem. 2011, 46, 5902–5909. [CrossRef] [PubMed] 21. Wang, X.-L.; Zhang, Y.-B.; Tang, J.-F.; Yang, Y.-S.; Chen, R.-Q.; Zhang, F.; Zhu, H.-L. Design, synthesis and antibacterial activities of vanillic acylhydrazone derivatives as potential β-ketoacyl-acyl carrier protein synthase III (FabH) inhibitors. Eur. J. Med. Chem. 2012, 57, 373–382. References 1. WHO. Gobal Tuberculosis Report 2016. 2016. Available online: http://www.who.int/tb/publications/ global_report/en/ (accessed on 14 October 2016). 1. WHO. Gobal Tuberculosis Report 2016. 2016. Available online: http://www.who.int/tb/publications/ global_report/en/ (accessed on 14 October 2016). 2. Cynamon, M.H.; Zhang, Y.; Harpster, T.; Cheng, S.; DeStefano, M.S. High-dose isoniazid therapy for isoniazid-resistant murine Mycobacterium tuberculosis infection. Antimicrob. Agents Chemother. 1999, 43, 2922–2924. [PubMed] 2. Cynamon, M.H.; Zhang, Y.; Harpster, T.; Cheng, S.; DeStefano, M.S. High-dose isoniazid therapy for isoniazid-resistant murine Mycobacterium tuberculosis infection. Antimicrob. Agents Chemother. 1999, 43, 2922–2924. [PubMed] 3. Bemer-Melchior, P.; Bryskier, A.; Drugeon, H.B. Comparison of the in vitro activities of rifapentine and rifampicin against Mycobacterium tuberculosis complex. J. Antimicrob. Chemother. 2000, 46, 571–576. [CrossRef] [PubMed] 3. Bemer-Melchior, P.; Bryskier, A.; Drugeon, H.B. Comparison of the in vitro activities of rifapentine and rifampicin against Mycobacterium tuberculosis complex. J. Antimicrob. Chemother. 2000, 46, 571–576. [CrossRef] [PubMed] 4. Jain, A.; Mondal, R. Extensively drug-resistant tuberculosis: Current challenges and threats. FEMS Immunol. Med. Microbiol. 2008, 53, 145–150. [CrossRef] [PubMed] 4. Jain, A.; Mondal, R. Extensively drug-resistant tuberculosis: Current challenges and threats. FEMS Immunol. Med. Microbiol. 2008, 53, 145–150. [CrossRef] [PubMed] 5. Parida, S.K.; Axelsson-Robertson, R.; Rao, M.V.; Singh, N.; Master, I.; Lutckii, A.; Keshavjee, S.; Andersson, J.; Zumla, A.; Maeurer, M. Totally drug-resistant tuberculosis and adjunct therapies. J. Intern. Med. 2015, 277, 388–405. [CrossRef] [PubMed] 5. Parida, S.K.; Axelsson-Robertson, R.; Rao, M.V.; Singh, N.; Master, I.; Lutckii, A.; Keshavjee, S.; Andersson, J.; Zumla, A.; Maeurer, M. Totally drug-resistant tuberculosis and adjunct therapies. J. Intern. Med. 2015, 277, 388–405. [CrossRef] [PubMed] 6. Food and Drug Administration. Sirturo (bedaquiline) Product Insert. Silver Spring MD: Food and Drug Administration, 2015. Available online: http://www.accessdata.fda.gov/drugsatfda_docs/label/2012/ 204384s000lbl.pdf (accessed on 11 July 2015). 6. Food and Drug Administration. Sirturo (bedaquiline) Product Insert. Silver Spring MD: Food and Drug Administration, 2015. Available online: http://www.accessdata.fda.gov/drugsatfda_docs/label/2012/ 204384s000lbl.pdf (accessed on 11 July 2015). 23 of 27 Molecules 2017, 22, 1457 7. European Medicines Agency C for MP for HU. European Medicines Agency, Assessment Report, Deltyba. European Medicines Agency C for MP for HU: London, England, 2013. Procedure No EMEA/H/C/002552. 2015. Available online: http://www.ema.europa.eu/ema/index.jsp?curl=pages/medicines/human/ medicines/002552/smops/Positive/human_smop_000572.jsp&mid=WC0b01ac058001d127 (accessed on 11 July 2015). 8. Banerjee, D.R.; Biswas, R.; Das, A.K.; Basak, A. Design, synthesis and characterization of dual inhibitors against new targets FabG4 and HtdX of Mycobacterium tuberculosis. Eur. J. Med. Chem. 2015, 100, 223–234. [CrossRef] [PubMed] 9. Rollas, S.; Küçükgüzel, S.G. Biological Activities of Hydrazone Derivatives. References [CrossRef] [PubMed] 22. Hearn, M.J.; Cynamon, M.H.; Chen, M.F.; Coppins, R.; Davis, J.; Joo-On Kang, H.; Noble, A.; Tu-Sekine, B.; Terrot, M.S.; Trombino, D.; et al. Preparation andantitubercular activities in vitro and in vivo of novel Schiff bases of isoniazid. Eur. J. Med. Chem. 2009, 44, 4169–4178. [CrossRef] [PubMed] 23. Hearn, M.J.; Cynamon, M.H. Desing and synthesis of antituberculars: Preparation and evaluation against Mycobacterium tuberculosis of an isoniazid Schiff base. J. Antimicrob. Chemother. 2004, 53, 185–191. [CrossRef] [PubMed] 24. Ventura, C.; Martins, F. Application of quantitative structure−activity relationships to the modeling of antitubercular compounds 1. The hydrazide family. J. Med. Chem. 2008, 51, 612–624. [CrossRef] [PubMed] Molecules 2017, 22, 1457 24 of 27 25. Martins, F.; Santos, S.; Ventura, C.; Elvas-Leitão, R.; Santos, L.; Vitorino, S.; Reis, M.; Miranda, V.; Correia, H.F.; et al. Design, synthesis and biological evaluation of novel isoniazid derivatives with potent antitubercular activity. Eur. J. Med. Chem. 2014, 81, 119–138. [CrossRef] [PubMed] 26. De, P.; Baltas, M.; Bedos-Belval, F. Cinnamic acid derivatives as anticancer agents—A Curr. Med. Chem. 2011, 18, 1672–1703. [CrossRef] [PubMed] 27. De, P.; Bedos-Belval, F.; Vanucci-Bacqué, C.; Baltas, M. Cinnamic acid derivatives in tuberculosis, malaria and cardiovascular diseases—A review. Curr. Org. Chem. 2012, 16, 747–768. [CrossRef] 28. De, P.; De, K.; Veau, D.; Bedos-Belval, F.; Chassaing, S.; Baltas, M. Recent advances in the development of cinnamic-like derivatives as antituberculosis agents. Expert Opin. Ther. Pat. 2012, 22, 155–168. [CrossRef] [PubMed] 29. De, P.; Veau, D.; Bedos-Belval, F.; Chassaing, S.; Baltas, M. Cinnamic Derivatives in Tuberculosis. In Understanding Tuberculosis—New Approaches to Fighting Against Drug Resistance; Cardona, P.-J., Ed.; InTech: Rijeka, Croatia, 2012; pp. 337–362. [CrossRef] 30. Menendez, C.; Chollet, A.; Rodriguez, F.; Inard, C.; Pasca, M.R.; Lherbet, C.; Baltas, M. Chemical synthesis and biological evaluation of triazole derivatives as inhibitors of InhA and antituberculosis agents. Eur. J. Med. Chem. 2012, 52, 275–283. [CrossRef] [PubMed] 31. Menendez, C.; Rodriguez, F.; Ribeiro, A.L.; Zara, F.; Frongia, C.; Lobjois, V.; Saffon, N.; Pasca, M.R.; Lherbet, C.; Baltas, M. Synthesis and evaluation of α-ketotriazoles and α,β-diketotriazoles as inhibitors of Mycobacterium tuberculosis. Eur. J. Med. Chem. 2013, 69, 167–173. [CrossRef] [PubMed] 32. Menendez, C.; Mori, G.; Maillot, M.; Fabing, I. Synthesis and evaluation of β-hydroxytriazoles and related compounds as antitubercular agents. French-Ukrainian J. Chem. 2015, 3, 82–96. [CrossRef] 33. Veau, D.; Krykun, S.; Mori, G.; Orena, B.S.; Pasca, M.R.; Frongia, C.; Lobjois, V.; Chassaing, S.; Lherbet, C.; Baltas, M. References Solid-state and solvent-free synthesis of azines, pyrazoles, and pyridazinones using solid hydrazine. Tetrahedron Lett. 2013, 54, 1384–1388. [CrossRef] 6. Lee, B.; Kang, P.; Lee, K.H.; Cho, J.; Nam, W.; Lee, W.K.; Hur, N.H. Solid-state and solvent-free synthes azines, pyrazoles, and pyridazinones using solid hydrazine. Tetrahedron Lett. 2013, 54, 1384–1388. [Cross 57. Estévez, V.; Villacampa, M.; Menéndez, J.C. Three-component access to pyrroles promoted by the CAN–silver nitrate system under high-speed vibration milling conditions: A generalization of the Hantzsch pyrrole synthesis. Chem. Commun. 2013, 49, 591–593. [CrossRef] [PubMed] 58. Schmeyers, J.; Toda, F.; Boy, J.; Kaupp, G. Quantitative solid–solid synthesis of azomethines. J. Chem. Soc. Perk. Trans. 2 1998, 4, 989–994. [CrossRef] 59. Dolotko, O.; Wiench, J.W.; Dennis, K.W.; Pecharsky, V.K.; Balema, V.P. Mechanically induced reactions in organic solids: Liquid eutectics or solid-state processes? New J. Chem. 2010, 34, 25–28. [CrossRef] 60. Kaupp, G.; Schmeyers, J.; Boy, J. Iminium Salts in Solid-State Syntheses Giving 100% Yield. J. Für Prakt. Chem. 2000 342 269–280 [CrossRef] 59. Dolotko, O.; Wiench, J.W.; Dennis, K.W.; Pecharsky, V.K.; Balema, V.P. Mechanically induced reactions in organic solids: Liquid eutectics or solid-state processes? New J. Chem. 2010, 34, 25–28. [CrossRef] 60 Kaupp G ; Schmeyers J ; Boy J Iminium Salts in Solid State Syntheses Giving 100% Yield J Für Prakt Chem 60. Kaupp, G.; Schmeyers, J.; Boy, J. Iminium Salts in Solid-State Syntheses Giving 100% Yield. J. Für Prakt. Chem. 2000, 342, 269–280. [CrossRef] 61. Mokhtari, J.; Naimi-Jamal, M.R.; Hamzeali, H.; Dekamin, M.G.; Kaupp, G. Kneading Ball-milling and stoichiometric melts for the quantitative derivatization of carbonyl compounds with gas-solid recovery. ChemSusChem 2009, 2, 248–254. [CrossRef] [PubMed] 62. Nun, P.; Martin, C.; Martinez, J.; Lamaty, F. Solvent-free synthesis of hydrazones and their subsequent N-alkylation in a Ball-mill. Tetrahedron 2011, 67, 8187–8194. [CrossRef] 63. Shalini, K.; Sharma, P.; Kumar, N. Imidazole and its biological activities: A review. Chem. Sin. 2010, 63. Shalini, K.; Sharma, P.; Kumar, N. Imidazole and its biological activities: A review. Chem. Sin. 2010, 1, 36–47. 64. Verma, A.; Joshi, S.; Singh, D. Imidazole: Having versatile biological activities. J. Chem. 2013, 2013, 1–12. [CrossRef] 64. Verma, A.; Joshi, S.; Singh, D. Imidazole: Having versatile biological activities. J. Chem. 2013, 2013, 1–12. [CrossRef] 65. Thangadurai, A.; Minu, M.; Wakode, S.; Agrawal, S.; Narasimhan, B. Indazole: A medicinally important heterocyclic moiety. Med. Chem. Res. 2012, 21, 1509–1523. [CrossRef] 66. De Luca, L. References Triazolophthalazines: Easily accessible compounds with potent antitubercular activity. Chem. Med. Chem. 2016, 11, 1078–1089. [CrossRef] [PubMed] 34. Matviiuk, T.; Madacki, J.; Mori, G.; Orena, B.S.; Menendez, C.; Kysil, A.; André-Barrès, C.; Rodriguez, F.; Korduláková, J.; Mallet-Ladeira, S.; et al. Pyrrolidinone and pyrrolidine derivatives: Evaluation as inhibitors of InhA and Mycobacterium tuberculosis. Eur. J. Med. Chem. 2016, 123, 462–475. [CrossRef] [PubMed] 35. Matviiuk, T.; Mori, G.; Lherbet, C.; Rodriguez, F.; Pasca, M.R.; Gorichko, M.; Guidetti, B.; Voitenko, Z.; Baltas, M. Synthesis of 3-heteryl substituted pyrrolidine-2,5-diones via catalytic Michael reaction and evaluation of their inhibitory activity against InhA and Mycobacterium tuberculosis. Eur. J. Med. Chem. 2014, 71, 46–52. [CrossRef] [PubMed] 36. Matviiuk, T.; Rodriguez, F.; Saffon, N.; Mallet-Ladeira, S.; Gorichko, M.; de Jesus Lopes Ribeiro, A.L.; Pasca, M.R.; Lherbet, C.; Voitenko, Z.; Baltas, M. Design, chemical synthesis of 3-(9H-fluoren-9-yl)pyrrolidine-2,5-dione derivatives and biological activity against enoyl-ACP reductase (InhA) and Mycobacterium tuberculosis. Eur. J. Med. Chem. 2013, 70, 37–48. [CrossRef] [PubMed] 37. Pavan, F.R.; da S Maia, P.I.; Leite, S.R.A.; Deflon, V.M.; Batista, A.A.; Sato, D.N.; Franzblau, S.G.; Leite, C.Q.F. Thiosemicarbazones, semicarbazones, dithiocarbazates and hydrazide/hydrazones: Anti- Mycobacterium tuberculosis activity and cytotoxicity. Eur. J. Med. Chem. 2010, 45, 1898–1905. [CrossRef] [PubMed] 38. Oliveira, P.F.M.; Baron, M.; Chamayou, A.; André-Barrès, C.; Guidetti, B.; Baltas, M. Solvent-free mechanochemical route for green synthesis of pharmaceutically attractive phenol-hydrazones. RSC Adv. 2014, 4, 56736–56742. [CrossRef] 39. Marques de Oliveira, P.F. Investigation of Mechanochemical Synthesis of Condensed 1,4-diazines and Pharmaceutically Attractive Hydrazones. Ph.D. Thesis, Ecole des mines d’Albi-Carmaux, Albi, France, October 2015. 40. Baláž, P. Mechanical activation in hydrometallurgy. Int. J. Miner. Process. 2003, 72, 341–354. [CrossR 41. Balema, V.P.; Wiench, J.W.; Pruski, M.; Pecharsky, V.K. Mechanically induced solid-state generation of phosphorus ylides and the solvent-free wittig reaction. J. Am. Chem. Soc. 2002, 124, 6244–6245. [CrossRef] [PubMed] 42. Watanabe, H.; Hiraoka, R.; Senna, M. A Diels-Alder reaction catalyzed by eutectic complexes autogenously formed from solid state phenols and quinones. Tetrahedron Lett. 2006, 47, 4481–4484. [CrossRef] 42. Watanabe, H.; Hiraoka, R.; Senna, M. A Diels-Alder reaction catalyzed by eutectic complexes autogenously formed from solid state phenols and quinones. Tetrahedron Lett. 2006, 47, 4481–4484. [CrossRef] 43. Zhang, Z.; Peng, Z.-W.; Hao, M.-F.; Gao, J.-G. Mechanochemical diels-alder cycloaddition reactions for straightforward synthesis of endo-norbornene derivatives Synlett 2010 2010 2895–2898 [CrossRef] 43. Zhang, Z.; Peng, Z.-W.; Hao, M.-F.; Gao, J.-G. Mechanochemical diels-alder cycloaddition reactions for straightforward synthesis of endo-norbornene derivatives. Synlett 2010, 2010, 2895–2898. References [CrossRef] 25 of 27 Molecules 2017, 22, 1457 44. Zhang, Z.; Dong, Y.-W.; Wang, G.-W.; Komatsu, K. Highly efficient mechanochemical reactions of 1,3-dicarbonyl compounds with chalcones and azachalcones catalyzed by potassium carbonate. Synlett 2004, 61–64. [CrossRef] 45. Zhang, Z.; Dong, Y.-W.; Wang, G.-W.; Komatsu, K. Mechanochemical Michael reactions of chalcones and azachalcones with ethyl acetoacetate catalyzed by K2CO3 under solvent-free conditions. Chem. Lett. 2004, 33, 168–169. [CrossRef] 46. Kaupp, G.; Naimi-Jamal, M.R.; Schmeyers, J. Quantitative reaction cascades of Ninhydrin in the solid state. Chem. Eur. J. 2002, 8, 594–600. [CrossRef] 47. Heintz, A.S.; Gonzales, J.E.; Fink, M.J.; Mitchell, B.S. Catalyzed self-aldol reaction of valeraldehyde via a mechanochemical method. J. Mol. Catal. A Chem. 2009, 304, 117–120. [CrossRef] 48. Burmeister, C.F.; Stolle, A.; Schmidt, R.; Jacob, K.; Breitung-Faes, S.; Kwade, A. Experimental and Computational Investigation of Knoevenagel Condensation in Planetary Ball Mills. Chem. Eng. Technol. 2014, 37, 857–864. [CrossRef] 49. Fulmer, D.A.; Shearouse, W.C.; Medonza, S.T.; Mack, J. Solvent-free Sonogashira coupling reaction via high speed ball milling. Green Chem. 2009, 11, 1821. [CrossRef] 50. Thorwirth, R.; Stolle, A.; Ondruschka, B. Fast copper-, ligand- and solvent-free Sonogashira coupling in a ball mill. Green Chem. 2010, 12, 985. [CrossRef] 51. Schneider, F.; Ondruschka, B. Mechanochemical solid-state Suzuki reactions using an in situ generated base. ChemSusChem 2008, 1, 622–625. [CrossRef] [PubMed] 52. Bernhardt, F.; Trotzki, R.; Szuppa, T.; Stolle, A.; Ondruschka, B. Solvent-free and time-efficient Suzuki-Miyaura reaction in a ball mill: The solid reagent system KF-Al2O3 under inspection. Beilstein J. Org. Chem. 2010, 6, 30–34. [CrossRef] [PubMed] 53. Tan, D.; Loots, L.; Frišˇci´c, T. Towards medicinal mechanochemistry: Evolution of milling from pharmaceutical solid form screening to the synthesis of active pharmaceutical ingredients (APIs). Chem. Commun. 2016. [CrossRef] [PubMed] 54. Mikhailenko, M.A.; Shakhtshneider, T.P.; Boldyrev, V.V. Acylation of sulfathiazole with maleic anhydride under mechanochemical activation. Mendeleev Commun. 2007, 17, 315–317. [CrossRef] 54. Mikhailenko, M.A.; Shakhtshneider, T.P.; Boldyrev, V.V. Acylation of sulfathiazole with maleic anhydride under mechanochemical activation. Mendeleev Commun. 2007, 17, 315–317. [CrossRef] 55. Carlier, L.; Baron, M.; Chamayou, A.; Couarraze, G. Use of co-grinding as a solvent-free solid state method 5. Carlier, L.; Baron, M.; Chamayou, A.; Couarraze, G. Use of co-grinding as a solvent-free solid state met to synthesize dibenzophenazines. Tetrahedron Lett. 2011, 52, 4686–4689. [CrossRef] y p , , [ ] 56. Lee, B.; Kang, P.; Lee, K.H.; Cho, J.; Nam, W.; Lee, W.K.; Hur, N.H. References Naturally occurring and synthetic imidazoles: Their chemistry and their biological activities. Curr. Med. Chem. 2006, 13, 1–23. [CrossRef] [PubMed] Molecules 2017, 22, 1457 26 of 27 26 of 27 67. Sharma, V.; Kumar, P.; Pathak, D. Biological importance of the indole nucleus in recent years: A comprehensive review. J. Heterocycl. Chem. 2010, 47, 491–502. [CrossRef] 68. Oliveira, P.F.M.; Haruta, N.; Chamayou, A.; Guidetti, B.; Baltas, M.; Tanaka, K.; Sato, T.; Baron, M. Comprehensive experimental investigation of mechanically induced 1,4-diazines synthesis in solid state. Tetrahedron 2017, 73, 2305–2310. [CrossRef] 69. Palla, G.; Predieri, G.; Domiano, P.; Vignali, C.; Turner, W. Conformational behaviour and/isomerization of -acyl and -aroylhydrazones. Tetrahedron 1986, 42, 3649–3654. [CrossRef] 70. Syakaev, V.V.; Podyachev, S.N.; Buzykin, B.I.; Latypov, S.K.; Habicher, W.D.; Konovalov, A.I. NMR study of conformation and isomerization of aryl- and heteroarylaldehyde 4-tert-butylphenoxyacetylhydrazones. J. Mol. Struct. 2006, 788, 55–62. [CrossRef] 71. Ünsal-Tan, O.; Özden, K.; Rauk, A.; Balkan, A. Synthesis and cyclooxygenase inhibitory activities of some N-acylhydrazone derivatives of isoxazolo[4,5-d]pyridazin-4(5H)-ones. Eur. J. Med. Chem. 2010, 45, 2345–2352. [CrossRef] 72. Patorski, P.; Wyrzykiewicz, E.; Bartkowiak, G. Synthesis and conformational assignment of N-(E)-stilbenyloxymethylenecarbonyl-substituted hydrazones of acetone and o- (m-and p-) chloro- (nitro-) benzaldehydes by means of and NMR spectroscopy. J. Spectrosc. 2013, 1–12. [CrossRef] 73. Lodewyk, M.W.; Siebert, M.R.; Tantillo, D.J. Computational prediction of 1 H and 13 C chemical shifts: A useful tool for natural product, mechanistic, and synthetic organic chemistry. Chem. Rev. 2012, 112, 1839–1862. [CrossRef] [PubMed] 74. Kalia, J.; Raines, R.T. Hydrolytic stability of hydrazones and oximes. Angew. Chemie Int. Ed. 2008, 47, 7523–7526. [CrossRef] [PubMed] 75. Wiberg, K.B.; Glaser, R. Resonance interactions in acyclic systems. 4. stereochemistry, energetics, and electron distributions in 3-center-four-.pi.-electron systems A:BC. J. Am. Chem. Soc. 1992, 114, 841–850. [CrossRef] 76. Doungdee, P.; Sarel, S.; Wongvisetsirikul, N.; Avramovici-Grisaru, S. Iron chelators of the pyridoxal 2-pyridyl hydrazone class. Part 4. pKa values of the chelators and their relevance to biological properties. J. Chem. Soc. Perkin Trans. 1995, 2, 319. [CrossRef] 77. Vilchèze, C.; Jacobs, W.R., Jr. The mechanism of isoniazid killing: Clarity through the scope of genetics. Annu. Rev. Microbiol. 2007, 61, 35–50. [CrossRef] [PubMed] 78. Johnsson, K.; Schultz, P.G. Mechanistic studies of the oxidation of isoniazid by the catalase peroxidase from Mycobacterium tuberculosis. J. Am. Chem. Soc. 1994, 116, 7425–7426. [CrossRef] 79. Rawat, R.; Whitty, A.; Tonge, P.J. References The isoniazid-NAD adduct is a slow, tight-binding inhibitor of InhA, the Mycobacterium tuberculosis enoyl reductase: Adduct affinity and drug resistance. Proc. Natl. Acad. Sci. USA 2003, 100, 13881–13886. [CrossRef] [PubMed] 80. Lei, B.; Wei, C.J.; Tu, S.C. Action mechanism of antitubercular isoniazid-activation by Mycobacterium tuberculosis KatG, isolation, and characterization of InhA inhibitor. J. Biol. Chem. 2000, 275, 2520–2526. [CrossRef] [PubMed] 81. Menendez, C.; Gau, S.; Lherbet, C.; Rodriguez, F.; Inard, C.; Pasca, M.R.; Baltas, M. Synthesis and biological activities of triazole derivatives as inhibitors of InhA and antituberculosis agents. Eur. J. Med. Chem. 2011, 46, 5524–5531. [CrossRef] [PubMed] 82. Campbell, P.J.; Morlock, G.P.; Sikes, R.D.; Dalton, T.L.; Metchock, B.; Starks, A.M.; Hooks, D.P.; Cowan, L.S.; Plikaytis, B.B.; Posey, J.E. Molecular detection of mutations associated with first- and second-line drug resistance compared with conventional drug susceptibility testing of Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 2011, 55, 2032–2041. [CrossRef] [PubMed] 83. Saranaya, S.; Haribabu, J.; Bhuvanesh, N.S.P.; Karvembu, R.; Gayathri, D. Crystal structures of the Schiff base derivatives (E)-N[(1H-indol-3-yl)methylidene]isonicotino-hydrazide ethanol monosolvate and (E)-N-methyl-2-[1-(2-oxo-2H-chromen-3-yl)ethyl-idene]hydrazinecarbothioamide. Acta Crystallogr. E Crystallogr. Commun. 2017, 73 Pt 4, 594–597. [CrossRef] [PubMed] 84. Mochon, M. Salicylaldehyde-1-phthalazinohydrazone as an analytical reagent. Talanta 1986, 33, 627–630. [CrossRef] 85. Chollet, A.; Mori, G.; Menendez, C.; Rodriguez, F.; Fabing, I.; Pasca, M.R.; Madacki, J.; Korduláková, J.; Constant, P.; Quémard, A.; et al. Design, synthesis and evaluation of new GEQ derivatives as inhibitors of InhA enzyme and Mycobacterium tuberculosis growth. Eur. J. Med. Chem. 2015, 101, 218–235. [CrossRef] [PubMed] 27 of 27 27 of 27 Molecules 2017, 22, 1457 86. Stadthagen, G.; Korduláková, J.; Griffin, R.; Constant, P.; Bottová, I.; Barilone, N.; Gicquel, B.; Daffé, M.; Jackson, M. p-Hydroxybenzoic acid synthesis in Mycobacterium tuberculosis. J. Biol. Chem. 2005, 280, 40699–40706. [CrossRef] [PubMed] 87. Phetsuksiri, B.; Baulard, A.R.; Cooper, A.M.; Minnikin, D.E.; Douglas, J.D.; Besra, G.S.; Brennan, P.J. Antimycobacterial activities of isoxyl and new derivatives through the inhibition of mycolic acid synthesis. Antimicrob. Agents Chemother. 1999, 43, 1042–1051. [PubMed] 88. Larsen, M.H.; Vilchèze, C.; Kremer, L.; Besra, G.S.; Parsons, L.; Salfinger, M.; Heifets, L.; Hazbon, M.H.; Alland, D.; Sacchettini, J.C.; et al. Overexpression of inhA, but not kasA, confers resistance to isoniazid and ethionamide in Mycobacterium smegmatis, M. bovis BCG and M. tuberculosis. Mol. Microbiol. 2002, 46, 453–466. [CrossRef] [PubMed] Sample Availability: Samples of the compounds 1a–d, 2–11 are available from the authors. © 2017 by the authors. Licensee MDPI, Basel, Switzerland. References This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
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Monitoring tumor response to the vascular disrupting agent CKD-516 in a rabbit VX2 intramuscular tumor model using PET/MRI: Simultaneous evaluation of vascular and metabolic parameters
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RESEARCH ARTICLE Materials and methods Editor: Gayle E. Woloschak, Northwestern University Feinberg School of Medicine, UNITED STATES With institutional Animal Care and Use Committee approval, 18 VX2 carcinoma tumors implanted in bilateral back muscles of 9 rabbits were evaluated. Serial PET/MRI were per- formed before, 4 hours after and 1-week after vascular disrupting agent, CKD-516 at a dose of 0.7 mg/kg (treated group, n = 10) or saline (control group, n = 8) administration. PET/MRI- derived parameters and their interval changes were compared between the treated and con- trol group by using the linear mixed model. Each parameter within each group was also com- pared by using the linear mixed model. Received: July 2, 2017 Accepted: January 29, 2018 Published: February 13, 2018 Copyright: © 2018 Ahn et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Objectives To determine whether the CKD-516 produces a significant change in vascular and meta- bolic parameters in PET/MRI Abstract Citation: Ahn SY, Goo JM, Lee KH, Ha S, Paeng JC (2018) Monitoring tumor response to the vascular disrupting agent CKD-516 in a rabbit VX2 intramuscular tumor model using PET/MRI: Simultaneous evaluation of vascular and metabolic parameters. PLoS ONE 13(2): e0192706. https:// doi.org/10.1371/journal.pone.0192706 Monitoring tumor response to the vascular disrupting agent CKD-516 in a rabbit VX2 intramuscular tumor model using PET/MRI: Simultaneous evaluation of vascular and metabolic parameters Su Yeon Ahn1, Jin Mo Goo1,2*, Kyung Hee Lee3, Seunggyun Ha4, Jin Chul Paeng4 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 1 Department of Radiology, Seoul National University College of Medicine, and Institute of Radiation Medicine, Seoul National University Medical Research Center, Seoul, Korea, 2 Cancer Research Institute, Seoul National University, Seoul, Korea, 3 Department of Radiology, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Korea, 4 Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, Korea * jmgoo@plaza.snu.ac.kr Conclusions PET/MRI is able to monitor the changes of vascular and metabolic parameters at different time points simultaneously, and confirmed that vascular changes precede the metabolic changes by VDA, CKD-516. Monitoring tumor response to the vascular disrupting agent using PET/MRI (P < 0.001), while total lesion glycolysis (TLG) did not show a significant difference between the time points. SUVmax and SUVmean did not show significant interval changes between time points (P > 0.05). Abbreviations: DCE-MRI, dynamic contrast- enhanced magnetic resonance imaging; FDG, fluorodeoxyglucose; iAUC, the initial area under the gadolinium concentration-time curve until 60 seconds; Ktrans, the volume transfer coefficient; MTV, metabolic tumor volume; PET, positron emission tomography; SUVmax, the maximum standardized uptake value; SUVmean, the average standardized uptake value; TLG, total lesion glycolysis; VDA, vascular disrupting agent. Results Changes of the volume transfer coefficient (Ktrans) and the initial area under the gadolinium concentration-time curve until 60 seconds (iAUC) in the treated group were significantly larger compared with those in the control group at 4-hour follow-up (mean, -39.91% vs. -6.04%, P = 0.018; and -49.71% vs. +6.23%, P = 0.013). Change of metabolic tumor volume (MTV) in the treated group was significantly smaller compared with that in the control group at 1-week follow-up (mean, +118.34% vs. +208.87%, P = 0.044). Serial measurements in the treated group revealed that Ktrans and iAUC decreased at 4-hour follow-up (P < 0.001) and partially recovered at 1-week follow-up (P = 0.001 and 0.024, respectively). MTV increased at a 4-hour follow-up (P = 0.038) and further increased at a 1-week follow-up Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2013R1A1A2063746). Competing interests: The authors have declared that no competing interests exist. 1 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 Introduction Supply of oxygen and nutrients via the surrounding vasculature is essential for tumor growth. Therefore, tumor vasculature has been a major target for cancer treatment. Apart from antian- giogenic drugs which compromise the formation of new blood vessels, vascular disrupting agents (VDAs) target the established tumor vasculature and cause a shutdown of blood flow, leading to subsequent tumor ischemia and necrosis [1]. Because of its cytostatic nature, con- ventional assessment of tumor response based on reduction in tumor size, using Response Evaluation Criteria in Solid Tumors [2] may not be adequate or prompt since there is a signifi- cant latency in determining the clinical effectiveness [3]. Physiologic or metabolic responses occur soon after the start of anticancer therapy, although clinical responses are slow. There- fore, functional molecular imaging techniques that depict physiologic and cellular processes within tumors such as vascularity or metabolism have been emphasized [4]. The depiction of these post-therapeutic events earlier than clinical endpoint is helpful for choosing the right treatment strategy, preventing unnecessarily long treatment courses with their inherent adverse events, as well as deciding whether to go or not in the development of anticancer pharmaceuticals [5, 6]. Several imaging techniques have been investigated to assess angiogenic vasculature and monitor the efficacy of vascular targeting agents noninvasively [3]. The major- ity of them were studied with dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) parameters for assessing the therapeutic effect of vascular targeting agents [3, 6– 10]. Furthermore, only a few previous studies were performed with [18F]-fluorodeoxyglucose (FDG) positron emission tomography (PET) for assessing metabolic change after the thera- peutic effect of anti-vascular drugs [11–13]. However, to our knowledge, until now, no studies dealing with post-treatment changes after VDA have been performed yet with the novel imag- ing modality PET/MRI, which can obtain multiparametric information simultaneously. Vascular disrupting agent, CKD-516 used in this experiment is a tubulin polymerization inhibitor that has a dual action mechanism of (a) rapid disruption of pre-existing tumor vascu- lature, resulting in hypoxia and necrosis, and (b) arresting the cell cycle, resulting in apoptosis [14]. Therefore, the aim of this study is to determine whether the CKD-516 produces a signifi- cant change in vascular and metabolic parameters in PET/MRI. All experiments were approved by the Institutional Animal Care and Use Committee in Seoul National University Hospital (SNUH-IACUC) (Permit Number: 15-0241-S1A0(1)) and Monitoring tumor response to the vascular disrupting agent using PET/MRI animals were maintained in the facility accredited AAALAC International (#001169) in accor- dance with Guide for the Care and Use of Laboratory Animals 8th edition, National Research Council (2010). The rabbits were monitored every 1–2 days. If one of the following conditions occurred during the experiment, the animals were humanely killed considered: weight loss (>20%) or if the animal became cachectic, had difficulty eating, drinking or moving around freely. All efforts were made to minimize suffering of animals during tumor implantation and image acquisition. Experimental protocol Sixteen rabbits were randomly allocated to receive injections of CKD-516 (Chong Kun Dang Pharmaceutical, Seoul, Korea) at a dose of 0.7 mg/kg (n = 11) or normal saline (n = 5) (treated group and control group, respectively). We set the dose of CKD-516 according to the safe dose in human (9 mg/m2) and converted it to the equivalent dose in rabbits (0.75mg/kg) [9]. One day after the baseline imaging, CKD-516 diluted in 3 mL of normal saline was administered slowly at a rate of 1 mL/min via the auricular vein to the treated group and the same dose of normal saline to the control group. Follow-up imaging was performed 4 hours and 1-week after the administration. After the last PET/MR imaging session, all rabbits were sacrificed by intravenous injection of 5 ml potassium chloride while under deep anesthesia. Animal model Sixteen male New Zealand White rabbits (Koatech Co. Ltd., Pyongtaek, Korea) weighing 3.0– 3.5 kg were used. The rationale for choosing rabbit VX2 model is as follows; rabbit VX2 tumor model is well established for studies of tumor and histopathological features are similar to humans [15], thus the results of animal studies can be extrapolated to humans; many previous studies have used the rabbit VX2 model for functional imaging [9, 16]; the VX2 carcinoma strain had been maintained by continuous transplantation into the hind limbs of carrier rab- bits at the preclinical animal experimental center of our institute, making it easily accessible in this study. To help the rabbits adapt to their environment, they were housed in individual cages with freely available food and water for 1–2 weeks in accordance with our humane ani- mal care protocol. For each rabbit, anesthesia was induced with intravenous ketamine hydro- chloride (50 mg per kg of body weight; Ketamine, Yuhan, Korea) and 2% xylazine (0.1 mL/kg; Rompun, Bayer, Germany). After anesthesia, bilateral back parallel to the spine was shaved and sterilized. Thereafter, 0.2 ml of VX2 tumor suspension was slowly implanted symmetrically in the bilateral paraver- tebral muscles at the level of the kidney each using 18-gauge Chiba needle under the guidance of ultrasonography (Accuvix XG, Samsung Medison, Seoul, Korea). Tumors were incubated for 10–12 days after the tumor implantation prior to baseline imaging. Among the 16 rabbits, the total number of tumors was 32. The longest diameter of the tumors on baseline T2-weighted axial MR images was 16.2 ± 3.5 mm (range, 9.3–22.2 mm). Ethics statement All experiments were approved by the Institutional Animal Care and Use Committee in Seoul National University Hospital (SNUH-IACUC) (Permit Number: 15-0241-S1A0(1)) and 2 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 PET/MRI image acquisition All acquisitions were performed by using an integrated PET/MRI scanner (Biograph mMR, Siemens Healthcare, Erlangen, Germany). All animals were fasted for at least 6 hours prior to the PET/MRI examination. Animals had an intravenous access established in the auricular vein at the day of PET/MRI acquisition. FDG (37 MBq) was intravenously injected and 1-bed PET image was obtained for 10 min, approximately 60 min after injection. MR acquisition was initiated as soon as the animals were placed in a supine position in the scanner. Using three- plane, true-fast imaging with steady-state precession (true-FISP) localizers, an axial MRI slab 3 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 Monitoring tumor response to the vascular disrupting agent using PET/MRI was placed covering the whole tumor implant in paravertebral muscles. T2-weighted images (T2WI) were obtained with the following parameters: repetition time/echo time (TR/TE), 4230/84 ms; matrix size, 128×128; slice thickness, 3 mm; and field of view (FOV), 160×160 mm. Unenhanced T1-weighted volumetric interpolated breath-hold examination (VIBE) images were acquired at each flip angle for T1 mapping using the following parameters: TR/ TE 3.2/1.1 ms; flip angles (α = 2˚, 5˚, 10˚ and 15˚); matrix size 128×128; slice thickness 3 mm; number of slices 20; and FOV 160 mm. Thereafter, dynamic contrast-enhanced MR imaging using the T1-weighted radial gradient echo sequence was then performed after an intravenous bolus injection via the auricular vein of 0.1 mmol/kg of gadoteric acid (Dotarem; Guerbet, Paris, France). DCE-MRI using the VIBE sequence was obtained at 5 seconds of temporal res- olution and the parameters were TR/TE 3.2/1.1 ms, flip angles (α = 15˚), matrix size 128×128, slice thickness 3 mm, number of slices 20, and FOV 160 mm. The total acquisition time of the dynamic scan was 10 minutes, including the first 4 phases of pre-contrast images. During MRI acquisition, emission data were collected from a single bed position of tumor implant level for 20 minutes and list-mode dataset was acquired for all animals. Reconstruc- tion of PET images was performed on the mMR console using 3D-ordered subset expectation maximization (3D-OSEM) with point spread function modeling with 3 iterations, 21 subsets, image matrix 256, a zoom factor of 2. Image analysis The most commonly used two DCE-MRI parameters, the volume transfer coefficient (Ktrans) and the initial area under the gadolinium concentration-time curve until 60 seconds (iAUC) were measured, according to the consensus opinion on DCE-MRI in evaluating vascular tar- geting agents in previous studies [1, 7, 17]. Using the DCE-MRI images, parametric maps of Ktrans and iAUC were generated with a post-processing software program (Tissue4D; Siemens Medical Solutions) based on Tofts model [18, 19]. We selected a representative section with the longest diameter of tumor and drew a region of interest manually by outlining the entire tumor boundary. The maximum and average standardized uptake value (SUVmax and SUVmean) were mea- sured to determine FDG avidity of the tumors using commercial software (Syngo.via, Siemens Healthcare). A sphere-shaped volume of interest (VOI) that included the entire lesion was drawn to determine FDG avidity. Metabolic tumor volume (MTV) was defined as total tumor volume with a margin threshold of 40% SUVmax. Total lesion glycolysis (TLG) was calculated as (SUVmean) × (MTV) in the same isocontour VOI. Tumor size was defined as the longest diameter measured on axial T2-weighted images. In addition, tumor volume was measured using a semi-automatic segmentation tool. Percentage changes in PET/MRI-derived parameters relative to the baseline were calculated as follows: Value Change = (Valuegiven time-Valuebaseline)/Valuebaseline × 100%. Sequential change in size and volume of tumor The size of tumors at baseline in the control and treated groups was 18 ± 4 mm and 16 ± 4 mm, respectively, and it showed no significant differences (P > 0.05). At 1-week follow-up, the tumors grew to 22 ± 3 mm and 20 ± 5 mm, respectively. Percentage change of size of tumors at 1-week follow-up did not show a significant difference between the two groups (30.9% vs. 21.9%, P = 0.198). The volume of tumors at baseline in the control and treated group was 6.0 ± 2.9 cm3 and 4.6 ± 2.3 cm3, respectively, and it showed no significant differences (P = 0.438). At 1-week fol- low-up, the tumors grew to 13.5 ± 5.3 cm3 and 8.1 ± 3.1 cm3, respectively. Percentage change of volume of tumors at 1-week follow-up showed no significant differences between the treated and control groups (139.3% vs. 89.6%, P = 0.115). Results Among 16 rabbits, data from 3 rabbits (2 in the treated group and 1 in the control group) were incomplete because 1-week follow-up imaging was not available due to technical problems. In addition, 4 rabbits in the treated group died unexpectedly before humane endpoints, mostly one or two days before 1-week follow-up. Although the dose of CKD-516 was within safe limits and we did not investigate the toxicity in our study, the toxicity may be related to animal’s death because all dead rabbits were in the treated group. However, stressful situation such as repeated handling, transportation and anesthesia may also be related. Therefore, 18 tumors in 9 rabbits (10 tumors in 5 rabbits in the treated group and 8 tumors in 4 rabbits in the control group) were available for all baselines, 4 hours and 1-week follow-up. Statistical analysis To determine whether there were differences in tumor size, volume, PET/MRI imaging values and their interval changes between the treated and control groups, the linear mixed model was used which made it possible to analyze clustered data because each rabbit has two tumors. Two fixed effects were included: one between-subjects group (control vs. treated) effect and one within-subject time effect (time: baseline, 4 hours, and 1 week). Spearman rank correlation test was performed to evaluate the correlation between the changes in PET/MR imaging values at each time point compared with the baseline. A P value of less than 0.05 was considered to 4 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 Monitoring tumor response to the vascular disrupting agent using PET/MRI indicate a significant difference. All statistical analyses were performed with SPSS version 21 (SPSS, Chicago, IL, USA). PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 Monitoring tumor response to the vascular disrupting agent using PET/MRI Table 1. Comparison of vascular and metabolic parameters between the control and treated groups at each time point and comparison of each parameter between time points in each group. Control (n = 8) P value Treated (n = 10) P value P value 4 Hours 1 Week 4 Hours 1 Week Ktrans (min-1) time × group: 0.023 Baseline 0.29 ± 0.13 0.137 0.049 0.28 ± 0.69 <0.001 0.001 0.816 4 Hours 0.26 ± 0.08 0.062 0.16 ± 0.05 0.081 0.055 1 Week 0.19 ± 0.06 0.20 ± 0.07 0.903 iAUC (mmol/sec) time × group: <0.001 Baseline 27.85 ± 10.39 0.853 0.037 26.49 ± 5.82 <0.001 0.024 0.819 4 Hours 28.31 ± 8.30 0.014 12.95 ± 5.44 <0.001 0.015 1 Week 18.58 ± 5.22 21.23 ± 7.76 0.555 SUVmax time × group: 0.143 Baseline 8.72 ± 2.91 NA NA 6.44 ± 2.00 NA NA NA 4 Hours 6.91 ± 3.01 NA 5.77 ± 1.80 NA NA 1 Week 8.79 ± 2.70 5.52 ± 2.59 NA SUVmean time × group: 0.237 Baseline 5.50 ± 2.02 NA NA 4.00± 1.22 NA NA NA 4 Hours 4.37 ± 1.91 NA 3.50 ± 1.14 NA NA 1 Week 5.21 ± 1.59 3.19 ± 1.56 NA MTV (cm3) time × group: 0.001 Baseline 3.78 ± 2.01 0.018 <0.001 2.81 ± 1.09 0.038 <0.001 0.374 4 Hours 4.65 ± 2.00 <0.001 3.66 ± 0.91 0.005 0.345 1 Week 10.69± 4.02 6.09 ± 2.17 0.035 TLG time × group: <0.001 Baseline 23.96 ± 21.28 0.627 0.001 10.66 ±3.64 0.341 0.066 0.225 4 Hours 21.67 ± 13.47 0.001 12.41 ± 4.33 0.126 0.193 1 Week 60.23 ± 35.20 18.93 ± 12.85 0.035 differences were observed in percentage changes in SUVmax, SUVmean, TLG, Ktrans and iAUC between the two groups at 1-week follow-up. Comparison of PET/MRI parameters at each time points and their changes between the treated and control groups The time × group interaction effect was found in Ktrans, iAUC, MTV and TLG (P = 0.023, <0.001, 0.001 and <0.001, respectively) on linear mixed model analysis. Mean values of vascu- lar and metabolic parameters and comparison of each parameter between treated and control group at each time points and comparison of each parameter between time points in each group are shown in Table 1. Percentage changes of those relative to baseline for each group at each time point are summarized in Table 2. There were no significant differences in all of PET/MRI parameters at baseline imaging between the two groups. At 4-hour follow-up, Ktrans in the treated group were lower than that in the control group, although the difference showed no statistical significance (P = 0.055). iAUC in the treated group were significantly lower than that in the control group (P = 0.015) at 4-hour follow-up. At 1-week follow-up, MTV and TLG were significantly lower in the treated group than those in the control group (P = 0.035). Percentage changes of PET/MRI parameters were also evaluated by using the linear mixed model. Changes of Ktrans and iAUC in the treated group were significantly larger compared with those in the control group at 4-hour follow-up (mean, -39.91% vs. -6.04%, P = 0.018; and -49.71% vs. +6.23%, P = 0.013). None of the relative changes in PET-derived parameters showed any statistically significant differences between the treated and control groups at 4-hour follow-up. MTV in the treated group is significantly less increased compared with those in the control group at 1-week follow-up (mean, +118.34% vs. +208.87%, P = 0.003). No statistical 5 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 https://doi.org/10.1371/journal.pone.0192706.t001 Sequential change in PET/MRI parameters of tumor within each group Comparisons between different time points in each parameter are shown in Figs 1 and 2. Serial measurements in the treated group revealed that Ktrans and iAUC decreased at 4-hour follow- up (P < 0.001) and partially recovered at 1-week follow-up (P = 0.001 and 0.024, respectively). MTV increased at 4-hour follow-up (P = 0.038) and further increased at 1-week follow-up (P < 0.001), while TLG increased at 1-week follow-up without a significant difference (P > 0.05). In the control group, Ktrans and iAUC showed no significant differences at 4-hours follow- up (P > 0.05) and decreased at 1-week follow-up (P = 0.049 and 0.037, respectively). MTV increased at 4-hour follow-up (P = 0.018) and further increased at 1-week follow-up (P < 6 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 Monitoring tumor response to the vascular disrupting agent using PET/MRI Table 2. Percentage changes of vascular and metabolic parameters compared with the baseline at each time point and P values of comparisons between the treated and control groups. Control (n = 8) Treated (n = 10) P Value Ktrans (min-1) 4 Hours -6.04(-21.04, 8.97) -39.91(-52.64, -27.18) 0.018 1 Week -29.90(-66.07, 6.27) -27.35(-45.62, -9.08) 0.822 iAUC (mmol/sec) 4 Hours 6.23(-17.75,30.21) -49.71(-65.47, -33.95) 0.013 1 Week -24.15(-53.84,5.55) -18.87(-38.17, 0.43) 0.797 SUVmax 4 Hours -15.57(-52.41, 21.27) -7.97(-25.83, 9.89) 0.757 1 Week 4.89(-23.17, 32.95) -16.42(-35.03, 2.18) 0.299 SUVmean 4 Hours -14.82(-51.87, 22.23) -10.05(-30.41, 10.30) 0.852 1 Week -0.76 (-27.03, 25.51) -21.92(-42.63, -1.21) 0.303 MTV (cm3) 4 Hours 30.74(14.05, 47.72) 37.82(16.61, 59.03) 0.660 1 Week 208.87(145.75, 272.00) 118.34(76.59, 160.10) 0.044 TLG 4 Hours 195.96(129.96, 261.97) 42.23(2.68, 81.77) 0.623 1 Week 209.64(108.00, 311.28) 79.43(3.74, 155.14) 0.101 Data are relative percentage changes determined by comparing the value at baseline with that at follow-up. Data in parentheses are 95% confidence intervals. Ktrans: volume transfer coefficient iAUC: initial area under the gadolinium concentration-time curve until 60 seconds SUV: standardized uptake value MTV: metabolic tumor volume TLG: total lesion glycolysis https://doi org/10 1371/journal pone 0192706 t002 Table 2. Percentage changes of vascular and metabolic parameters compared with the baseline at each time point and P values of comparisons between the treated and control groups. 0.001), while TLG showed no significant difference at 4-hour follow-up and increased at 1-week follow-up (P = 0.001) in the control group. Correlation analysis with tumor response To determine whether there is correlation between the percentage changes in parameters at 4-hour follow-up and change of tumor size or volume at 1-week follow-up for early prediction of tumor response, correlation analysis was performed in the treated group. Any change of parameters at 4-hour follow-up was not correlated with the change of size or volume at 1-week follow-up. (P> 0.05). In addition, we have checked the correlations between vascular and met- abolic parameters (Ktrans or iAUC and 4 metabolic parameters, respectively) and we’ve found that there were no correlation between these parameters at any time (p>0.05). Discussion Our study demonstrated that PET/MRI can monitor serial vascular and metabolic changes of intramuscular VX2 tumor model after the administration of VDA, CKD-516. Vascular and metabolic parameters changed at different times and we confirmed that vascular changes pre- cede the metabolic changes by VDA, CKD-516. Significant differences in vascular parameters including Ktrans and iAUC occurred after 4 hours, whereas significant differences in metabolic PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 7 / 14 Monitoring tumor response to the vascular disrupting agent using PET/MRI Fig 1. Serial changes of PET/MRI parameters before and after the treatment with CKD-516. (a) Axial T2-weighted images demonstrated target tumors with high signal intensity in bilateral paravertebral muscles. (b) DCE-MRI revealed peripheral enhancement of tumors suggesting central necrosis. (c) Ktrans map and (d) iAUC map demonstrated a reduction of values at 4 hours and partial recovery at 1 week follow-up. (e) PET images and (f) fusion images showed no significant differences of SUVmax or SUVmean. https://doi org/10 1371/journal pone 0192706 g001 Fig 1. Serial changes of PET/MRI parameters before and after the treatment with CKD-516. (a) Axial T2-weighted images demonstrated target tumors with high signal intensity in bilateral paravertebral muscles. (b) DCE-MRI revealed peripheral enhancement of tumors suggesting central necrosis. (c) Ktrans map and (d) iAUC map demonstrated a reduction of values at 4 hours and partial recovery at 1 week follow-up. (e) PET images and (f) fusion images showed no significant differences of SUVmax or SUVmean. Fig 1. Serial changes of PET/MRI parameters before and after the treatment with CKD-516. (a) Axial T2-weighted images demonstrated target tumors with high signal intensity in bilateral paravertebral muscles. (b) DCE-MRI revealed peripheral enhancement of tumors suggesting central necrosis. (c) Ktrans map and (d) iAUC map demonstrated a reduction of values at 4 hours and partial recovery at 1 week follow-up. (e) PET images and (f) fusion images showed no significant differences of SUVmax or SUVmean. https://doi.org/10.1371/journal.pone.0192706.g001 https://doi.org/10.1371/journal.pone.0192706.g001 parameters of MTV and TLG were noted at 1-week after VDA treatment between the control and treated groups. Our results of vascular parameters are similar to previous studies that have demonstrated that Ktrans and iAUC values changed within a few hours after the treatment with VDA [7–9, 20]. Both parameters reflect blood flow and permeability [3]. Discussion Tumor blood vessels are imma- ture and highly permeable without supporting connective tissues, and VDA perturbs these preexisting vessels, leading to collapse of tumor vasculature and subsequent necrosis [21]. PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 8 / 14 Monitoring tumor response to the vascular disrupting agent using PET/MRI Fig 2. Serial measurement of (a) Ktrans, (b) iAUC, (c) SUVmax, (d) SUVmean, (e) MTV and (f) TLG at different time points.  is a significant change compared to the baseline. Ktrans: volume transfer coefficient iAUC: initial area under the gadolinium concentration-time curve until 60 seconds SUV: standardized uptake value MTV: metabolic tumor volume TLG: total lesion glycolysis. Fig 2. Serial measurement of (a) Ktrans, (b) iAUC, (c) SUVmax, (d) SUVmean, (e) MTV and (f) TLG at different time points.  is a significant change compared to the baseline. Ktrans: volume transfer coefficient iAUC: initial area under the gadolinium concentration-time curve until 60 seconds SUV: standardized uptake value MTV: metabolic tumor volume TLG: total lesion glycolysis. https://doi.org/10.1371/journal.pone.0192706.g002 Fig 2. Serial measurement of (a) Ktrans, (b) iAUC, (c) SUVmax, (d) SUVmean, (e) MTV and (f) TLG at different time points.  is a significant change compared to the baseline. Ktrans: volume transfer coefficient iAUC i iti l d th d li i t ti ti til 60 d https://doi.org/10.1371/journal.pone.0192706.g002 Thus, a decrease of Ktrans and iAUC reflects a decrease in blood flow and permeability in a tumor. Interestingly, serial measurement of Ktrans and iAUC in control group also showed significant decrease at 1 week follow-up in our study. One of our hypothesis is that it is due to the nature of VX2 tumors. VX2 tumor grows quickly in the first three week and showed necro- sis and cysts at advanced stages [22]. In our study, at 1-week follow-up, control group as well as treated group also showed areas of high signal intensity within tumors on T2 weighted images, suggestive of necrosis (Fig 3). According to Moon et al. [23]’s study, Ktrans value of complete necrotic area is lower than that of partial necrotic area, and Ktrans value of partial necrotic area is lower than that of viable tumor area. It suggests that necrosis can affect the value of Ktrans. Therefore, we assume that necrotic portion of tumors in control group at 1 week follow-up could cause the decrease of Ktrans. PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 Monitoring tumor response to the vascular disrupting agent using PET/MRI expression of hypoxia-inducible factor-1 alpha, which involves in angiogenesis, glycolysis, and microenvironment acidification of tumors [24]. Although VDA induces tumor necrosis, viable tumors at the peripheral rim adapt to hypoxia by providing nutrients through newly formed vessels and promote growth and proliferation. El-Emir et al. [25] demonstrated the effect of combretastatin A-4 phosphate, one of VDA, in colorectal xenograft model and revealed that hypoxia reaches its maximum 1 hour and is relieved and returned to normal after 24 hours. Increase of Ktrans reflects tumor resistance to VDA, recovering tumor perfusion and relapse of tumors [24, 26]. Thus, rapid decrease of perfusion parameters might not be directly associated with size reduction, as shown in our results. In addition to vascular parameters, we also demonstrated simultaneous changes of meta- bolic parameters after the administration of CKD-516. Among PET-derived parameters, MTV and TLG showed significant differences at 1-week follow-up between the two groups. Further- more, an increase in MTV at 1-week follow-up in the treated group was smaller than in the control group. MTV and TLG are potential biomarkers for predicting response to treatment as well as for predicting prognosis in various solid tumors, including head and neck cancer, lung cancer, esophageal cancer, cervical cancer, epithelial ovarian cancer, etc [27]. However, we could not identify prognostic or predictive factors for tumor response in this experiment. None of the changes of parameters including MTV and TLG at 4 hours follow-up was corre- lated with changes in tumor size at 1-week follow-up. This may be because the follow-up period was too short to cause a change of size. To our knowledge, this is the first study that depicts multiparametric monitoring of tumor response after the administration of VDA, using the novel imaging technique, PET/ MRI. Multimodality imaging is a rapidly growing field in clinical practice, but most are per- formed on separate machines, which requires time-consuming processing and manipulating a vast amount of imaging. Also, interpreting images side-by-side results in diagnostic inaccu- racy [28]. Recently, the potential of simultaneous acquisition of in vivo functional informa- tion with PET/MRI has been investigated [16]. We believe that simultaneity is one of the advantages of PET/MR imaging in comparison with separate PET and MRI. Simultaneous acquisition provides better alignment quality and is especially beneficial when temporally varying multi-functional information from PET and MRI are acquired [29]. PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 Discussion However, Ktrans and iAUC of baseline and 1 week follow-up did not show significant difference between the treated and control group. Significant differences of values and its changes at 4 hours are important issue in discriminat- ing physiological response to therapy. Although histologic examination is not available in this study, there were several studies which investigated the correlation of histologic parameters such as necrosis and microvessel density with changes in DCE-MRI parameters. Necrosis can affect the value of Ktrans [23], which would explain our results of changes of Ktrans. For the microvessel density, there is a controversy whether it could be a validation biomarker for effect of VDA. Because many counted microvessels collapsed 4 hours after CKD-516, microvessel density could not repre- sent the functional vascular profile [9]. Despite the rapid shutdown of tumor vasculature, we could not identify the correlation between changes of vascular parameters and tumor response. The potential mechanism is tumor resistance to VDA. In hypoxic condition induced by VDA, tumors upregulate the 9 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 Monitoring tumor response to the vascular disrupting agent using PET/MRI Fig 3. Serial changes of PET/MRI parameters in control group. (a) Axial T2-weighted images demonstrated target tumors with high signal intensity in bilateral paravertebral muscles. At 1-week follow-up, there were areas of high signal intensity within tumors on T2 weighted images, suggestive of necrosis (arrows). (b) DCE-MRI, (c) Ktrans map, (d) iAUC, (e) PET images and (f) fusion images. https://doi.org/10.1371/journal.pone.0192706.g003 Fig 3. Serial changes of PET/MRI parameters in control group. (a) Axial T2-weighted images demonstrated target tumors with high signal intensity in bilateral paravertebral muscles. At 1-week follow-up, there were areas of high signal intensity within tumors on T2 weighted images, suggestive of necrosis (arrows). (b) DCE-MRI, (c) Ktrans map, (d) iAUC, (e) PET images and (f) fusion images. Fig 3. Serial changes of PET/MRI parameters in control group. (a) Axial T2-weighted images demonstrated target tumors with high signal intensity in bilateral paravertebral muscles. At 1-week follow-up, there were areas of high signal intensity within tumors on T2 weighted images, suggestive of necrosis (arrows). (b) DCE-MRI, (c) Ktrans map, (d) iAUC, (e) PET images and (f) fusion images. https://doi.org/10.1371/journal.pone.0192706.g003 https://doi.org/10.1371/journal.pone.0192706.g003 10 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 Although, there is no comparable data acquiring vascular and metabolic parameters separately and simulta- neously, we believe that simultaneous PET/MR acquisition is suitable for monitoring multi parametric changes after VDA treatment because they changes at different time points as shown in our study. Our study has several limitations. First, we conducted baseline imaging 1 day before the administration of CKD-516 considering the elimination of previously injected FDG. Because the VX2 tumor is highly aggressive and grows rapidly [30], the microenvironment of the tumor would change within a day. Thus, changes of parameters at 4 hours after the treatment may include not only the effect of drugs but also an intrinsic change of tumor characteristics. Second, DCE-MRI parameters are measured with one axial cross- sectional image, which might be less representative of the entire tumor. Third, it is not validated whether early changes in vascular and metabolic parameters in PET/MRI after the treatment with VDA are relevant to clinical outcome such as overall survival, so further studies must be performed. Forth, the histopathologic examination or quantification is not available to support the changes of vascular and metabolic of parameters. Although sev- eral studies dealing with vascular parameters have provided the histologic correlations, fur- ther studies on correlation between the histologic examination and PET parameters are warranted. 11 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 Monitoring tumor response to the vascular disrupting agent using PET/MRI In conclusion, PET/MRI is able to monitor the change of vascular and metabolic parame- ters at different time points simultaneously and confirmed that vascular changes precede the metabolic changes by VDA, CKD-516. Conceptualization: Jin Mo Goo. Writing – original draft: Su Yeon Ahn, Jin Mo Goo. Writing – review & editing: Kyung Hee Lee, Seunggyun Ha, Jin Chul Paeng. Writing – review & editing: Kyung Hee Lee, Seunggyun Ha, Jin Chul Paeng. Writing – review & editing: Kyung Hee Lee, Seunggyun Ha, Jin Chul Paeng. 9. Kim KW, Lee JM, Jeon YS, Lee IJ, Choi Y, Park J, et al. Vascular disrupting effect of CKD-516: preclini- cal study using DCE-MRI. Invest New Drugs. 2013; 31:1097–106. https://doi.org/10.1007/s10637-012- 9915-6 PMID: 23299389. S1 File. Dataset for sequential changes in PET/MRI parameters of all rabbits. (XLSX) S1 File. Dataset for sequential changes in PET/MRI parameters of all rabbits. (XLSX) S2 File. Animal Research: Reporting In Vivo Experiments (ARRIVE) guidelines checklist. (DOCX) Author Contributions Conceptualization: Jin Mo Goo. Formal analysis: Su Yeon Ahn, Seunggyun Ha, Jin Chul Paeng. Investigation: Su Yeon Ahn, Jin Mo Goo, Kyung Hee Lee, Jin Chul Paeng. Methodology: Su Yeon Ahn, Jin Mo Goo, Kyung Hee Lee, Seunggyun Ha. Resources: Jin Mo Goo, Seunggyun Ha, Jin Chul Paeng. Supervision: Jin Mo Goo. Conceptualization: Jin Mo Goo. References Phase I evaluation of a fully human anti-alphav integrin monoclonal antibody (CNTO 95) in patients with advanced solid tumors. Clin Cancer Res. 2007; 13:2128–35. https://doi.org/10.1158/1078-0432.CCR-06-2779 PMID: 17404096. 12. Thomas JP, Arzoomanian RZ, Alberti D, Marnocha R, Lee F, Friedl A, et al. Phase I pharmacokinetic and pharmacodynamic study of recombinant human endostatin in patients with advanced solid tumors. J Clin Oncol. 2003; 21:223–31. https://doi.org/10.1200/JCO.2003.12.120 PMID: 12525513. 13. Herbst RS, Mullani NA, Davis DW, Hess KR, McConkey DJ, Charnsangavej C, et al. Development of biologic markers of response and assessment of antiangiogenic activity in a clinical trial of human recombinant endostatin. J Clin Oncol. 2002; 20:3804–14. https://doi.org/10.1200/JCO.2002.05.102 PMID: 12228200. 14. Lee J, Kim SJ, Choi H, Kim YH, Lim IT, Yang HM, et al. Identification of CKD-516: a potent tubulin poly- merization inhibitor with marked antitumor activity against murine and human solid tumors. J Med Chem. 2010; 53:6337–54. https://doi.org/10.1021/jm1002414 PMID: 20690624. 15. Shiomi M. Rabbit as a Model for the Study of Human Diseases. In: Houdebine L-M, Fan J, editors. Rab- bit Biotechnology. Dordrecht: Springer Netherlands; 2009. p. 49–63. 16. Lee KH, Kang SK, Goo JM, Lee JS, Cheon GJ, Seo S, et al. Relationship Between Ktrans and K1 with Simultaneous Versus Separate MR/PET in Rabbits with VX2 Tumors. Anticancer Res. 2017; 37:1139– 48. Epub 2017/03/21. https://doi.org/10.21873/anticanres.11427 PMID: 28314275. 17. Mross K, Fasol U, Frost A, Benkelmann R, Kuhlmann J, Buchert M, et al. DCE-MRI assessment of the effect of vandetanib on tumor vasculature in patients with advanced colorectal cancer and liver metasta- ses: a randomized phase I study. J Angiogenes Res. 2009; 1:5. https://doi.org/10.1186/2040-2384-1-5 PMID: 19946413. 18. Tofts PS, Brix G, Buckley DL, Evelhoch JL, Henderson E, Knopp MV, et al. Estimating kinetic parame- ters from dynamic contrast-enhanced T(1)-weighted MRI of a diffusable tracer: standardized quantities and symbols. J Magn Reson Imaging. 1999; 10:223–32. PMID: 10508281. 19. Tofts PS, Kermode AG. Measurement of the blood-brain barrier permeability and leakage space using dynamic MR imaging. 1. Fundamental concepts. Magn Reson Med. 1991; 17:357–67. PMID: 2062210. 20. Thoeny HC, De Keyzer F, Vandecaveye V, Chen F, Sun X, Bosmans H, et al. Effect of vascular target- ing agent in rat tumor model: dynamic contrast-enhanced versus diffusion-weighted MR imaging. Radi- ology. 2005; 237:492–9. https://doi.org/10.1148/radiol.2372041638 PMID: 16192323. 21. Spear MA, LoRusso P, Mita A, Mita M. Vascular disrupting agents (VDA) in oncology: advancing towards new therapeutic paradigms in the clinic. Curr Drug Targets. References 1. O’Connor JP, Jackson A, Parker GJ, Jayson GC. DCE-MRI biomarkers in the clinical evaluation of anti- angiogenic and vascular disrupting agents. Br J Cancer. 2007; 96:189–95. https://doi.org/10.1038/sj. bjc.6603515 PMID: 17211479. 2. Eisenhauer EA, Therasse P, Bogaerts J, Schwartz LH, Sargent D, Ford R, et al. New response evalua- tion criteria in solid tumours: revised RECIST guideline (version 1.1). Eur J Cancer. 2009; 45:228–47. https://doi.org/10.1016/j.ejca.2008.10.026 PMID: 19097774. 3. Miller JC, Pien HH, Sahani D, Sorensen AG, Thrall JH. Imaging angiogenesis: applications and poten- tial for drug development. J Natl Cancer Inst. 2005; 97:172–87. https://doi.org/10.1093/jnci/dji023 PMID: 15687360. 4. Padhani AR, Miles KA. Multiparametric imaging of tumor response to therapy. Radiology. 2010; 256:348–64. https://doi.org/10.1148/radiol.10091760 PMID: 20656830. 5. Desar IM, van Herpen CM, van Laarhoven HW, Barentsz JO, Oyen WJ, van der Graaf WT. Beyond RECIST: molecular and functional imaging techniques for evaluation of response to targeted therapy. Cancer Treat Rev. 2009; 35:309–21. https://doi.org/10.1016/j.ctrv.2008.12.001 PMID: 19136215. 6. Wang H, Li J, Chen F, De Keyzer F, Yu J, Feng Y, et al. Morphological, functional and metabolic imag- ing biomarkers: assessment of vascular-disrupting effect on rodent liver tumours. Eur Radiol. 2010; 20:2013–26. https://doi.org/10.1007/s00330-010-1743-5 PMID: 20182730. 7. Joo I, Lee JM, Grimm R, Han JK, Choi BI. Monitoring Vascular Disrupting Therapy in a Rabbit Liver Tumor Model: Relationship between Tumor Perfusion Parameters at IVIM Diffusion-weighted MR Imag- ing and Those at Dynamic Contrast-enhanced MR Imaging. Radiology. 2016; 278:104–13. https://doi. org/10.1148/radiol.2015141974 PMID: 26200601. 8. Joo I, Lee JM, Han JK, Choi BI. Intravoxel incoherent motion diffusion-weighted MR imaging for moni- toring the therapeutic efficacy of the vascular disrupting agent CKD-516 in rabbit VX2 liver tumors. Radi- ology. 2014; 272:417–26. https://doi.org/10.1148/radiol.14131165 PMID: 24697148. 9. Kim KW, Lee JM, Jeon YS, Lee IJ, Choi Y, Park J, et al. Vascular disrupting effect of CKD-516: preclini- cal study using DCE-MRI. Invest New Drugs. 2013; 31:1097–106. https://doi.org/10.1007/s10637-012- 9915-6 PMID: 23299389. PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 12 / 14 Monitoring tumor response to the vascular disrupting agent using PET/MRI 10. Galbraith SM, Maxwell RJ, Lodge MA, Tozer GM, Wilson J, Taylor NJ, et al. Combretastatin A4 phos- phate has tumor antivascular activity in rat and man as demonstrated by dynamic magnetic resonance imaging. J Clin Oncol. 2003; 21:2831–42. https://doi.org/10.1200/JCO.2003.05.187 PMID: 12807936. 11. Mullamitha SA, Ton NC, Parker GJ, Jackson A, Julyan PJ, Roberts C, et al. 29. Wehrl HF, Judenhofer MS, Wiehr S, Pichler BJ. Pre-clinical PET/MR: technological advances and new perspectives in biomedical research. European Journal of Nuclear Medicine and Molecular Imaging. 2009; 36:56–68. https://doi.org/10.1007/s00259-009-1078-0 PMID: 19194703 PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 30. Kidd JG, Rous P. A Transplantable Rabbit Carcinoma Originating in a Virus-Induced Papilloma and Containing the Virus in Masked or Altered Form. J Exp Med. 1940; 71:813–38. PMID: 19871000. 29. Wehrl HF, Judenhofer MS, Wiehr S, Pichler BJ. Pre-clinical PET/MR: technological advances and new perspectives in biomedical research. European Journal of Nuclear Medicine and Molecular Imaging. 2009; 36:56–68. https://doi.org/10.1007/s00259-009-1078-0 PMID: 19194703 30. Kidd JG, Rous P. A Transplantable Rabbit Carcinoma Originating in a Virus-Induced Papilloma and Containing the Virus in Masked or Altered Form. J Exp Med. 1940; 71:813–38. PMID: 19871000. References 2011; 12:2009–15. PMID: 21777190. 22. Liu Y, Ren W, Liu C, Huang K, Feng Y, Wang X, et al. Contrast-enhanced ultrasonography of the rabbit VX2 tumor model: Analysis of vascular pathology. Oncol Lett. 2012; 4:685–90. https://doi.org/10.3892/ ol.2012.819 PMID: 23205083. 23. Moon J, Kim JH, Choi D, Yang J, Lee MW, Choi YL, et al. Correlation of quantitative dynamic contrast- enhanced MRI with microvascular density in necrotic, partial necrotic, and viable liver tumors in a rabbit model. J Appl Clin Med Phys. 2016; 17:6314. Epub 2016/09/30. https://doi.org/10.1120/jacmp.v17i5. 6314 PMID: 27685133. 24. Liang W, Ni Y, Chen F. Tumor resistance to vascular disrupting agents: mechanisms, imaging, and solutions. Oncotarget. 2016; 7:15444–59. https://doi.org/10.18632/oncotarget.6999 PMID: 26812886. 25. El-Emir E, Boxer GM, Petrie IA, Boden RW, Dearling JL, Begent RH, et al. Tumour parameters affected by combretastatin A-4 phosphate therapy in a human colorectal xenograft model in nude mice. Eur J Cancer. 2005; 41:799–806. https://doi.org/10.1016/j.ejca.2005.01.001 PMID: 15763657. 26. Chen F, Feng Y, Zheng K, De Keyzer F, Li J, Feng Y, et al. Enhanced antitumor efficacy of a vascular disrupting agent combined with an antiangiogenic in a rat liver tumor model evaluated by multipara- metric MRI. PLoS One. 2012; 7:e41140. https://doi.org/10.1371/journal.pone.0041140 PMID: 22815943. 27. Van de Wiele C, Kruse V, Smeets P, Sathekge M, Maes A. Predictive and prognostic value of metabolic tumour volume and total lesion glycolysis in solid tumours. Eur J Nucl Med Mol Imaging. 2013; 40:290– 301. https://doi.org/10.1007/s00259-012-2280-z PMID: 23151913. 28. Pichler BJ, Kolb A, Nagele T, Schlemmer HP. PET/MRI: paving the way for the next generation of clini- cal multimodality imaging applications. J Nucl Med. 2010; 51:333–6. https://doi.org/10.2967/jnumed. 109.061853 PMID: 20150252. 13 / 14 PLOS ONE | https://doi.org/10.1371/journal.pone.0192706 February 13, 2018 Monitoring tumor response to the vascular disrupting agent using PET/MRI Monitoring tumor response to the vascular disrupting agent using PET/MRI 14 / 14
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Investigation of Adding Microscopic Slide Glass Nano Particles on the Metallurgical Characterization and Mechanical Properties of Cast Aluminum 7075 Composites
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Advances in Science and Technology Research Journal Received: 2023.03.21 Accepted: 2023.05.18 Published: 2023.06.01 Advances in Science and Technology Research Journal 2023, 17(3), 214–225 https://doi.org/10.12913/22998624/166282 ISSN 2299-8624, License CC-BY 4.0 ABSTRACT Metal matrix composite (MCC) exhibits significantly better properties, like hardness, low density, high tensile strength, and good wear resistance compared to any alloy or other metals. In the present study, the effect of using different proportions (2, 4, 8 and 10 wt.%) of microscopic slide glass nanoparticles (MSGNPs) on the properties of Al-7075 alloy was investigated. The results of the experimental study of the metallurgical characterization and mechanical properties of aluminum MMC that formed by stir casting method were obtained. Stir casting is a pro­ cess of introducing a reinforcing material into a molten metal by stirring action. Also, the results of the aluminum MMC were compared with those for the base alloy material. Optical microscopy, scanning electron microscope (SEM), energy dispersive spectroscopy (EDS), and X-ray diffraction study (XRD) were carried out to analyze the microstructure and the dispersion of the (MSGNPs) into the composite alloy specimens. Regarding the mechani­ cal properties, the Rockwell hardness gradually increased when the addition of MSGNPs was raised from 0 to 10 wt.%. Additionally, there was a rise in the ultimate tensile strength, peaking at the incorporation rate of 4 wt.% MSGNPs and thereafter, this strength declined. Therefore, the addition of microscopic slide glass nanoparticles to the Al-7075 is virtuous to enhance the properties of this alloy for the engineering application. Keywords: microscopic slide glass nanoparticles, aluminum 7075, metal matrix composite. Investigation of Adding Microscopic Slide Glass Nano Particles on the Metallurgical Characterization and Mechanical Properties of Cast Aluminum 7075 Composites Haneen Lateef1*, Shukry H. Aghdeab1, Baha S. Mahdi1 1 Production Engineering and Metallurgy Department, University of Technology-Iraq, Baghdad, Iraq * Corresponding author’s email: haneenlateef92@gmail.com INTRODUCTION Aluminum is an ecological agreeable materi­ al because of its proficiency to be recycled as well as its different uses proving the elevated alumi­ num’s manufacture need. The solid wastes, like the cullet (broken glasses) and the metals aren’t water soluble and biodegradable. The recycling of these solid wastes for making fresh products could reduce the challenge it poses upon the natu­ ral environment. Thus, the merely choice left is to recycle them for getting rid of them from the environment [3, 4]. The current investigation is participation to the efforts aiming to develop the Aluminum- based Matrix Composites (AMCs) with elevat­ ed indices of performance at a decreased cost. AMCs are a class of Metal Matrix Composites (MMCs) presently used in the industries of au­ tomobile and aerospace. Aluminum is preferred as a structural material in such applications due to its light weight. And, among the series of alu­ minum alloys, aluminum 7075 alloy possesses numerous promising properties, such as high stiffness, high toughness, high strength, and vir­ tuous resistance to wear. Ceramic particulates are supplemented to the aluminum base matrix as reinforcement for fabricating AMCs, which gave an enhanced strength [1, 2]. Glass has a predominant content of Si, so it is one of the most widely used materials as a re­ inforcing. [5]. On the Mohs scale, the oxide glass has a hardness ranging from 5 to 7 with silica glass having the highest hardness [6]. Therefore, it can be used as a reinforcement that increases the hardness of aluminum matrix composites. 214 Advances in Science and Technology Research Journal 2023, 17(3), 214–225 Investigators are vigorously experimenting and discovering methods for strengthening the alu­ minum and its alloys utilizing the particles of ceramic.f were improved by raising the additive fraction. Also, it was noticed that the impact strength and elongation were decreased; nevertheless, the in­ vestigational analysis upon the tribological char­ acteristics wasn’t assessed [20, 21]. i Numerous methods, like different casting techniques, powder metallurgy, and mechanical milling have been utilized in the AMCs formula­ tion through the previous few decades. Amongst the whole such methods, the method of melting and casting is the highly favorable for the manu­ facturing since it’s comparatively inexpensive and facilitates the manufacture [7]. INTRODUCTION Besides its low price, the method of stir casting provides a big span of material as well as treating circumstances, and also it can synthesize composites with up to a (30%) reinforcement volume fraction with en­ hanced bonding between the matrix of metal and the reinforcements owing to the action of stirring. Regarding the all such advantages, the method of stir casting was chosen, especially for such inves­ tigation for the composites manufacture [8]. The literature clarifies that the aluminum al­ loys and the microscopic slide glass nanoparticles are commonly utilized in engineering. However, no attempt has been made to stir casting AA7075/ MSGNP composites and explore the effect of the weight percentage of MSGNPs on the physi­ cal and mechanical properties of the compos­ ites. The present study focuses on the evaluation of the properties of AMCs fabrication with the AA7075 as the matrix and the microscopic slide glass nanoparticles (MSGNPs) sieved to 35 nm at various percentages of weight fractions as the reinforcements employing the technique of stir- casting. It’s visualized that the additive’s fine particulate reinforcement will perform better performance than the coarse ones. The mechani­ cal properties and the metallurgical features of the specimens have been investigated utilizing mechanical tests and SEM micrographs, respec­ tively, thus raising the knowledge upon the waste materials’ effect upon the AA7075 properties as well as observing the AA7075/MSGNPs compos­ ite properties. Utilization of SiC particulates utilization in the AA7075 matrix manifested that the whole mechanical properties evinced improved values, with the exception of elongation to the failure [9]. For the manufactured nano-composites em­ ploying a stir-casting procedure via SiC carbide nanoparticles (mechanically pulverized) into a metal matrix of Al alloy, the outcomes of research elucidated enhancements of 45% in ultimate ten­ sile strength, 41% in yield strength, and 125% in hardness, and also the compressive strength enhancement from (311 MPa) to (603 MPa) at a (5%) SiC inclusion [10]. The used SiC for rein­ forcing the AA6061 illustrated the yield as well as maximum tensile strength improvement with (0-4 wt.%) inclusion, whereas the elongation was noted for reducing increasingly as the content augmented from (0) to (4%). And, it was seen that the SiC is a virtuous strengthener in the alumi­ num alloy [11]. MATERIALS The materials analyzed in the work are listed below: • Matrix material –Aluminum (AA7075) alloy, • Matrix material –Aluminum (AA7075) alloy, • Reinforcement material – microscopic slide glass nanoparticles (MSGNPs). • Matrix material –Aluminum (AA7075) alloy, • Reinforcement material – microscopic slide glass nanoparticles (MSGNPs). INTRODUCTION Also, other used additives in the preceding investigations are TiC [12], WC [13], Al2O3 [14], Si3N4 [15], and AlN [16], and the out­ comes demonstrated that the supplement of such reinforcements improved the Al and its alloys performance. As well, the use of waste in rein­ forcing and strengthening the aluminum alloys has proved successful [17]. The use of wastes like rice husk ash [18], and fly ash [19], and glass, was searched. −90 μm was employed for enhancing the Al scrap properties as well as the outcome portrayed that the maximum compres­ sive strength and the maximum tensile strength Processing of MMCs by stir casting (OES) test and the properties of base material were taken as per ASM material data sheet. Stir casting is the simplest and least expen­ sive way of making AMCs. This method includes mechanically mixing the reinforcing particles into a molten metal bath, and the resulting mix­ ture is then transferred to a formed mold just be­ fore it completely solidifies. The important issue in this process is to get a good wetting between the molten metal and the particle reinforcement. The composite specimen was made using stir casting technique, whose experimental setup is shown in Figure 2 [22], to ensure a more uniform Matrix material AA7075 alloy was used as the matrix material because it is a precipitation hardened aluminum alloy containing zinc, magnesium, copper, and chromium as the main alloying elements, accord­ ing to the chemical composition given in in the Table 1 together with that for the standard alloy for comparison purpose. It is strong and has good mechanical properties, including strength com­ parable to numerous steels, fatigue strength, and corrosion resistance. The physical and mechani­ cal properties of AA7075 are shown in the Table 2. The whole data of chemical analysis were obtained via the optical emission spectroscopy 215 Advances in Science and Technology Research Journal 2023, 17(3), 214–225 Table 1. Chemical compositions of the used AA7075 aluminum alloy (wt.%) and standard alloy Element Mg Fe Ti Si Mn Zn Cu Cr Al Wt.% 2.5 0.5 0.02 0.4 0.3 5.6 1.5 0.15 Balance Standard alloy 2.1-2.9 0-05 0-0.2 0-0.4 0-0.3 5.1-6.1 1.2-2 0.18-0.28 Balance Table 2. Physical and mechanical properties of the used AA7075 Table 2. Physical and mechanical properties of the used AA7075 glass into smaller particles by a milling process using a ball mill to obtain a powdery form. This process was pursued by sieving process employ­ ing a laboratory sieve shaker whose upper aper­ ture was 2.38 mm. The fine glass powder sieved to 35 nm was collected and then oven dried at 120°C for 24 h to remove the volatile content. Figure 1 reveals the SEM image of MSGNPs, and the chemical composition of MSGNPs is depicted in Table 3. The particle size, physical, mechani­ cal, and thermal properties of MSGNPs are given in Table 4. Table 2. Physical and mechanical properties of the used AA7075 Property Unit Values Density gm/cm3 2.81 Hardness (HB 500) HB 60 compressive strength MPa 330 Ultimate tensile strength MPa 200 Elongation % 11 Modulus of elasticity GPa 71.7 Poisson s of Ratio -- 0.33 Machinability % 70 Melting temperature °C 477-700 Shear modulus GPa 26.9 Shear strength MPa 331 Reinforcement metal Physical and mechanical properties of MSGNPs Property Unit Values Particle size nm 35 Density g/cc 2.48 Hardness Mohs 6 Light transmission, total solar % 91.5 Reflective index at 546.07 Nm 1.517 Coefficient of expansion °C 90.6 × 10-7 Poisson s of Ratio -- 0.2 Strain point °C 494 Annealing temperature °C 545 Softening temperature °C 720 Composite preparation The proposed metal matrix composite was fabricated at four different compositions, as listed in Table 5, where the amount of added magne­ sium was kept constant at 2%, and the added glass proportion was varied from 0 to 10%. Thus, the potential compositions of the novel composite are listed in this table. In addition to that, 1wt.% of flux was used to remove the slug. Figure 2. Stir casting setup [22] Figure 2. Stir casting setup [22] Reinforcement metal In this research, glass powder was used as the major reinforcement in form of particles obtained from a microscope slide. The particles were washed thoroughly under the running water to re­ move all impurities, after which they were dried in the open air for one day. Then, these particles were crushed and ground from microscopic-slide Figure 1. The SEM image of MSGNPs Figure 1. The SEM image of MSGNPs 216 Advances in Science and Technology Research Journal 2023, 17(3), 214–225 Table 3. Chemical composition of microscopic-slide gla Element SiO2 Al2O3 Fe2O3 Na2O % 72.2 1.2 0.03 14.3 Table 4. Physical and mechanical properties of MSGNPs Property Unit Values Particle size nm 35 Density g/cc 2.48 Hardness Mohs 6 Light transmission, total solar % 91.5 Reflective index at 546.07 Nm 1.517 Coefficient of expansion °C 90.6 × 10-7 Poisson s of Ratio -- 0.2 Strain point °C 494 Annealing temperature °C 545 Softening temperature °C 720 Figure 2. Stir casting setup [22] Table 3. Chemical composition of microscopic-slide glass nanoparticles MSGNP Element SiO2 Al2O3 Fe2O3 Na2O CaO K2O MgO SO3 TiO2 % 72.2 1.2 0.03 14.3 6.4 1.2 4.3 0.03 0.01 Table 4. Physical and mechanical properties of MSGNPs Property Unit Values Particle size nm 35 Density g/cc 2.48 Hardness Mohs 6 Light transmission, total solar % 91.5 Reflective index at 546.07 Nm 1.517 Coefficient of expansion °C 90.6 × 10-7 Poisson s of Ratio -- 0.2 Strain point °C 494 Annealing temperature °C 545 Softening temperature °C 720 slurry at 720°C and stirred with a stainless steel stirrer to avoid the agglomeration of powder and to ensure its uniform distribution. This process was done with the help of Argon gas that was pumped through a side tube. The slurry tempera­ ture was augmented to a totally liquid-state, and the automatic stirring was continued to around 2 min with a (450 rpm) average stirring speed. Then, the molten composite was directly decant­ ed into a steel mold (heated to 500°C) to prepare specimens for the testing purpose. Table 4. Physical and mechanical properties of MSGNPs Table 4. Reinforcement particles preheating Preheating the particulates is important to pre­ vent the moisture from entering the particulate; oth­ erwise, the moisture and gases can cause particulate agglomeration. Before mixing with the aluminum melt, the temperature was increased to 400°C for one hour in a muffle furnace to improve the wet­ tability and remove any type of other gases. Thus, reducing the humidity of the particles increases the surface energy and enhances its interaction with the aluminum, as it produces more effective particles in the aluminum matrix and less porosity in the casting [23]. Care was taken to put each gram of powder in foil before being introduced into the oven. Figure 2. Stir casting setup [22] dispersion of the reinforcing particles. The ma­ trix alloy (AA7075) was initially superheated at 700°C. After Al was completely melted, flux powder was added as a melt aiding to remove the slag from the molten. When the slag was re­ moved, magnesium strips were added to the mol­ ten, because Mg evaporates at a temperature of 450°C. The warmed glass particles of 2%, 4%, 8% and 10% (by weight) were slowly put into the Table 5: Concentrations of the composite material [%] Sample Al7075 Magnesium Glass 1 100 0 0 2 96 2 2 3 94 2 4 4 90 2 8 5 88 2 10 Table 5: Concentrations of the composite material [%] 217 Advances in Science and Technology Research Journal 2023, 17(3), 214–225 Stirring speed were improved via raising the grit size of the re­ inforcement particles of SiC. Therefore, the ef­ fect of using various percentages of MSGNPs on the mechanical properties (hardness and tensile strength) of the Al7075/MSGNP composites has been investigated in the present study. The stir casting method relies heavily on the stirring speed parameter. The distribution of rein­ forcing particles in molten metal is caused by a vortex that is created as a result of the influence by the speed of stirring. Therefore, it is evident that the stirring increases the wettability. The rate of stirring has a direct impact on the flow pattern of molten metal [24]. High-speed rotary mechan­ ical stirrers or ultrasonic stirrers can be used to achieve effective mechanical stirring to improve the wetting between the melted metal and the re­ inforcing particles, which is considered to be a crucial factor in the homogeneous distribution of reinforcement particles in the molten metal [25]. Therefore, in the present work, the average used stirring speed was selected to be 450 rpm and continued for about 2 min. Experimental details The microstructure and mechanical proper­ ties were considered for AA7075 reinforced with 0%, 2%, 4%, 8%, and 10% microscopic-slide glass nanoparticles subjected based on the tests of specimens. For each test, five samples from each mix were assessed, and the mean outcome was calculated for the analysis. Wetting element (magnesium) added to molten The wettability of aluminum melt with rein­ forcement particles can be improved by adding alloying elements, like calcium and magnesium. After the slag was removed from the molten, magnesium strips were added to the molten to in­ crease the wettability of liquid aluminum since it lowers the surface tension. Magnesium does not only increase the alloy’s strength but also causes magnesium oxide to form when it reacts with oxygen, which reduces the amount of blowholes that appear in the casting [26]. Size of reinforcement The size of reinforcement, the distance be­ tween the mold and the crucible, the pouring rate, and the pouring temperature are all significant de­ terminants in the quality of casting. To prevent the gas entrapment, the pouring rate and tem­ perature should be uniform [28]. The influence of using different grit sizes of SiC upon the me­ chanical properties of AMC (Al+4%Cu+5%Sic) by stir casting process with changing the pouring temperatures (700, 725, and 750°C) was studied [29]. It was found that the mechanical properties (impact strength, tensile strength, and hardness Mold preheating temperature A steel mold used for preparing the test speci­ mens was heated to 500°C. Preheating this mold is vital because it aids in the removal of trapped gas from the slurry, which would otherwise cause porosity [27]. Temperature for pouring Pouring temperature plays an important role for improving the mechanical properties of Aluminum-based metal matrix composites. Several researchers have studied the influence of the pouring temperature on the mechanical properties of AMCs using stir casting process. Investigated. The influence using three pouring temperatures (800°C, 820°C and 840°C) of Al/ TiB2 as well as (730°C, 750°C and 770°C) of Al/ SiCp metal matrix composites manufactured em­ ploying stir casting technique was investigated [30]. It was found that a higher tensile and frac­ ture strength were occurred at the MMCs of Al/ TiB2 in comparison with the Al/SiCp MMCs and the aluminum base alloy. The maximum hardness was reached at the pouring temperatures of 820°C and 750°C in the MMCs of Al/TiB2 and Al/SiCp, correspondingly. The influence of utilizing three pouring temperatures whilst fabricating Alumi­ num SiC metal matrix composites, with further advantages of Mg and Cu by stir casting method was studied [31]. It was concluded that the pour­ ing temperature possesses a significant effect upon the microstructure and mechanical conduct, creating it as a vigorous factor for synthesizing the Al/SiC/Mg/Cu composites. Thus, in the pres­ ent work, the pouring temperature of the molten composite was within the range of (700–720°C). Microstructural examination The distribution of glass particles into the produced composites was assessed using micro­ structural examination. It was intended to obtain a fair MSGNPs distribution into the AA-7075 matrix. The microstructural characteristics of 218 Advances in Science and Technology Research Journal 2023, 17(3), 214–225 Hardness test The specimens of hardness test were prepared by grinding with various grit sizes of grinding pa­ per, followed by polishing with a polishing ma­ chine to achieve mirror-like smooth surfaces. A Rockwell hardness apparatus was used to conduct the hardness test in accordance with ASTM E-18 standard, and the smooth-surfaced samples that have already been prepared were indented for 10 seconds with a (100 kg) load. The value of hardness was determined by measuring the average of four readings that were recorded for each position on the specimen surface. Rockwell hardness number was calculated according to the following formula [33]. Tensile strength test the created composites were examined employ­ ing an optical microscope. Using a JSM-7800F extreme resolution analytical field emission (SEM) fitted with EDX spectroscopy, the sur­ face morphology as well as the elemental com­ position was measured by (EDX) spectroscopy. The samples underwent a variety of grinding, polishing, and gold coating procedures before being prepared for the microscopic analysis, as manifested in the Figure 3. In order to etch the samples, Keller’s reagent (1.0 ml HF, 1.5 ml HCl, 2.5 ml HNO3, and 95 ml water) was used. Tensile testing was performed in accordance with standard (ASTM-E8) at the room tempera­ ture using a machine of type WDW-200E with an applied load capacity of (20 kN) and a strain rate of 0.5 mm/min. The standard specimen used in the tensile test is evinced in Figure 4. Analysis of SEM and EDX spectroscopy Figure 6 manifests the SEM image and EDX patterns of 7075 alloy, and the EDX analysis was carried out to examine the glass adsorption in the aluminum matrix as well as any other elements that might be present in the matrices. Figure 6a views the SEM image of AA7075-8%wt.%SiO2 composite. Figure 6b displays the EDX analysis demonstrating the increase of Si element in the composites than that in the base material, con­ firming the presence of Si. The alloying elements of the AA7075 base matrix are represented by the peaks for Na, C, O, Si and Al. The results of the EDX study for all AA7075-SiO2 compositions were similar; therefore, the 8% MSGNPs result shown in Figure 5d was chosen to serve as an ex­ ample of the oxidation and the presence of SiO2. In Table 7, the chemical composition of AA7075 is listed in accordance with the EDX. Microstructure Microstructural characterization of the com­ posites was used to determine how the glass particles were distributed inside the resulting composites. Figure 5a illustrates the microstruc­ ture of AA7075 alloy at 0 wt% microscopic- slide glass nanoparticles, and the microstructure of AA7075 portrayed a virtuous metallurgical bonding among the Al particles. Figures from 5b to 5e depict the microstructure of AA7075 al­ loy with different percentages of glass (2%, 4%, 8%, and 10%), and it has been observed that the MSGNPs are found in the matrix at sites, such as those on the grain boundaries and within the grains. When the MSGNPs concentration was increased to around 8% in figure 5d, the equally scattered microscopic-slide glass nanoparticles (MSGNPs) were found, and the open porosity de­ creased in figure 5d compared to figure 5c when Chemical composition of Al7075/MSGNP The chemical composition for the fabricated composite material is elucidated in the Table 6; therefore the 8% was chosen, the metal matrix composite contains aluminum, magnesium, iron and silicon, and the last element, which increased by the added glass, works to improve the tensile strength, hardness, and resistance to pitting, mak­ ing the composite material more resistant to cor­ rosion and rupture at the elevated temperature. The sample was tested in the Central Organiza­ tion for Standardization and Quality Control, Baghdad, Iraq. XRD characterization The phases present in the composites formed were identified using the analysis of X-Ray Dif­ fraction (XRD). Samples were scanned in the range from 10° to 90° at a speed of 2°/min while the XRD was running at (40 kV) and (30 mA). The XRD examination of the materials was per­ formed utilizing a back loading preparation tech­ nique [32]. The materials were examined using a PANalytical Empyrean diffractometer equipped with a PIXcel detector, fixed slits, and Cu-Ka1 ra­ diation with a Fe filter (= 1.540598 A). The used software is called Crystal. Impact match was used to identify the stage. RHN = E − 0.002 h (1) (1) where: E – a constant relying upon the indenter form (100 for the diamond indenter and 130 for the steel ball indenter), Figure 3. Microstructural examination: (a) grinding machine, (b) polishing machine, and (c) gold coating machine Figure 4. Tensile test specimen according to ASTM E8M-13a Figure 3. Microstructural examination: (a) grinding machine, (b) polishing machine, and (c) gold coating machine Figure 3. Microstructural examination: (a) grinding machine, (b) polishing machine, and (c) gold coating machine Figure 3. Microstructural examination: (a) grinding machine, (b) polishing machine, and (c) gold coating machine (b) polishing machine, and (c) gold coating machine Figure 4. Tensile test specimen according to ASTM E8M-13a Figure 4. Tensile test specimen according to ASTM E8M-13a Figure 4. Tensile test specimen according to ASTM E8M-13a 219 Advances in Science and Technology Research Journal 2023, 17(3), 214–225 h – the permanent increment in the pen­ etration depth owing to the main load, in mm. h – the permanent increment in the pen­ etration depth owing to the main load, in mm. the MSGNPs concentration was 4%. Such en­ hancement was ascribed to the sufficiency of re­ inforcement as well as the uniform distribution of MSGNPs with an addition of 8 wt.%. However, when the reinforcement (MSGNPs) content has been increased to around 10 wt.%, Figure 5e, the nano glass particles begin to agglomerate, creat­ ing dark black regions in the AA7075 matrix. In general, the MSGNPs have a fair distribution in composites, which is attributable to the fact that the quality of AMCs is controlled by the wetting of glass particles in aluminum. There is a signifi­ cant chemical reaction between the nano glass powder and the aluminum particles. XRD Analysis Figure 7 evinces the XRD result, displaying the various 2theta value-generated diffraction pat­ terns of the phases. The phases in the composites changed as a result of different two theta values. The phases being identified by the analysis of XRD, which were described via their robust peak Table 6: The chemical composition of the fabricated AA7075/MSGNPs Element Wt.% composition Element Wt.% composition Mg 1.11 Ni 0.01 Fe 0.20 Ti 0.02 Si 1.83 Ca 0.007 Cu 1.37 Ga 0.01 Mn 0.14 Zr 0.01 Zn 5.84 Al 89.2 220 Advances in Science and Technology Research Journal 2023, 17(3), 214–225 Figure 5. The microstructure image of Al 7075 MMCs (0%, 2%, 4%, 8%, and 10%): (a) 0 wt.%, (b) 2 wt.%, (c) 4 wt.%, and (d) 8 wt.%, and (e) 10 wt.% MSGNPs at 200X Figure 5. The microstructure image of Al 7075 MMCs (0%, 2%, 4%, 8%, and 10%): (a) 0 wt.%, (b) 2 wt.%, (c) 4 wt.%, and (d) 8 wt.%, and (e) 10 wt.% MSGNPs at 200X Figure 6. AA7075-8wt.% glass spectrum for: (a) The SEM micrographs of MMCs, and (b) The EDX spectra result of MMCs Figure 6. AA7075-8wt.% glass spectrum for: (a) The SEM micrographs of MMCs, and (b) The EDX spectra result of MMCs 221 Advances in Science and Technology Research Journal 2023, 17(3), 214–225 Table 7: Chemical composition of AA7075 by EDX Element Wt.% composition Element Wt.% composition Mg 1.12 Ni 0.01 Fe 0.22 Ti 0.02 Si 1.83 Na 2.1 Cu 1.37 C 0.02 Mn 0.14 O 0.01 Zn 5.84 Al Balance Figure 7. The XRD analysis of MMCs Table 7: Chemical composition of AA7075 by EDX Element Wt.% composition Element Wt.% composition Mg 1.12 Ni 0.01 Fe 0.22 Ti 0.02 Si 1.83 Na 2.1 Cu 1.37 C 0.02 Mn 0.14 O 0.01 Zn 5.84 Al Balance Figure 7. The XRD analysis of MMCs agglomeration. When AMCs are stressed, the particles act as agents that impede the mobility of dislocation inside the matrix, restricting the plastic flow. This might explain why AMCs’ ten­ sile properties have improved, as well as other mechanical qualities, such as stiffness and com­ pressive strength [34]. With an increase in glass of 10%, there was a small reduction into the ultimate tensile strength compared to the value achieved when adding 4%. Tensile strength Figure 8 elucidates the ultimate tensile strength of the AA7075 specimens reinforced with MSGNPs. The average values of tensile strength for 0%, 2%, 4%, 8%, and 10% speci­ mens were measured to be 50, 71.2, 89.16, 60, and 58.3 MPa, respectively. The tensile strength value of the created composite also improved, as shown in this figure 7. The greatest ultimate ten­ sile strength was found for the sample 3, which includes 4% MSGNPs. As demonstrated in fig­ ure 7, the ultimate tensile strength improves as the proportion of MSGNPs increases. This is owing to the high wettability of glass particles with the aluminum melts. The bonding strength between the aluminum alloy and the reinforc­ ing particles is reduced due to the particles XRD Analysis However, 10% still results in an improvement in yield, ultimate ten­ sile strength, and the final tensile strength was comparatively compared to the control. And, the reason for this decrease is attributed to the ef­ fect of dislocation multiplication, which leads to the accumulation of dislocation impeding fur­ ther deformation, and the result of this is up to failure. intensities, certainly contained SiO2. Also, this figure exhibits that the MSGNP and aluminum are the two main components of the composite, which is consistent with the optical microstruc­ ture of the composite. Hardness analysis The Al7075/MSGNP composites were manu­ factured using the stir casting technique, which demonstrated a consistent dispersion of nano glass particles at 8%. the porosity increased with a proportional rise in the MSGNP. In­ creased porosity can be linked to entrapped gas and bubbles during the production process. 2. The microstructural analysis of Al-7075 re­ vealed a good metallurgical bonding between the Al particles and the microscopic slide glass nano particles uniformly dispersed at the opti­ mum addition of 8 wt.%. 3. As MSGNPs was raised, the composite’s hard­ ness increased from 30 HRC to 60 HRC, while the tensile strength having maximum value of 89 MPa at 4% of MSGNPs, where the base metal was 50 MPa. 4. XRD manifested that the two main components of the composite were aluminium and glass. CONCLUSIONS In this experiment, Al7075/MSGNP compos­ ites were fabricated by stir casting with increas­ ing volume percentage of reinforcement particles. Mechanical behaviour and microstructure of the prepared AMMCs were analysed and obtained the appropriate level of MSGNP reinforcement required to produce Al-7075 composites. The outcomes were concise below. Hardness analysis Figure 9 portrays that after adding the MS­ GNP reinforcement to an aluminum alloy, the av­ erage values of hardness for 0%, 2%, 4%, 8%, and 10% specimens were measured to be 30, 35, 47, 61, and 60 RHC, respectively. The composite 222 Advances in Science and Technology Research Journal 2023, 17(3), 214–225 Figure 8. Ultimate tensile strength of aluminium MMC Figure 9. Microhardness of aluminium MMC Figure 8. Ultimate tensile strength of aluminium MMC Figure 8. Ultimate tensile strength of aluminium MMC Figure 9. Microhardness of aluminium MMC Figure 9. Microhardness of aluminium MMC Figure 9. Microhardness of aluminium MMC with 8% MSGNP has the highest hardness val­ ue in the present study. This means the hardness of the composite material increases with the in­ crease in the weight percentage of the reinforced particles (MSGNP). This is due to the presence of extremely hard ceramics (MSGNP) particles in the aluminum alloy matrix, a stronger limit on the localized matrix deformation during indentation [35], and a homogenous distribution of MSGN particles. Although the hardness is directly pro­ portional to the weight percentage, a decrease in the hardness was observed at 10% wt compared value obtained at 8%wt of MSGNP, the reason is due to nano glass particles begin to agglomerate in the Al-7075 matrix. Thus, causing a decrease in the hardness. 1. The Al7075/MSGNP composites were manu­ factured using the stir casting technique, which demonstrated a consistent dispersion of nano glass particles at 8%. the porosity increased with a proportional rise in the MSGNP. In­ creased porosity can be linked to entrapped gas and bubbles during the production process. with 8% MSGNP has the highest hardness val­ ue in the present study. This means the hardness of the composite material increases with the in­ crease in the weight percentage of the reinforced particles (MSGNP). This is due to the presence of extremely hard ceramics (MSGNP) particles in the aluminum alloy matrix, a stronger limit on the localized matrix deformation during indentation [35], and a homogenous distribution of MSGN particles. Although the hardness is directly pro­ portional to the weight percentage, a decrease in the hardness was observed at 10% wt compared value obtained at 8%wt of MSGNP, the reason is due to nano glass particles begin to agglomerate in the Al-7075 matrix. Thus, causing a decrease in the hardness. 1. 2. Aynalem G.F., Processing methods and mechanical properties of aluminium matrix composites, Adv. REFERENCES 1. Korkut M.H., Effect of particulate reinforcement on wear behaviour of aluminium matrix composites, Mater. Sci. Technol. 20(1), 2004: 73–81. 1. Korkut M.H., Effect of particulate reinforcement on wear behaviour of aluminium matrix composites, Mater. Sci. Technol. 20(1), 2004: 73–81. 2. Aynalem G.F., Processing methods and mechanical properties of aluminium matrix composites, Adv. 2. Aynalem G.F., Processing methods and mechanical properties of aluminium matrix composites, Adv. 223 Advances in Science and Technology Research Journal 2023, 17(3), 214–225 15. Sharma P., S. Sharma, D. Khanduja, Production and some properties of Si3N4 reinforced aluminium alloy composites, J. Asian Ceram. Soc. 3, 2018: 352–361. Mater. Sci. Eng., 2020, 20: 3765791. Mater. Sci. Eng., 2020, 20: 3765791. 3. Al-imari J.H.G. Fabrication and mechanical prop­ erties of economic composite materials using alu­ mimium scrap and wasted glass. 3rd International Conference on Mechanical, Automobile and Robot­ ics Engineering (ICMAR’2014), Singapore, Feb. 11-12, 2014, 356: 812-824. 16. Mohanavel V., K. Rajan, M. Ravichandran, Syn­ thesis, characterization and properties of stir cast AA 6351-aluminium nitride (AlN) composites, J. Mater. Res. 31(24), 2016: 3824–3831, http://doi. org/10.1557/jmr.2016.460. 4. Nuhu A.H., Jikan S.S., Asman S., Azam N., Zago D.M., Bano N. Fabrication and characterization of direct recycled Al-Cu - cullet metal composite. Jour­ nal of Science and Technology 9(4), 2017: 15-18 . 17. Adediran A.A., K.K. Alaneme, I.O. Oladele, E.T. Akinlabi, Microstructural characteristics and me­ chanical behaviour of aluminium matrix composites reinforced with Si-based refractory compounds de­ rived from rice husk, Cogent Eng. 8(1), 2021: 1–16, http://doi.org/10.1080/23311916.2021.1897928. 5. Parghi A. and Alam M.S. Physical and mechanical properties of cementitious composites containing recycled glass powder (RGP) and styrene butadin rubber (SBR). Construction and Buliding Materials, 104, 2016: 34-43. 18. Kumar S.D., M.S. Saravanan, Effect of mechanical properties on rice husk ash reinforced aluminium alloy (AlSi10Mg) matrix composites. Procedia En­ gineering, 64, 2013: 1505-1513. 6. Yamane M. and Mackenzie J.D. Vicker’s hardness of glass. Journal of Noncrystalline Solids, 15(2), 1974: 153-164. 7. Anis A.L., Ramli R., Darham W., Microstructure and mechanical properties investigation of in situ TiB2 and ZrB2 reinforced Al-4Cu composites. Mate­ rials Science and Engineering, 114, 2016: 1-5, http:// doi.org/10.1088/1757-899X/114/1/012120. 19. Kulkarni S.G., J.V. Meghnani, L. Achchhe, Effect of fly ash hybrid reinforcement on mechanical prop­ erty and density of aluminium 356 alloy. Procedia Materials Science, 5, 2014: 746-754 20. Al-Imari J.H.G. Fabrication and mechanical proper­ ties of economic composite materials using alumin­ ium scrap and wasted glass, 3rd Int. REFERENCES Conference on Mechanical, Automobile and Robotics Engineering, Scientific African, 12, 2021: e00812. 8. Sharma P., Sharma S., Khanduja D.A. Study on microstructure of aluminium matrix composites. Journal of Asian Ceramic Societies, 157, 2015: 1-5, http://doi.org/10.1016/j.jascer.2015.04.001 9. Komai K., Minoshima K., Ryoson H., Tensile and fatigue fracture behavior and water-environment ef­ fects in a SiC-whisker/7075-aluminum composite. Composites Science and Technology, 46, 1993: 59-66. 21. Akhil R. Effect of heat treatment on mechanical and microstructural properties of PbO glass reinforced metal matrix composite, Int. J. Sci. Res. 7(11), 2016: 1595-1598. 10. Md T.A., Ansari A., Arif S., Alam Md.N., Me­ chanical properties and morphology of aluminium metal matrix nanocomposites – stir cast products. Adavances in Materials and Processing Technolo­ gies, 2017: 1-15, http://doi.org/10.1080/2374068X. 2017.1350543 22. Kaw A.K. Mechanics of Composite materials. 2nd Edition, 2006. 23. Suresha S. and Sridhara B.K. Effect of silicon car­ bide particulates on wear resistance of graphitic aluminum matrix composites. Mater. Des., 31(9), 2010: 4470-4477. 11. Taha M.A., R. Youness, M. Ibrahim, Evolution of the physical, mechanical and electrical properties of SiC-reinforced Al 6061 composites prepared by stir cast method, Biointerface Res. Appl. Chem., 11(2), 2021: 8946–8956. 24. Ramakoteswara Rao.V., Ramanaiah. N., Sarcar. M.M.M., Fabrication and investigation on proper­ ties of TiC reinforced Al7075 metal matrix compos­ ites. Appl. Mech. Mater., 592-594, 2014: 349-353. 25. Singh J. and Chauhan A. A review of microstruc­ ture, mechanical properties and wear behavior of hybrid aluminum matrix composites fabricated via stir casting route. Sādhanā, 44, 2019: 1-18, 10.1007/ s12046-018-1025-5 12. Ravikumar K., K. Kiran, V.S. Sreebalaji, Micro structural characteristics and mechanical behaviour of aluminium matrix composites reinforced with ti­ tanium carbide, J. Alloys Compd. 723, 2017: 795– 801, http://doi.org/10.1016/j.jallcom.2017.06.309. 26. Stojanovic B., M. Babic, S. Velickovic, J. Blago­ jevic, Tribological behavior of aluminum hybrid composites studied by application of factorial tech­ niques. Tribol. Trans., 59(3), 2016: 522-529. 13. Ravikumar K., K. Kiran, V.S. Sreebalaji, Charac­ terization of mechanical properties of aluminium/ tungsten carbide composites, Measurement, 102, 2017: 142–149. 14. Pugalenthi P., M. Jayaraman, V. Subburam, Study of the microstructures and mechanical properties of aluminium hybrid composites with SiC and Al2O3. Mater. Technol., 53, 2019: 49-55. 27. Ramanathan A., P.K. Krishnan, R. Muraliraja, A review on the production of metal matrix com­ posites through stir casting Furnace design, prop­ erties, challenges, and research opportunities. J. 224 Advances in Science and Technology Research Journal 2023, 17(3), 214–225 Manuf. Process. 42, 2019:  213-245,  10.1016/j. REFERENCES jmapro.2019.04.017 S., Infuence of pouring temperature on stir cast­ ing of Al/SiC/Mg/Cu composite. March 2021, DOI:10.21203/rs.3.rs-314471/v1. 28. S. Soltani, R. Azari Khosroshahi, R. Taherzadeh Mousavian, Z.-Y. Jiang, A. Fadavi Boostani, and D. Brabazon, “Stir casting process for manufacture of Al–SiC composites”, Rare Metals, vol. 36, 2017, pp. 581–590, doi: 10.1007/s12598-015-0565-7 Google Scholar. 32. Ramezani A.H., Hoseinzadeh S., Ebrahiminejad, Z., Hantehzadeh M.R., Shafiee M. The study of mechanical and statistical properties of nitrogen ion-implanted Tantalum bulk. Optik, 225(1), 2021: 65628. 29. Suhail M., Alam M., Rahim R., The effect of Process parameter on metal matrix composite (Al+4%Cu+5%Sic) by stir casting. International Journal of Engineering Trends and Applications, 2(1), 2015. 33. ASTM E18-19, Standard Test Method for Rockwell Hardness of Metallic Materials, ASTM Internation­ al, West Conshohocken, PA., 2019. 34. Anilkumar H.C., H.S. Hebbar, K.S. Ravishankar, mechanical properties of fly ash reinforced alumin­ ium alloy (Al6061) composites. Int. J. Mech. Mater Eng. 6, 2011: 41-45. 30. Rajaravi C., B. Gobalakrishnan, P.R. Lakshmina­ rayanan, Effect of pouring temperature on cast Al/ SiCp and Al/TiB2 metal matrix composites. Journal of the Mechanical Behavior of Materials, 2019. 35. Lu L., Lim C.Y.H., Yeong W.M., Effect of reinforce­ ment on strength of Mg 9%Al composite. Compos­ ite’s Structure, 66, 2004: 41-45. 31. Tamilanban T., Ravikumar T.S., Kanthasamy 225
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The Evolving Role of Fetuin-A in Nonalcoholic Fatty Liver Disease: An Overview from Liver to the Heart
International journal of molecular sciences
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  Citation: Dogru, T.; Kirik, A.; Gurel, H.; Rizvi, A.A.; Rizzo, M.; Sonmez, A. The Evolving Role of Fetuin-A in Nonalcoholic Fatty Liver Disease: An Overview from Liver to the Heart. Int. J. Mol. Sci. 2021, 22, 6627. https:// doi.org/10.3390/ijms22126627 Academic Editor: Yoshio Fujitani Academic Editor: Yoshio Fujitani Keywords: NAFLD; Fetuin-A; CVD Keywords: NAFLD; Fetuin-A; CVD Received: 5 May 2021 Accepted: 17 June 2021 Published: 21 June 2021 Received: 5 May 2021 Accepted: 17 June 2021 Published: 21 June 2021 Review The Evolving Role of Fetuin-A in Nonalcoholic Fatty Liver Disease: An Overview from Liver to the Heart https:// doi.org/10.3390/ijms22126627 Academic Editor: Yoshio Fujitani Received: 5 May 2021 Accepted: 17 June 2021 Published: 21 June 2021 Review The Evolving Role of Fetuin-A in Nonalcoholic Fatty Liver Disease: An Overview from Liver to the Heart li Kirik 2, Hasan Gurel 3 , Ali A. Rizvi 4,5 , Manfredi Rizzo 5,6 and Alper Sonmez 7,* Teoman Dogru 1, Ali Kirik 2, Hasan Gurel 3 , Ali A. Rizvi 4,5 , Manfredi Rizzo 5,6 and Alp 1 Department of Gastroenterology, Balikesir University Medical School, Cagis, Balikesir 10145, Turkey; teomandogru@balikesir.edu.tr g 2 Department of Internal Medicine, Balikesir University Medical School, Cagis, Balikesir 10145, Turkey; ali.kirik@balikesir.edu.tr 2 Department of Internal Medicine, Balikesir University Medical School, Cagis, Balikesir 10145, Turkey; ali.kirik@balikesir.edu.tr 3 Department of Gastroenterology, Samsun Education and Research Hospital, University of Health Sciences, Ilkadim, Samsun 55090, Turkey; hasan.gurel1@saglik.gov.tr y g g g 4 Division of Endocrinology, Metabolism, and Lipids, Department of Medicine, Emory University, Atlanta, GA 30322, USA; ali.abbas.rizvi@emory.edu y 5 Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of South Carolina, Columbia, SC 29208, USA; manfredi.rizzo@unipa.it p 6 Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, 90133 Palermo, Italy p y y 7 Department of Endocrinology and Metabolism, Gulhane Medical School, University of Health Sciences, Ankara 06010, Turkey 7 Department of Endocrinology and Metabolism, Gulhane Medical School, University of Health Sciences, A k 1 T k * Correspondence: yusufalper.sonmez@sbu.edu.tr Abstract: Nonalcoholic fatty liver disease (NAFLD) is strongly associated to the features of metabolic syndrome which can progress to cirrhosis, liver failure and hepatocellular carcinoma. However, the most common cause of mortality in people with NAFLD is not liver-related but stems from atherosclerotic cardiovascular disease (CVD). The prevalence of NAFLD is on the rise, mainly as a consequence of its close association with two major worldwide epidemics, obesity and type 2 diabetes (T2D). The exact pathogenesis of NAFLD and especially the mechanisms leading to disease progression and CVD have not been completely elucidated. Human fetuin-A (alpha-2- Heremans Schmid glycoprotein), a glycoprotein produced by the liver and abundantly secreted into the circulation appears to play a role in insulin resistance, metabolic syndrome and inflammation. This review discusses the links between NAFLD and CVD by specifically focusing on fetuin-A’s function in the pathogenesis of NAFLD and atherosclerotic CVD.   Citation: Dogru, T.; Kirik, A.; Gurel, H.; Rizvi, A.A.; Rizzo, M.; Sonmez, A. The Evolving Role of Fetuin-A in Nonalcoholic Fatty Liver Disease: An Overview from Liver to the Heart. Int. J. Mol. Sci. 2021, 22, 6627. International Journal of Molecular Sciences 1. Introduction On the other hand, several studies show that atherogenic dyslipidemia, hyperinsulinemia and impaired liver glucose output are the possible players in the interaction between NAFLD and CVD [24–26]. So far, the pathogenesis of CVD in people with NAFLD is not clear and the search for the missing link is still in progress. 2 of 12 cesses of hepatic lipid uptake, synthesis, oxidation and secretion is modified by the hepa- tokines, which are proteins secreted by the liver. The alterations in the secretion and phos- phorylation of hepatokines play a role in the pathogenesis of NAFLD [14,15]. CVD is the most common cause of mortality in patients with NAFLD [16,17]. The focus of this article is to explore the relation of NAFLD to increased CVD risk. A growing body of evidence suggests that NAFLD increases the risk of CVD, alt- hough the exact pathogenesis is not clear [18–21]. Whether this is an independent effect of NAFLD or is confounded by the shared risk factors of insulin resistance, diabetes mellitus, dyslipidemia or hypertension is not clearly identified [16,17]. Prospective cohort studies performed in patients with T2D reported the role of NAFLD as an independent predictor Fetuin-A, also known as alpha-2-Heremans-Schmid glycoprotein, is abundantly syn- thesized and secreted by the liver. It is found in the extracellular space throughout the body [27]. Fetuin-A is a multifaceted protein playing a role in various cellular pathways including calcium and bone metabolism, insulin resistance and inflammation. The genes encoding fetuin-A are involved in diseases like MetS and T2D [15]. It is an important in- hibitor molecule of the insulin receptor tyrosine kinase in studies of insulin-resistant animal model [28–30]. In addition, fetuin-A is thought to support the formation of insulin resis- tance with its proinflammatory effect, apart from its direct effect on the insulin receptor [31]. It is thought that fetuin-A, which has a direct effect on insulin resistance, modulates for inflammatory reactions and causes various metabolic alterations [32]. Consistent with these findings, many epidemiologic studies showed that higher serum fetuin-A concentrations were independently associated with T2D, insulin resistance, MetS and CVD [33–35]. On the other hand, there are limited and conflicting data about the relationship between fetuin-A and NAFLD. The current review focuses on the role of fetuin-A in the pathogenesis of NAFLD and NAFLD-associated CVD risk (Figure 1). 1. Introduction NAFLD is the most common liver disorder, affecting 30–40% of the adult popula- tion [1–3] and up to 95% of patients with obesity [4–6]. It is characterized by chronic accumulation of fat in the liver (>5% of hepatocytes by histology) in the absence of sub- stantial alcohol consumption or other causes of liver disease such as viral or autoimmune hepatitis and medications. It refers to a spectrum of disorders ranging from benign simple steatosis (SS) to potentially more rapidly progressive histological phenotype, such as non- alcoholic steatohepatitis (NASH), which can progress to advanced fibrosis, cirrhosis and hepatocellular carcinoma [7–9]. A large body of evidence indicates that NAFLD is closely related to metabolic syndrome (MetS), and this association is mutual and bi-directional [10]. Insulin resistance seems to play a key role in the pathogenesis of NAFLD [11–13]. The pathophysiologic mechanisms underlying NAFLD and its progression have not been com- pletely elucidated so far. The interplay between the delivery of lipids to the liver and the processes of hepatic lipid uptake, synthesis, oxidation and secretion is modified by the hepatokines, which are proteins secreted by the liver. The alterations in the secretion and Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). https://www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2021, 22, 6627. https://doi.org/10.3390/ijms22126627 Int. J. Mol. Sci. 2021, 22, 6627 2 of 12 phosphorylation of hepatokines play a role in the pathogenesis of NAFLD [14,15]. CVD is the most common cause of mortality in patients with NAFLD [16,17]. The focus of this article is to explore the relation of NAFLD to increased CVD risk. A growing body of evidence suggests that NAFLD increases the risk of CVD, although the exact pathogenesis is not clear [18–21]. Whether this is an independent effect of NAFLD or is confounded by the shared risk factors of insulin resistance, diabetes mellitus, dyslipidemia or hypertension is not clearly identified [16,17]. Prospective cohort studies performed in patients with T2D reported the role of NAFLD as an independent predictor of the future risk of incident CVD [22,23]. 1. Introduction performed in patients with T2D reported the role of NAFLD as an independent predictor of the future risk of incident CVD [22,23]. On the other hand, several studies show that atherogenic dyslipidemia, hyperinsulinemia and impaired liver glucose output are the possible players in the interaction between NAFLD and CVD [24–26]. So far, the patho- genesis of CVD in people with NAFLD is not clear and the search for the missing link is still in progress. Fetuin-A, also known as alpha-2-Heremans-Schmid glycoprotein, is abundantly syn- thesized and secreted by the liver. It is found in the extracellular space throughout the body [27]. Fetuin-A is a multifaceted protein playing a role in various cellular pathways including calcium and bone metabolism, insulin resistance and inflammation. The genes encoding fetuin-A are involved in diseases like MetS and T2D [15]. It is an important in- hibitor molecule of the insulin receptor tyrosine kinase in studies of insulin-resistant ani- mal model [28–30]. In addition, fetuin-A is thought to support the formation of insulin resistance with its proinflammatory effect, apart from its direct effect on the insulin recep- tor [31]. It is thought that fetuin-A, which has a direct effect on insulin resistance, modu- lates for inflammatory reactions and causes various metabolic alterations [32]. Consistent with these findings, many epidemiologic studies showed that higher serum fetuin-A con- centrations were independently associated with T2D, insulin resistance, MetS and CVD [33–35]. On the other hand, there are limited and conflicting data about the relationship between fetuin-A and NAFLD. The current review focuses on the role of fetuin-A in the pathogenesis of NAFLD and NAFLD-associated CVD risk (Figure 1) Figure 1. The pathophysiological relationship of fetuin-A with NAFLD and CVD. Increased fetuin- A in plasma exerts an insulin pathway inhibitory effect by modulating the kinase reaction on the Figure 1. The pathophysiological relationship of fetuin-A with NAFLD and CVD. Increased fetuin-A in plasma exerts an insulin pathway inhibitory effect by modulating the kinase reaction on the insulin-receptor tyrosine kinase; it leads to the development of insulin resistance in insulin-sensitive tissues (muscle tissue, adipose tissue, liver, etc.) Furthermore, fetuin-A stimulates the release of inflammatory cytokines through Toll-like receptor 4 (TLR4) and it causes systemic inflammation. On the other hand, fetuin-A is an important calcium- and phosphate-binding protein and decreased fetuin-A levels strongly correlate with excessive vascular calcification and heart failure. 2.1. Studies Investigating Fetuin-A in Subjects with Radiologically Diagnosed NAFLD In a prospective study, Lebensztejn et al. investigated circulating fetuin-A levels in 45 obese children with NAFLD diagnosed with abdominal ultrasonography (US). Serum fetuin-A concentration was significantly higher in patients with NAFLD when compared to 30 healthy controls. However, there was no association of fetuin-A with any other parameters studied both in children with NAFLD and obese children without NAFLD [38]. Reinehr et al. studied the relationships between fetuin-A, NAFLD and MetS in a total of 36 obese and 14 lean children. The 12 obese children with NAFLD had significantly higher fetuin-A levels than the 24 obese children without NAFLD and the 14 normal-weight children. Fetuin-A levels were independent of age, pubertal stage and gender. Fetuin-A correlated significantly with systolic and diastolic blood pressure, homeostasis model assessment for insulin resistance (HOMA-IR) and high-density lipoprotein cholesterol (HDL-C) [39]. In a cross-sectional case-control study, Ou HY et al. investigated the re- lationship between serum fetuin-A levels and prediabetes in subjects with or without ultrasound-diagnosed NAFLD. A total of 510 age- and sex-matched subjects with normal glucose tolerance (NGT), impaired fasting glucose (IFG) and impaired glucose tolerance (IGT) with or without NAFLD were recruited. Fetuin-A levels were significantly higher in subjects with NAFLD when compared to subjects with NGT and prediabetes. Fetuin-A levels were positively associated with postload 2 h glucose, body mass index (BMI), triglyc- eride and HOMA-IR but negatively associated with age, HDL-C and adiponectin [40]. In a population-based cross-sectional study, Huang et al. investigated the association of serum fetuin-A with fatty liver index (FLI), the indicator of NAFLD in a total of 5219 middle-aged and elderly participants. Fetuin-A was positively associated with FLI, alanine aminotrans- ferase (ALT), aspartate aminotransferease (AST), and gamma-glutamyl transferase (GGT) after adjustment for the confounding factors. Multivariate logistic regression analysis showed that each one-standard-deviation increase in fetuin-A level was associated with 12%, 13%, and 10% increased risk of elevated FLI, ALT, and AST, respectively. Categori- cal analysis showed that compared to the lowest quartile, the highest quartile of serum fetuin-A was associated with a 35%, 50% and 33% increased risk of elevated FLI, ALT and AST, respectively [41]. Thompson et al. investigated the relationship of blood fetuin-A with fatty liver in 78 nonobese persons of African origin. Liver and abdominal fat were evaluated using computed tomography (CT). No association was found between fetuin-A and liver fat content [42]. Cui et al. 1. Introduction As a result, fetuin-A protein shows a multifunctional effect in the MetS and it plays a key role in the pathogenesis of NAFLD, T2D, obesity and CVD. Figure 1. The pathophysiological relationship of fetuin-A with NAFLD and CVD. Increased fetuin- A in plasma exerts an insulin pathway inhibitory effect by modulating the kinase reaction on the Figure 1. The pathophysiological relationship of fetuin-A with NAFLD and CVD. Increased fetuin-A in plasma exerts an insulin pathway inhibitory effect by modulating the kinase reaction on the insulin-receptor tyrosine kinase; it leads to the development of insulin resistance in insulin-sensitive tissues (muscle tissue, adipose tissue, liver, etc.) Furthermore, fetuin-A stimulates the release of inflammatory cytokines through Toll-like receptor 4 (TLR4) and it causes systemic inflammation. On the other hand, fetuin-A is an important calcium- and phosphate-binding protein and decreased fetuin-A levels strongly correlate with excessive vascular calcification and heart failure. As a result, fetuin-A protein shows a multifunctional effect in the MetS and it plays a key role in the pathogenesis of NAFLD, T2D, obesity and CVD. Int. J. Mol. Sci. 2021, 22, 6627 3 of 12 2. The Role of Fetuin-A in NAFLD; from Hepatic Steatosis to Inflammation and Fibrosis NAFLD occurs due to increased uptake and deposition of lipids in the hepatocytes which surpasses the rate of mitochondrial fatty acid oxidation and triglyceride secretion as the very low density lipoprotein particles. The disruption of the balance between lipid uptake and secretion is related to the impaired synthesis and secretion of hepatokines, leading to the development of insulin resistance, glucose intolerance and inflammation [14]. Fetuin-A, the major protein of the alpha-2-globulin fraction in serum electrophoresis, is among the hepatokines highly related to the pathogenesis of NAFLD and its metabolic com- plications [15]. Fetuin-A expression is significantly increased in subjects with NAFLD [35,36] and decrease after the improvement of NAFLD [37]. However, there are conflicting data re- garding the relationship of circulating fetuin-A with NAFLD and other metabolic disorders. 2.1. Studies Investigating Fetuin-A in Subjects with Radiologically Diagnosed NAFLD investigated the association of serum fetuin-A with NAFLD in 79 Chinese subjects. NAFLD was diagnosed and graded based on abdominal US. Serum fetuin-A level in NAFLD patients was significantly lower than that the controls. In addition, compared with controls, mild NAFLD and moderate NAFLD had significantly lower concentration of fetuin-A, while fetuin-A level tended to increase slightly with the severity of NAFLD [43]. Studies investigating fetuin-A in subjects with radiologically diagnosed NAFLD are given in Table 1. Int. J. Mol. Sci. 2021, 22, 6627 4 of 12 Table 1. Studies investigating circulating fetuin-A levels in subjects with NAFLD. Author (Reference) Study Population Diagnosis of NAFLD Fetuin-A Levels in NAFLD (Compared to Controls) Association of Fetuin-A with NAFLD Lebensztejn et al. [38] 45 obese children with NAFLD and 30 controls US Higher None Reinehr et al. [39] 36 obese children with NAFLD and 14 controls US Higher None Ou HY et al. [40] 255 subjects with NAFLD and 255 controls US Higher None Huang et al. [41] 5219 middle-aged and elderly subjects US NE Positive Cui et al. [43] 79 subjects with NAFLD and 79 controls US Lower Positive Sato et al. [44] 295 subjects with NAFLD US NE Negative Thompson et al. [42] 78 subjects with NAFLD CT NE None Yilmaz et al. [45] 99 subjects with NAFLD and 75 controls Liver bx Higher Positive Haukeland et al. [46] 111 subjects with NAFLD and 131 controls Liver bx Higher Positive Ou et al. [47] 90 subjects with NAFLD and 90 controls Liver bx Higher NE Celebi et al. [48] 105 subjects with NAFLD Liver bx NE None Kahraman et al. [49] 108 morbidly obese subjects with NAFLD and 10 controls Liver bx NS Negative Rametta et al. [50] 137 subjects with NAFLD and 260 controls Liver bx Higher Positive Von Loeffelholz et al. [51] 58 subjects with NAFLD Liver bx NE Positive Pampanini et al. [52] 160 subjects with NAFLD and 23 controls US and Liver bx Higher None NAFLD: nonalcoholic fatty liver disease, Bx: biopsy, NE: not evaluated, NS: no significant difference, US: ultrasonography, CT: computed tomography. Table 1. Studies investigating circulating fetuin-A levels in subjects with NAFLD. 2.2. Studies Investigating Fetuin-A in Histologically Diagnosed Subjects with NAFLD Yilmaz et al. investigated circulating fetuin-A in 99 patients with biopsy-proven NAFLD and 75 age- and gender-matched healthy controls. 2.1. Studies Investigating Fetuin-A in Subjects with Radiologically Diagnosed NAFLD Fetuin-A serum concentrations were not different between NAFLD patients (or subgroups) and controls. In liver tissue, expression of fetuin-A was significantly elevated in SS compared with controls. The NASH group exhibited an even stronger increased mRNA expression than SS patients. In correlation analysis, a significant positive association of fetuin-A with liver mRNA was observed. In addition, a significant negative association was found for the fibrosis stage and serum fetuin-A [49]. In a cross-sectional study, Rametta et al. evaluated the causal relationship between fatty liver and serum fetuin-A levels in 137 patients with histologically diagnosed NAFLD and 260 healthy subjects. They also analyzed whether the inherited PNPLA3 I148M variant modulates fetuin-A. Fetuin-A levels were higher in NAFLD patients than in the controls, independently of age, sex, BMI, insulin resistance, dyslipidemia, adiponectin, PNPLA3 I148M and ALT levels. In NAFLD patients, fetuin-A was associated with steatosis severity and MetS, but not with hepatic inflammation. At multivariate analysis, fetuin-A levels were associated with BMI, triglycerides, hyperglycemia and PNPLA3 I148M independently also of age, sex and ALT levels [50]. In their study, Von Loeffelholz et al. studied the role of fetuin-A in 58 patients with NAFLD/NASH undergoing open abdominal surgery. Compared to non-NAFLD sub- jects, fetuin-A levels were found to be significantly increased in subjects with NAFLD and NASH. In addition, fetuin-A correlated with the extent liver steatosis and hepatocellular ballooning degeneration [51]. However, on multivariate analysis, only hepatic steatosis was related with fetuin-A. In their study, Peter et al. reported in 55 NAFLD subjects, hepatic mRNA expression of fetuin-A associated positively with liver triglyceride content and HOMA-IR. In 220 subjects who underwent precise metabolic phenotyping, circulating fetuin-A was associated positively with liver fat content, and negatively with insulin sensi- tivity measured with the oral glucose tolerance test (OGTT) and during the euglycemic, hyperinsulinemic clamp [53]. Pampanini et al. studied fetuin-A levels in 81 obese children with NAFLD diagnosed by biopsy, 79 obese children with NAFLD defined by liver US and 23 lean subjects. Obese children with NAFLD detected by US had significantly higher fetuin-A levels compared to those with normal liver. In obese children who underwent liver biopsy, no significant differences were detected in fetuin-A levels between subject with NASH and those with SS [52]. Studies investigating fetuin-A in histologically diagnosed NAFLD are listed in Table 1. 2.1. Studies Investigating Fetuin-A in Subjects with Radiologically Diagnosed NAFLD Fetuin-A levels were signifi- cantly higher in subjects with NAFLD when compared to the controls. Multivariate analysis revealed a significant association of fetuin-A with insulin resistance as assessed by the HOMA-IR and the liver fibrosis. Moreover, the relationship between fetuin-A and fibrosis remained statistically significant even after adjustment for potential confounders, including the insulin resistance [45]. In a randomized controlled trial, Haukeland et al. investigated 111 subjects with histologically proven NAFLD. One hundred and thirty-one healthy sub- jects served as healthy controls. The main outcome variables were circulating levels of fetuin-A according to the presence of NAFLD, hepatic gene expression of fetuin-A and key enzymes in glucose and lipid metabolism. Fetuin-A levels were significantly higher in patients with NAFLD compared to controls. NAFLD was a significant predictor of elevated fetuin-A independent of BMI, age, sex, fasting glucose and triglycerides. Hepatic fetuin-A mRNA levels correlated significantly with hepatic mRNA levels of key enzymes in lipid (sterol regulatory element-binding protein-1c, carnitine palmitoyltransferase-1) and glucose (phosphoenol pyruvate kinase-1, glucose-6-phosphatase) metabolism [46]. Ou et al. aimed to investigate the levels of fetuin-A in 180 age- and sex-matched subjects with 5 of 12 Int. J. Mol. Sci. 2021, 22, 6627 NGT, NAFLD, newly diagnosed T2D (NDT2D) and NDT2D with NAFLD. They observed that fetuin-A levels were significantly higher in NDT2D with NAFLD as compared with NDT2D or NAFLD subjects [47]. In our previous study, we investigated circulating concen- trations of fetuin-A and its possible association with hepatic and systemic inflammation in a total of 105 nondiabetic male subjects with biopsy-proven NAFLD (NASH, n = 86 and SS, n = 19). Plasma levels of fetuin-A and markers of inflammation [high-sensitivity C-reactive protein (hsCRP), tumor necrosis factor alpha (TNF-α), interleukin-6 (IL-6) and adiponectin] were determined. In multivariate analysis, fetuin-A was negatively correlated with age, however, there was no association between fetuin-A and BMI, waist circumference (WC), glucose, insulin, HOMA-IR, lipid parameters, and inflammatory markers. In addition, no significant association was observed between fetuin-A and histological findings includ- ing liver fibrosis [48]. Kahraman et al. examined the hepatic fetuin-A expression in 108 morbidly obese NAFLD patients (50 with NASH and 58 with SS) undergoing bariatric surgery. A total of 10 subjects were used as healthy controls. In addition, primary human hepatocytes were treated with non-esterified fatty acid (NEFA) to investigate changes in fetuin-A expression. Treatment of hepatocytes with NEFA led to up-regulation of fetuin-A expression. 2.1. Studies Investigating Fetuin-A in Subjects with Radiologically Diagnosed NAFLD It is clear that there are significant differences regarding the relationship of circu- lating fetuin-A with NAFLD in literature. We suggest some possible explanations for the conflicting findings of these studies. First, when the abovementioned studies were analyzed separately, it can be seen that some of the subjects with NAFLD had metabolic confounders such as morbid obesity, T2D, hypertension and MetS. It has been reported that circulating levels of fetuin-A may be easily affected by these metabolic risk factors [31,46]. In addition, some of these patients were also using medications related to these metabolic Int. J. Mol. Sci. 2021, 22, 6627 6 of 12 problems [49,54]. It is well known that certain agents such as metformin, pioglitazone and niacin may affect the fetuin-A concentrations. Therefore, data regarding the association of fetuin-A with NAFLD might be affected by these confounders. Liver biopsy is the gold standard in diagnosing NAFLD, and the most accurate tool for the determination and grading of inflammation and fibrosis. However, in the abovementioned studies, the diagnosis of NAFLD was mostly performed by US or CT, and not all subjects received a liver biopsy. Therefore, the use of the various techniques for diagnosing of NAFLD may also contribute to contradictory results regarding the association of fetuin-A with liver inflammation and fibrosis. Circulating fetuin-A has been inversely associated with age in subjects with NAFLD. Although it has been hypothesized that low levels of fetuin-A may be the result of decreased hepatic fetuin-A production in older people, the exact mecha- nism responsible for this relationship remains unclear [44,47,48]. Thus, age may be another factor that influences the levels of circulating fetuin-A in NAFLD. The different methods of measuring the concentrations of circulating fetuin-A (such as different ELISA kits) might be another reason for discrepant findings in various studies [45,48,49]. Another reason might be the polymorphisms of the fetuin-A gene which cause variations in the serum assays [55]. On the other hand, as recently reported, genetic factors may also affect the fetuin-A con- centrations independently from inflammation [53]. Lastly, other possible confounders that may affect the association of fetuin-A with NAFLD might include arbitrary definitions of “apparently healthy” controls and different definitions regarding the “normal levels of serum aminotransferases”. 2.1. Studies Investigating Fetuin-A in Subjects with Radiologically Diagnosed NAFLD In light of these data, we think that it is still uncertain whether fetuin-A directly contributes to the development of NAFLD, whether elevated blood levels reflect the presence or severity of NAFLD, or if other unidentified factors simultaneously influence both. Going forward, research should investigate whether fetuin-A has a role in the progression of liver inflammation and fibrosis that may occur during the natural history of NAFLD. Further studies are also needed to search the modulation of fetuin-A as a potential therapeutic strategy in this clinically relevant condition. 3. The Relationship of Fetuin-A with NAFLD Associated CVD Risk The metabolic or cardiovascular risk is not only related to the serum levels of fetuin-A, but also to such factors such as renal function, concomitant disorders, medications and the type of serum assay used [15]. It is noteworthy that serum levels of fetuin-A may not clearly reflect the functionality of this hepatokine. Fetuin-A presents in circulation in two different forms in a soluble form in plasma as well as in colloidal fractions [71]. Phosphorylation of fetuin-A is needed for it be effective on insulin receptors [28,29]. Fetuin-A is fully phosphorylated only when it is in colloidal fractions [30]. Thus, simply measuring serum levels of fetuin-A may not be an accurate way to assess its functionality. y CVD is the most common cause of mortality in individuals with NAFLD. The lat- ter is associated with an increased risk of incident CVD that is independent of the risk conferred by traditional cardiovascular risk factors (e.g., dyslipidemia, T2D and smok- ing) [13]. However, there is limited and conflicting data regarding the role of fetuin-A in the pathogenesis of increased CVD risk in NAFLD. Sato et al. investigated the relationship between circulating fetuin-A levels and liver/vessel fibrosis-related markers (platelet count, NAFLD fibrosis score and carotid intima–media thickness (cIMT)) in 295 subjects with NAFLD. Multivariate analysis revealed that fetuin-A concentration was a significant and independent determinant of platelet count, NAFLD fibrosis score and mean cIMT [44]. Our group investigated the relationship of circulating fetuin-A with markers of endothe- lial dysfunction (asymmetric dimethyl arginine (ADMA) and adiponectin) and cIMT in 115 patients with biopsy-confirmed NAFLD and 74 age-matched healthy subjects. Fetuin- A and ADMA levels were significantly higher and adiponectin level was significantly lower in the NAFLD group than the control group. In addition, the NAFLD group had greater cIMT levels than the controls. However, no difference was observed for fetuin-A, ADMA, adiponectin and cIMT between the two groups when the findings were adjusted for glucose, lipids and HOMA-IR index. In univariate analysis, fetuin-A was found to be positively associated with triglyceride, HOMA-IR, ADMA and cIMT values, and negatively associated with HDL-C and adiponectin. Multiple linear regression analysis showed that fetuin-A was independently associated with ADMA and cIMT levels [72]. In contrast, Ballestri et al. investigated fetuin-A levels in 70 subjects who underwent elective coronary angiography for suspected coronary artery disease (CAD) in a prospective, cross-sectional study. 3. The Relationship of Fetuin-A with NAFLD Associated CVD Risk 3. The Relationship of Fetuin-A with NAFLD Associated CVD Risk The relationship of fetuin-A with CVD is Janus-faced. Both low and high fetuin-A levels have been reported to increase the risk of CVD-related mortality and morbidity [15]. Fetuin-A is a significant regulator of calcium, phosphate and bone metabolism, and a prominent inhibitor of extraosseous calcification [56,57]. Low serum fetuin-A levels are found in patients with chronic kidney disease (CKD), which in turn is associated with arterial stiffness and increased all-cause and cardiovascular mortality [58,59]. On the other hand, high fetuin-A levels may also increase the risk of CVD through effects on insulin resistance and subclinical inflammation [15]. As NAFLD is a significant risk factor for the development of MetS and T2D [60], the relation of fetuin-A to CVD is likely to be stronger in the presence of NAFLD [61]. Few studies have investigated the association of circulating fetuin-A levels and risk of CVD prospectively. In a study of 3810 individuals older than 65 years, it was reported that higher fetuin-A levels were associated with lower risk of CVD among participants without T2D [62]. These findings are similar to the previous Rancho Bernardo Study that showed higher fetuin-A levels were associated with lower risk of CVD mortality in participants without T2D [63]. On the other hand, in the Nurses’ Health Study, higher fetuin-A levels were associated with lower CVD risk when CRP levels were high, but no association was observed among participants with lower CRP levels [64]. Moreover, we and others have demonstrated that fetuin-A level is inversely associated with calcification scores, CV events and mortality from CVD in subjects with CKD [65,66]. However, contradictory to these findings, it was reported that subjects with high fetuin-A levels had a 4-fold increased risk for myocardial infarction and ischemic stroke compared to subjects with low fetuin-A levels [67]. In addition, individuals with previous myocardial infarction had significantly higher concentrations of fetuin-A than healthy controls [68]. A positive association of Int. J. Mol. Sci. 2021, 22, 6627 7 of 12 fetuin-A with arterial stiffness and increased intima–media thickness has been observed in healthy subjects and in patients with normal renal function [68–70]. fetuin-A with arterial stiffness and increased intima–media thickness has been observed in healthy subjects and in patients with normal renal function [68–70]. In view of the above data, it seems that the relationship between circulating fetuin-A and CVD is complicated. 3. The Relationship of Fetuin-A with NAFLD Associated CVD Risk Twenty-four patients had no CAD (9 with and 15 without NAFLD) and 46 had CAD (20 with and 26 without NAFLD). Fetuin-A was significantly lower in patients with CAD compared to those without CAD. In addition, at multivariate analysis, they reported high fetuin-A levels to be independently associated with NAFLD and a lower risk of CAD [73]. Finally, Nascimbeni et al. investigated fetuin-A values and their relationship with symp- tomatic atherosclerosis in 149 patients with coronary artery disease (CAD) and peripheral arterial disease (PAD). Fetuin-A levels were positively associated with both CAD and NAFLD [74]. Studies investigating the relationship of fetuin-A with NAFLD-associated CVD risk are given in Table 2. g In light of these results, although the reason for the inconsistencies in the obtained data is not clear, various explanations have been suggested. It has been suggested that as a result of the detrimental effect of fetuin-A on insulin resistance and plasma lipid levels, it aggravates CVD in the initial period of the disease. However, in the later stages of the CVD, high fetuin-A levels have been observed to have a positive effect by preventing vascular calcification [75]. Therefore, it has been shown that the deficiency of fetuin- A, an inhibitor of vascular calcification, develops severe soft tissue and intravascular calcifications in animal studies with fetuin-A knockout mice [76]. On the other hand, as mentioned above, we observed a significant negative association of fetuin-A with HDL- C and adiponectin concentrations in our NAFLD cohort [72]. Since elevated levels of adiponectin and HDL-C are known to protect against atherosclerosis, we propose that the Int. J. Mol. Sci. 2021, 22, 6627 8 of 12 8 of 12 modulation of adiponectin and/or HDL-C by fetuin-A might be an important contributor in the pathogenesis of atherosclerosis and CVD in NAFLD. These data suggest that the relationship of fetuin-A with CVD is more complex than previously thought. Longitudinal studies with a greater number of subjects are needed to determine the contributory effects of fetuin-A on CVD risk in NAFLD. Table 2. Studies investigating the relationship of fetuin-A with CVD in subjects with and without NAFLD. Author (Reference) Study Population Study Design CVD Risk Assessment Association of Fetuin-A with CVD Risk Jensen et al. [62] 3810 older subjects Prospective CVD event or CVD death Negative Laughlin et al. [63] 1688 women Prospective CVD event or CVD death Negative Sun et al. 3. The Relationship of Fetuin-A with NAFLD Associated CVD Risk [64] 466 patients with IS Prospective IS None Caglar et al. [65] 198 nondiabetic patients with CKD Retrospective FMD and cIMT Positive Zhao et al. [75] 241 patients with T2D Retrospective Coronary angiography Positive Weikert et al. [67] 227 patients with MI and 168 patients with IS Prospective MI or IS Positive Vörös et al. [68] 171 patients with CVD and 81 controls Cross-sectional Biomarkers of ED Positive Mori et al. [70] 141 healthy subjects Cross-sectional Carotid arterial stiffness Positive Sato et al. [44] 295 subjects with NAFLD Cross-sectional cIMT Negative Dogru et al. [72] 115 subjects with NAFLD Cross-sectional Biomarkers of ED and cIMT Positive Ballestri et al. [73] 70 subjects with and without CVD Cross-sectional Coronary angiography Negative Nascimbeni et al. [74] 45 patients with CVD and 104 patients with PAD Cross-sectional CAD PAD Positive NAFLD: nonalcoholic fatty liver disease, CVD: cardiovascular disease, IS: ischemic stroke, CKD: chronic kidney disease, FMD: flow mediated dilation, cIMT: carotid intima–media thickness, T2D: type 2 diabetes, MI: myocardial infarction, ED: endothelial dysfunction, PAD: peripheral artery disease, CAD: coronary artery disease. able 2. Studies investigating the relationship of fetuin-A with CVD in subjects with and without NAFLD. NAFLD: nonalcoholic fatty liver disease, CVD: cardiovascular disease, IS: ischemic stroke, CKD: chronic kidney disease, FMD: flow mediated dilation, cIMT: carotid intima–media thickness, T2D: type 2 diabetes, MI: myocardial infarction, ED: endothelial dysfunction, PAD: peripheral artery disease, CAD: coronary artery disease. Institutional Review Board Statement: Not applicable. Informed Consent Statement: Not applicable. Data Availability Statement: Not applicable. Data Availability Statement: Not applicable. Conflicts of Interest: The authors declare that the current research was conducted independently, in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Rizzo is a full-time Professor of Internal Medicine at University of Palermo, Italy and currently Medical Director, Novo Nordisk Eastern Europe; he has given lectures, received honoraria and research support, and participated in conferences, advisory boards and clinical trials sponsored by many pharmaceutical companies including Amgen, AstraZeneca, Boehringer Ingelheim, Kowa, Eli Lilly, Meda, Mylan, Merck Sharp & Dohme, Novo Nordisk, Novartis, Roche Diagnostics, Sanofi and Servier. Sonmez has received honoraria and research support, and participated in conferences, advisory boards and clinical trials sponsored by many pharmaceutical companies including As- traZeneca, Novo Nordisk, Novartis, Eli Lilly and Sanofi. None of the above had any role in this article, which has been written independently, without any financial or professional help, and reflects only the opinion of the authors, without any role of the industry. References 1. Li, J.; Zou, B.; Yeo, Y.H.; Feng, Y.; Xie, X.; Lee, D.H.; Fujii, H.; Wu, Y.; Kam, L.Y.; Ji, F.; et al. Prevalence, incidence, and outcome of nonalcoholic fatty liver disease in Asia, 1999–2019: A systematic review and meta-analysis. Lancet Gastroenterol. Hepatol. 2019, 4, 389–398. [CrossRef] 2. Browning, J.D.; Szczepaniak, L.S.; Dobbins, R.; Nuremberg, P.; Horton, J.D.; Cohen, J.C.; Grundy, S.M.; Hobbs, H.H. Prevalence of hepatic steatosis in an urban population in the United States: Impact of ethnicity. Hepatology 2004, 40, 1387–1395. [CrossRef] 2. Browning, J.D.; Szczepaniak, L.S.; Dobbins, R.; Nuremberg, P.; Horton, J.D.; Cohen, J.C.; Grundy, S.M.; Hobbs, H.H. Prevalence of hepatic steatosis in an urban population in the United States: Impact of ethnicity. Hepatology 2004, 40, 1387–1395. [CrossRef] 3. Younossi, Z.M.; Koenig, A.B.; Abdelatif, D.; Fazel, Y.; Henry, L.; Wymer, M. Global epidemiology of nonalcoholic fatty liver disease-meta-analytic assessment of prevalence, incidence, and outcomes. Hepatology 2016, 64, 73–84. [CrossRef] [PubMed] p p p p y p gy 3. Younossi, Z.M.; Koenig, A.B.; Abdelatif, D.; Fazel, Y.; Henry, L.; Wymer, M. Global epidemiology of nonalcoholic fatty liver disease-meta-analytic assessment of prevalence, incidence, and outcomes. Hepatology 2016, 64, 73–84. [CrossRef] [PubMed] y p p gy 4. Silverman, J.F.; O’Brien, K.F.; Long, S.; Leggett, N.; Khazanie, P.G.; Pories, W.J.; Norris, H.T.; Caro, J.F. Liver pathology in morbidly obese patients with and without diabetes. Am. J. Gastroenterol. 1990, 85, 1349–1355. [PubMed] 5. Subichin, M.; Clanton, J.; Makuszewski, M.; Bohon, A.; Zografakis, J.G.; Dan, A. Liver disease in the morbidly obese: A review of 1000 consecutive patients undergoing weight loss surgery. Surg. Obes. Relat. Dis. 2015, 11, 137–141. [CrossRef] [PubMed] 6. Sasaki, A.; Nitta, H.; Otsuka, K.; Umemura, A.; Baba, S.; Obuchi, T.; Wakabayashi, G. Bariatric surgery and nonalcoholic fatty liver disease: Current and potential future treatments. Front. Endocrinol. 2014, 5, 164. [CrossRef] [PubMed] p 7. Toplak, H.; Stauber, R.; Sourij, H. EASL-EASD-EASO clinical practice guidelines for the management o disease: Guidelines, clinical reality and health economic aspects. Diabetologia 2016, 59, 1148–1149. [Cro R.; Sourij, H. EASL-EASD-EASO clinical practice guidelines for the management of nonalcoholic fatty liver clinical reality and health economic aspects. Diabetologia 2016, 59, 1148–1149. [CrossRef] y p g 8. Chalasani, N.; Younossi, Z.; Lavine, J.E.; Charlton, M.; Cusi, K.; Rinella, M.; Harrison, S.A.; Brunt, E.M.; Sanyal, A.J. The diagnosis and management of nonalcoholic fatty liver disease: Practice guidance from the American Association for the Study of Liver Diseases. References Hepatology 2018, 67, 328–357. [CrossRef] Diseases. Hepatology 2018, 67, 328–357. [CrossRe p gy 9. Singh, S.; Allen, A.M.; Wang, Z.; Prokop, L.J.; Murad, M.H.; Loomba, R. Fibrosis progression in nonalcoholic fatty liver vs nonalcoholic steatohepatitis: A systematic review and meta-analysis of paired-biopsy studies. Clin. Gastroenterol. Hepatol. 2015, 13, 643–654.e9. [CrossRef] 10. Lonardo, A.; Leoni, S.; Alswat, K.A.; Fouad, Y. History of nonalcoholic fatty liver disease. Int. J. Mol. Sci. 2020, 21, 5888. [CrossRef] 11. Yki-Järvinen, H. Nonalcoholic fatty liver disease as a cause and a consequence of metabolic syndrome. Lancet Diabetes Endocrinol. 2014, 2, 901–910. [CrossRef] 10. Lonardo, A.; Leoni, S.; Alswat, K.A.; Fouad, Y. History of nonalcoholic fatty liver disease. Int. J. Mol. k l h l f l d d f b l d y y 11. Yki-Järvinen, H. Nonalcoholic fatty liver disease as a cause and a consequence of metabolic syndrome. Lancet Diabetes Endocrinol. 2014, 2, 901–910. [CrossRef] 12. Ercin, C.N.; Dogru, T.; Genc, H.; Celebi, G.; Aslan, F.; Gurel, H.; Kara, M.; Sertoglu, E.; Tapan, S.; Bagci, S.; et al. Insulin resistance but not visceral adiposity index is associated with liver fibrosis in nondiabetic subjects with nonalcoholic fatty liver disease. Metab. Syndr. Relat. Disord. 2015, 13, 319–325. [CrossRef] y 13. Byrne, C.D.; Targher, G. NAFLD: A multisystem disease. J. Hepatol. 2015, 62, S47–S64. [CrossRef] 14. Meex, R.C.R.; Watt, M.J. Hepatokines: Linking nonalcoholic fatty liver disease and insulin resistance. Nat. Rev. Endocrinol. 2017, 13, 509–520. [CrossRef] messer, L.; Moré, E.; Franzen, M.; Topf, A.; Mirna, M.; Paar, V.; Pistulli, R.; Kretzschmar, D.; Wernly, B.; e ions of fetuin-A. Int. Rev. Cytol. 2019, 89, 79–130. [CrossRef] 15. Jirak, P.; Stechemesser, L.; Moré, E.; Franzen, M.; Topf, A.; Mirna, M.; Paar, V.; Pistulli, R.; Kretzsch Clinical implications of fetuin-A. Int. Rev. Cytol. 2019, 89, 79–130. [CrossRef] 16. Bril, F.; Cusi, K. Nonalcoholic fatty liver disease. Endocrinol. Metab. Clin. N. Am. 2016, 45, 765–781. [CrossRef] [PubMed] 17 A t M Ad L A C b A S W K E t h ti li ti f l h li f tt li di H t l 16. Bril, F.; Cusi, K. Nonalcoholic fatty liver disease. Endocrinol. Metab. Clin. N. Am. 2016, 45, 765–781. 16. Bril, F.; Cusi, K. Nonalcoholic fatty liver disease. Endocrinol. Metab. Clin. N. Am. 2016, 45, 765–781. [CrossRef] [PubMed] 17. Armstrong, M.; Adams, L.A.; Canbay, A.; Syn, W.K. Extrahepatic complications of nonalcoholic fatty liver disease. 1. Li, J.; Zou, B.; Yeo, Y.H.; Feng, Y.; Xie, X.; Lee, D.H.; Fujii, H.; Wu, Y.; Kam, L.Y.; Ji, F.; et al. Prevalence, incidence, and outcome of nonalcoholic fatty liver disease in Asia, 1999–2019: A systematic review and meta-analysis. Lancet Gastroenterol. Hepatol. 2019, 4, 389–398. [CrossRef] 4. Conclusions NAFLD, considered a hepatic manifestation of MetS, independently increases the risk of developing both T2D and CVD. Hepatokines that are mainly secreted from the liver are known to affect glucose and lipid metabolism. They can also modulate inflam- matory processes that in turn mediate the atherosclerotic process. Fetuin-A is a novel hepatokine and a pleotropic molecule with diverse and well-established proinflammatory and anti-inflammatory properties impacting a multitude of systems. As a proinflammatory compound, fetuin-A contributes to insulin resistance and is an important link between liver, adipose tissue and skeletal muscle. Although the significance of fetuin-A in NAFLD has been increasingly recognized, its pathogenetic role is still not completely understood. The relationship between circulating fetuin-A and CVD risk associated with NAFLD appears to be complex and in need of further research. Author Contributions: T.D., A.S.—conceived the original idea; A.K., H.G.—performed the patient data collection; T.D., A.K.—analyzed the data and designed the tables and figures; T.D., A.K., A.S.— designed the study; T.D., A.S., M.R., A.A.R.—wrote the manuscript. All authors have read and agreed to the published version of the manuscript. Funding: This research received no external fundings. Funding: This research received no external fundings. 9 of 12 Int. J. Mol. Sci. 2021, 22, 6627 Institutional Review Board Statement: Not applicable. References Hepatology 2014, 59, 1174–1197. [CrossRef] [PubMed] y 17. Armstrong, M.; Adams, L.A.; Canbay, A.; Syn, W.K. Extrahepatic complications of nonalcoholic fatty liver disease. Hepatology 2014, 59, 1174–1197. [CrossRef] [PubMed] 18. Lu, H.; Zeng, L.; Liang, B.; Shu, X.; Xie, D. High prevalence of coronary heart disease in type 2 diabetic p fatty liver disease. Arch. Med. Res. 2009, 40, 571–575. [CrossRef] Liang, B.; Shu, X.; Xie, D. High prevalence of coronary heart disease in type 2 diabetic patients with nonalcoh e. Arch. Med. Res. 2009, 40, 571–575. [CrossRef] 19. Targher, G.; Bertolini, L.; Padovani, R.; Poli, F.; Scala, L.; Tessari, R.; Zenari, L.; Falezza, G. Increased prevalence of cardiovascular disease in type 2 diabetic patients with nonalcoholic fatty liver disease. Diabet. Med. 2006, 23, 403–409. [CrossRef] 10 of 12 Int. J. Mol. Sci. 2021, 22, 6627 10 of 12 20. Stepanova, M.; Rafiq, N.; Makhlouf, H.; Agrawal, R.; Kaur, I.; Younoszai, Z.; McCullough, A.; Goodman, Z.; Younossi, Z.M. Predictors of all-cause mortality and liver-related mortality in patients with nonalcoholic fatty liver disease (NAFLD). Dig. Dis. Sci. 2013, 58, 3017–3023. [CrossRef] 21. Söderberg, C.; Stål, P.; Askling, J.; Glaumann, H.; Lindberg, G.; Marmur, J.; Hultcrantz, R. Decreased survival of subjects with elevated liver function tests during a 28-year follow-up. Hepatology 2010, 51, 595–602. [CrossRef] 22. Targher, G.; Bertolini, L.; Rodella, S.; Tessari, R.; Zenari, L.; Lippi, G.; Arcaro, G. Nonalcoholic fatty liver disease is independently associated with an increased incidence of cardiovascular events in type 2 diabetic patients. Diabetes Care 2007, 30, 2119–2121. [CrossRef] 23. Targher, G.; Bertolini, L.; Poli, F.; Rodella, S.; Scala, L.; Tessari, R.; Zenari, L.; Falezza, G. Nonalcoholic fatty liver disease and risk of future cardiovascular events among type 2 diabetic patients. Diabetes 2005, 54, 3541–3546. [CrossRef] 24. Bril, F.; Sninsky, J.J.; Baca, A.M.; Superko, H.R.; Sanchez, P.P.; Biernacki, D.; Maximos, M.; Lomonaco, R.; Orsak, B.; Suman, A.; et al. Hepatic steatosis and insulin resistance, but not steatohepatitis, promote atherogenic dyslipidemia in NAFLD. J. Clin. Endocrinol. Metab. 2016, 101, 644–652. [CrossRef] 25. Lomonaco, R.; Bril, F.; Portillo-Sanchez, P.; Ortiz-Lopez, C.; Orsak, B.; Biernacki, D.; Lo, M.; Suman, A.; Weber, M.H.; Cusi, K. Metabolic impact of nonalcoholic steatohepatitis in obese patients with type 2 diabetes. Diabetes Care 2016, 39, 632–638. [CrossRef] 26. Bril, F.; Lomonaco, R.; Orsak, B.; Ortiz-Lopez, C.; Webb, A.; Tio, F.; Hecht, J.; Cusi, K. References Fully phosphorylated fetuin-A forms a mineral complex in the serum of rats with adenine-induced renal failure. Kidney Int. 2009, 75, 915 928 [CrossRef] 30. Matsui, I.; Hamano, T.; Mikami, S.; Fujii, N.; Takabatake, Y.; Nagasawa, Y.; Kawada, N.; Ito, T.; Rakugi, H.; Imai, E.; et al. Fully phosphorylated fetuin-A forms a mineral complex in the serum of rats with adenine-induced renal failure. Kidney Int. 2009, 75, 915–928. [CrossRef] 31. Mori, K.; Emoto, M.; Inaba, M. Fetuin-A: A multifunctional protein. Recent Pat. Endocr. Metab. Immune Drug Discov. 2011, 5, 124–146. [CrossRef] 32. Trepanowski, J.F.; Mey, J.; Varady, K.A. Fetuin-A: A novel link between obesity and related complications. Int. J. Obes. 2015, 39, 734–741. [CrossRef] 33. Ou, H.-Y.; Yang, Y.; Wu, H.-T.; Wu, J.-S.; Lu, F.-H.; Chang, C. Serum fetuin-A concentrations are elevated glucose tolerance and newly diagnosed type 2 diabetes. Clin. Endocrinol. 2011, 75, 450–455. [CrossRef] 34. Ix, J.H.; Shlipak, M.G.; Brandenburg, V.M.; Ali, S.; Ketteler, M.; Whooley, M.A. Association between human fetuin-A and the metabolic syndrome. Circulation 2006, 113, 1760–1767. [CrossRef] 35. Aroner, S.A.; St-Jules, D.E.; Mukamal, K.J.; Katz, R.; Shlipak, M.G.; Criqui, M.H.; Kestenbaum, B.; Siscovick, D.S.; De Boer, I.H.; Jenny, N.S.; et al. Fetuin-A, glycemic status, and risk of cardiovascular disease: The multi-ethnic study of atherosclerosis. Atherosclerosis 2016, 248, 224–229. [CrossRef] [PubMed] 36. Stefan, N.; Hennige, A.M.; Staiger, H.; Machann, J.; Schick, F.; Kröber, S.M.; Machicao, F.; Fritsche, A.; Häring, H.U. Alpha2- Heremans-Schmid glycoprotein/ fetuin-A is associated with insulin resistance and fat accumulation in the liver in humans. Diabetes Care 2006, 29, 853–857. [CrossRef] 37. Stefan, N.; Häring, H.-U. The role of hepatokines in metabolism. Nat. Rev. Endocrinol. 2013, 9, 144–152. [CrossRef] 38. Lebensztejn, D.M.; Białokoz-Kalinowska, I.; Kłusek-Oksiuta, M.; Tarasów, E.; Wojtkowska, M.; Kaczmarski, M. Serum fetuin A concentration is elevated in children with nonalcoholic fatty liver disease Adv Med Sci 2014, 59, 81–84 [CrossRef] 37. Stefan, N.; Häring, H. U. The role of hepatokines in metabolism. Nat. Rev. Endocrinol. 2013, 9, 144 152. [CrossRef] 38. Lebensztejn, D.M.; Białokoz-Kalinowska, I.; Kłusek-Oksiuta, M.; Tarasów, E.; Wojtkowska, M.; Kaczmarski, M. Serum fetuin A concentration is elevated in children with nonalcoholic fatty liver disease. Adv. Med. Sci. 2014, 59, 81–84. [CrossRef] y 39. Reinehr, T.; Roth, C.L. Fetuin-A and its relation to metabolic syndrome and fatty liver disease in obese children before and after weight loss. J. Clin. Endocrinol. Metab. 2008, 93, 4479–4485. [CrossRef] 40. References Relationship between disease severity, hyperinsulinemia, and impaired insulin clearance in patients with nonalcoholic steatohepatitis. Hepatology 2014, 59, 2178–2187. [CrossRef] 25. Lomonaco, R.; Bril, F.; Portillo-Sanchez, P.; Ortiz-Lopez, C.; Orsak, B.; Biernacki, D.; Lo, M.; Suman, A.; Weber, M.H.; Cusi, K. Metabolic impact of nonalcoholic steatohepatitis in obese patients with type 2 diabetes. Diabetes Care 2016, 39, 632–638. [CrossRef] 26. Bril, F.; Lomonaco, R.; Orsak, B.; Ortiz-Lopez, C.; Webb, A.; Tio, F.; Hecht, J.; Cusi, K. Relationship between disease severity, 26. Bril, F.; Lomonaco, R.; Orsak, B.; Ortiz-Lopez, C.; Webb, A.; Tio, F.; Hecht, J.; Cusi, K. Relationship between disease severity, hyperinsulinemia, and impaired insulin clearance in patients with nonalcoholic steatohepatitis. Hepatology 2014, 59, 2178–2187. [CrossRef] 27. Nangami, G.N.; Watson, K.; Parker-Johnson, K.; Okereke, K.O.; Sakwe, A.; Thompson, P.; Frimpong, N.; Ochieng, J. Fetuin-A (α2HS-glycoprotein) is a serum chemo-attractant that also promotes invasion of tumor cells through Matrigel. Biochem. Biophys. Res. Commun. 2013, 438, 660–665. [CrossRef] , , [ ] 28. Auberger, P.; Falquerho, L.; Contreres, J.O.; Pages, G.; Le Cam, G.; Rossi, B.; Le Cam, A. Characterization of a natural inhibitor of the insulin receptor tyrosine kinase: cDNA cloning, purification, and anti-mitogenic activity. Cell 1989, 58, 631–640. [CrossRef] 28. Auberger, P.; Falquerho, L.; Contreres, J.O.; Pages, G.; Le Cam, G.; Rossi, B.; Le Cam, A. Characterization of a natural inhibitor of the insulin receptor tyrosine kinase: cDNA cloning, purification, and anti-mitogenic activity. Cell 1989, 58, 631–640. [CrossRef] 29. Kalabay, L.; Mathur, S.; Bobin, S.; Arnaud, P. Electrophoretic and isoelectric focusing analysis of human recombinant alpha2-HS 29. Kalabay, L.; Mathur, S.; Bobin, S.; Arnaud, P. Electrophoretic and isoelectric focusing analysis of human recombinant alpha2-HS glycoprotein produced in insect cells: Analysis of the post-translational events. Electrophoresis 1996, 17, 529–532. [CrossRef] 29. Kalabay, L.; Mathur, S.; Bobin, S.; Arnaud, P. Electrophoretic and isoelectric focusing analysis of human recombinant alpha2 HS glycoprotein produced in insect cells: Analysis of the post-translational events. Electrophoresis 1996, 17, 529–532. [CrossRef] 30. Matsui, I.; Hamano, T.; Mikami, S.; Fujii, N.; Takabatake, Y.; Nagasawa, Y.; Kawada, N.; Ito, T.; Rakugi, H.; Imai, E.; et al. Fully y p g y p glycoprotein produced in insect cells: Analysis of the post-translational events. Electrophoresis 1996, 17, 529–532. [CrossRef] 30. Matsui, I.; Hamano, T.; Mikami, S.; Fujii, N.; Takabatake, Y.; Nagasawa, Y.; Kawada, N.; Ito, T.; Rakugi, H.; Imai, E.; et al. References Stenvinkel, P.; Wang, K.; Qureshi, A.R.; Axelsson, J.; Pecoits-Filho, R.; Gao, P.; Barany, P.; Lindholm, B.; Jogestrand, T.; Heimberger, O.; et al. Low fetuin-A levels are associated with cardiovascular death: Impact of variations in the gene encoding fetuin. Kidney Int. 2005, 67, 2383–2392. [CrossRef] [PubMed] 56. Schäfer, C.; Heiss, A.; Schwarz, A.; Westenfeld, R.; Ketteler, M.; Floege, J.; Müller-Esterl, W.; Schinke, T.; Jahnen-Dechent, W. The serum protein α2–Heremans-Schmid glycoprotein/fetuin-A is a systemically acting inhibitor of ectopic calcification. J. Clin. Investig. 2003, 112, 357–366. [CrossRef] 57. Westenfeld, R.; Schäfer, C.; Krüger, T.; Haarmann, C.; Schurgers, L.J.; Reutelingsperger, C.; Ivanovski, O.; Drueke, T.B.; Massy, Z.A.; Ketteler, M.; et al. Fetuin-A protects against atherosclerotic calcification in CKD. J. Am. Soc. Nephrol. 2009, 20, 1264–1274. [CrossRef] [PubMed] 58. Ford, M.L.; Tomlinson, L.A.; Smith, E.R.; Rajkumar, C.; Holt, S.G. Fetuin-A is an independent det stiffness over 1 year in non-diabetic patients with CKD stages 3 and 4. Nephrol. Dial. Transplant. 20 58. Ford, M.L.; Tomlinson, L.A.; Smith, E.R.; Rajkumar, C.; Holt, S.G. Fetuin-A is an independent determinant of change of aortic stiffness over 1 year in non-diabetic patients with CKD stages 3 and 4. Nephrol. Dial. Transplant. 2010, 25, 1853–1858. [CrossRef] 59. Ketteler, M.; Bongartz, P.; Westenfeld, R.; Wildberger, J.E.; Mahnken, A.H.; Böhm, R.; Metzger, T.; Wanner, C.; Jahnen-Dechent, W.; Floege, J. Association of low fetuin-A (AHSG) concentrations in serum with cardiovascular mortality in patients on dialysis: A cross-sectional study. Lancet 2003, 361, 827–833. [CrossRef] y p g p p [ ] 59. Ketteler, M.; Bongartz, P.; Westenfeld, R.; Wildberger, J.E.; Mahnken, A.H.; Böhm, R.; Metzger, T.; Wanner, C.; Jahnen-Dechent, W.; Floege, J. Association of low fetuin-A (AHSG) concentrations in serum with cardiovascular mortality in patients on dialysis: A cross-sectional study. Lancet 2003, 361, 827–833. [CrossRef] 60. Adams, L.A.; Waters, O.R.; Knuiman, M.W.; Elliott, R.R.; Olynyk, J.K. NAFLD as a risk factor for the development of diabetes and the metabolic syndrome: An eleven-year follow-up study. Am. J. Gastroenterol. 2009, 104, 861–867. [CrossRef] ic fat in insulin resistance, dyslipidemia, and cardiometabolic disease. N. Engl. J. Med. 2014, 371, 1131–1141 61. Shulman, G.I. Ectopic fat in insulin resistance, dyslipidemia, and cardiometabolic disease. N. Engl. J. M [CrossRef] 62. Jensen, M.K.; Bartz, T.M.; Mukamal, K.J.; Djoussé, L.; Kizer, J.R.; Tracy, R.P.; Zieman, S.J.; Rimm, E.B.; Siscovick, D.S.; Shlipak, M.; et al. Fetuin-A, type 2 diabetes, and risk of cardiovascular disease in older adults: The cardiovascular health study. References Fetuin-A mRNA expression is elevated in NASH compared with NAFL patients. Clin. Sci. 2013, 125, 391–400. [CrossRef] 49. Kahraman, A.; Sowa, J.-P.; Schlattjan, M.; Sydor, S.; Pronadl, M.; Wree, A.; Beilfuss, A.; Kilicarslan, A.; Altinba¸s, A.; Bechmann, L.P.; et al. Fetuin-A mRNA expression is elevated in NASH compared with NAFL patients. Clin. Sci. 2013, 125, 391–400. [CrossRef] 50. Rametta, R.; Ruscica, M.; Dongiovanni, P.; Macchi, C.; Fracanzani, A.L.; Steffani, L.; Fargion, S.; Magni, P.; Valenti, L. Hepatic steatosis and PNPLA3 I148M variant are associated with serum fetuin-A independently of insulin resistance. Eur. J. Clin. Investig. 49. Kahraman, A.; Sowa, J.-P.; Schlattjan, M.; Sydor, S.; Pronadl, M.; Wree, A.; Beilfuss, A.; Kilicarslan, A.; Altinba¸s, A.; Bechmann, L.P.; et al. Fetuin-A mRNA expression is elevated in NASH compared with NAFL patients. Clin. Sci. 2013, 125, 391–400. [CrossRef] 50. Rametta, R.; Ruscica, M.; Dongiovanni, P.; Macchi, C.; Fracanzani, A.L.; Steffani, L.; Fargion, S.; Magni, P.; Valenti, L. Hepatic steatosis and PNPLA3 I148M variant are associated with serum fetuin-A independently of insulin resistance. Eur. J. Clin. Investig. 2014, 44, 627–633. [CrossRef] 50. Rametta, R.; Ruscica, M.; Dongiovanni, P.; Macchi, C.; Fracanzani, A.L.; Steffani, L.; Fargion, S.; Magni, P.; Valenti, L. Hepatic steatosis and PNPLA3 I148M variant are associated with serum fetuin-A independently of insulin resistance. Eur. J. Clin. Investig. 2014, 44, 627–633. [CrossRef] 51. Von Loeffelholz, C.; Horn, P.; Birkenfeld, A.; Claus, R.; Metzing, B.; Döcke, S.; Jahreis, G.; Heller, R.; Hoppe, S.; Stockmann, M.; et al. Fetuin A is a predictor of liver fat in preoperative patients with nonalcoholic fatty liver disease. J. Investig. Surg. 2016, 29, 266–274. [CrossRef] 52. Pampanini, V.; Inzaghi, E.; Germani, D.; Alterio, A.; Puglianiello, A.; Alisi, A.; Nobili, V.; Cianfarani, S. Serum fetuin-A levels in obese children with biopsy proven nonalcoholic fatty liver disease. Nutr. Metab. Cardiovasc. Dis. 2018, 28, 71–76. [CrossRef] [PubMed] 53. Peter, A.; Kovarova, M.; Staiger, H.; Machann, J.; Schick, F.; Königsrainer, A.; Königsrainer, I.; Schleicher, E.; Fritsche, A.; Häring, H.-U.; et al. The hepatokines fetuin-A and fetuin-B are upregulated in the state of hepatic steatosis and may differently impact on glucose homeostasis in humans. Am. J. Physiol. Metab. 2018, 314, E266–E273. [CrossRef] 54. Kaushik, S.V.; Plaisance, E.P.; Kim, T.; Huang, E.Y.; Mahurin, A.J.; Grandjean, P.W.; Mathews, S.T. Extended-release niacin decreases serum fetuin-A concentrations in individuals with metabolic syndrome. Diabetes/Metab. Res. Rev. 2009, 25, 427–434. [CrossRef] 55. References Ou, H.-Y.; Yang, Y.-C.; Wu, H.-T.; Wu, J.-S.; Lu, F.-H.; Chang, C.-J. Increased fetuin-A concentrations in impaired glucose tolerance with or without nonalcoholic fatty liver disease, but not impaired fasting glucose. J. Clin. Endocrinol. Metab. 2012, 97, 4717–4723. [CrossRef] 41. Huang, Y.; Huang, X.; Ding, L.; Wang, P.; Peng, K.; Chen, Y.; Dai, M.; Zhang, D.; Xu, M.; Bi, Y.; et al. Serum fetuin-A associated with fatty liver index, early indicator of nonalcoholic fatty liver disease. Medicine 2015, 94, e1517. [CrossRef] 42. Thompson, D.S.; Tennant, I.A.; Soares, D.P.; Osmond, C.; Byrne, C.D.; Forrester, T.E.; Boyne, M. Nonalcoholic fatty liver disease in nonobese subjects of African origin has atypical metabolic characteristics. J. Endocr. Soc. 2019, 3, 2051–2063. [CrossRef] 43. Cui, Z.; Xuan, R.; Yang, Y. Serum fetuin A level is associated with nonalcoholic fatty liver dis Oncotarget 2017, 8, 107149–107156. [CrossRef] 44. Sato, M.; Kamada, Y.; Takeda, Y.; Kida, S.; Ohara, Y.; Fujii, H.; Akita, M.; Mizutani, K.; Yoshida, Y.; Yamada, M.; et al. Fetuin-A negatively correlates with liver and vascular fibrosis in nonalcoholic fatty liver disease subjects. Liver Int. 2014, 35, 925–935. [CrossRef] 11 of 12 11 of 12 Int. J. Mol. Sci. 2021, 22, 6627 45. Yilmaz, Y.; Yonal, O.; Kurt, R.; Ari, F.; Oral, A.Y.; Celikel, C.A.; Korkmaz, S.; Ulukaya, E.; Ozdogan, O.; Imeryuz, N.; et al. Serum fetuin-A/α2HS-glycoprotein levels in patients with nonalcoholic fatty liver disease: Relation with liver fibrosis. Ann. Clin. Biochem. Int. J. Lab. Med. 2010, 47, 549–553. [CrossRef] 46. Haukeland, J.W.; Dahl, T.B.; Yndestad, A.; Gladhaug, I.P.; Løberg, E.M.; Haaland, T.; Konopski, Z.; Wium, C.; Aasheim, E.T.; Johansen, O.E.; et al. Fetuin-A in nonalcoholic fatty liver disease: In vivo and in vitro studies. Eur. J. Endocrinol. 2012, 166, 503–510. [CrossRef] 47. Ou, H.-Y.; Wu, H.-T.; Hung, H.-C.; Yang, Y.-C.; Wu, J.-S.; Chang, C.-J. Endoplasmic reticulum stress induces the expression of fetuin-A to develop insulin resistance. Endocrinology 2012, 153, 2974–2984. [CrossRef] 48. Çelebi, G.; Genc, H.; Gurel, H.; Sertoglu, E.; Kara, M.; Tapan, S.; Acikel, C.; Karslioglu, Y.; Ercin, C.N.; Dogru, T. The relationship of circulating fetuin-A with liver histology and biomarkers of systemic inflammation in nondiabetic subjects with nonalcoholic fatty liver disease. Saudi J. Gastroenterol. 2015, 21, 139–145. [CrossRef] [PubMed] y 49. Kahraman, A.; Sowa, J.-P.; Schlattjan, M.; Sydor, S.; Pronadl, M.; Wree, A.; Beilfuss, A.; Kilicarslan, A.; Altinba¸s, A.; Bechmann, L.P.; et al. References [CrossRef] [PubMed] y p y p y g 69. Brix, J.M.; Stingl, H.; Höllerl, F.; Schernthaner, G.H.; Kopp, H.-P.; Schernthaner, G. Elevated fetuin-A concentrations in morbid obesity decrease after dramatic weight loss. J. Clin. Endocrinol. Metab. 2010, 95, 4877–4881. [CrossRef] g , M.; Araki, T.; Yokoyama, H.; Teramura, M.; Lee, E.; Motoyama, K.; Koyama, H.; Shoji, T.; Inaba, M.; e y g 70. Mori, K.; Emoto, M.; Araki, T.; Yokoyama, H.; Teramura, M.; Lee, E.; Motoyama, K.; Koyama, H.; Shoji, T.; Inaba, M.; et al. Association of serum fetuin-A with carotid arterial stiffness. Clin. Endocrinol. 2006, 66, 246–250. [CrossRef] [PubMed] 70. Mori, K.; Emoto, M.; Araki, T.; Yokoyama, H.; Teramura, M.; Lee, E.; Motoyama, K.; Koyama, H.; Shoji, T.; Inaba, M.; et al. Association of serum fetuin A with carotid arterial stiffness Clin Endocrinol 2006 66 246 250 [CrossRef] [PubMed] 71. Haglund, Å.C.; Ek, B.; Ek, P. Phosphorylation of human plasma α2-Heremans-Schmid glycopro Biochem. J. 2001, 357, 437–445. [CrossRef] 71. Haglund, Å.C.; Ek, B.; Ek, P. Phosphorylation of human plasma α2-Heremans-Schmid glycoprotein (human fetuin) in vivo. Biochem. J. 2001, 357, 437–445. [CrossRef] 72. Dogru, T.; Genc, H.; Tapan, S.; Aslan, F.; Ercin, C.N.; Ors, F.; Kara, M.; Sertoglu, E.; Karslioglu, Y.; Bagci, S.; et al. Plasma fetuin-A is associated with endothelial dysfunction and subclinical atherosclerosis in subjects with nonalcoholic fatty liver disease. Clin. Endocrinol. 2013, 78, 712–717. [CrossRef] 73. Ballestri, S.; Meschiari, E.; Baldelli, E.; Musumeci, F.E.; Romagnoli, D.; Trenti, T.; Zennaro, R.G.; Lonardo, A.; Loria, P. Relationship of serum fetuin-A levels with coronary atherosclerotic burden and NAFLD in patients undergoing elective coronary angiography. Metab. Syndr. Relat. Disord. 2013, 11, 289–295. [CrossRef] 74. Nascimbeni, F.; Romagnoli, D.; Ballestri, S.; Baldelli, E.; Lugari, S.; Sirotti, V.; Giampaoli, V.; Lonardo, A. Do nonalcoholic fatty liver disease and fetuin-A play different roles in symptomatic coronary artery disease and peripheral arterial disease? Diseases 2018, 6, 17. [CrossRef] 75. Zhao, Z.-W.; Lin, C.-G.; Wu, L.-Z.; Luo, Y.-K.; Fan, L.; Dong, X.-F.; Zheng, H. Serum fetuin-A levels are associated with the presence and severity of coronary artery disease in patients with type 2 diabetes. Biomarkers 2013, 18, 160–164. [CrossRef] 75. Zhao, Z.-W.; Lin, C.-G.; Wu, L.-Z.; Luo, Y.-K.; Fan, L.; Dong, X.-F.; Zheng, H. Serum fetuin-A levels are associated with the presence and severity of coronary artery disease in patients with type 2 diabetes. Biomarkers 2013, 18, 160–164. [CrossRef] 76. References Diabetes Care 2012, 36, 1222–1228. [CrossRef] 63. Laughlin, G.A.; Cummins, K.M.; Wassel, C.L.; Daniels, L.B.; Ix, J.H. The Association of fetuin-A with cardiovascular disease mortality in older community-dwelling adults: The rancho bernardo study. J. Am. Coll. Cardiol. 2012, 59, 1688–1696. [CrossRef] 64. Sun, Q.; Jiménez, M.C.; Townsend, M.K.; Rimm, E.B.; Manson, J.E.; Albert, C.; Rexrode, K.M. Plasma levels of fetuin-A and risk of coronary heart disease in US women: The nurses’ health study. J. Am. Heart Assoc. 2014, 3, e000939. [CrossRef] y y 65. Caglar, K.; Yilmaz, M.I.; Saglam, M.; Cakir, E.; Kilic, S.; Sonmez, A.; Eyileten, T.; Yenicesu, M.; Oguz, Y.; Tasar, M.; et al. Serum fetuin-A concentration and endothelial dysfunction in chronic kidney disease. Nephron 2008, 108, c233–c240. [CrossRef] [PubMed] 65. Caglar, K.; Yilmaz, M.I.; Saglam, M.; Cakir, E.; Kilic, S.; Sonmez, A.; Eyileten, T.; Yenicesu, M.; Oguz, Y.; Tasar, M.; et al. Serum fetuin-A concentration and endothelial dysfunction in chronic kidney disease. Nephron 2008, 108, c233–c240. [CrossRef] [PubMed] 66. Hruska, K.A.; Mathew, S.; Lund, R.J.; Memon, I.; Saab, G. The pathogenesis of vascular calcification in the chronic kidney disease mineral bone disorder: The links between bone and the vasculature. Semin. Nephrol. 2009, 29, 156–165. [CrossRef] 66. Hruska, K.A.; Mathew, S.; Lund, R.J.; Memon, I.; Saab, G. The pathogenesis of vascular calcification in the chronic kidney disease mineral bone disorder: The links between bone and the vasculature. Semin. Nephrol. 2009, 29, 156–165. [CrossRef] p 67. Weikert, C.; Stefan, N.; Schulze, M.B.; Pischon, T.; Berger, K.; Joost, H.-G.; Häring, H.-U.; Boeing, H.; Fritsche, A. Plasma fetuin-A levels and the risk of myocardial infarction and ischemic stroke. Circulation 2008, 118, 2555–2562. [CrossRef] Int. J. Mol. Sci. 2021, 22, 6627 12 of 12 12 of 12 68. Vörös, K.; Gráf, L., Jr.; Prohászka, Z.; Gráf, L.; Szenthe, P.; Kaszás, E.; Böröcz, Z.; Cseh, K.; Kalabay, L. Serum fetuin-A in metabolic and inflammatory pathways in patients with myocardial infarction. Eur. J. Clin. Investig. 2011, 41, 703–709. [CrossRef] [PubMed] 69. Brix, J.M.; Stingl, H.; Höllerl, F.; Schernthaner, G.H.; Kopp, H.-P.; Schernthaner, G. Elevated fetuin-A concentrations in morbid obesity decrease after dramatic weight loss. J. Clin. Endocrinol. Metab. 2010, 95, 4877–4881. [CrossRef] 68. Vörös, K.; Gráf, L., Jr.; Prohászka, Z.; Gráf, L.; Szenthe, P.; Kaszás, E.; Böröcz, Z.; Cseh, K.; Kalabay, L. Serum fetuin-A in metabolic and inflammatory pathways in patients with myocardial infarction. Eur. J. Clin. Investig. 2011, 41, 703–709. References Herrmann, M.; Babler, A.; Moshkova, I.; Gremse, F.; Kiessling, F.; Kusebauch, U.; Nelea, V.; Kramann, R.; Moritz, R.L.; McKee, M.D.; et al. Lumenal calcification and microvasculopathy in fetuin-A-deficient mice lead to multiple organ morbidity. PLoS ONE 2020, 15, e0228503. [CrossRef] 76. Herrmann, M.; Babler, A.; Moshkova, I.; Gremse, F.; Kiessling, F.; Kusebauch, U.; Nelea, V.; Kramann, R.; Moritz, R.L.; McKee, M.D.; et al. Lumenal calcification and microvasculopathy in fetuin-A-deficient mice lead to multiple organ morbidity. PLoS ONE 2020, 15, e0228503. [CrossRef]
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Role of professional associations in the development of a young specialist
Kardiovaskulârnaâ terapiâ i profilaktika
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Кардиоваскулярная терапия и профилактика. 2022;21(10):3446. doi:10.15829/1728-8800-2022-3446 ISSN 1728-8800 (Print) ISSN 2619-0125 (Online) Кардиоваскулярная терапия и профилактика. 2022;21(10):3446. doi:10.15829/1728-8800-2022-3446 ISSN 1728-8800 (Print) ISSN 2619-0125 (Online) ISSN 2619-0125 (Online) g g [Иванова А. А. — врач-кардиолог, м.н.с. отдела фундаментальных и прикладных аспектов ожирения, ORCID: 0000-0002-2812-959X, Макогон Н. В.* — врач-кардиолог, м.н.с. отдела фундаментальных и прикладных аспектов ожирения, ORCID: 0000-0003-3288-7315]. РОПНИЗ — Российское общество профилактики неинфекционных заболеваний. *Автор, ответственный за переписку (Corresponding author): e-mail: nikimakogon@gmail.com [Иванова А. А. — врач-кардиолог, м.н.с. отдела фундаментальных и прикладных аспектов ожирения, ORCID: 0000-0002-2812-959X, Макогон Н. В.* — врач-кардиолог, м.н.с. отдела фундаментальных и прикладных аспектов ожирения, ORCID: 0000-0003-3288-7315]. Role of professional associations in the development of a young specialist Role of professional associations in the development of a young specialist Ivanova A. A., Makogon N. V. 1National Medical Research Center for Therapy and Preventive Medicine. Moscow; 2Russian Society for the Prevention of Non-Communicable Diseases (ROPNIZ). Moscow, Russia Role of professional associations in the development of a young specialist Ivanova A. A., Makogon N. V. 1National Medical Research Center for Therapy and Preventive Medicine. Moscow; 2Russian Society for the Prevention of Non-Communicable Diseases (ROPNIZ). Moscow, Russia Role of professional associations in the development of a young specialist Ivanova A. A., Makogon N. V. 1National Medical Research Center for Therapy and Preventive Medicine. Moscow; 2Russian Society for the Prevention of Non-Communicable Diseases (ROPNIZ). Moscow, Russia Keywords: professional medical associations, new generation, youth sections. Relationships and Activities: none. Ivanova A. A. ORCID:  0000-0002-2812-959X, Makogon N. V.* ORCID: 0000-0003-3288-7315. *Corresponding author: nikimakogon@gmail com Received: 18/10-2022 Accepted: 20/10-2022 For citation: Ivanova A. A., Makogon N. V. Role of professional asso­ ciations in the development of a young specialist. Cardiovascular Therapy and Prevention. 2022;21(10):3446. doi:10.15829/1728-8800- 2022-3446. EDN RQHMBU Keywords: professional medical associations, new generation, youth sections. Received: 18/10-2022 Accepted: 20/10-2022 For citation: Ivanova A. A., Makogon N. V. Role of professional asso­ ciations in the development of a young specialist. Cardiovascular Therapy and Prevention. 2022;21(10):3446. doi:10.15829/1728-8800- 2022-3446. EDN RQHMBU e-mail: nikimakogon@gmail.com Роль профессиональных сообществ в становлении молодого специалиста Иванова А. А.1,2, Макогон Н. В.1,2 ГБУ "Национальный медицинский исследовательский центр терапии и профилактической медицины" Минздрава осква; 2Российское общество профилактики неинфекционных заболеваний (РОПНИЗ). Москва, Россия 1ФГБУ "Национальный медицинский исследовательский центр терапии и профилакт ФГБУ Национальный медицинский исследовательский центр терапии и профилактической медицины Ми Москва; 2Российское общество профилактики неинфекционных заболеваний (РОПНИЗ). Москва, Россия Москва; 2Российское общество профилактики неинфекционных заболеваний (РОПН Москва; 2Российское общество профилактики неинфекционных заболеваний (РОПНИЗ). Москва, Росс Ключевые слова: профессиональные медицинские сообщества, новое поколение, молодежные секции. Отношения и деятельность: нет. Поступила 18/10-2022 Принята к публикации 20/10-2022 Ключевые слова: профессиональные медицинские сообщества, новое поколение, молодежные секции. Отношения и деятельность: нет. Поступила 18/10-2022 Принята к публикации 20/10-2022 Для цитирования: Иванова А. А., Макогон Н. В. Роль профес- сиональных сообществ в  становлении молодого специалиста. Кардиоваскулярная терапия и  профилактика. 2022;21(10):3446. doi:10.15829/1728-8800-2022-3446. EDN RQHMBU [Иванова А. А. — врач-кардиолог, м.н.с. отдела фундаментальных и прикладных аспектов ожирения, ORCID: 0000-0002-2812-959X, Макогон Н. В.* — врач-кардиолог, м и прикладных аспектов ожирения, ORCID: 0000-0003-3288-7315]. *Автор, ответственный за переписку (Corresponding author): e-mail: nikimakogon@gmail.com [Иванова А. А. — врач-кардиолог, м.н.с. отдела фундаментальных и прикладных аспект и прикладных аспектов ожирения, ORCID: 0000-0003-3288-7315]. •  координацию деятельности специалистов по всей стране [1]. По окончании программ профессионального медицинского образования молодой специалист приступает к трудовой деятельности на своем пер- вом рабочем месте. Значительная часть выпускни- ков программ специалитета становится врачами первичного звена здравоохранения в амбулаторно- поликлинических учреждениях, где научные под- разделения часто отсутствуют. Определенная часть выпускников становятся врачами частных меди- цинских учреждений, где в  большинстве случаев также отсутствуют научные подразделения. На дан- ном этапе у молодого специалиста формируется за- прос на самореализацию, ответ на который способ- ны дать профессиональные медицинские ассоциа- ции, а именно, их молодежные подразделения [7]. Образовательная деятельность профессио- нальных ассоциаций является важнейшим звеном системы непрерывного профессионального об- разования, играет решающую роль в поддержании квалификации специалистов. Примером этому мо- гут служить многочисленные программы, которые разрабатываются ведущими университетами стра- ны совместно с профессиональными сообществами [2]. В большинстве случаев образовательные меро- приятия носят односторонний характер: эксперты делятся своими знаниями, а менее опытные моло- дые специалисты выступают в  роли слушателей. Очевидно, что для активной работы в составе про- фессионального сообщества необходимо обладать клиническим и научным опытом, быть экспертом в определенной области. У молодых специалистов также есть потребность в  самореализации, пред- ставлении собственных научных данных, практике публичных выступлений, однако недостаток опы- та, неуверенность в  себе или отсутствие профес- сиональных связей со старшими коллегами могут препятствовать их развитию в профессиональных ассоциациях. ции, а именно, их молодежные подразделения [7]. В большинстве крупных профессиональных медицинских сообществ созданы рабочие группы, секции и общества, которые ведут активную дея- тельность, направленную на поддержку молодых специалистов. Например, в  составе Российского общества профилактики неинфекционных заболе- ваний (РОПНИЗ) функционирует секция "Специ- алисты нового поколения", основной целью кото- рой является формирование комфортной рабочей и научной среды для молодых специалистов здра- воохранения, обеспечение возможностей для само- реализации молодежи со всей страны при помощи очного и  дистанционного взаимодействия с  ис- пользованием инновационных подходов [8]. Сре- ди ключевых задач секции — содействие молодым специалистам в планировании, организации и про- ведении научных исследований и лечебной работы, организация образовательных мероприятий для обмена знаниями и опытом, обеспечение взаимо- действия начинающих специалистов и  экспертов в различных областях медицины. Работа в секции открывает возможности для взаимодействия с дру- гими секциями РОПНИЗ, закладывает фундамент для построения личного бренда врача, что обеспе- чивает закономерный личностный и  профессио­ нальный рост [9]. В  течение 2021 и  2022гг члены секции представляли РОПНИЗ на всероссийских конференциях и конгрессах, выступали организа- торами ряда молодежных мероприятий и  симпо- зиумов, активно взаимодействовали с молодежны- ми ассоциациями других профессио­нальных со- обществ, становились победителями и призерами всероссийских конкурсов и олимпиад. Российское общество профилактики неинфекционных заболеваний Российское общество профилактики неинфекционных заболеваний •  координацию деятельности специалистов по всей стране [1]. Relationships and Activities: none. Ivanova A. A. ORCID:  0000-0002-2812-959X, Makogon N. V.* ORCID: 0000-0003-3288-7315. *Corresponding author: nikimakogon@gmail.com РОПНИЗ — Российское общество профилактики неинфекционных заболеваний. важнейших функций профессиональных обществ можно выделить: Профессиональные медицинские сообщества объединяют специалистов различных областей ме- дицины, ведущих активную научную и  практиче- скую деятельность. Под эгидой всероссийских об- ществ и  ассоциаций проводятся крупнейшие кон- грессы, съезды и  конференции, где специалисты имеют возможность представлять результаты своих исследований, обмениваться опытом, укреплять международное и межрегиональное взаимодействие. Подобные сообщества возглавляют эксперты и ве- дущие специалисты своих областей знаний. Среди •  образовательную деятельность, •  образовательную деятельность, •  образовательную деятельность, •  организацию тематических мероприятий, •  формирование рабочих групп и секций, зани- мающихся узкоспециализированными проблемами, •  разработку клинических рекомендаций, •  выявление проблем системы здравоохранения и предложение их решений, •  внедрение новых программ медицинской по- мощи, 92 •  координацию деятельности специалистов по всей стране [1]. Члены сек- ции "Специалисты нового поколения" отмечают, что членство в секции открывает возможности для реализации собственных идей, позволяет получить опыт публичных выступлений, уникальный орга- низаторский, научный и клинический опыт. П ф В настоящее время медицинское образование представляет собой непрерывный континуум, яв- ляясь частью которого будущий специалист полу- чает доступ к неограниченным информационным ресурсам, а  также имеет возможность восполь- зоваться поддержкой той организации, где он по- лучает образование [3]. В  большинстве ведущих медицинских университетов страны учреждены многочисленные студенческие организации с раз- нообразным функционалом. Студенческие науч- ные общества занимаются организацией студенче- ских научных кружков, молодежных конференций, фестивалей и  съездов, профкомы обучающихся координируют работу общественных, культурных и  спортивных секций и  сообществ, налаживают взаимодействие профессорско-преподавательского состава и учащихся [4]. Студенты имеют возмож- ность обратиться за поддержкой к членам студен- ческих организаций или вступить в их состав и по- лучить первый опыт научной деятельности, подго- товить свои первые публичные выступления. Более того, во время обучения студенты могут присоеди- ниться к работе клинических и научных подразде- лений своего высшего учебного заведения. В рам- ках внеучебной деятельности совершенствуются и так называемые "soft skills" — коммуникативные навыки, навыки презентации докладов, взаимодей- ствие с коллегами и пациентами [5]. Во время обу­ чения в ординатуре и аспирантуре молодым специ- алистам также оказывается помощь и содействие со стороны организации, в которой они получают об- разование [6]. Профессиональные компетенции, которые по- лучают участники молодежных подразделений ме- дицинских ассоциаций, способствуют более бы- строму профессиональному росту и всестороннему 93 Кардиоваскулярная терапия и профилактика. 2022;21 дежные секции и  рабочие группы всероссийских медицинских обществ являются важнейшим звеном системы, которая направлена на повышение про- фессионального уровня молодых врачей и ученых. развитию. Накопленный опыт и  взаимодействие с ведущими специалистами интересующей области знаний обеспечивают эффективную интеграцию в профессиональную среду. Таким образом, моло- Литература/References 1. Astanina SYu. Issues of reforming professional me-dical education in Russia. Cardiovascular Therapy and Prevention. 2022;21(1):3192. (In Russ.) Астанина С. Ю. Вопросы рефор- мирования профессионального медицинского образова- ния в России. Кардиоваскулярная терапия и профилактика. 2022;21(1):3192. doi:10.15829/1728-8800-2022-3192. 6. Artyukhina AI, Chizhova VM, Chumakov VI. Personalized peda­gogical learning of highly qualified residents and postgraduate students. Cardiovascular Therapy and Prevention. 2022;21(S1):3160. (In Russ.) Артюхина А. И., Чижова В. М., Чумаков В. И. Персонализированный подход к  педагогиче- ской подготовке кадров высшей квалификации в ординатуре и аспирантуре. Кардиоваскулярная терапия и профилактика. 2022;21(1S):3160. doi:10.15829/1728-8800-2022-3160. 2. Sirotkina OV, Ishchuk TN, Parmon EV Shlyakhto EV. Issues of medical specialists education. foundation of institute of independent professional experts. Russian Journal of Cardiology. 2016;(9):41-5. (In Russ.) Сироткина О. В., Ищук Т. Н., Пар­ мон Е. В., Шляхто Е. В. Вопросы качества подготовки меди- цинских специалистов. Формирование института независимых профессиональных экспертов. Российский кардио­логический журнал. 2016;(9):41-5. doi:10.15829/1560-4071-2016-9-41-45. 2. Sirotkina OV, Ishchuk TN, Parmon EV Shlyakhto EV. Issues of medical specialists education. foundation of institute of independent professional experts. Russian Journal of Cardiology. 2016;(9):41-5. (In Russ.) Сироткина О. В., Ищук Т. Н., Пар­ мон Е. В., Шляхто Е. В. Вопросы качества подготовки меди- цинских специалистов. Формирование института независимых профессиональных экспертов. Российский кардио­логический журнал. 2016;(9):41-5. doi:10.15829/1560-4071-2016-9-41-45. 7. Vertkin AL. Polyclinics physician education  — in the center of a problematic triangle. Cardiovascular Therapy and Prevention. 2017;16(2):4-7. (In Russ.) Верткин А. Л. Образование поли­ клинического врача  — в  центре треугольника проблем. Кардиоваскулярная терапия и профилактика. 2017;16(2):4-7. doi:10.15829/1728-8800-2017-2-4-7. 3. Astanina SYu. Innovations in medical education  — advanta­ ges and risks. Cardiovascular Therapy and Prevention. 2022;21(3S):3359. (In Russ.) Астанина С. Ю. Инновации в ме- дицинском образовании — преимущества и риски. Кардио­ васкулярная терапия и  профилактика. 2022;21(3S):3359. doi:10.15829/1728-8800-2022-3359. 8. Drapkina OM. Information technologies in cardiology: potential for further development. Russian Journal of Cardiology. 2013;(4):23-7. (In Russ.) Драпкина О. М. Информационные тех- нологии в кардиологии. Перспективы развития. Российский кардиологический журнал. 2013;(4):23-7. doi:10.15829/1560- 4071-2013-4-23-27. 4. Sirotkina OV, Ischuk TN, Golubeva IS, et al. Improvement of continuing medical education. Russian Journal of Cardiology. 2020;25(11):4176. (In Russ.) Сироткина О. В., Ищук Т. Н., Пар­мон Е. В. и  др. Совершенствование непрерывного ме- дицинского развития специалистов лечебного дела. Рос­ сийский кардиологический журнал. 2020;25(11):4176. doi:10.15829/29/1560-4071-2020-4176. 9. Bezzubenko OI. The brand status of a doctor as the basis of professional and personal growth of a medical specialist. Cardiovascular Therapy and Prevention. 2022;21(7):3349. (In Russ.) Беззубенко О. И. Vertkin AL. Polyclinics physician education  — in the center of a problematic triangle. Cardiovascular Therapy and Prevention. 2017;16(2):4-7. (In Russ.) Верткин А. Л. Образование поли­ клинического врача  — в  центре треугольника проблем. Кардиоваскулярная терапия и профилактика. 2017;16(2):4-7. doi:10.15829/1728-8800-2017-2-4-7. Необходимость развития личностных компетенций вра- ча-кардиолога. Российский кардиологический журнал. 2021;26(9):4680. doi:10.15829/1560-4071-2021-4680. Литература/References Бренд-статус врача как основа про- фессионального и  личностного роста медицинского спе- циалиста. Кардиоваскулярная терапия и  профилактика. 2022;21(7):3349. doi:10.15829/1728-8800-2022-3349. 5. Kudinova MA, Shaydyuk OYu. Development of personal competencies of a cardiologist. Russian Journal of Cardiology. 2021;26(9):4680. (In Russ.) Кудинова М. А., Шайдюк О. Ю. 94
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<i>The Turing Test as Interactive Proof</i>
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Permanent link http://nrs.harvard.edu/urn-3:HUL.InstRepos:2027203 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA Citation Stuart M. Shieber. The Turing test as interactive proof. Noûs, 41(4):686-713, December 2007. The definitive version is available at www.blackwell-synergy.com. Published Version http://dx.doi.org/10.1111/j.1468-0068.2007.00636.x 1I take the term “sensible sequence of verbal responses” directly from Block to mean whatever criterion of human indistinguishability that the judge in a Turing Test is verifying. It may be that the term is not entirely felicitous for that purpose. For instance, there may be sequences of responses that are sensible in the informal sense of the term, yet reveal the non-human character of the generator by being stilted in some way. Under certain circumstances, even clearly nonsensical responses are appropriate in a Turing Test, as in Block’s example of a judge requesting “Let’s see you talk nonsense.” (Block, 1981, pages 19–20) Nonetheless, for consistency hereafter I will follow Block in using the phrase, with the request that the reader interpret it in the intended manner. Share Your Story The Harvard community has made this article openly available. Please share how this access benefits you. Submit a story . The Harvard community has made this article openly available. Please share how this access benefits you. Submit a story . Accessibility THE TURING TEST AS INTERACTIVE PROOF STUART M. SHIEBER 1. Introduction For instance, the underlying idea could be implemented in a simpler form, in which a judge merely stipulates whether or not a machine has exhibited human-level behavior, except that without some sort of forced choice, a gaming of the test would be possible. Indeed, Turing presents this simpler more direct form in a little known 1952 BBC interview in which he describes the test as follows: The idea of the test is that the machine has to pretend to be a man, by answering questions put to it, and it will only pass if the pretence is reasonably convincing. . . . We had better suppose that each jury has to judge quite a number of times, and that sometimes they really are dealing with a man and not a machine. That will prevent them saying “It must be a machine” every time without proper consideration. (Newman, Turing, Jefferson, and Braithwaite, 1952) Here, he describes the point of the Test directly in the first sentence, and makes clear that the comparison issue (whether through repeated trials, as described in this selection, or one-on-one, as in the original paper) is an expedient to make the forced choice a real one. Thus, at base, the Turing Test is a test based on the idea that ability to produce sensible verbal behavior is an indication of intelligence. The syllogism that underlies the appropriateness of the Turing Test as a criterion for intelligence proceeds something like this: Premise 1: If an agent passes a Turing Test, then it produces a sensible sequence of verbal responses to a sequence of verbal stimuli. Premise 2: If an agent produces a sensible sequence of verbal responses to a sequence of verbal stimuli, then it is intelligent. Premise 2: If an agent produces a sensible sequence of verbal responses to a sequence of verbal stimuli, then it is intelligent. q , g Conclusion: Therefore, if an agent passes a Turing Test, then it is intelligent. Block refers to a premise such as the second one as the “Turing Test conception of intelligence”, and his (and others’) repudiation of the Turing Test as a criterion for intelligence is based on a denial of this premise. 1.2. The Conceptual Basis for Turing-Test Denial. 1. Introduction In this paper, I attempt to reconcile two mutually contradictory but well-founded attitudes towards the Turing Test, Alan Turing’s proposed replacement for the question “Can machines think?” On the one hand is the attitude that has become philosophical conventional wisdom, viz., that the Turing Test is hopelessly flawed as a sufficient condition for intelligence, while on the other hand is the overwhelming sense that were a machine to pass a real live full-fledged Turing Test, it would be a sign of nothing but our orneriness to deny it the attribution of intelligence. The arguments against the sufficiency of the Turing Test for determining intelligence rely on showing that some extra conditions are logically necessary for intelligence beyond the behavioral properties exhibited by an agent under a Turing Test. Therefore, it cannot follow logically from passing a Turing Test that the agent is intelligent. I will argue that these extra conditions can be revealed by the Turing Test, so long as we allow a very slight weakening of the criterion from one of logical proof to one of statistical proof under weak realizability assumptions. Crucially, this weakening is so slight as to make no conceivable difference from a practical standpoint. Thus, the Gordian knot between the two opposing views of the sufficiency of the Turing Test can be cut. 1.1. The Essence of the Turing Test. The Turing Test is, at its heart, a test of the adequacy of an agent’s verbal behavior. Block (1981) characterizes it as a test of the ability to “produce a sensible sequence of verbal responses to a sequence of verbal stimuli”.1 Turing’s original presentation of the Test is couched in terms of an imitation game between two entities, a person and a machine, with the goal of seeing if in repeated forced choices a judge can do no better than chance at determining which is which on the basis of verbal interactions with each. Much of this setup (and the preliminaries that he introduces regarding a gender-based version of the game) are incidental to the underlying goal, which is to determine if a machine has human-level verbal behavior. The introduction of the human confederate and the forced choice merely serve to make more clear and operational what constitutes “sensibility” of the 1 STUART M. SHIEBER 2 machine’s responses, but there are other ways to achieve the same goal. THE TURING TEST AS INTERACTIVE PROOF 3 Now imagine a scenario in which Peter has been getting straight A’s in school and just got two 800’s on the SAT. Victoria says “Oh, Peter’s not really intelligent; he’s just faking it to get into a good school.” Intelligence in this sense (which is not, of course, the sense that the Turing Test is meant to test for) is clearly like fluency in Italian, which is why the statement sounds ridiculous. Finally, imagine Victoria takes you to a Searlian “Italian room” where you can insert slips of paper with Italian written on them through a slot in the door and get back other slips of paper with perfectly fluent Italian responses, sometimes clever, sometimes amusing, always insightful; the room is a brilliant conversationalist. After an hour or so of this, you’re quite impressed, but Victoria, ever the spoilsport, says “Oh, that room isn’t intelligent; it’s just faking it.” If you think that sounds silly prima facie, you can see why the Turing-Test deniers’ view is so counter-intuitive. They seem to think that one could have the symptoms without the germ. Different philosophers diagnose this necessary causal agent differently. Searle (1980) thinks the germ is intentionality (though Dennett (1987) objects that Searle thinks it’s consciousness); Davidson (1990) thinks it’s semantics; Gunderson (1964) thinks it’s flexibility of behavior; Block (1981) thinks it’s “richness of information processing”. But all (except Dennett) agree that intelligence is not testable in purely behavioral terms. On the other hand, many find it hard to shake the intuition that a Turing-Test-passing entity must surely be intelligent. To such Turing-Test approvers, like Dennett (1985), no germ is necessary. “[T]he Turing test, conceived as he conceived it, is (as he thought) plenty strong enough as a test of thinking. I defy anyone to improve upon it.” This intuition is quite strong. Nonetheless, intuitions may be wrong and a little philosophy might be just the thing to lead us to accept previously counterintuitive conclusions, for instance, that sentences like “that machine is just faking intelligence” aren’t ridiculous at all. 1.3. The Argument Against Behaviorist Tests. In “Psychologism and Behaviorism”, Block (1981) presents what I take to be the strongest argument to date of the inadequacy of the Turing Test as a criterion of intelligence. 1. Introduction Philosophers of mind fall, roughly speaking, into two camps, the Turing-Test deniers, who think that passing a Turing Test cannot be used as a sufficient condition for intelligence, and the Turing-Test approvers, who think that it can. Turing-Test deniers think of intelligence like a bad cold. It has a hidden cause, a germ. Victoria can say of her friend Peter without sounding ridiculous things like “Oh, Peter’s not really sick; he’s just faking it, to get out of school.” Sickness can’t be cashed out in terms of some disposition to exhibit sickness symptoms (coughing, complaining of stomach pain, staying in bed). There has to be a germ. ) Turing-Test approvers, on the other hand, think of intelligence like being fluent in Italian. (In fact, they think it’s exactly like being fluent in Italian.) Imagine you’ve been talking for an hour with Victoria’s friend Pietro using perfect Italian. Now suppose Victoria were to say, “Oh, Pietro’s not really fluent in Italian; he’s just faking it, to be eligible for an Italians-only scholarship.” Such a statement is clearly silly. One can’t exhibit the symptoms of being fluent in Italian and be faking, missing some essential “germ” of fluency; the symptoms are the fluency. THE TURING TEST AS INTERACTIVE PROOF THE TURING TEST AS INTERACTIVE PROOF Through a series of thought experiments, Block argues that no conception of intelligence that relies solely on external behavior (as manifested in Premise 2) can be sufficient; some (at least minimal) internal conditions on the means by which the behavior is generated must be included. In particular, he faults the Turing Test for failing to demonstrate not only the fact of producing “a sensible sequence of verbal responses to a sequence of verbal stimuli” but of a general capacity for such behavior, and further, one derived from sufficient “richness of information processing”; the antecedent in Premise 2 is too weak. Because I think this is the strongest argument against the Turing Test as a sufficient condition of intelligence, it is the argument that I address in this paper. I argue that the Turing Test can in fact provide such a demonstration, thereby vitiating Block’s argument against the sufficiency of the Turing Test as a test of intelligence. Searle, in his “Minds, Brains, and Programs” (1980), presents a different argument against the Turing Test, his “Chinese room”. This argument is based on an article of faith that is too woolly to argue against, namely, that no formal system that merely manipulates symbols could bear intelligence. But Block doesn’t go that STUART M. SHIEBER 4 far,2 and indeed has argued against Searle on this point (Block, 1980). Block is saying something simpler, that it is logically possible that some thing that not only is merely a symbol manipulator but also is a trivial one could pass the Turing Test. Furthermore, it not only can pass the Turing Test, but has a general capacity to do so. But if Block is right, why would we be inclined to attribute intelligence to a machine that passed a Turing Test? far,2 and indeed has argued against Searle on this point (Block, 1980). Block is saying something simpler, that it is logically possible that some thing that not only is merely a symbol manipulator but also is a trivial one could pass the Turing Test. Furthermore, it not only can pass the Turing Test, but has a general capacity to do so. But if Block is right, why would we be inclined to attribute intelligence to a machine that passed a Turing Test? THE TURING TEST AS INTERACTIVE PROOF It seems to me that Block is right in principle: Such a machine is conceptually possible; hence the Turing Test is not logically sufficient as a condition of intelligence. Let us suppose this view is correct and, as Block argues, some further criterion is needed regarding the manner in which the machine works. Some further criterion is needed, but how much of a criterion is that, and can the Turing Test test for it? Although Block calls this further internal property ‘nonbehavioral’, I will argue that the mere behavior of passing a Turing Test can reveal the property. Borrowing an idea from theoretical computer science, I argue that the Turing Test can be viewed as an interactive proof not only of the fact of sensible verbal behavior, but of a capacity to generate sensible verbal behavior, and to do so “in the right way”. Assuming some extraordinarily weak conditions on physical realizability, any Turing-Test-passing agent must possess a sufficient property to vitiate Block’s argument. In summary, Block’s arguments are not sufficient to negate the Turing Test as a criterion of intelligence, at least under a very slight weakening of the notion of ‘criterion’. The argument I present does not demonstrate that the Turing Test is sufficient as a criterion for intelligence. It merely shows that Block’s argument against its sufficiency fails. However, some other argument might hold; this possibility remains open. 2At the end of “Psychologism and Behaviorism”, Block presents claims that an agent that exhibits intelligent behavior on the basis of exact emulation of the neurological processes of a person would arguably still not be intelligent. 2. Motivation Before I argue for the resurrection of the Turing Test as a sufficient condition of intelligence, it merits mention of why such an argument is worth undertaking in the first place. Discussions such as the present one (and Block’s) for or against the Turing Test as a definition or necessary or sufficient condition for 2At the end of “Psychologism and Behaviorism”, Block presents claims that an agent that exhibits intelligent behavior on the basis of exact emulation of the neurological processes of a person would arguably still not be intelligent. Consider a device that simulates you by using a theory of your psychological processes. It is a robot that looks and acts as you would in any stimulus situation. Instead of a brain it has a computer equipped with a description of your psychological mechanisms. You receive a certain input, cogitate about it, and emit a certain output. If your robot doppelganger receives that input, a transducer converts the input into a description of the input. The computer uses its description of your cognitive mechanisms to deduce the product of your cogitations; it then transmits a description of your output to a mechanism that causes the robot body to execute the output. It is hardly obvious that the robot’s process of manipulation of descriptions of your cogitation is itself cogitation. It is still less obvious that the robot’s manipulation of descriptions of your experiential and emotional processes are themselves experiential and emotional processes. It is hard to know how this claim could be distinguished in spirit from Searle’s, and Block (personal communication, 2002) has since stated that, though the various hedges make it possibly literally true, it goes too far. THE TURING TEST AS INTERACTIVE PROOF 5 intelligence might be denigrated (and have been) on the grounds that Turing didn’t propose his Test as a criterion of intelligence. Rather, Turing wanted to replace the question “Can machines think?” with the question “Can machines pass the Turing Test?”. But philosophers just won’t listen. They insist on investigating the issue of whether the Turing Test is a good definition of intelligence, despite Turing’s best efforts to avoid definitions entirely. A few voices have kept up pressure to stop such useless bickering. “It is a sad irony that Turing’s proposal has had exactly the opposite effect on the discussion of that which he intended,” says Dennett (1985). 2. Motivation “Alas, philosophers — amateur and professional — have instead taken Turing’s proposal as the pretext for just the sort of definitional haggling and interminable arguing about imaginary counterexamples he was hoping to squelch.” Chomsky’s view is that “Turing’s sensible admonitions should also be borne in mind, more seriously than they sometimes have been, in my opinion.” (Chomsky, 2004) ( ) But how can we know that Turing’s test is an adequate replacement for the question “Can machines think?” if we can’t compare the results of the Test with the corresponding answers to the question? I could request replacing the question “Can machines think?” with a test of their ability to perform arbitrary precision square roots, but one would be within rights to note that this is not a useful replacement. As Moor (1976, page 250) points out, “if Turing intends that the question of the success of the machine at the imitation game replace the question about machines thinking, then it is difficult to understand how we are to judge the propriety and adequacy of the replacement if the question being replaced is too meaningless to deserve discussion. Our potential interest in the imitation game is aroused not by the fact that a computer might learn to play yet another game, but that in some way this test reveals a connection between possible computer activities and our ordinary concept of human thinking.” Thus, philosophers have been inexorably led to the question of the relationship between a machine’s passing of the test and its thinking capacity. Turing finds himself sliding down the slippery slope from replacement to definition for just this reason. “We cannot altogether abandon the original form of the problem, for opinions will differ as to the appropriateness of the substitution and we must at least listen to what has been said in this connection” (Turing, 1950). He discusses, for instance, whether the test should be thought of as a necessary or sufficient condition for attributing intelligence, finding for the latter only. I therefore take seriously the issue as to whether passing a Turing Test is a sufficient criterion for intelligence. (The arguments against the Turing Test as a necessary condition, and therefore as a definition, of intelligence are simple, clear, uncontroversial, and need not be restated. 2. Motivation The views of French (1990) are particularly trenchant on the matter.) In the next section, I rehearse conventional philosophical wisdom on the matter (Dennett notwithstanding). 3The conceptions highlighted here correspond roughly to Block’s “operationalist proposal”, “neo-Turing Test conception”, and “amended neo-Turing Test conception”, respectively, except that crucially they are phrased as conditionals to better accord with the view of the Test as an ostensible sufficient condition, not an ostensible definition. In particular, Block states his conceptions in the form of definitions, e.g., “Intelligence (or more accurately, conversational intelligence) is the capacity to produce a sensible sequence of verbal responses to a sequence of verbal stimuli, whatever they may be.” Compare this to my capacity conception below. 3. Turing Test Conceptions of Intelligence Whether one thinks that the Turing Test is a sufficient condition for intelligence or not depends in large part on one’s interpretation of particular aspects of the role of the Turing Test in the stating of the condition. In Block’s phraseology, it depends on the “Turing Test conception of intelligence” that one has in mind. Block takes the upshot of passing a Turing Test as demonstrating STUART M. SHIEBER 6 that the subject-under-test can “produce a sensible sequence of verbal responses to a sequence of verbal stimuli”. The Turing Test conception of intelligence thus provides the connection between such production and the possession of intelligence. In its most direct form, the relation is expressed as in Premise 2 above, repeated here under the name “the occasional conception of intelligence”.3 The occasional conception: If an agent produces a sensible sequence of verbal responses to a sequence of verbal stimuli, then it is intelligent. The occasional conception: If an agent produces a sensible sequence of verbal responses to a sequence of verbal stimuli, then it is intelligent. In particular, how could the fact of passing one or more Turing Tests allow one to conclude the antecedent of this conception? I will pay this promissory note later. But Block is willing to grant capacities to the Turing-Test approvers anyway, ex hypothesi, because he has an argument even against this conception. Imagine (with Block) a hypothetical machine that stores a tree of interactions providing a sensible response for each possible interrogator’s input in each possible conversational context of up to, say, one hour long. (These responses might be modeled on those that Block’s fictional Aunt Bertha would have given.) Such a tree would undeniably be large, but processing in it would be conceptually straightforward. By hypothesis, such an “Aunt Bertha machine” would pass a Turing Test of up to one hour, because its responses would be indistinguishable from that of Aunt Bertha, whose responses it recorded. Such a machine is clearly not intelligent, by the same token that the teletype that the interrogator interacts with in conversation with the human confederate in a Turing Test is not intelligent; it is merely the conduit for some other person’s intelligence, the human confederate. Similarly, the Aunt Bertha machine is merely the conduit for the intelligence of Aunt Bertha. Yet just as surely, it can pass a Turing Test, and more, has the capacity to pass arbitrary Turing Tests of up to an hour. The mere logical possibility of an Aunt Bertha machine is sufficient to undermine the capacity conception.4 Block pursues a number of potential objections to his argument that the capacity conception is flawed, the most significant of which (his Objection 8) is based on the fact that the Aunt Bertha machine is exponentially large, that is, its size is exponential in the length of the conversation. Objection 8 leads to his “amended neo-Turing-Test conception”: “Intelligence is the capacity to emit sensible sequences of responses to stimuli, so long as this is accomplished in a way that averts exponential explosion of search.” (Emphasis in original.) It is not exactly clear what “exponential explosion of search” is intended to indicate in general. In the case of the Aunt Bertha Machine, exponentiality surfaces in the size of the machine, not the time complexity of the search. Further, the aspect of the Aunt Bertha machine that conflicts with our intuitions about intelligence is its reliance upon memorization. 4This anti-behaviorist argument was apparently first proposed in sketch form by Shannon and McCarthy (1956, page vi): “A disadvantage of the Turing definition of thinking is that it is possible, in principle, to design a machine with a complete set of arbitrarily chosen responses to all possible input stimuli. . . . With a suitable dictionary such a machine would surely satisfy Turing’s definition but does not reflect our usual intuitive concept of thinking.” 5For this reason, adding this extra condition to the conception of intelligence is not ad hoc. It amounts to saying, in a precise way, that the agent must have the capacity to produce sensible responses without having memorized them. The occasional conception: If an agent produces a sensible sequence of verbal responses to a sequence of verbal stimuli, then it is intelligent. This conception, together with Premise 1 — which asserts that passing a Turing Test demonstrates the antecedent — allows the conclusion that the agent is intelligent. It is simple to argue that this conception (admittedly a straw man, as no one to my knowledge, including Turing, has ever claimed it) is flawed. Imagine a machine that responds to the interrogator’s queries by emitting a random sequence of keystrokes. (The idea is conventionally implemented using monkeys and typewriters.) There is some (admittedly astronomically small) probability that these keystrokes will fortuitously spell out perfectly plausible responses to the queries, and the interrogator would therefore be fooled into confusing the random keystroke generator with a human. If one holds the stance that the random typing responses were not true intelligent behavior (and why would they be?), then the mere possibility of such an occurrence, by itself, demonstrates that passing the Turing test is not a sufficient condition for intelligent behavior, at least under the occasional conception. Of course, even Turing admitted as much. He thought of the test as having a statistical component, requiring more than a single occasion of passing. This is clear from his 1952 interview, quoted above. His statements about passing the Test were statistical too, as in his famous prediction that “an average interrogator will not have more than 70 per cent. chance of making the right identification after five minutes of questioning” (Turing, 1950). But subjecting the monkeys to multiple Tests, or longer ones, doesn’t solve this problem; it merely adjusts the odds of a false positive. Instead, what is needed is a change in the conception of intelligence, along the lines that Block argues for in “Psychologism and Behaviorism”. I skip ahead to his “neo-Turing-Test conception of intelligence”, which I will call The capacity conception: If an agent has the capacity to produce a sensible sequence of verbal responses to a sequence of verbal stimuli, whatever they may be, then it is intelligent. Arguably, this revised conception already gives up on a purely behaviorist view. How could one know that an agent has a (counterfactual) capacity without resort to analysis of its internal workings, that is, to a theory of its behavior, rather THE TURING TEST AS INTERACTIVE PROOF 7 than a mere sample of it? 6Hobbs, Stickel, Martin, and Edwards (1988) present a similar symmetrical view of the three types of reasoning. The occasional conception: If an agent produces a sensible sequence of verbal responses to a sequence of verbal stimuli, then it is intelligent. Removing the possibility of exponential storage amounts to a prohibition against memorization.5 C tl i t h i f thi ti i Consequently, an appropriate rephrasing of this conception is The compact conception: If an agent has the capacity to produce a sensible sequence of verbal responses to a sequence of verbal stimuli, whatever they may be, and without requiring storage exponential in the length of the sequence, then the agent is intelligent. Again, Block notes that this additional condition is psychologistic in mentioning a nonbehavioral condition, viz., that the manner of the processing must avert STUART M. SHIEBER 8 combinatorial explosion of storage. He claims that insofar as the condition is psychologistic, a Turing Test cannot test for it. combinatorial explosion of storage. He claims that insofar as the condition is psychologistic, a Turing Test cannot test for it. To summarize, Block’s Aunt Bertha argument forces us to pay up on two promissory notes. For the purely behavioral Turing Test to demonstrate intelligence, it must suffice as a demonstration of the antecedent of the compact conception of intelligence, that is, it must indicate a general capacity to produce a sensible sequence of verbal responses and it must demonstrate compactness of storage of the agent. It requires us to demonstrate a basis for an alternative to Premise 1: Premise 1′: If an agent passes a Turing Test, then it has the capacity to produce a sensible sequence of verbal responses to a sequence of verbal stimuli, whatever they may be, and without requiring storage exponential in the length of the sequence. To invalidate Block’s argument, then, it is sufficient to provide a basis for the new, stronger, view of the Turing Test codified in Premise 1′. 4. The Deductive, Inductive, and Abductive Basis for the Turing Test (What “best” means is a tricky issue, of course; it is where all the action is in formalizing abductive reasoning.) cases where Q →P holds because Q is a cause of P, and if there are multiple Qi such that Qi →P, we select the Qi that serves as the “best” explanation as cause of P. (What “best” means is a tricky issue, of course; it is where all the action is in formalizing abductive reasoning.) In the case at hand, we take P to be the passing of the Turing Test and Q to be the bearing of intelligence. Abduction then allows us to reason from an agent passing the Turing Test, along with the view that intelligence (at least of a certain sort) implies the ability to pass the Turing Test, to the conclusion that the agent is intelligent. Stalker points out that abductive reasoning requires an argument that the particular Q →P that one chooses must be the best explanation, not just any one, and he thinks he has a better one, namely, that the machine is merely following a particular computational procedure. Moor’s reply amounts to arguing that the intelligence view is, as an abductive explanation, just as good, if not better. Abductive reasoning in general has the following problem: The explanation that is best may still be wrong. Moor implies as much when he talks about the possibility that new evidence can cause one to change one’s conclusions. So the move to viewing the Turing Test as abductive evidence of intelligence probably won’t satisfy those (like Searle) who believe themselves in possession of a priori arguments against the possibility of mechanical intelligence. No matter how much “evidence” of this sort accumulates, the deductive conclusion from the premise “machines can’t think” will trump the abductive evidence to the contrary. It may also not satisfy Block, as it is hard to see how to rate the relative quality of the explanation “the machine is intelligent” and “the machine is looking up the replies in a table” without begging the question. Nonetheless, the attempt to salvage the Turing Test as a test for intelligence by changing the kind of demonstration that we take it to be is a promising one. 4. The Deductive, Inductive, and Abductive Basis for the Turing Test In the next section, I argue that the Turing Test can serve as a proof of the antecedent in the compact conception, and therefore a sufficient condition for intelligence, under a notion of proof that is very slightly weakened. By going from a requirement of deductive proof to that of interactive proof, and adding a weak condition of physical realizability, we can resurrect the Turing Test as a criterion of intelligence. 4. The Deductive, Inductive, and Abductive Basis for the Turing Test One potential way of salvaging the Turing Test is to change the notion of “demonstrate” in the claim that passing a Turing Test demonstrates intelligence. For instance, James Moor’s view (1976) is that Turing Tests should be viewed not as deductive proofs of intelligence (as Block would have it), but as “a source of good inductive evidence”. He calls the evidence inductive evidence, but what kind of induction could a Turing Test be evidence for? Induction, in one guise at least, is the form of reasoning from instances of a universal to the universal. The instances we see in a Turing Test are the agent “producing a sensible sequence of verbal responses to a sequence of verbal stimuli” as Block would say. The natural inductive conclusion to draw from such data is that the agent has the “capacity to produce a sensible sequence of verbal responses to arbitrary sequences of verbal stimuli”. Moor’s inductive evidence is evidence for the antecedent in the capacity conception of intelligence. Already, we see that by relaxing our notion of demonstration, we can make some headway on the path from Premise 1 to 1′. Nonetheless, the Test is only inductive evidence for the consequent if the capacity conception is sound. Thus, if Block is right, and the capacity conception fails, so does the inductive evidence reconstruction. But what Moor is getting at goes beyond the inductive view of the Turing Test, and is made clearer by Stalker’s reply (1978) and Moor’s response (1978). Stalker refers to the evidence not as inductive evidence, but as explanatory evidence. More properly, though Stalker doesn’t use the terminology, it appeals to reasoning by abduction, that is, reasoning to the best explanation. We can caricature the types of reasoning as follows: Deduction is reasoning from P and P →Q to Q; induction is reasoning from (repeated instances of) P and Q to P →Q; abduction is reasoning from P and Q →P to Q.6 Of course, such abductive reasoning is deductively unsound, and is appropriately limited to special THE TURING TEST AS INTERACTIVE PROOF 9 cases where Q →P holds because Q is a cause of P, and if there are multiple Qi such that Qi →P, we select the Qi that serves as the “best” explanation as cause of P. 5. The Interactive Proof Alternative To review, there are two psychologistic promissory notes out in the compact conception of the Turing Test. First, we must ascertain a general capacity to pass the test. Second, the manner of passing must satisfy a compactness limitation. I will pay the capacity promissory note first, and then turn to the compactness issue. Certainly, there is no deductive move that allows one to go from observation of the passing of one or more Turing Tests to a conclusion of a general capacity; the monkeys and typewriters argument shows that. This is the Humean problem of induction. But it does not follow that there is no method of reasoning from the former to the latter. I will argue that the powerful notion of an interactive proof, taken from theoretical computer science, is exactly such a reasoning method. Furthermore, as I will show in Section 6, Turing Tests bear some of the tell-tale signs of interactive proofs that have been investigated in the computer science literature. Although interactive proof is a mathematical notion, the argument I will provide is not a formal one. I do not propose that the Turing Test is an interactive 10 STUART M. SHIEBER proof in the mathematical sense, but rather, that interactive proofs provide the right metaphor or analogy for thinking about what Turing Tests provide.7 Interactive proofs are protocols designed to convince a verifier conventionally denoted V that a prover P has certain knowledge or abilities, which we will think of as being encapsulated in an assertion s.8 In a classical (deductive) proof system, P would merely reveal a deductive proof of s, which V then verifies. This provides V with knowledge of s and perhaps other knowledge implicit in the proof. Interactive proofs augment classical proof systems by adding notions of randomization and interaction between prover and verifier. (The interaction implicit in classical proof systems — P’s presenting V with the proof — is essentially trivial.) Interaction is added by allowing V and P to engage in rounds of message-passing. Randomization is introduced in two ways: First, the verifier may make use of random bits in constructing her messages. Second, she may be required to be satisfied with a probabilistic notion of proof. When we state that P proves s with an interactive proof, we mean (implicitly) that s has been proved but with a certain determinable residual probability of error. 7In independent work, Bradford and Wollowski (1994) do attempt to provide a mathematical argument relating interactive proofs and the Turing Test, but of a quite different flavor. For instance, they assume that the subject-under-test is polynomially bounded, and take the subject-under-test and confederate to be the verifiers, and the judge to be the prover. It is safe to say that the upshot of their analysis is unclear given the strong assumptions that they make. 8The roles of verifier and prover are analogous to those of Victoria and Peter/Pietro above. For convenience in reference, we will therefore refer to them using gendered pronouns “her” and “him” respectively. 9The probabilistic nature of interactive proof conclusions constitutes a very important distinction between interactive proofs and general inductive evidence (as appealed to by Moor). Inductive arguments may, like interactive proofs, be thought of as statistically founded, but they end in a step of acceptance of the general conclusion of which the instances form the inductive evidence. (We select many marbles from a jar and note that all are red. Statistics and independence assumptions allow us to compute a probability distribution over proportions of red marbles in the jar, with 100 percent being the most likely. By inductive acceptance, we conclude that all of the marbles in the jar are red.) Pollock (1990, Chapter 5) reviews problems with the statistical foundations of induction, and in particular, the acceptance step. But by virtue of yielding probabilistic conclusions, interactive proofs have no acceptance step, and thus do not fall prey to these problems. 9The probabilistic nature of interactive proof conclusions constitutes a very important distinction between interactive proofs and general inductive evidence (as appealed to by Moor). Inductive arguments may, like interactive proofs, be thought of as statistically founded, but they end in a step of acceptance of the general conclusion of which the instances form the inductive evidence. (We select many marbles from a jar and note that all are red. Statistics and independence assumptions allow us to compute a probability distribution over proportions of red marbles in the jar, with 100 percent being the most likely. By inductive acceptance, we conclude that all of the marbles in the jar are red.) Pollock (1990, Chapter 5) reviews problems with the statistical foundations of induction, and in particular, the acceptance step. But by virtue of yielding probabilistic conclusions, interactive proofs have no acceptance step, and thus do not fall prey to these problems. 10I digress to discuss a technical issue in order to forestall confusion about the graph nonisomorphism protocol. In order for the interactive proof of graph nonisomorphism to be of interest, we must assume that the verifier is computationally limited. Otherwise, the verifier could check whether G0 is isomorphic to G1 herself. It is standard, therefore, to restrict V to amounts of computation polynomial in the size of the graph. Under this assumption (and, again, current assumptions in the foundations of computational complexity), the verifier cannot herself determine if the two graphs are nonisomorphic. There is, of course, no reason to assume such computational limitations on the prover, and it is standard not to do so. For this reason, the interactive proof protocol can involve the prover carrying out actions for which no such computationally limited method is known, such as the computation of graph isomorphism in Step 2. The issue is discussed in detail by Goldreich et al. (1991). Interactive proof protocols for other problems, such as Graph 3-Colorability, are known for which computationally limited provers are sufficient. 11Informally speaking, a random permutation of a graph is just an isomorphic copy of the graph whose relation to the original has been lost. 5. The Interactive Proof Alternative That is, the verifier may need to be satisfied with some small and quantifiable chance that the protocol indicates that s is true when in fact it is not, or vice versa. The residual error is the reason that moving to a notion of interactive proofs is a weakening relative to a view as a deductive proof. The fact that the residual error can rapidly be made vanishingly small through repeated protocols is the reason that the weakening is referred to as “very slight”.9 The idea of interactive proofs has been absolutely revolutionary in computer science since their introduction by Goldwasser, Micali, and Rackoff (1985). It has had two major payoffs. First, there are efficient interactive proofs of assertions for which classical proofs are hopelessly inefficient. Second, there are interactive proofs of theorems that reveal to V much less knowledge about s; in the case of so-called zero-knowledge proofs, they reveal nothing but the fact of the assertion’s truth. The idea is perhaps best grasped through an example, a variation on the Graph Nonisomorphism interactive proof system of Goldreich, Micali, and Wigderson (1991). A graph is a mathematical object consisting of a set of nodes THE TURING TEST AS INTERACTIVE PROOF THE TURING TEST AS INTERACTIVE PROOF 11 11 (a) (b) (c) 1 2 3 4 5 1 2 3 4 5 Figure 1. Example graphs 5 Figure 1. Example graphs and a set of edges connecting some of them. Two graphs are isomorphic if there is a one-to-one mapping from the nodes of one to the nodes of the other such that there is an edge between a pair of nodes in the one if and only if there is an edge between the pair of nodes in the other that they map to. Figure 1 presents a graphical depiction of some graphs. Although all have the same number of vertices and edges, only graphs (a) and (b) are isomorphic, under a mapping of the vertices given by the node numberings in the figure. Neither is isomorphic to (c). This is easily seen, as (c) has a minimal cycle (that is, a set of vertices connected in a cycle no subset of which forms a cycle) of four vertices, while neither (a) nor (b) do. In the general case, determining that two graphs are nonisomorphic is not so straightforward. 11Informally speaking, a random permutation of a graph is just an isomorphic copy of the graph whose relation to the original has been lost. Formally, a random permutation G′ of the graph Gb is a graph isomorphic to Gb constructed as follows: The nodes of G′ are a set of the same cardinality as the set of nodes of Gb. A one-to-one mapping π from the nodes of Gb to the nodes of G′ is chosen at random from all possible such mappings. For each edge in Gb connecting nodes n1 and n2, there is an edge of G′ connecting nodes π(n1) and π(n2), and there are no other edges in G′. 5. The Interactive Proof Alternative SHIEBER assertion is true, this new graph is isomorphic to Gb but not G1−b. If the assertion is false, G′ is isomorphic to both the original graphs.) V sends G′ to P as a message. assertion is true, this new graph is isomorphic to Gb but not G1−b. If the assertion is false, G′ is isomorphic to both the original graphs.) V sends G′ to P as a message. (2) P checks if G′ is isomorphic to G0. If so, he sends the message “0”, otherwise the message “1”. (2) P checks if G′ is isomorphic to G0. If so, he sends the message “0”, otherwise the message “1”. (2) P checks if G′ is isomorphic to G0. If so, he sends the message “0”, otherwise the message “1”. (3) V receives the bit b′ that P sent. If b′ = b, V accepts the proof; the assertion has been proved. If b′ ̸= b, V rejects the proof. (3) V receives the bit b′ that P sent. If b′ = b, V accepts the proof; the assertion has been proved. If b′ ̸= b, V rejects the proof. (We will call a series of messages generated according to a protocol such as this a transcript. An accepting transcript is one in which the verifier accepts the proof in the final step, and correspondingly for a rejecting transcript.) The protocol is a bit like a mentalist’s mind-reading trick. The verifier thinks of a number between 0 and 1, and the prover must guess that number. The prover gets a clue, namely the knowledge that if the verifier is thinking of the number 0, the graph she sent is isomorphic to G0, and similarly for 1. If G0 and G1 are nonisomorphic (that is, the proposition is true), the clue is enough information to reconstruct the verifier’s number. P will be able to reconstruct the bit b and the verifier will accept the proof. If the graphs are isomorphic (the proposition is false), the clue provides no help in guessing the verifier’s number. In that case, the prover can do no better than guessing randomly, and will thus be wrong about half the time, causing V to reject the proof. The other half of the time, she will erroneously accept the proof; the prover “got lucky”. It is in this sense that the interactive proof is probabilistic. 5. The Interactive Proof Alternative It is important for the purposes of this example to understand that (given current assumptions in the foundations of computational complexity) the time required to determine if two graphs are isomorphic is exponential in the number of nodes in each graph, that is to say, the problem is very difficult. and a set of edges connecting some of them. Two graphs are isomorphic if there is a one-to-one mapping from the nodes of one to the nodes of the other such that there is an edge between a pair of nodes in the one if and only if there is an edge between the pair of nodes in the other that they map to. Figure 1 presents a graphical depiction of some graphs. Although all have the same number of vertices and edges, only graphs (a) and (b) are isomorphic, under a mapping of the vertices given by the node numberings in the figure. Neither is isomorphic to (c). This is easily seen, as (c) has a minimal cycle (that is, a set of vertices connected in a cycle no subset of which forms a cycle) of four vertices, while neither (a) nor (b) do. In the general case, determining that two graphs are nonisomorphic is not so straightforward. It is important for the purposes of this example to understand that (given current assumptions in the foundations of computational complexity) the time required to determine if two graphs are isomorphic is exponential in the number of nodes in each graph, that is to say, the problem is very difficult. Suppose P claims to know that the following assertion s is true: Graphs G0 and G1 are not isomorphic. Graphs G0 and G1 are not isomorphic. V wants to be convinced of this. We can imagine that the graphs G0 and G1 are quite large, say thousands of nodes. It would thus be impractical for V to determine by direct computation the truth of s.10 The following interactive proof protocol achieves this goal. The following interactive proof protocol achieves this goal. (1) V selects one of the two graphs G0 or G1 at random by choosing a random bit b, a 0 or 1; the selected graph is then Gb, the unselected graph G1−b. V then computes a random permutation11 G′ of the chosen graph Gb. (If the 12 STUART M. 5. The Interactive Proof Alternative By the time you have thrown one hundred darts with 75 landing in the red, the likelihood that the red region is less than 50% is, intuitively at least, much lower. This line of reasoning can be made precise and quantified. In so doing, the intuition is proved correct, and in fact, the probability that the sample fails to represent the whole can be shown to be exponentially small in the number of samples. Crucially, this method allows us to reason from the behavior of a sample (the dart throws) to the space undergoing sampling (the entire dartboard). Identical reasoning can be applied to extrapolate from a sample of verbal behavior to a general capacity. Such reasoning is exactly what is needed to argue from the passing of a Turing Test to the attribution of a general capacity to do so. I now describe how to use a rigorous form of the dartboard method to generate an interactive proof of a general capacity. Suppose that P claims a general capacity to compute a function f over possible inputs from a (presumably large and perhaps infinite) space S. How can V verify this claim by testing P in computing f on a sample of S? First, we must make more precise what we mean by a general capacity to compute a function. We may not (and, in the case at hand, do not) want to require perfect performance in computing the function; P may get the answer wrong on occasion for incidental reasons, even though in general P can compute the function. Let tp be the fraction of the space for which P performs correctly. We can pick a threshold tl to serve as a lower bound on the size of the subspace. We will say that if tp > tl, P has a general capacity to compute f. For the purpose of concreteness, we might take tl to be 1/2. Then we are saying that if P computes f correctly on at least 50% of all possible inputs, it has a general capacity to compute f. Figure 2 depicts the general setup. In this way, we can make precise a notion of having a general capacity. 5. The Interactive Proof Alternative If the verifier doesn’t like these 50-50 odds of false positives, V can rerun the test several times. The more rounds, the less likely it is that the prover can guess right every time, unless the clues are actually helping (that is, unless the proposition to be proved is actually true). The probability of a false positive after k rounds of this protocol are 1 in 2k, because the prover would have to get lucky k times in a row. 5.1. Interactive Proofs of Capacity. If a Turing Test is a kind of interactive proof, it needs to be a proof not of knowledge, but (as argued above) of a capacity. In the parlance of theoretical computer science, it is a proof of an ability. Bellare and Goldreich (1992) extend the notion of an interactive proof of knowledge to an interactive proof of an ability. Their method is quite sophisticated and general; in essence, they demonstrate that (with arbitrarily high probability) playing the role of P successfully in a proof system to compute some function is tantamount to computing the function itself. We don’t require such a general setup. Rather, I present a simple mechanism for making statistical conclusions about a general capacity based on an interactive proof. I start with an analogy. Suppose you are given a dartboard that is painted black, except for a single region of red. You throw some darts at the board uniformly at random, and note that 75% of them land in the red region. Intuitively, this should indicate to you that roughly 75% of the dartboard is red, but of course this depends on how many darts you threw. If you threw only four darts, there is a reasonable chance that the red region is relatively small (say less than 50%), and yet three THE TURING TEST AS INTERACTIVE PROOF THE TURING TEST AS INTERACTIVE PROOF 13 Figure 2. Sampling inputs to a function to test a general capacity for a prover to compute the function correctly on a given fraction of inputs. Figure 2. Sampling inputs to a function to test a general capacity for a prover to compute the function correctly on a given fraction of inputs. of the four happened to land in that region. 5. The Interactive Proof Alternative In general, Pr[t > ts] < e−ck where c = (tl−ts)2 2(1−tl) . Thus, it has the behavior of an interactive proof: As the number of samples k increases, the probability of a false positive decreases exponentially. where c = (tl−ts)2 2(1−tl) . Thus, it has the behavior of an interactive proof: As the number of samples k increases, the probability of a false positive decreases exponentially. It is important to realize that the probabilities of error that we are talking about can be literally astronomically small. For the bounds that we have been talking about, if we let k be, say, 100, we are already in the realm of false positive probabilities on the order of 1 in 500. At k = 300, the false positive probability is on the order of 1 in 1010; at that rate, if a population the size of all humanity were tested, one would expect to see no false positives. At k = 1000, the false positive rate of some 1 in 1027 is truly astronomically small. A similar argument shows that the probability of false negatives decreases exponentially in sample size as well. We suppose there to be another bound tu > ts such that there is an agent that performs correctly on a fraction of the space given by tu. A false negative occurs if t < ts for such an agent. For example, suppose tu to be 90%, and suppose P computes f correctly on more than 90% of inputs, yet V happens to choose more than 25% of the samples on the less than 10% of the subspace that P fails to compute f on. Then for this sample, the apparent performance t will be less than the sample bound ts = 3/4, a false negative. Again, the probability of such an occurrence can be shown to be exponentially small in k. 5.2. The Turing Test as an Interactive Proof of Capacity. I view the Turing Test as an interactive proof for the antecedent of the capacity conception of intelligence, that is, it is a proof that P “has the capacity to produce a sensible sequence of verbal responses to a sequence of verbal stimuli, whatever they may be”. Consider the (perhaps infinite) space of all possible sequences of verbal stimuli. 5. The Interactive Proof Alternative Nonetheless, this definition of general capacity still requires that we determine how P performs on all possible inputs, not just a subsample, in order to (deductively) verify that the subspace on which P performs correctly is larger than the threshold tl. An interactive proof protocol can be used to prove this general capacity. V 14 STUART M. SHIEBER can sample k inputs x1, . . . , xk uniformly from S, and have P compute f on these inputs. V then verifies the correctness of each f(xi). can sample k inputs x1, . . . , xk uniformly from S, and have P compute f on these inputs. V then verifies the correctness of each f(xi). Suppose that P generates correct answers on some percentage ts of samples greater than tl; in the case at hand, we might take ts to be 75% of the samples. Can we conclude that P has a general capacity to compute f (in the sense of computing f correctly on at least 50% of all inputs)? Such a conclusion does not logically follow. Perhaps P computes f correctly on less than 50% of all inputs, but V happened to select 75% of the samples from this smaller subspace. This would constitute a “false positive”, reasoning incorrectly from the sample to the space as a whole. A false positive occurs when a sample of k inputs is selected for which f is computed correctly on t of these, where t > ts (the prover outperforms the sample threshold on the sample), yet tp < tl (the subspace is smaller than the definitional threshold). Using the method of Chernoffbounds (see, e.g., Chapter 5 of the text by Motwani (1995)), it can be shown that the probability of a false positive is Pr[t > ts] < e−µδ2/2 Pr[t > ts] < e−µδ2/2 where µ = (1 −tl)k and δ = 1 −1−ts 1−tl . For the example in which tl = 1/2 and ts = 3/4, we have µ = k/2 and δ = 1/2, so Pr[t > 3/4] = e−(k/2)(1/2)2/2 = e−k/16 . Pr[t > ts] < e−µδ2/2 where µ = (1 −tl)k and δ = 1 −1−ts 1−tl . For the example in which tl = 1/2 and ts = 3/4, we have µ = k/2 and δ = 1/2, so Pr[t > 3/4] = e−(k/2)(1/2)2/2 = e−k/16 . 5. The Interactive Proof Alternative An agent without a general capacity to produce sensible sequences of responses would fail to do so on some nontrivial fraction of this space. Block notes that a 100% THE TURING TEST AS INTERACTIVE PROOF 15 criterion is neither necessary nor appropriate. One wants to be able to “ask of a system that fails the test whether the failure really does indicate that the system lacks the disposition to pass the test.” Indeed, people put under similar tests would at least occasionally perform in such a way that a judge might deem the responses not sensible. So there is some percentage, less than 100%, such that if an agent produced sensible sequences of responses on that percentage of the space, we can attribute a general capacity, sufficient for the antecedent of the capacity conception. Let us say, for the sake of argument that this threshold is 50%. That is, if an agent produces sensible responses to 50% of the space of possible verbal stimuli, we will consider it to have a general capacity to produce such responses. Importantly, we are not saying that the agent must merely produce sensible responses to 50% of some subsample of possible stimuli that we confront it with, but with 50% of all possible stimuli, in a counterfactual sense, whether we ever test it with these stimuli or not. The interactive proof approach of the previous section is directly applicable to this problem, with tl = 1/2. Suppose we sample k sequences of verbal stimuli uniformly from this space, and test some agent as to whether it generates sensible sequences of responses to them. Suppose further that the agent does so on 75% of these stimuli (that is, ts > 3/4). On this sample, then, the agent performs well above our 50% cut-off. The analysis of the previous section shows that the probability that the agent does not have a general capacity at the 50% level is exponentially small.12 What about false negatives? If we assume that people generate sensible responses on, say, 99% of the space (recalling that 100% is not required here), then again the odds of a sample showing a performance of less than 75% is exponentially small in k. 12The bounds presented here showing exponentially vanishing probabilities of error in adjudging capacities are predicated on the k samples being taken uniformly and independently. In the case of repeated Turing Tests, of course, the judge is free, and apt, to construct new Tests based on the behavior noted in previous Tests so as to maximize the information received. Such nonindependent sampling can lead to dramatically smaller rates of error, in theory, for randomized tests of this sort. 5. The Interactive Proof Alternative When all we know is the system’s performance on a fixed sample of stimuli, the storage requirements to generate these responses is linear in the length of the stimuli. But the size of any fixed fraction of the space of possible stimuli is exponential in their length. By being able to reason from the sample to the fraction of the space as a whole — as the interactive proof approach allows — we can conclude that an agent using a memorization strategy (as the Aunt Bertha machine) would require exponential storage capacity to achieve this performance. Conversely, any agent not possessing exponential storage capacity would fail the interactive proof. Nonetheless, how can a Turing Test reveal that the machine doesn’t have exponential storage capacity? Recall that the modified compact conception requires that the agent pass Turing tests at least logarithmic in its storage capacity. Thus, without bounding its storage capacity, we can’t bound the length of the Test we would need. There is no purely logical argument against this possibility; the Aunt Bertha argument shows this. Some further assumption must be made to pay the compactness promissory note. I now turn to how weak an assumption is required. Suppose we could bound the amount of information in the universe. Then any physically realizable agent that could pass Turing Tests whose length exceeded the logarithm of this amount would satisfy the compact conception. We would be able to bound the length of the Turing Test required under the compact conception, at least for any agent that is no larger than the universe. (And of course, no agent is larger than the universe.) We will call this length bound the critical Turing Test length. One might worry that the critical Turing Test length might be centuries or millennia long. In the paragraphs that follow, we show that the critical Turing Test length is actually quite short. A crude upper bound on the information capacity of the universe can be constructed by examining the fine structure of space-time itself. (We will refine the estimate shortly.) Quantum theory predicts that the basic structure of space-time is strongly fluctuating on length scales of order 10−35 meters (the Planck scale). Any attempt to resolve phenomena below this scale, as would be necessary to store information, would require so much energy that the region being resolved would collapse into a black hole. 5. The Interactive Proof Alternative In summary, a protocol in which we run k Turing Tests and receive sensible responses on at least, say, 75% provides exponentially strong evidence that the agent satisfies the antecedent of the capacity conception, that is, has a general capacity to produce sensible responses to verbal stimuli, whatever they may be. Of course, one might think that a 50% capacity is insufficient to characterize a general capacity for verbal fluency. Perhaps 80% would be better. (We had better not get too greedy, though, as people don’t deliver 100% performance.) Or one might think that some people, and even intelligent ones, don’t approach 99% performance; maybe 85% is all we can guarantee. As long as there is a differential between the two bounds, we can place the threshold ts between them and still achieve an exponentially small rate of both false positives and negatives. The difference between the two bounds merely determines a constant in the exponent. One can think of this as adjusting the number of samples needed before the knee in the exponential curve. (If one doesn’t think there is a differential between the two bounds, one is denying the capacity conception itself.) Thus, under the notion of proof provided by interactive proofs, the Turing Test can provide a proof of a general capacity to produce a sensible sequence of STUART M. SHIEBER 16 verbal responses to a sequence of verbal stimuli, whatever they may be. It can therefore unmask the monkeys on typewriters. 5.3. The Turing Test as an Interactive Proof of Compactness. Now to the question of compactness. First, I rephrase the compact conception of intelligence; rather than placing an upper limit on the size of the agent, I place an equivalent lower limit on the length of the test. The modified compact conception: If an agent has the capacity The modified compact conception: If an agent has the capacity to produce a sensible sequence of verbal responses to a sequence of verbal stimuli that is at least logarithmic in the storage capacity of the agent, whatever they may be, then the agent is intelligent. The modified compact conception is logically equivalent to the compact conception; the difference is just in the phraseology. The interactive proof approach provides leverage for demonstrating this compactness as well. 5. The Interactive Proof Alternative It is thus reasonable to take a volume of this linear size as the smallest region in which one could store a bit. Let us assume one could actually store bits uniformly at this level of granularity. (We return to this THE TURING TEST AS INTERACTIVE PROOF 17 assumption below.) This gives a volume at this primitive level of 10105 bits per cubic meter. assumption below.) This gives a volume at this primitive level of 10105 bits per cubic meter. To obtain a value for the information capacity of the universe as viewed from a given location, we need a further estimate of the volume that could in principle affect that location. For any given distance in the past, the volume of the accessible universe is a sphere corresponding to a three-dimensional slice through the four-dimensional space-time light cone. For example, the volume of the universe of a minute ago accessible to a location now is a sphere centered on the location with radius of one light-minute (approximately 17 million kilometers). As we look farther backwards in time, the volume grows, but not without limit. The big bang serves as a second point of reference. At that point, the universe volume was effectively zero. The accessible volume, then starts at zero with the big bang, grows to some maximal volume, and then shrinks again to zero as we approach the given location in space-time. A two-dimensional depiction of the situation is given in Figure 3. The point in question is how large this maximal volume is. However large this maximal volume is, it can be no larger than a volume of diameter given by the time since the big bang some 15×109 years ago, which is the maximal volume if no contraction in the accessible volume occurs as we look back in time beyond that governed by the expansion of the universe since the big bang. Thus, the maximal accessible volume of the universe — which we can think of for our purposes, talking loosely, as the volume of the universe — must be less than (15 × 109)3 cubic light years. Recalling that a light year is about 1016 meters, the volume of the universe is thus bounded by 1079 cubic meters, and the total storage capacity is bounded by 10184 bits. Call it 10200 (thereby increasing the estimate by 16 orders of magnitude). 13The estimate based on the holographic principle is far lower than our previous estimate because it respects the fact that any attempt to store bits as densely by volume as the previous estimate would have energy requirements that would cause the system to collapse under gravitational forces. 5. The Interactive Proof Alternative ) Descending now from these ethereal considerations to the concrete goal of analyzing the Turing Test conceptions of intelligence, under the modified compact conception, we would require an agent with this literally astronomical storage capacity to have a capacity to pass Turing Tests of on the order of log2 10200 ≈670 bits. The entropy of English is about one bit per character or five bits per word (Shannon, 1951), so we require a critical Turing Test length of around 670 characters or 140 words. At a natural speaking rate of some 200 words per minute, a conversation of less than a minute would therefore unmask a Turing-Test subject whose performance, like that of the Aunt Bertha machine, is based on memorization. Current results in quantum gravity yield even smaller estimates of the information-storage capacity of the universe. Work on the so-called holographic principle (regarding which see the survey by Bousso (2002) for a review) limits the information stored in a volume based on its surface area rather than volume. Thus, the exponent in our estimate is offby a factor of 3/2; a more accurate estimate would be some 10120. An important property of this result is that (unlike the estimate of the previous paragraph,13 in which we assumed that we could store only one bit per Planck volume) it does not depend on any assumptions about the fine structure of physical theory. It is a pure principle of physics, like relativity; STUART M. SHIEBER 18 Figure 3. The volume of the universe accessible to a point in space time (here-now). The volume grows starting with the big bang, reaches some maximal volume, and then shrinks back to zero at here-now. The size of the maximal volume is bounded by a sphere whose diameter is given by the time since the big bang. Figure 3. The volume of the universe accessible to a point in space time (here-now). The volume grows starting with the big bang, reaches some maximal volume, and then shrinks back to zero at here-now. The size of the maximal volume is bounded by a sphere whose diameter is given by the time since the big bang. regardless of future discoveries of more and more finely differentiated particles, say, this limit on information content will hold. 5. The Interactive Proof Alternative As a side note, Block claims that Nothing in contemporary physics prohibits the possibility of matter in some part of the universe that is infinitely divisible. . . . Suppose there is a part of the universe (possibly this one) in which matter is infinitely divisible. In that part of the universe there need be no upper bound on the amount of information storable in a given finite space. So my machine could perhaps exist, its tapes stored in a volume the size of, e.g., a human head. Current physics shows that this claim is incorrect — the holographic bound on the information content of the universe holds regardless of the divisibility of matter — and limitations on the information-carrying capacity of the universe can allow us to THE TURING TEST AS INTERACTIVE PROOF 19 draw conclusions from the fact of passing a Turing Test of sufficient (supercritical) length. Further, this length is a perfectly practical one. An even smaller bound on the informational capacity of the universe has been developed by Seth Lloyd (2002), based on the total number of distinct quantum states in the universe. His estimate based on this methodology (which ignores the ability to store bits using gravitational degrees of freedom) is 1090. (He notes as well that adding in the gravitational degrees of freedom gives a limit of 10120, in agreement with the estimate above derived above.) Thus, the critical Turing Test length might be even smaller than the one minute we estimated initially. Nonetheless, the skeptic might wonder how sensitive our estimates of the critical Turing Test length are to these numbers. Suppose our estimates of the information content of the universe were offby, say, 1000 orders of magnitude, and there might be as many as 101200 bits in the universe. Even then, the required Turing Test length would be around 4000 characters or 800 words, the size of a very short essay and far less than a five-minute conversation. Thus, under extraordinarily conservative (but admittedly not logically necessary) assumptions, even quite short Turing Tests are sufficient to pay the compactness promissory note. It might seem counterintuitive (especially to those familiar with toy programs designed to engage in conversation on this or that topic) that the critical Turing Test length should be so short. 6. Interactive Proof Properties Shared by the Turing Test Several previously unexplored properties of Turing Tests follow from properties of interactive proofs that have been demonstrated in the computer science literature. Such properties inhere to interactive proofs as opposed to classical proofs. Their applicability to Turing Tests thus provides a further argument for the view of Turing Tests as interactive proofs. I discuss two such properties here: nontransferability and lack of closure under composition. 6.1. Nontransferability. Interactive proofs typically are nontransferable; they provide proof only to the verifier and no one else. In a classical proof system, an accepting transcript includes a record of the prover submitting to the verifier an independently checkable proof of the proposition. Thus, the transcript can serve as a proof to a third party as well. But a third party who is given an accepting transcript of an interactive proof protocol does not thereby gain proof of the truth of the proposition being proved. This follows from the fact that accepting transcripts can be generated without knowledge of the truth of the proposition being proved. For the graph nonisomorphism case, the only message from the prover to the verifier in an accepting transcript is a bit the identity of which the verifier already knows. Such a transcript is therefore trivial to generate. Another reason that third parties do not gain evidence from an accepting transcript, even if they watch it being generated, is that they do not have access to crucial facts concerning whether the protocol is being accurately followed. The evidence provided by an interactive proof depends, for instance, on certain bits being generated randomly by the verifier and kept private from the prover. Only the verifier knows that the bits were random and secret, as only the verifier generated them and held them. If the bits were generated nonrandomly (for instance, according to a prior collusive agreement with a “prover”14) or were not kept secret (communicated to a “prover” after being generated randomly), the recipient could use the knowledge of the bits to complete an accepting protocol instance without knowledge of the proposition being proved. Turing Tests are also nontransferable in this sense. Accepting transcripts (that is, sensible conversations) can be generated by the verifier (judge) independently and without knowledge that the prover (subject-under-test) possesses the ability in question. 14The quotes are used to indicate that the entity playing the prover role is not acting as a true prover. 5. The Interactive Proof Alternative Keep in mind that the Test here is the unrestricted Turing Test — any and all queries on any topic of any sort are allowed — and that the machine that we are trying to unmask is of a particular sort, namely one that has memorized answers to every possible such query. As it turns out, the combinatorics of language are such that only a short time is required to generate a vast number of possible queries, and the design of the Aunt Bertha Machine is such that we need only find one that is unhandled to unmask it. It is important to understand that the physical calculations performed here, by themselves, are insufficient to provide grounding to the compact conception. The argument requires the interactive proof notion as well, for it is the interactive proof view of the Turing Test that lets us go from a conclusion about a sample of verbal behavior to a conclusion about possible untested behaviors, and the storage capacity required by a sample is merely linear in the sample size, but the storage capacity required by the possible untested behaviors is exponential in the sample size. What I have argued is not that one can deduce from an agent passing a Turing Test the agent’s intelligence, but rather, that one can prove this under a conception of proof that admits false positives with astronomically small probability, and that makes physical assumptions of an astronomically weak nature. Further, the proof is of the strong antecedent to the compact conception of intelligence, including the capacity requirement and the compactness limitations on the agent. In essence, I have argued for the following recasting of the basic syllogism supporting the sufficiency of the Turing Test: Premise 1: If an agent passes k rounds of a Turing Test of at least one minute in length, then (with probability of error exponentially small in k) it has the capacity to produce a sensible sequence of verbal responses to a sequence of verbal stimuli that is logarithmic in the storage capacity of the agent, whatever they may be. STUART M. SHIEBER 20 Premise 2 (= Modified Compact Conception): If an agent has the capacity to produce a sensible sequence of verbal responses to a sequence of verbal stimuli that is logarithmic in the storage capacity of the agent, whatever they may be, then it is intelligent. 5. The Interactive Proof Alternative Conclusion: Therefore, if an agent passes k rounds of a Turing Test of at least one minute in length, then (with probability of error exponentially small in k) it is intelligent. 15For this reason, many of us in the natural-language-processing field have come to be healthily skeptical of published transcripts of the behavior of natural-language-processing systems. 16An anonymous reviewer urges correctly that we not make too much of the nontransferability of Turing Tests, noting that the same could be said about scientific proofs as documented in research papers. “A scientist can publish a result that is incorrect or even cooked. How can published results become knowledge for others who haven’t run the experiment?” The answer, of course, is trust in the scholarly publishing system, a trust founded in large part on statistical evidence; incorrect results fail to replicate and cooked results occasionally come to light, and we can note empirically the rarity of both types of failures. In fact, the nontransferability of scientific proof reminds us of the degree to which the scientific enterprise is founded on an interactive notion of proof as well. 6. Interactive Proof Properties Shared by the Turing Test Similarly, if a “verifier” fails to obey the randomness or secrecy requirements of the protocol, an accepting transcript can be generated even though the “prover” lacks the general capacity to respond sensibly to verbal stimuli. For example, if V restricts her questioning to a particular line of conversation that she knows P has been programmed to handle well, the transcript THE TURING TEST AS INTERACTIVE PROOF 21 will appear to an outside observer to be an accepting one, even though it provides no information about the general capacities of P to respond sensibly. This is the phenomenon of the “cooked demo”, which can appear very convincing to an observer while of course being completely unconvincing to the participants. The observer lacks the crucial knowledge possessed by the participants that the protocol was apparently, but not actually, being followed.15 The only way for you to know that a demo hasn’t been cooked is to act as the verifier yourself.16 Of course, nontransferability is an intended property of typical interactive proof protocols — the typical cryptographic applications of interactive proofs make nontransferability a desirable property — whereas nontransferability is an inadvertent property of Turing Tests. Nonetheless, the similarity is real. 6.2. Lack of Closure under Composition. It can easily be shown that interactive proofs are not closed under composition. In particular, if agents participate in multiple interactive proofs at the same time, the conclusions that can be drawn from the set of proofs can be much weaker than those that could have been drawn by similar proofs generated independently (that is without shared participation). Block alludes to this issue with his example of the simultaneous chess player. Jones plays brilliant chess against two of the world’s foremost grandmasters at once. You think him a genius until you find out that his method is as follows. He goes second against grandmaster G1 and first against G2. He notes G1’s first move against him, and then makes the same move against G2. He awaits G2’s response, and makes the same move against G1, and so on. Since Jones’s method itself was one he read about in a comic book, Jones’s performance is no evidence of his intelligence. (Block, 1981) Failures of interactive proofs of this sort have been noted in the computer science literature as well. 7. Conclusion I have argued that the Turing Test is appropriately viewed not as a deductive or inductive proof but as an interactive proof of the intelligence of a subject-under-test. This view is evidenced both by the similarity in form between Turing Tests and interactive proof protocols and by the sharing of important properties between Turing Tests and interactive proofs. In so doing, I provide a counterargument against Block’s demonstration that the Turing Test is not a sufficient criterion of intelligence. Our counterargument requires a (very slight) weakening of the conditions required of the Turing Test — weakening the notion of proof (from classical deductive proof to interactive proof with its exponentially small residual error probability) and strengthening the notion of possible agent (from one of logical possibility to one with a trivial realizability requirement essentially of nomological possibility). These weakenings are sufficiently mild that they can be seen as providing foundation for the view that the Turing Test is a sound sufficient condition for intelligence. Block is right, yet Dennett may be too. It merits pointing out that this view of the Turing Test is consonant with (though by no means implicit in) Turing’s view of the Test as presented in his writings. His view of the Test as being statistical in nature and his pragmatic orientation toward its efficacy are of a piece with its status as an interactive rather than classical proof. 6. Interactive Proof Properties Shared by the Turing Test Desmedt, Goutier, and Bengio (1987), for instance, describe what they term the “mafia fraud”, which is a failure of the Fiat-Shamir interactive proof method for authentication (Fiat and Shamir, 1986). In an authentication protocol, P proves his identity to V ; the Fiat-Shamir protocol does so by proving (via interaction, and in the normal probabilistic sense) to V that P has knowledge of a certain private key known only to P, without revealing that key to V (or anyone else). In the “mafia fraud”, P ′, who has no knowledge of P’s private key succeeds in authenticating himself to V by carrying out a separate authentication protocol with P. Whatever messages V sends to P ′, P ′ sends on to P; whatever responses P ′ receives, he sends on to V . The two instances of the protocol being carried out STUART M. SHIEBER 22 are accepting ones, hence P is authenticated to P ′ and P ′ is authenticated to V . The composition of the two protocol instances thus fails to ensure the correctness of the conclusions (at least in the case of the authentication of P ′). This technique of composing interactive proofs and playing one participant offagainst another can trip up Turing Tests as well. Here is a six-line program, clearly unintelligent, that can pass two simultaneous Turing Tests. (Here, query(judgei) returns the next query sent by the i-th judge, and respond(judgei, r) sends a given response r to the i-th judge.) repeat i1 := query(judge1); respond(judge2, i1); i2 := query(judge2); respond(judge1, i2); untilfinished repeat i1 := query(judge1); respond(judge2, i1); i2 := query(judge2); respond(judge1, i2); untilfinished repeat i1 := query(judge1); d( d ) respond(judge2, i1); ( ) i2 := query(judge2); ( ) respond(judge1, i2); f It merely shuttles the responses of each of the judges to the other, just as the chess player shuttles the moves of the two grandmasters to each other and as the mafia defrauder shuttles protocol messages from P to V . Engaging in two Turing Tests at once does not necessarily provide twice the evidence generated by a single Turing Test, and may provide no evidence at all, just as simultaneous Fiat-Shamir proofs fail to provide the authentication guarantee that single Fiat-Shamir proofs do. Acknowledgments I would like to thank Ned Block, Raphael Bousso, Daniel Fisher, David Israel, Michael Rabin, Ken Shan, Andrew Strominger, Salil Vadhan, and the members of the Artificial Intelligence Research Group at Harvard University for THE TURING TEST AS INTERACTIVE PROOF 23 valuable discussions and insights regarding the issues discussed in this paper. I also thank the anonymous reviewers for their comments that led to several clarifications. Much of the work on this paper was done while visiting the Centro per la Ricerca Scientifica e Tecnologica (itc-IRST), Trento, Italy during the spring of 2002. My deep appreciation goes to Oliviero Stock and itc-IRST for space and support to work on this material during my visit. References Bellare, Mihir, and Oded Goldreich. 1992. Proving computational ability. Available at http://www.wisdom.weizmann.ac.il/~oded/PS/poa.ps. Block, Ned. 1980. What intuitions about homunculi don’t show. Behavioral and Brain Sciences 3:425–426. ———. 1981. Psychologism and behaviorism. Philosophical Review XC(1):5–43. Bousso, Raphael. 2002. The holographic principle. Reviews of Modern Physics 74: 825–874. Available as hep-th/0203101. Bradford, Phillip G., and Michael Wollowski. 1994. A formalization of the Turing test. Tech. Rep. 399, Department of Computer Science, Indiana University. Available at http://www.cs.indiana.edu/pub/techreports/TR399.html. An extended abstract appeared in the Proceedings of the 5th Midwest Artificial Intelligence and Cognitive Science Conference, ed. T. E. Ahlswede, pages 83–87, April 1993. Chomsky, Noam. 2004. Turing on the “imitation game”. In The Turing Test, ed. Stuart M. Shieber, chap. 20. Cambridge, MA: MIT Press. Davidson, Donald. 1990. Turing’s test. In Modelling the mind, ed. K. A. Mohyeldin Said, W. H. Newton-Smith, R. Viale, and K. V. Wilkes, chap. 1, 1–11. Oxford, England: Clarendon Press. Dennett, Daniel. 1985. Can machines think? In How we know, ed. Michael Shafto, 121–145. San Francisco, CA: Harper & Row. Dennett, Daniel. 1985. Can machines think? In How we know, ed. Michael Shafto, 121–145. San Francisco, CA: Harper & Row. ———. 1987. Fast thinking. In The intentional stance, chap. 9, 323–337. Cambridge, MA: MIT Press. ———. 1987. Fast thinking. In The intentional stance, chap. 9, 323–337. Cambridge, MA: MIT Press. Desmedt, Yvo, Claude Goutier, and Samy Bengio. 1987. Special uses and abuses of the Fiat-Shamir passport protocol. In Advances in cryptology—CRYPTO ’87, ed. Carl Pomerance, vol. 293 of Lecture Notes in Computer Science, 21–39. Berlin, Germany: Springer-Verlag. Fiat, Amos, and Adi Shamir. 1986. How to prove yourself: Practical solutions to identification and signature problems. In Advances in cryptology—CRYPTO ’86, ed. A. M. Odlyzko, vol. 263 of Lecture Notes in Computer Science, 171–185. Berlin, Germany: Springer-Verlag. French, Robert. 1990. Subcognition and the limits of the Turing test. Mind 99(393): 53–65. Goldreich, Oded, Silvio Micali, and Avi Wigderson. 1991. Proofs that yield nothing but their validity or all languages in NP have zero-knowledge proofs. Journal of the Association for Computing Machinery 38(3):691–729. Goldwasser, Shafi, Silvio Micali, and Charles Rackoff. 1985. The knowledge complexity of interactive proof-systems (extended abstract). In Proceedings of the 17th ACM Symposium on the Theory of Computing, 291–304. Providence, RI. Gunderson, Keith. 1964. The imitation game. Mind 73(290):234–245. STUART M. SHIEBER 24 Hobbs, Jerry R., Mark Stickel, Paul Martin, and Douglas D. Edwards. 1988. Interpretation as abduction. References In Proceedings of the 26th annual meeting of the association for computational linguistics, 95–103. Buffalo, New York. Lloyd, Seth. 2002. Computational capacity of the universe. Physical Review Letters 88(23). Moor, James H. 1976. An analysis of the Turing test. Philosophical Studies 30: 249–257. ———. 1978. Explaining computer behavior. Philosophical Studies 34:325–327. Motwani, Rajeev. 1995. Randomized algorithms. Cambridge, England: Cambridge University Press. Newman, M. H. A., Alan M. Turing, Sir Geoffrey Jefferson, and R. B. Braithwaite. 1952. Can automatic calculating machines be said to think? Radio interview, recorded 10 January 1952 and broadcast 14 and 23 January 1952. Turing Archives reference number B.6. Pollock, John L. 1990. Nomic probability and the foundations of induction. Oxford, England: Oxford University Press. Searle, John R. 1980. Minds, brains, and programs. Behavioral and Brain Sciences 3:417–457. Shannon, C. E. 1951. Prediction and entropy of printed English. Bell Systems Technical Journal 30(1):50–64. ( ) Shannon, Claude E., and John McCarthy, eds. 1956. Automata studies. Princeton, NJ: Princeton University Press. Stalker, Douglas F. 1978. Why machines can’t think: A reply to James Moor. Philosophical Studies 34:317–320. Turing, Alan M. 1950. Computing machinery and intelligence. Mind LIX(236): 433–460. Harvard University
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Expression of zebrafish Brn1.2 (Pou3f2) and two Brn-3a (Pou4f1) POU genes in brain and sensory structures
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Expression of zebrafish Brn1.2 (Pou3f2) and two Brn-3a (Pou4f1) POU genes in brain and sensory structures Satish Srinivas Kitambi1,2,+*, Gayathri Chandrasekar1,2 1School of Life Sciences, Södertörns University College 2Department of Biosciences and Nutrition, Karolinska Institutet 14152 Huddinge, Sweden +Current Address:Institute for Healthcare Education and Translational Sciences, India. Expression of zebrafish Brn1.2 (Pou3f2) and two Brn-3a (Pou4f1) POU genes in brain and sensory structures Satish Srinivas Kitambi1,2,+*, Gayathri Chandrasekar1,2 1School of Life Sciences, Södertörns University College 2Department of Biosciences and Nutrition, Karolinska Institutet 14152 Huddinge, Sweden +Current Address:Institute for Healthcare Education and Translational Sciences, India. . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: oRxiv preprint Expression of zebrafish Brn1.2 (Pou3f2) and two Brn-3a (Pou4f1) POU genes in brain and sensory structures *Corresponding author Professor. Satish Srinivas Kitambi, Research Director Institute for Healthcare Education and Translational Sciences, 10-2-311, Plot 187, Cama Manor, W. Marredpally, Sec-Bad, India 500026. Tel: +914027805176 Email: kitambi1979@gmail.com Keywords: retina, zebrafish, lateral line, POU, brn1.2 brn3a. *Corresponding author Professor. Satish Srinivas Kitambi, Research Director Institute for Healthcare Education and Translational Sciences, 10-2-311, Plot 187, Cama Manor, W. Marredpally, Sec-Bad, India 500026. Tel: +914027805176 Email: kitambi1979@gmail.com Keywords: retina, zebrafish, lateral line, POU, brn1.2 brn3a. *Corresponding author Professor. Satish Srinivas Kitambi, Research Director Institute for Healthcare Education and Translational Sciences, 10-2-311, Plot 187, Cama Manor, W. Marredpally, Sec-Bad, India 500026. Tel: +914027805176 Email: kitambi1979@gmail.com Keywords: retina, zebrafish, lateral line, POU, brn1.2 brn3a. 1 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: oRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint Introduction POU genes encode a subclass of sequence-specific DNA-binding proteins within the family of homeodomain transcription factors. They are defined by the conserved POU DNA-binding domain, that was originally identified by sequence comparison of the mammalian Pit-1, Oct-1, Oct-2 homeodomain proteins and the Caenorhabditis elegans transcription factor unc-86 (Herr et al., 1988). Based on their sequence homologies, POU genes have been divided into six subclasses (I to VI) (Latchman, 1999; Ryan and Rosenfeld, 1997). Mammalian class III POU genes include four members, Brn-1, Brn-2, Brn-4 and Oct-6/SCIP/Tst-1 that are predominantly expressed in the developing and adult nervous system (He et al., 1989; Monuki et al., 1989; Meijer et al., 1990; Hara et al., 1992; Mathis et al., 1992; Alvarez-Bolado et al., 1995; Zwart et al., 1996). POU class III genes are important for the neuronal cell differentiation. Knock out of the mouse Brn -2 gene results in the loss of neurons that produce oxytocin, vasopressin and corticotropin-releasing hormone (Nakai et al., 1995; Schonemann et al., 1995). Brn-4 mutants in mice show developmental defects in the inner ear causing deafness (Phippard et al., 1999). In humans, DFN3, an X- chromosome linked non-syndromic mixed deafness is caused by the naturally occurring mutations in Brn-4 gene (de Kok et al., 1995). Targeted deletion of Tst-1 has shown that Tst-1 is essential for the terminal differentiation of myelinating Schwann cells in the peripheral nervous system (Bermingham et al., 1996; Jaegle et al., 1996). In zebrafish, five POU class III genes have been identified and characterized (Matsuzaki et al., 1992; Sampath and Stuart 1996; Spaniol et al., 1996; Hauptmann and Gerster 1996; Hauptmann and Gerster 2000). They include zp12, zp23, zp47, brn1.2 and zp50. The zebrafish POU class III genes show high sequence identity with their corresponding mammalian genes. Similar to their mammalian members, zebrafish class III POU genes lack introns within their POU-domain encoding sequences. zp50 is orthologous to mammalian Oct-6 (Levavasseur et al., 1998). zp12 and zp23 are the zebrafish orthologs of mammalian Brn-1 and are identical with each other (Spaniol et al., 1996). zp47 and brn1.2 are related to each other and are the zebrafish orthologs of mammalian Brn-2 gene (Spaniol et al., 1996; Sampath and Stuart 1996). The presence of additional genes in zebrafish could be attributed to the gene duplication in the genomic sequence of the teleost lineage. Abstract POU genes are characterized by a conserved POU DNA-binding domain, and are divided into six subclasses. Class III and IV POU genes are predominantly expressed in the developing nervous system. POU class III genes are critical for several neuronal cell differentiation and class IV POU genes serve important functions in the differentiation and survival of sensory neurons. In this study, we attempted to identify POU genes in the zebrafish and pufferfish genomes by using existing bioinformatics tools. We analysed the expression of zebrafish brn1.2 and brn3a genes (brn3a1 and brn3a2)) using whole-mount in situ hybridisation. Similarly to the mammalian orthologue, zebrafish brn1.2 was widely expressed in the forebrain, midbrain and hindbrain. During the late stages of embryogenesis, brn1.2 expressing cells were located in the preoptic area and in the auditory vesicles. Expression of both zebrafish brn3a genes was detected in trigeminal ganglia, cranial sensory ganglia, sensory neurons along the dorsal spinal cord, in the anterior and posterior lateral line placodes (ALL and PLL), retinal ganglion cell layer, optic tectum and in small cell clusters in the forebrain and hindbrain. Similar to mammalian Brn3a, zebrafish brn3a genes were detected in the retina and sensory structures. However, different domains of expression were also observed, namely in spinal sensory neurons, and lateral line system. 2 2 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: oRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint Introduction Previously only a partial sequence of brn1.2 was deduced and a detailed developmental expression 3 3 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: oRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint analysis of this gene was not described (Sampath and Stuart et al., 1996). Therefore, we have attempted to describe the developmental expression pattern of zebrafish brn1.2 using whole-mount in situ hybridization. Members of the class IV group of POU genes are characterized by an additional amino terminal consensus sequence, the POU-IV box (Gerrero et al., 1993; Xiang et al., 1995; Xiang et al., 1993) and are known to play important roles during development of the nervous system (Latchman, 1999; Ryan and Rosenfeld, 1997). Drosophila I-POU (Acj6) and Caenorhabditis elegans unc-86 are the invertebrate homologues of mammalian class IV POU genes (Gruber et al., 1997). The three mammalian class IV POU genes, POU4F1 (also called Brn-3.0, Brn-3a, RDC1), POU4F2 (Brn-3.2, Brn-3b), and POU4F3 (Brn-3.1, Brn-3c) display high sequence similarities and distinct but overlapping expression patterns in the developing CNS and PNS (Latchman, 1999). Murine Brn-3a is mainly expressed in dorsal root and trigeminal ganglia, medial habenula, red nucleus and inferior olivary nucleus (Xiang et al., 1996). Loss of Brn-3a function by targeted deletion in mice causes loss of neurons in the brain stem and trigeminal ganglion and leads to uncoordinated limb movement and impaired suckling (Xiang et al., 1996). Human Brn-3a is localised on chromosome 13 and was found expressed in subsets of peripheral nervous system tumours (Collum et al., 1992). Human Brn-3a has been reported to activate expression of p53 in human tumour cells (Budhram-Mahadeo et al., 2002). It has also been shown that human Brn3a can activate the NGF1-A promoter in primary neurons and neuronal cell lines (Smith et al., 1999). Zebrafish brn3b and brn3c homologues have recently been characterized, while a brn3a gene of zebrafish has not been described. 1. Results and discussion 1.1 Phylogenetic analysis of the zebrafish Pou gene class. Studies on vertebrate genome evolution provide increasing evidence of a whole genome duplication in the teleost lineage. In order to determine the effect of the proposed teleost genome duplication on the number of POU genes, we searched the zebrafish and pufferfish genome databases (Zebrafish version 3 and 4 (Zv3, Zv4) and FUGU 2.0) (www.ensemble.org). Our database search revealed 18 POU genes in zebrafish and 17 POU genes in pufferfish. To classify the identified POU genes into different subclasses, multiple sequence alignment was performed using the identified POU domain sequences and a phylogenetic tree was constructed (Fig 1A). The phylogenetic tree clustered the different zebrafish and pufferfish genes into the known six subclasses. Zebrafish and pufferfish genes corresponding to each of the six subclasses were identified. When compared to the mammalian set of 15 POU genes, it became eveident that several POU genes were present in two copies, while others were missing in the two teleost genomes. Surprisingly, genes corresponding to POU5F2 (Sprm-1) and POU3F4 (brn-4) could not be identified through the genome search in zebrafish and pufferfish. Perhaps, zebrafish and pufferfish sprm-1 and brn-4 may be secondarily lost during evolution (Fig 1A). Introduction In zebrafish two brn3b cDNAs, a long and a short isoform, have been cloned and their expression reported in the retina, optic tectum, migrating posterior lateral line primordium and larval neuromast (DeCarvalho et al., 2004). Zebrafish brn-3c has also been cloned and was found to be expressed in the developing otic vesicle (DeCarvalho et al., 2004; Sampath and Stuart, 1996). In an effort to determine the complete set of POU genes in teleost fish by search through available genome sequence and EST databases, we identified two brn3a zebrafish orthologues named brn3a1 and brn3a2,. Similarly to brn3b, brn3a2 was found to be expressed as a long (brn3a2 (l)) and a short (brn3a2(s)) isoform. The 4 . 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It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: oRxiv preprint developmental expression patterns of the two-zebrafish brn3a genes were analyzed by whole-mount in situ hybridisation (WISH). 1.2 Identification of zebrafish brn1.2 cDNA We identified the zebrafish brn1.2, fugu brn1.2 and zp47 gene by TBLASTN search of the genomic zebrafish and fugu sequence at wwww.ensemble.org using zebrafish zp47 (acc.no. P79746). The constructed sequence was used to screen the zebrafish EST database for zebrafish brn1.2 ESTs. Two ESTS for zebrafish brn1.2 were identified and sequenced. We found that only one of them contained the complete open reading frame, therefore we used this clone for further analysis. This clone contained only a partial fragment of the 5ÚTR (20nt), 1639nt 3ÚTR and 1014nt ORF. Multiple sequence comparison between the zebrafish POU class III proteins Zp47 and Brn1.2 with the corresponding proteins of other species revealed high conservation in the POU domain region (Fig 1B). The POU domain sequence of zp47 and brn1.2 are highly similar to human, mouse and pufferfish. zp47 showed an overall sequence 5 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: Rxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint identity of 97.4% to human, mouse and pufferfish while brn1.2 was 95.5% identical to human and mouse and 96.8% identical to pufferfish. 1.3 Identification of zebrafish brn3a cDNAs. Through the zebrafish genome search ENSDARP00000007850 and ENSDARP00000013808 were identified. Similarity search with Blast program followed by multiple sequence alignment of POU domain and phylogenetic tree construction was performed to identify the class of POU genes these hits belonged. The similarity analyses revealed that ENSDARP00000007850 and ENSDARP00000013808 were paralogues to each other and orthologues to mammalian Brn3a. For the murine Brn3a gene a short and a long cDNA isoform has been characterized (acc. Nos: AAO60105, AAO60106) (Thomas et al., 2004). In order to explore the possible existence of zebrafish brn3a1 and brn3a2 isoforms, we attempted to theoretically construct a long and a short isoform transcript form the available genome sequence using in silico methods. 1.2 Identification of zebrafish brn1.2 cDNA It was possible to construct a long and a short isoform for zebrafish brn3a2 (brn3a2(l) and brn3a2(s)) but not for zebrafish brn3a1. The coding region of zebrafish brn3a2(l) was derived from two exons (E1,E2) separated by an intron (I1). Incontrast, brn3a2(s) was made up from the 3’ region of intron (I1) and exon E2 (Fig 1D). The genome sequence analyses of the members of the brn3 family in zebrafish and fugu demonstrated that the mRNA was mainly derived from two exons and some members of the family also formed shorter isoforms (Fig 1D). The amino acid sequences from the assembled zebrafish brn3a1, brn3a2(l) and brn3a2(s) were taken to mine the zebrafish expressed sequence tag database available at NCBI (www.ncbi.nlm.nih.gov). One EST for zebrafish brn3a1 was identified and sequenced. The sequence contained 165 nt 5’ UTR and 1133 nt 3’UTR and an open reading frame encoding 344 amino acids . Two EST’s for zebrafish brn3a2(l) were identified and sequenced. The sequence data revealed an open reading frame of 366 amino acids and 17nt 5’UTR and 1254nt 3’UTR. Similarly one EST for brn3a2(s) was identified and sequenced revealing an open reading frame of 367 amino acid and 7nt 5’UTR and 1254nt 3’UTR. The sequences of all Ests matched the in silico sequence prediction from the zebrafish genome. Similar in silico sequence analyses of pufferfish genome lead to the identification and construction of pufferfish brn3a1, 6 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: oRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint brn3a2(l) and brn3a2(s) sequences. Sequence Identity of the POU domain region between the zebrafish brn3a genes and mammalian Brn3a was very high (Human and Mouse Brn3a is 93.7% identical to zebrafish brn3a1 and 96.2% identical to zebrafish brn3a2). 1.4 Multiple sequence alignment of Pou class IV sequences. 1.4 Multiple sequence alignment of Pou class IV sequences. Multiple sequence alignment of class IV amino acid sequences revealed a high conservation of the POU domain region (POU+Linker+Homeodomain) between different species, but significant conservation was also observed outside of the POU domain (Fig 1C). A poly-glycine stretch at the N-terminus of mammalian Brn-3b and in mammalian Brn-3a was seen; this region was absent in the zebrafish and pufferfish sequences. Distinct region specific for brn3b sequences, mammalian brn3a, brn3b sequences were observed (Fig 1C). A specific region of 11 amino acid was identified to be present in fish (zebrafish and pufferfish) brn3a2 and mammalian brn3a. This region was absent from the fish brn3a1 (Fig 1C). Analysis of the genomic sequence of Pou class IV genes from human, mouse, zebrafish, and pufferfish showed that the coding region is derived from two exons. The position of the intron was conserved among all the species compared. The length of the exons of different brn3 genes in zebrafish and fugu were very similar and zebrafish brn3a2 and brn3b also formed shorter isoforms (Fig 1D). 1.2 Identification of zebrafish brn1.2 cDNA Even higher sequence identity was found between zebrafish and pufferfish class IV POU domain sequences (pufferfish brn3a1 is 97.5% identical to zebrafish brn3a1 and pufferfish brn3a2 is 97.5% identical to zebrafish brn3a2). 1.5 Developmental expression pattern of zebrafish brn1.2 We performed whole-mount in situ hybridization (WISH) (Hauptmann and Gerster, 1994, 2000) to characterize the spatial expression of brn1.2 in the developing zebrafish brain. Expression of brn1.2 was first detected at the tail bud stage in an area that corresponds to the midbrain primordium (Fig 2A). At the 3-, 5- and 10- somite stages the expression became quite strong in the midbrain region. From the 5-somite stage on brn1.2 was also detected in the hindbrain and spinal cord (Fig 2B,C,D). A weak expression of brn1.2 transcripts was found in the ventral diencephalic region at the 10-somite stage (Fig 2D). We compared the expression of brn1.2 with pax2.1 (Krauss et al., 1991) and krx-20 (Oxtoby and Jowett, 1993) in order to locate the position of brn1.2 transcripts in the midbrain and hindbrain. Two color in situ 7 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: oRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint hybridisation with pax2.1 showed that brn1.2 was located anterior to pax2.1 expression domain indicating that brn1.2 expression domain was located in the anterior midbrain (Fig 2E). Co-labelling studies with krx-20 revealed that brn1.2 expression in the hindbrain is confined to r3 and r5 (Fig 2G,H). From 24hpf on, brn1.2 showed a widespread expression in the CNS. In the forebrain, brn1.2 was detected in the diencephalon, epiphysis, ventral thalamus, dorsal thalamus and pretectum while the telencephalon was devoid of brn1.2 expression. At 1dpf, brn1.2 was expressed throughout the hindbrain with strong expression levels in r3 and r5 (Fig 2I). At 30hpf a lamda shaped expression domain with two arms were observed in the diencephalon (Fig 2J). To define the position of the two arms more precisely we performed whole-mount in situ hybridisation to visualize brn1.2 followed by immunohistochemistry to detect acetylated α-tubulin (Piperno and Fueller, 1985). 1.5 Developmental expression pattern of zebrafish brn1.2 One arm of the lamba domain was found to be lying in-between the optic recess and the tract of the postoptic commissure. The other arm extending from the ventral thalamus was broader in shape and was widespread across the tract of the commissure of the posterior tuberculum (Fig 2J). At 36hpf and 2dpf the expression of brn1.2 became more complex in the brain (Fig. 2K,L). At 2dpf, few brn1.2 positive cells were found scattered in the telecephalon (Fig. 2L). Additionally, brn1.2 expression was detected for the first time in the auditory vesicles at this stage of development (Fig. 2F). Interestingly, at 36hpf and 48dpf few cells expressing brn1.2 were concentrated in the preoptic area of the forebrain (Fig. 2K & L). The mammalian neuro-hypophyseal hormones oxytocin and arginine vasopressin are represented as isotocin and vasotocin in fish. Two color in situ hybridization with zebrafish isotocin-neurophysin (itnp) and vasotocin- neurophysin (vt) was performed to determine whether brn1.2 was co-expressed with itnp and vt. In zebrafish, itnp mRNA is expressed as bilateral cell clusters in the dorsal preoptic region of the brain (Unger and Glasgow, 2003). Zebrafish vt is first detected at 24hpf in the anterior diencephalon (not shown). At 48 hpf, vt is expressed as bilateral cell clusters in the preoptic area and in the ventral hypothalamus (Fig. 3E). Co-labelling experiments performed on 48hpf embryos revealed that brn1.2, itnp and vt expressing cells are located in the same region in the preoptic area (Fig. 3A-F). In a separate study it was demonstrated that the isotocin expressing cells are co-distributed with corticotropin-releasing hormone (CRH) producing cells in the preoptic region of 8 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: oRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint the forebrain (Fig. 3G-I) (Chandrasekar et al., 2007). Therefore it is likely that the CRH expression domain lies within the brn1.2 expression domain in the preoptic area. 1.5 Developmental expression pattern of zebrafish brn1.2 In mammals, so far, four transcription factors, namely, Sim1, Arnt 2, Otp and Brn-2 have been known to be required for the development of specific neuroendocrine cell types located within the paraventricular nuclei (PVN) and supraoptic nuclei (SON) of the hypothalamus. Sim1 and its heterodimerization partner Arnt2 belong to the bHLH- PAS family of transcription factors. Both Sim1 and Arnt2 are critical for the development of the neurosecretory cell types that produce oxytocin (OT), arginine vasopressin (AVP), corticotropin-releasing hormone (CRH), thyrotropin-releasing hormone (TRH) and somatostatin (Keith et al., 2001; Michaud et al., 2000; Michaud et al., 1998). Brn-2 is the downstream target of Sim1 and is required for the terminal differentiation of OT, AVP and CRH expressing neurons (Nakai et al., 1995; Schonemann et al., 1995). Brn-2 also regulates the transcription of CRH by binding to its promoter (Li et al., 1993). The homeobox gene orthopedia (Otp) function in parallel with Sim1 and both are required for the maintenance of Brn-2 expression (Acampora et al., 1999). A recent study in zebrafish shows that sim1 and otp are required for isotocin cell development and they act in parallel to direct the differentiation of isotocin cells in zebrafish (Eaton and Glasgow, 2006; Eaton and Glasgow, 2007). Considering our results from the co-expression studies we are tempted to speculate that similar to the mammalian Brn-2 gene, zebrafish brn1.2 could also have a role in the differentiation of isotocin, vasotocin and CRH producing cell types. In conclusion, we have analyzed the developmental expression pattern of brn1.2 in the embryonic brain. Our results show that zebrafish brn1.2 exhibits a very complex expression pattern in the developing brain very much similar to its paralog zp47 (Hauptmann and Gerster, 2000a). Overlapping expression domains of brn1.2, itnp and vtnp in the preoptic area suggests a possible role for brn1.2 in the development of specific neuroendocrine cell types. 1.6 Expression of zebrafish brn3a genes during development. From the 7 somite stage onwards to 15 somite stage, brn3a1 expression was also found in the forming anterior and posterior lateral line placodes (ALL and PLL) (Fig. 4J,K,M,N, 5I) in addition to the longitudinal stripes along the developing spinal cord. At 25 hpf, brn3a1 expression had spread to various cranial sensory placodes, including anterior dorsal (AD), anterior ventral (AV), facial (F), middle lateral line placode (M) and posterior lateral line placode (PLL) Fig. (5A-C) and remained unchanged at 30 hpf and 36h pf (Fig 5F, G, J, K). By 48hpf, brn3a1 expression in cranial ganglia was decreased and restricted to the neuromast of ALL and PLL (Fig 5L). Apart from these regions, brn3a1 was also expressed in cluster of cells in the forebrain and hindbrain (fig. 5J). The expression of brn3a1 in Rohan Beard neurons was transient and disappeared by 30 hpf. The retinal ganglion cells (RGC) are the first neurons to become post mitotic (Brown et al., 2001; Hu and Easter, 1999; Kay et al., 2001; Wang et al., 2001). The laminar pattern of the eye is formed by 60hpf (Hu and Easter, 1999) and the RGC’s are the first neurons to be born (Brown et al., 2001; Hu and Easter, 1999; Kay et al., 2001; Wang et al., 2001) and require Ath5 expression for its determination (Brown et al., 2001; Kay et al., 2001; Liu et al., 2000; Liu et al., 2001; Wang et al., 2001). In mammals Brn3a is expressed in the RGC cells (Xiang et al., 1996). Zebrafish brn3a1 was found to be expressed in the ventronasal region of the retina at 25 hpf (Fig 5D). Retinal brn3a1 expression spread dorsally and temporally and throughout the RGC layer by 36hpf (Fig. 5J). The three retinal layers (ganglion cell layer, inner nuclear layer and outer nuclear layer) are clearly visible at 48hpf, and intense expression of brn3a1 was seen throughout the RGC layer (Fig 5M-N). The early expression profile of zebrafish brn3a1 indicated that brn3a1 may precede the expression of brn3b and brn3c. The sequence of expression of Brn3a, Brn3b and Brn3c is different in mouse where the expression of Brn3b precedes the expression of Brn3a and Brn3c (Xiang, 1998). Axonal projections from the RGC’s exit the retina by 34hpf and innervate optic tectum by 72hpf (Burrill and Easter, 1995). Expression of brn3a1 was also found in the optic tectum. 1.6 Expression of zebrafish brn3a genes during development. Whole-mount in situ hybridization was used to study the developmental expression profile of brn3a1 and brn3a2. Fluorescein labelled neuroD was used to identify the sensory structures (Blader et al., 1997; Kim et al., 1997; Korzh et al., 1998). Initial expression of brn3a1 was detected at the tailbud stage. brn3a1 expression was 9 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: oRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint confined to the trigeminal placode and to longitudinal stripes along the lateral aspects of the neural plate, presumably Rohon beard sensory neuron precursors (Fig. 4A-C, 5H). This expression pattern stayed essentially the same up to the 5 somite stage (Fig. 4D-I). From the 7 somite stage onwards to 15 somite stage, brn3a1 expression was also found in the forming anterior and posterior lateral line placodes (ALL and PLL) (Fig. 4J,K,M,N, 5I) in addition to the longitudinal stripes along the developing spinal cord. At 25 hpf, brn3a1 expression had spread to various cranial sensory placodes, including anterior dorsal (AD), anterior ventral (AV), facial (F), middle lateral line placode (M) and posterior lateral line placode (PLL) Fig. (5A-C) and remained unchanged at 30 hpf and 36h pf (Fig 5F, G, J, K). By 48hpf, brn3a1 expression in cranial ganglia was decreased and restricted to the neuromast of ALL and PLL (Fig 5L). Apart from these regions, brn3a1 was also expressed in cluster of cells in the forebrain and hindbrain (fig. 5J). The expression of brn3a1 in Rohan Beard neurons was transient and disappeared by 30 hpf. confined to the trigeminal placode and to longitudinal stripes along the lateral aspects of the neural plate, presumably Rohon beard sensory neuron precursors (Fig. 4A-C, 5H). This expression pattern stayed essentially the same up to the 5 somite stage (Fig. 4D-I). 2.1 Zebrafish maintenance Wild type Zebrafish were maintained at 28.5 °C and under standard conditions of feeding, care and egg collection. Embryos were collected by natural mating . The collected embryos were staged according to Kimmel et al. (1995). Embryos were staged in hours post fertilization (hpf) and days post fertilization (dpf), and embryo stages older than 24hpf were subjected to 0.03% phenylthiourea treatment. The collected embryos were fixed at different stages in 4% paraformaldehyde overnight and then washed with phosphate buffered saline containing 0.1% Tween-20 (PBSTw) and stored in 100% methanol until usage for in situ hybridization. 1.6 Expression of zebrafish brn3a genes during development. Tectal expression of brn3a1 was detected at 30 hpf (Fig 5F) 10 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: Rxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint and fully established by 48 hpf (Fig 5L-M), Zebrafish brn3a2 was very similarly expressed as brn3a1. Expression of brn3a2(l) in the trigeminal placode and presumed Rohon Beard sensory neurons started around the 7 somite stage (Fig. 6A,B) and became stronger by 10 somite stage (Fig 6C,D). Expression in the trigeminal ganglion ceased at 24 hpf. Expression of brn3a2(l) was detected in the anterior lateral line (ALL) and posterior lateral line (PLL) by 15 somites and continued to be expressed there until 48hpf (Fig 6E-J, 7A-M). Clusters of cells expressing brn3a2(l) were also seen in the forebrain, hindbrain (Fig 7A,D,G,I) and along the dorsal cells of the spinal cord (Fig 7C,F). The expression in the spinal cord goes down by 48hpf (Fig 7M).In the midrain tectum and RGC layer, brn3a2(l) expression was established by 48hpf (Fig 7I,J,L,M). In summary, apart from expression of both brn3a genes in the RGC layer and sensory ganglia, expression of these genes was also detected in sensory neurons along the dorsal spinal cord and in small cell clusters within the forebrain and hindbrain. Similar to zebrafish brn3b (DeCarvalho et al., 2004), brn3a1 and brn3a2(l) were also detected in the lateral line system. 2.2 Sequence analysis Zebrafish and Pufferfish genome sequence databases were mined to identify and construct POU class genes. Mammalian POU genes were used as query. A database using Filemaker Pro software was developed to collect and maintain the assembled POU sequences from zebrafish and pufferfish as well as published sequences from other species. The assembled sequences were translated and POU, Linker region and 11 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: oRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint Homeodomain were extracted and multiple sequence alignments were performed with the Clustal X program (Thompson et al., 1997). A neighbour joining tree with bootstrap value of 1000 was constructed based on the multiple sequence alignment obtained in the Clustal X program. The neighbour joining tree helped to cluster the newly found zebrafish and pufferfish sequences to their mammalian counterparts. The tree was viewed with NJ plot software (Perriere and Gouy, 1996). Zebrafish brn1.2, brn3a1 and brn3a2 genomic sequences (ENSDARG00000023662, ENSDARP00000007850 and ENSDARP00000013808) were identified using zebrafish zp47 for brn1.2 and murine Brn3a protein sequences (acc No P79746 and acc. Nos. S69350) as query against the ongoing zebrafish genome project (Zv3) using TBLASTN search. The long and the short isoforms of brn3a2 were assembled manually using conceptual translation. Amino acid sequences of brn3a1, brn3a2(l), brn3a2(s) were obtained by conceptual translation. The constructed zebrafish protein sequence of brn1.2, brn3a1, brn3a2(l) and brn3a2(s) were used as query to identify corresponding cDNAs from the zebrafish EST database. The database search revealed two EST’s for brn1.2 (LLKMp964N034Q2, IMAGp998L14324Q3), two EST’s for brn3a1 (IMAGp998K1214311Q3, IMAGp998I1314318Q3), one EST for brn3a2(l) (IMAGp998P1314603Q3) and one EST for brn3a2(s) (IMAGp998A1414316Q1). The ESTs were purchased from the German Resource Center for Genome Research (www.rzpd.de), fully sequenced by MWG and submitted to GenBank (acc. Nos.). The zebrafish Brn3a1 and Brn3a2 protein sequences were compared to the Brn3 sequences of other species. 2.2 Sequence analysis Multiple sequence alignments were performed with the Clustal X program (Thompson et al., 1997). The accession numbers for the used sequences were as follows: AAU13951, NP_620395, NP_620394 of (Mm) Mus musculus, NP_006228, NP_002691, NP_004566 (Hs) Homo sapiens, NP_571353, NP_997972, ENSDARP00000007850, ENSDARP00000013808 (Dr) Danio rerio, SINFRUP00000143813, SINFRUP00000162286, SINFRUP00000133796, SINFRUP00000133155 (Fr) Fugu rubripes. 2.3 Whole-mount in situ hybridisation (WISH) Single color and two-color WISH was performed as described previously (Hauptmann and Gerster, 1994; 2000). brn1.2, brn3a1 and brn3a2(l) specific digoxigenin-labeled antisense riboprobes were synthesized by KpnI (ASP718) linearization and T7 polymerase transcription. brn1.2, brn3a1 and brn3a2(l) transcripts were visualized 12 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: oRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint with anti digoxigenin-alkaline phosphatase conjugates and BCIP/NBT or BM purple substrates (Roche). For two color WISH krx-20 (Oxytoby and Jowett, 1993), neuroD (Blader et al., 1997; Kim et al., 1997; Korzh et al., 1998) and pax2.1 (Krauss et al., 1991) fluorescein labelled probe was used. The fluorescein labelled probe was detected with anti-fluorescein-alkaline phosphatase conjugates and Fast Red substrate. A Zeiss Axioplan DIC compound microscope and a Leica MZ16 dissecting microscope were used to view the embryos. Embryos were photographed with a Zeiss Axiocam digital camera and Leica DFC300FX digital camera. Image processing and composite figures were assembled with Adobe Photoshop 7.0 software. 2.4 Immunohistochemistry Some embryos processed for WISH to visualize brn1.2 were further processed for immunohistochemical detection of the position of the primary axons using a monoclonal antibody against acetylated alpha-tubulin (Piperno and Fuller, 1985). The experiments were performed as described previously (Hauptmann and Gerster, 1996). Axon tracts were visualized in red using Fast red as alkaline phosphatase substrate. Reference: Acampora, D., Postiglione, M.P., Avantaggiato, V., Di Bonito, M., Vaccarino, F.M., Michaud, J., Simeone, A., 1999. Progressive impairment of developing neuroendocrine cell lineages in the hypothalamus of mice lacking the orthopedia gene. Genes dev. 13, 2787-2800. Alvarez-Bolado, G., Rosenfeld, M.G., Swanson, L.W., 1995. Model of forebrain regionalization based on spatiotemporal patterns of POU-III homeobox gene expression, birthdates, and morphological features. J.Comp.Neurol. 355, 237-295. Bermingham, J.R.Jr., Scherer, S., O’Connell, S., Arroyo, E., Kalla, K.A., Powell, F.L., Rosenfeld, M.G., 1996. Tst-1/Oct-6/SCIP regulates a unique step in peripheral myelination and is required for normal respiration. Genes Dev. 10, 1395-1410. Blader, P., Fischer, N., Gradwohl, G., Guillemot, F.Strahle, U., 1997. The activity of neurogenin1 is controlled by local cues in the zebrafish embryo. Development 124, 4557-4569. Brown, N.L., Patel, S., Brzezinski, J.Glaser, T., 2001. Math5 is required for retinal ganglion cell and optic nerve formation. Development 128, 2497-2508. Budhram-Mahadeo, V., Morris, P., Ndisang, D., Irshad, S., Lozano, G., Pedley, B.Latchman, D.S., 2002. The Brn-3a POU family transcription factor stimulates p53 gene expression in human and mouse tumour cells. Neurosci Lett 334, 1-4. Burrill, J.D.Easter, S.S., Jr., 1995. The first retinal axons and their microenvironment in zebrafish: cryptic pioneers and the pretract. J Neurosci 15, 2935-2947. Collum, R.G., Fisher, P.E., Datta, M., Mellis, S., Thiele, C., Huebner, K., Croce, C.M., Israel, M.A., Theil, T., Moroy, T.et al., 1992. A novel POU homeodomain gene specifically expressed in cells of the developing mammalian nervous system. Nucleic Acids Res 20, 4919-4925. Cumming, R., Reaves, T.A. Jr., Hayward, J.N., 1982. Ultrastructural immunocytochemical characterization of isotocin, vasotocin and neurophysin neurons in the magnocellular preoptic nucleus of the goldfish. Cell Tissue Res 223, 685-694. DeCarvalho, A.C., Cappendijk, S.L.Fadool, J.M., 2004. Developmental expression of the POU domain transcription factor Brn-3b (Pou4f2) in the lateral line and visual system of zebrafish. Dev Dyn 229, 869-876. de Kok, Y.J.M., van der Maarel, S.M., Bitner-Glindzicz, M., Huber, I., Monaco, A.P., Malcolm, S., Pembrey, M.E., Ropers, H-h., Cremers, F.P.M., 1995. Association between X-linked mixed deafness and mutations in the POU domain gene POU3f4. Science 267, 685-688. g f Eaton, J.L., Glasgow, E., 2006. The zebrafish bHLH PAS transcriptional regulator, single-minded 1 (sim1), is required for isotocin cell development. Dev. Dyn. 235, 2071-2072. Eaton, J.L., Glasgow, E., 2006. zebrafish orthopedia (otp) is required for isotocin cell development. in press. Gerrero, M.R., McEvilly, R.J., Turner, E., Lin, C.R., O'Connell, S., Jenne, K.J., Hobbs, M.V.Rosenfeld, M.G., 1993. Acknowledgements We thank School of Lifesciences, Sodertorns Hogskola, Department of Biosciences, Karolinska Institutet, Institute for Healthcare Education and Translational Science (IHETS) and Kitambi Foundation for financial support. Dr. Giselbert Hauptmann for providing useful inputs into this study. 13 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint Reference: Brn-3.0: a POU-domain protein expressed in the sensory, immune, and endocrine systems that functions on elements distinct from known octamer motifs. Proc Natl Acad Sci U S A 90, 10841-10845. 14 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: oRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint Goossens, N., Dierickx, K., Vandesande, F., 1977. Immunohistochemical localization of vasotocin and isotocin in the preopticohypophysial neurosecretory system of teleosts. Gen Comp Endocrinol 32, 371-375. Gruber, C.A., Rhee, J.M., Gleiberman, A.Turner, E.E., 1997. POU domain factors of the Brn-3 class recognize functional DNA elements which are distinctive, symmetrical, and highly conserved in evolution. Mol Cell Biol 17, 2391-2400. Hara, Y., Rovescalli, A.C., Kim, Y., Nierenberg, M., 1992. Structure and evolution of four POU domain genes expressed in mouse brain. Proc. Natl. Acad. Sci. USA 89, 3280-3284. Hauptmann, G., Gerster, T., 1994. Two-color whole-mount in situ hybridization to vertebrate and Drosophila embryos Trends genet. 10, 266. Hauptmann, G., Gerster, T., 1996. Complex expression of the zp-50 POU gene in the embryonic zebrafish brain is altered by overexpression of sonic hedgehog. Development 122, 1769-1780. Hauptmann, G., Gerster, T., 2000. Combinatorial expression of zebrafish Brn-1- and Brn-2- related POU genes in the embryonic brain, pronephric primordium and pharyngeal arches. Developmental Dyn. 218, 345-358. Hauptmann, G., Gerster, T., 2000. Multicolor whole-mount in situ hybridization Methods Mol. Biol. 137, 139-148. He, X., Treacy, M. N., Simmons, D.M., Ingraham, H.A., Swanson, L.W., Rosenfeld, M.G., 1989. Expression of a large family of POU-domain regulatory genes in mammalian brain development. Nature 340, 35-42. Herr, W., Sturm, R.A., Clerc, R.G., Corcoran, L.M., Baltimore, D., Sharp, P.A., Ingraham, H.A., Rosenfeld, M.G., Finney, M., Ruvkun, G.et al., 1988. The POU domain: a large conserved region in the mammalian pit-1, oct-1, oct-2, and Caenorhabditis elegans unc-86 gene products. Genes Dev 2, 1513-1516. Holmqvist, B.I., Ekstrom, P., 1995. Hypophysiotropic systems in the brain of the Atlantic salmon. . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint Reference: Neuronal innervation of the pituitary and the origin of pituitary dopamine and nonapeptides identified by means of combined carbocyanine tract tracing and immunocytochemistry. J Chem Neuroanat 8, 125-145. Hu, M.Easter, S.S., 1999. Retinal neurogenesis: the formation of the initial central patch of postmitotic cells. Dev Biol 207, 309-321. Jaegle, M., Mandemakers, W., Broos, L., Zwart, R., Karis, A., Visser, P., Grosveld, F., Meijer, D., 1996. The POU factor Oct-6 and Schwann cell differentiation. Science 273, 507-510. Kay, J.N., Finger-Baier, K.C., Roeser, T., Staub, W.Baier, H., 2001. Retinal ganglion cell genesis requires lakritz, a Zebrafish atonal Homolog. Neuron 30, 725-736. Keith, B., Adelman, D.M., Simon, M.C., 2001. Targeted mutation of the murine arylhydrocarbon receptor nuclear translocator 2 (Arnt2) gene reveals partial redundancy with Arnt. Proc. Natl. Acad. Sci. USA. 98, 6692-6697. Kim, C.H., Bae, Y.K., Yamanaka, Y., Yamashita, S., Shimizu, T., Fujii, R., Park, H.C., Yeo, S.Y., Huh, T.L., Hibi, M.Hirano, T., 1997. Overexpression of neurogenin induces ectopic expression of HuC in zebrafish. Neurosci Lett 239, 113-116. 15 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: oRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint Korzh, V., Sleptsova, I., Liao, J., He, J.Gong, Z., 1998. Expression of zebrafish bHLH genes ngn1 and nrd defines distinct stages of neural differentiation. Dev Dyn 213, 92-104. Krauss, S., Johansen, T., Korzh, V., Fjose, A., 1991. Expression pattern of zebrafish pax genes suggests a role in early barin regionalization. Nature 353, 267-270. Latchman, D.S., 1999. POU family transcription factors in the nervous system. J Cell Physiol 179, 126-133. Levavasseur, F., Mandemakers, W., Visser, P., Broos, L., Grosveld, F., Zivkovic, Meijer, D., 1998. Comparison of sequence and function of the Oct-6 genes in zebrafish, chicken and mouse. Mech. Dev. 74, 89-98. Li, P., He, H., Gerrero, M.R., Mok, M., Aggarwal, A., Rosenfeld, M.G., 1993. Spacing and orientation of bipartite DNA- binding motifs as potential functional determinants for POU domain factors. Genes Dev. Reference: ; https://doi.org/10.1101/2021.05.26.445703 doi: oRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint Piperno, G., Fuller, M.T., 1985. Monoclonal antibodies specific for an acetylated form of alpha-tubulin recognize the antigen in cilia and flagella from a variety of organisms. J. cell Biol. 101, 2085-2094. Ryan, A.K.Rosenfeld, M.G., 1997. POU domain family values: flexibility partnerships, and developmental codes. Genes Dev 11, 1207-1225. Sampath, K.Stuart, G.W., 1996. Developmental expression of class III and IV POU domain genes in the zebrafish. Biochem Biophys Res Commun 219, 565-571. Schonemann, M.D., Ryan, A.K., McEvilly, R.J., O'Conell, S.M., Arias, C.A., Kalla, K.A., Li, P., Sawchnko, P.E., Rosenfeld, M.G., 1995. Development and survival of the endocrine hypothalamus and posterior pituitary gland requires the neuronal POU domain factor Brn-2. Genes Dev. 9, 3122-3135. Smith, M.D., Ensor, E.A., Stohl, L., Wagner, J.A.Latchman, D.S., 1999. Regulation of NGFI-A (Egr-1) gene expression by the POU domain transcription factor Brn-3a. Brain Res Mol Brain Res 74, 117-125. Spaniol, P., Bornmann, C., Hauptmann, G., Gerster, T., 1996. Class III POU genes of zebrafish are predominantly expressed in the central nervous system. Nucleic Acids res. 24, 4874-4881. y Swanson, L.W., Sawchenko, P.E., 1983. Hypothalamic integration: Organization of the paraventricular and supraoptic nuclei. Annu Rev Neurosci 6, 269-324. Thomas, G.R., Faulkes, D.J., Gascoyne, D.Latchman, D.S., 2004. EWS differentially activates transcription of the Brn-3a long and short isoform mRNAs from distinct promoters. Biochem Biophys Res Commun 318, 1045- 1051. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F.Higgins, D.G., 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876-4882. Unger, J.L., Glasgow, E., 2003. Expression of isotocin-neurophysin mRNA in developing zebrafish. Gene Express. Patterns 3, 105-108. Wang, S.W., Kim, B.S., Ding, K., Wang, H., Sun, D., Johnson, R.L., Klein, W.H.Gan, L., 2001. Requirement for math5 in the development of retinal ganglion cells. Genes Dev 15, 24-29. Xiang, M., 1998. Requirement for Brn-3b in early differentiation of postmitotic retinal ganglion cell precursors. Dev Biol 197, 155-169. Xiang, M., Gan, L., Zhou, L., Klein, W.H.Nathans, J., 1996. Reference: 7, 2483-2496. Liu, W., Khare, S.L., Liang, X., Peters, M.A., Liu, X., Cepko, C.L.Xiang, M., 2000. All Brn3 genes can promote retinal ganglion cell differentiation in the chick. Development 127, 3237-3247. p Liu, W., Mo, Z.Xiang, M., 2001. The Ath5 proneural genes function upstream of Brn3 POU domain transcription factor genes to promote retinal ganglion cell development. Proc Natl Acad Sci U S A 98, 1649-1654. Mathis, J.M., Simmons, D.M., He, X., Swanson, L.W., Rosenfeld, M.G., 1992. Brain 4. a novel mammalian POU domain transcription factor exhibiting restricted brain-specific expression. Embo J 11, 2551-2561. p p , Matsuzaki, T., Amanuma, H., Takeda, H., 1992. A POU-domain gene of zebrafish, zfpou1, specifically expressed in the developing neural tissues. Biochem. Biophys. Res. Commun. 187, 1446-1463. Meijer, D., Graus, A., Kraay, R., Langeveld, A., Mulder, M.P., Grosveld, G., 1990. The octamer binding factor Oct-6: cDNA cloning and expression in early embryonic cells. Nucleic Acids. Res. 18, 7357-7365. Michaud, J.L., Rosenquist, T., May, N.R., Fan, C.M., 1998. Development of neuroendocrine lineages requires the bHLH-PAS transcription factor SIM1. Genes Dev. 12, 3264-3275. Michaud, J.L., DeRossi, C., May, N.R., Holdener, B.C., Fan, C.M., 2000. ARNT2 acts as the dimerization partner of SIM1 for the development of the hypothalamus. Mech. Dev. 90, 253-261. yp Monuki, E.S., Kuhn, R., Weinmaster, G., Lemke, G., 1989. SCIP: A glial POU domain gene regulated by cyclic AMP. Neuron 3, 783-793. Nakai, S., Kawano, H., Yudate, T., Nishi, M., Kuno, J., Nagata, A., Jishage, K., Hamada, H., Fujii, H., Kawamura, K., Shiba, K., Noda, T., 1995. The POU domain transcription factor Brn-2 is required for the determination of specific neuronal lineages in the hypothalamus of the mouse. Genes Dev. 9, 3109- 3121. Oxtoby, E., Jowett, T., 1993. Cloning of the zebrafish Krox-20 gene (krx-20) and its expression during hindbrain development. Nucleic Acids. Res. 21, 1087- 1095. Perriere, G.Gouy, M., 1996. WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 78, 364-369. Phippard, D., Lu, L., Lee, D., Saunders, J.C., Crenshaw III, E.B., 1999. Targeted Mutagenesis of the POU-domain gene Brn4/Pou3f4 causes developmental defects in the inner ear. J. Neurosci. 19, 5980-5989. 16 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. Figure 1: POU Family tree and sequence analyses of POU class III and IV. a) Phylogenetic tree showing the clustering of new zebrafish and pufferfish POU sequences into six different classes. Multiple sequence alignment of POU domain and phylogenetic tree was done with CLUSTAL X software and the phylogenetic tree was viewed with NJ plot software. Zebrafish oct2b could not be fully assembled and hence not included in the tree. B) Multiple sequence alignment of mammalian brn2 with zp47 and brn1.2 from zebrafish and fugu. The POU-specific (POU-S), linker and the POU-homeodomain (POU-Hs) are demarcated below the sequence and showed high degree of conservation. C) Multiple sequence alignment of POU class IV protein sequences. The arrowhead indicates the intron position. Arrows indicate POUIV box, POU specific, linker and homeobox domain region. The black box indicates region specific for mammalian brn3a class and the green box indicates region specific to mammalian Brn3a and fish brn3a2, brn3a1 of zebrafish and pufferfish lacks this region. The red box indicated the glycine rich region specific to mammalian Brn3b and the blue box indicates region specific for Brn3b. D) Zebrafish brn3 family gene structure. The arrows indicate that all members of brn3 form mRNA with two exons (lon form) and some of them form a shorter isoform. Zebrafish brn3b and brn3a2 forms a longer (l) and shorter (s) isoforms, the full length coding sequence is made up of two exons and the shorter isoform is made up of one exon and a part of intron. The length of nucleotides (nt) of the exons and the part of the intron from different brn3 sequences of zebrafish and fugu is indicated below. Reference: Targeted deletion of the mouse POU domain gene Brn-3a causes selective loss of neurons in the brainstem and trigeminal ganglion, uncoordinated limb movement, and impaired suckling. Proc Natl Acad Sci U S A 93, 11950-11955. Xiang, M., Zhou, L., Macke, J.P., Yoshioka, T., Hendry, S.H., Eddy, R.L., Shows, T.B.Nathans, J., 1995. The Brn-3 family of POU-domain factors: primary structure, binding specificity, and expression in subsets of retinal ganglion cells and somatosensory neurons. J Neurosci 15, 4762-4785. g g y Xiang, M., Zhou, L., Peng, Y.W., Eddy, R.L., Shows, T.B.Nathans, J., 1993. Brn- 3b: a POU domain gene expressed in a subset of retinal ganglion cells. Neuron 11, 689-701. Zwart, R., Broos, L., Grosveld, G., Meijer, D., 1996. The restricted expression pattern of the POU factor Oct-6 during early development of the mouse nervous system. Mech. Dev. 54, 185-194. 17 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: oRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint Figure 4: Early expression of zebrafish brn3a1. Anterior to the left. Lateral (A,D,G,J,M) and dorsal (B,C,E,F,H,I,K,L,N,O) views are shown. Expression is observed in Rohon beard neurons (Rb) and in the trigeminal (t), anterior lateral line ganglia (a), posterior lateral line ganglia (p). Figure 2: Expression of brn1.2 in the developing zebrafish brain. Embryos were subjected to WISH to visualize brn 1.2 in blue, pax2.1 in red (E) and krx-20 in red (G, H). Embryo in panel J was subjected to immunohistochemistry to visualize the primary axons in red after detecting brn1.2 in blue via WISH. Panels A, B, C, D, G, I, J, K, L show lateral views with the anterior to the left. Panels E, F, H show dorsal views with the anterior to the left. Developmental stages are indicated on the right hand corner of each panel. Arrowhead in panel K and L indicate the preoptic region of the brain. Abbreviations: ce, cerebellum, dt, dorsal thalamus, h, hindbrain, hy, hypothalamus, m, midbrain, ov, otic vesicle, pr, pretectum, r3, rhombomere 3, r5, 18 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: Rxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint rhombomere 5, sc, spinal cord, tc, tectum, tg, tegmentum, t, telencephalon, vt, ventral thalamus. Figure 3: Localization of brn1.2 in the preoptic area of the hypothalamus. Two-color in situ hybridization was performed to examine co-expression of brn 1.2 with itnp and vt and also crh with itnp. Embryos were subjected to WISH to visualize brn 1.2 in blue (A, C, D, F), itnp in blue (B, H) and in red (C, I), vt in blue (E) and in red (F) and crh in blue (G, I). Dorsal views of 48hpf embryos are shown (A-I). Anterior is facing up. itnp and vt expression domain in the preoptic area are indicated by arrowheads (B, D). Arrows in (C, F) indicates the localization of itnp and vtnp within brn1.2 expression domain in the preoptic area. Abbreviations: po, preoptic area. Figure 5: Late spatial expression of zebrafish brn3a1 In all panels, anterior is to the left. Lateral (D, E, F, H, I, J, K, L), dorsal (A, M, N) and oblique lateral (B, C, G) views of embryos are shown. Expression is seen in the anterior dorsal (ad), anterior ventral (av), glossopharyngeal (g), posterior lateral line (p), rohan beard neurons (Rb), optic tectum (ot), ganglion cell layer (GCL),. Images H and I show expression in trigeminal ganglia (t), Arrowheads indicate expression in ventronasal region (image D), cluster of hindbrain cells (image J), neuromast (image L). Zebrafish brn3a1 is stained in blue and zebrafish neuroD in red (C, G, H, I, K). Figure 6: Expression of zebrafish brn3a2(l) from 7 to 20 somite stage. Images present lateral (A, C, E, G, I) and dorsal (B, D, F, H, J) views of the embryos. The figures are arranged with anterior to the left. Arrowheads indicate trigeminal ganglia (A, C, E) and otic placode (G, H, I). Arrows mark dorsal cells of the spinalcord. Expression is seen in the trigeminal ganglia (t), dorsal cells of the spinal 19 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: oRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint cord (represented by arrows), anterior lateral line (a), posterior lateral line (p). Eye is represented by (e). Figure 7: Expression of zebrafish brn3a2(l) from 25 hpf - 48 hpf . Embryos are arranged with anterior to the left. Expression is seen in anterior dorsal (ad), anterior ventral (av), otic (o), glassopharyngeal (g), posterior lateral line (p), optic tectum (ot), ganglion cell layer (GCL), dorsal cells of the spinal cord (represented by arrows), cluster of cells of the fore-, mid-, and hind brain (represented by double sided arrows). Lense of the eye is represented by (L). Expression of zebrafish brn3a2(l) is visualized in blue and zebrafish neuroD is shown in red. 20 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint . CC-BY 4.0 International license available under a not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: reprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint de which . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint . CC-BY 4.0 International license available under a not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: reprint . CC-BY 4.0 International license available under a is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; 0.1101/2021.05.26.445703 . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to disp T this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint ay the preprint in perpetuity. It is made he copyright holder for this preprint (which ay the preprint in perpetuity. It is made he copyright holder for this preprint (which . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to disp this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint . CC-BY 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to disp T this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: bioRxiv preprint . CC-BY 4.0 International license available under a s not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which this version posted May 27, 2021. ; https://doi.org/10.1101/2021.05.26.445703 doi: v preprint . CC-BY 4.0 International license available under a
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In‐depth echocardiographic analysis of left atrial function in healthy adults using speckle tracking echocardiography and volumetric analysis
Echocardiography
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6,549
Received: 13 August 2018  |  Revised: 25 September 2018  |  Accepted: 27 September 2018 DOI: 10.1111/echo.14174 Received: 13 August 2018  |  Revised: 25 September 2018  |  Accepted: 27 September 2018 DOI: 10.1111/echo.14174 3 August 2018  |  Revised: 25 September 2018  |  Accepted: 27 September 2018 DOI: 10.1111/echo.14174 O R I G I N A L I N V E S T I G AT I O N O R I G I N A L I N V E S T I G AT I O N wileyonlinelibrary.com/journal/echo  |  1 Roderick W. J. van Grootel MD1  | Mihai Strachinaru MD1 | Myrthe E. Menting PhD2 |  Jackie McGhie MSc1 | Jolien W. Roos-Hesselink PhD1 | Annemien E. van den Bosch PhD1 Roderick W. J. van Grootel MD1  | Mihai Strachinaru MD1 | Myrthe E. Menting PhD2 |  Jackie McGhie MSc1 | Jolien W. Roos-Hesselink PhD1 | Annemien E. van den Bosch PhD1 Roderick W. J. van Grootel MD1  | Mihai Strachinaru MD1 | Myrthe E. Menting PhD2 |  Jackie McGhie MSc1 | Jolien W. Roos-Hesselink PhD1 | Annemien E. van den Bosch PhD1 1Department of Cardiology, Erasmus MC, Rotterdam, The Netherlands 2Department of Radiology, Erasmus MC, Rotterdam, The Netherlands 1Department of Cardiology, Erasmus MC, Rotterdam, The Netherlands 2Department of Radiology, Erasmus MC, Rotterdam, The Netherlands 1Department of Cardiology, Erasmus MC, Rotterdam, The Netherlands Purpose: Left atrial (LA) dilatation is predictive for complications in a multitude of cardiac diseases; therefore, adequate assessment is essential. Technological ad- vances have made it possible to quantify LA function with Speckle Tracking Echocardiography (STE); however, there are currently no recommendations for nor- mal values with regard to LA function. We aimed to assess LA myocardial and volu- metric function in a healthy cohort and investigate correlations with baseline characteristics. 2Department of Radiology, Erasmus MC, Rotterdam, The Netherlands Correspondence Conclusion: This study provides normal values for the three phasic functions of the LA, assessed with STE and volumetric function. Our results suggest the need for age-­ specific reference ranges, and normal values for this cohort have been calculated. K E Y W O R D S Conclusion: This study provides normal values for the three phasic functions of the LA, assessed with STE and volumetric function. Our results suggest the need for age-­ specific reference ranges, and normal values for this cohort have been calculated. Correspondence Correspondence Annemien E. van den Bosch, Department of Cardiology, Erasmus University Medical Center, Rotterdam, The Netherlands. Email: a.e.vandenbosch@erasmusmc.nl Methods: This prospective cohort study included 147 (aged 20–72) healthy individu- als and assessed LA volumetric function using maximum, minimum and pre-­a-­wave volumes and myocardial function using reservoir function using peak strain in LA relaxation (LA-­strain), conduit function using peak strain rate in early LA contraction (LA-­SRe) and pump function using peak strain rate in late LA contraction (LA-­SRa). Results: Mean LA-­strain was 39.7 ± 6.2%, LA-­SRe −2.78 ± 0.62 s−1 and LA-­SRa −2.56 ± 0.62 s−1. Subjects were divided into 5 age decades (each 50% female). LA-­ strain and LA-­SRe were lower in the oldest groups, whereas LA-­SRa was higher. LA-­ SRa was higher in males(−2.69 ± 0.68 s−1 vs −2.42 ± 0.52 s−1). Age-­specific values are provided. Age proved to be an independent predictor for LA-­SRa after correction for blood pressure and heart rate. LA expansion index and passive emptying fraction decreased with age, while active emptying fraction increased with age. LA maximum volume did not increase with age. Methods: This prospective cohort study included 147 (aged 20–72) healthy individu- als and assessed LA volumetric function using maximum, minimum and pre-­a-­wave volumes and myocardial function using reservoir function using peak strain in LA relaxation (LA-­strain), conduit function using peak strain rate in early LA contraction (LA-­SRe) and pump function using peak strain rate in late LA contraction (LA-­SRa). Funding information This manuscript is supported by a grant from the ErasmusMC Thorax Foundation. Funding information This manuscript is supported by a grant from the ErasmusMC Thorax Foundation. (LA ­SRe) and pump function using peak strain rate in late LA contraction (LA ­SRa). Results: Mean LA-­strain was 39.7 ± 6.2%, LA-­SRe −2.78 ± 0.62 s−1 and LA-­SRa −2.56 ± 0.62 s−1. Subjects were divided into 5 age decades (each 50% female). LA-­ strain and LA-­SRe were lower in the oldest groups, whereas LA-­SRa was higher. LA-­ SRa was higher in males(−2.69 ± 0.68 s−1 vs −2.42 ± 0.52 s−1). Age-­specific values are provided. Age proved to be an independent predictor for LA-­SRa after correction for blood pressure and heart rate. LA expansion index and passive emptying fraction decreased with age, while active emptying fraction increased with age. LA maximum volume did not increase with age. K E Y W O R D S atrial function, left atrium, myocardial function, reference values, speckle tracking echocardiography All authors take responsibility for all aspects of the reliability and freedom from bias of the data presented and their discussed interpretation. Echocardiography. 2018;1–10. wileyonlinelibrary.com/journal/echo  |  1 All authors take responsibility for all aspects of the reliability and freedom from bias of the data presented and their discussed interpretation. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2018 The Authors. Echocardiography Published by Wiley Periodicals, Inc. he terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, y cited. wileyonlinelibrary.com/journal/echo  |  1 Echocardiography. 2018;1–10. 2 | METHODS • Left atrial expansion index = TEV/LA minimum volume. Left atrial conduit function: Left atrial conduit function: 2  |     1 | INTRODUCTION van GROOTEL et al. 2.1 | Study design and population • Left atrial passive emptying volume (PEV) = LA maximum vol- ume–LA pre-a-wave volume. Healthy volunteers were enrolled in 2014–2015 for this prospective cross-­sectional study and stratified into 5 age groups: 20–29, 30–39, 40–49, 50–59, 60–72 years (n ≥ 28 for each group, each 50% female). Details have been published earlier.13 Briefly, subjects were recruited via advertisement and underwent a questionnaire regarding medi- cal history and current health status, physical examination, venous blood sampling, 12-­lead ECG, and an echocardiogram. Subjects were excluded if one or more of the following criteria were present: (prior) cardiovascular disease, systemic disease, the finding of cardiac abnor- malities during the examination (including any valvular abnormalities) or risk factors including hypertension (cutoff values: 140/80 mm Hg), diabetes mellitus, impaired renal function or hypercholesterolemia. In case of elevated blood pressures, follow-­up measurements were per- formed by the general practitioner to confirm this. If follow-­up revealed normal blood pressures, the subject was included. Reasons for exclu- sion due to abnormalities on ECG were conduction disorders: Atrial fibrillation, right or left bundle branch block, prolonged PR interval, and prolonged QRS. Professional athletes, people who were morbidly obese (BMI > 40 kg/m2), having breast implants or pregnant were ex- cluded. This study was carried out according to the principles of the Declaration of Helsinki and approved by the local ethics committee. Written informed consent was obtained from every participant. • Left atrial passive emptying fraction = PEV/LA maximum volume. Left atrial pump function: Left atrial pump function: • Left atrial active emptying volume (AEV) = LA pre-a-wave vol- ume–LA minimum volume. • Left atrial active emptying fraction = AEV/LA pre-a-wave volume. • Left atrial active emptying fraction = AEV/LA pre-a-wave volume. All reported volumes are indexed for BSA. Since the Dutch popula- tion is the tallest in the world,15 we indexed for an allometric function of height2.7.16 LV diastolic function was assessed according to the EAE-­ ASE recommendations for diastolic function.17 2.3 | Volumetric analysis In order to assess LA maximum volume, the revised recommenda- tions for cardiac chamber quantification were used.1 LA minimum volume (measured at mitral valve closure) and pre-­a-­wave volume (one frame before atrial contraction starts) were measured using the biplane method-­of-­disk summation technique (Figure 1) and the area-­length method. All measurements were performed with Xcelera (Philips Medical Systems). Using the above volumes, LA function can be assessed as follows: The clinical value of LA volumetric and myocardial function has not been translated into recommendations to be used in clinical practice. This is in part because solid reference ranges have not been established, neither for volumetric measurements4–6 nor for strain measurements.7–12 Left atrial reservoir function: Therefore this study aims to provide reference ranges for LA myocardial and volumetric function in healthy adults and investi- gates the impact of age, sex, and BSA. • Left atrial total emptying volume (TEV) = LA maximum volume– LA minimum volume. • Left atrial total emptying volume (TEV) = LA maximum volume– LA minimum volume. • Left atrial total emptying fraction = TEV/LA maximum volume. 2.2 | Echocardiographic image acquisition Echocardiographic studies were performed by one of two experi- enced sonographers. Two-­dimensional grayscale harmonic images were obtained in the left lateral decubitus position using a iE33 or EPIQ7 ultrasound system (Philips Medical Systems, Best, The Netherlands) equipped with a transthoracic broadband X5-­1 matrix transducer (composed of 3040 elements with 1–5 MHz). The LA was acquired in dedicated apical four-­ and two-­chamber views with frame rates ≥ 50 frames/s.14 At least 2 consecutive heartbeats were recorded. Assessment of the left atrium (LA) is gaining increased attention as it reflects the severity and chronicity of many different conditions and is associated with significant morbidity and mortality.1 In the absence of valvular disease, LA volume reflects the presence of elevated left ventricular (LV) diastolic pressure and dysfunction.2 LA maximum volume is the most often described pa- rameter, but LA phasic function could be a more sensitive measure in patients with heart failure, valvular disease, and atrial fibrilla- tion. LA function can be assessed by volumetric measurements and includes reservoir, conduit, and pump function which can be expressed as absolute volumes or fractions. Recently speckle tracking echocardiography (STE) has been validated for LA mea- surements3; LA strain and strain rate can be measured which re- flect LA myocardial function without the need for geometrical assumptions. 2.4 | Speckle tracking analysis Offline analysis was performed using QLAB10 (Philips Medical Systems). LA myocardial function was assessed according to an earlier published guideline and a recent validation study,18,19 using the api- cal four-­ and two-­chamber views and the R-­wave as reference point. LA reservoir function can be expressed as peak strain (LA-­strain) and van GROOTEL et al. FI G U R E 1 Example of the volumetric measurements using the method-­of-­disk summation technique in dedicated apical four-­ and two-­chamber views. From top to bottom: the left atrial minimum, maximum, and pre-­a-­wave volume van GROOTEL et al. 3 3.3 | Correlations Besides age, LA reservoir function did not correlate with baseline characteristics (Table 6). Conduit function decreased slightly with increasing weight, BMI, and blood pressure, while pump function in- creased with BMI, heart rate, and blood pressure. Conduit and pump function correlated well with LV diastolic parameters. LA-­strain, LA-­ Sre, and LA-­Sra correlated well with their volumetric counterparts, LA expansion index and passive and active emptying fraction(r: 0.471 P: <0.001, r: −0.613 P: <0.001, r: −0.541 P: <0.001). 4  | van GROOTEL et al. LA conduit and pump function with LA strain rate. The negative peak in early diastole represents LA conduit function (LA-­SRe) and the negative peak in late diastole represents LA pump function (LA-­SRa) (Figure 2). 3 | RESULTS Out of the 155 eligible subjects, 147 subjects were included (me- dian age 43.8 [32.7–56.2], 50% female) into 5 age groups (n ≥ 28 per group). In total, 8 subjects were excluded: 2 due to having breast implants, 2 subjects had valvular pathology, 1 had a surgically closed ductus, 1 had hypertension, 1 with morbid obesity, and 1 with a right bundle branch block. Table 1 shows the baseline characteristics of the study population. 2.5 | Statistical analysis Normal distribution was checked using histograms and Shapiro-­Wilk tests. Depending on data distribution, continuous data are presented as mean ± standard deviation (SD) or median with first-­third quar- tile. Categorical data are presented as frequencies and percentages. Student’s t-­test, the Mann–Whitney U test, chi-­square test or Fisher’s exact test was used when appropriate. Correlations between LA meas- urements and baseline characteristics were assessed using the Pearson correlation test. When a variable was statistically significant and did not show collinearity with another variable, they were included in a multi- variable linear regression model. In case of collinearity, the one with the strongest correlation was selected. Statistical analysis was done with the Statistical Package for Social Sciences version 21 (IBM DPDD Statistics for Windows, Armonk, NY, USA). A P-­value of ≤0.05 (two-­ sided) was considered statistically significant. 3.2 | LA myocardial function Left atrial-­strain analysis results are shown in Table 4, including the feasibility, which ranged from 78.2% to 80.3%. LA-­strain was low- est in the oldest age groups as was LA-­Sre, but LA-­Sra increased with age (Figure 3). LA-­Sra was significantly more negative in men than women, no sex-­dependent differences were found in LA-­strain and LA-­Sre (Figure 4). The limits of normal (mean ± 2 SD) were also calculated (Table 5). Interobserver (RG, MS) agreement was assessed for LA volumet- ric and strain parameters using Bland–Altman plots in a sample of 30 random subjects.20 Measurements were done while being blinded for the other measurement approximately 1 month later. Agreement between two measurements was determined as the mean of the difference ± 1.96 SD. |  3 |  3 FI G U R E 1 Example of the volumetric measurements using the method-­of-­disk summation technique in dedicated apical four-­ and two-­chamber views. From top to bottom: the left atrial minimum, maximum, and pre-­a-­wave volume FI G U R E 1 Example of the volumetric measurements using the method-­of-­disk summation technique in dedicated apical four-­ and two-­chamber views. From top to bottom: the left atrial minimum, maximum, and pre-­a-­wave volume FI G U R E 2 Example of left atrial (LA)-­strain measurement in a apical four-­chamber view. LA-­strain(A) is measured as the maximum strain value during atrial diastole. Conduit (B) and pump (C) function are measured using strain rate FI G U R E 1 Example of the volumetric measurements using the method-­of-­disk summation technique in dedicated apical four-­ and two-­chamber views. From top to bottom: the left atrial minimum, maximum, and pre-­a-­wave volume FI G U R E 2 Example of left atrial (LA)-­strain measurement in a apical four-­chamber view. LA-­strain(A) is measured as the maximum strain value during atrial diastole. Conduit (B) and pump (C) function are measured using strain rate FI G U R E 2 Example of left atrial (LA)-­strain measurement in a apical four-­chamber view. LA-­strain(A) is measured as the maximum strain value during atrial diastole. Conduit (B) and pump (C) function are measured using strain rate FI G U R E 2 Example of left atrial (LA)-­strain measurement in a apical four-­chamber view. LA-­strain(A) is measured as the maximum strain value during atrial diastole. Conduit (B) and pump (C) function are measured using strain rate 3.1 Feasibility for volumetric measurements was good, ranging from 92.5% to 95.9% (Table 2). LA volumes were indexed for BSA (Table 2), and an additional analysis was performed with height indexed pa- rameters (Table 3). Changes in volumes can be seen between the age groups regardless of the indexation method. LA minimum and pre-­a-­wave volumes increased with each age decade. With regard to function, LA reservoir and conduit function decreased while pump function increased with age (Table 4). 4 | DISCUSSION This prospective study shows that LA function assessed with volu- metric and myocardial methods is feasible in a healthy population and that age and LV diastolic function are important determinants of LA function. This study presents values per age decade for LA volumetric and myocardial function in a healthy population. The largest body of evidence with regard to LA assessment is on LA maximum volume; this reflects remodeling due to increased LV filling pressures. The upper limit of normal is set at 34 mL/m2, regardless of age, though recent studies showed that LA maximum volume increases with age.3–5,21 This is especially true in the elderly; no correlation was found in our cohort which included individuals up to 72 years old. We speculated that by using STE, LA dysfunction could be detected earlier, which suggests that LV diastolic dysfunc- tion can be detected before apparent LA dilatation, providing clini- cians a possibility to intervene earlier. Our results show that LA peak strain did increase with age, which may implicate that strain is a more sensitive marker for LA remodeling in an earlier stage. A recent study also demonstrated that LA myocardial function was diminished in patients with LV diastolic dysfunction while there was no apparent LA dilatation.19 4.1 | LA volumetric vs myocardial function This study demonstrates that LA volumetric and myocardial assess- ment is highly feasible. We recognize that the BSA-­indexed maxi- mum volume in our study was large according to current guidelines. However, with parameters such as LA expansion index, passive and active emptying fraction this is no longer relevant, since these measurements are relative.22 Therefore, the reference values of LA volumetric and myocardial function can be extrapolated to other populations. However, there are certain disadvantages to volumetric assessment, like the assumption of geometrical shapes and relatively low reproducibility of especially smaller volumes. STE can overcome these shortcomings because strain analysis does not rely on geo- metrical assumptions. measurements, mean difference for LA peak strain, early and late strain rate were 1.83 ± 7.91%, −0.04 ± 0.63, and 0.03 ± 0.67 s−1, respectively. measurements, mean difference for LA peak strain, early and late strain rate were 1.83 ± 7.91%, −0.04 ± 0.63, and 0.03 ± 0.67 s−1, respectively. TA B LE 2 Left atrial echocardiographic volumes indexed for BSA per age decade Feasibility (%) Entire study 20–29 y 30–39 y 40–49 y 50–59 y 60–72 y r P-­value n = 147 n = 32 n = 28 n = 28 n = 31 n = 28 Method-­of-­disk summation technique LA maximum volume (mL/m²) n = 136 (92.5%) 28.8 ± 7.2 27.8 ± 5.7 28.1 ± 6.6 29.0 ± 9.2 29.4 ± 5.5 30.0 ± 9.1 ns ns LA minimum volume (mL/m²) n = 141 (95.9%) 10.1 ± 3.7 8.7 ± 2.5 9.4 ± 2.8 10.8 ± 4.0 10.4 ± 3.2 11.9 ± 5.2 0.252 0.003 LA pre-­a-­wave volume (mL/m²) n = 141 (95.9%) 18.1 ± 5.5 14.5 ± 3.8 16.4 ± 3.9 18.8 ± 5.9 19.4 ± 4.0 21.9 ± 6.9 0.437 <0.001 Area-­length method LA maximum volume (mL/m²) n = 136 (92.5%) 31.0 ± 7.5 29.9 ± 6.0 30.2 ± 6.7 31.1 ± 9.4 31.7 ± 6.1 32.3 ± 9.6 ns ns LA minimum volume (mL/m²) n = 141 (95.9%) 10.9 ± 3.9 9.4 ± 2.8 10.0 ± 3.1 11.5 ± 4.2 11.3 ± 3.3 13.0 ± 5.4 0.273 0.001 LA pre-­a-­wave volume (mL/m²) n = 141 (95.9%) 19.4 ± 5.7 15.8 ± 3.9 17.5 ± 3.9 19.9 ± 6.1 21.0 ± 4.2 23.7 ± 7.1 0.463 <0.001 C l ti ith d di P l t d 3.4 | Reproducibility Interobserver agreement was assessed for volumetric and strain measurements: Mean difference for LA maximum volume was −5.2 ± 12.1 mL. For pre-­a-­wave and minimum volume, this was −0.9 ± 10.2 and −1.0 ± 8.4 mL, respectively. Regarding strain TA B LE 1 Baseline table Total n = 147 Male n = 73 Female n = 74 P-­value Age (years) 44.6 ± 13.8 44.0 ± 13.7 45.3 ± 13.8 ns Height (cm) 175 ± 9 181 ± 7 169 ± 6 <0.001 Weight (kg) 74.6 ± 12.8 82.4 ± 11.2 66.9 ± 9.0 <0.001 Body mass index (kg/ m²) 24.4 ± 3.3 25.2 ± 3.3 23.6 ± 3.0 0.002 Body surface area (m²) 1.89 ± 0.19 2.03 ± 0.15 1.76 ± 0.12 <0.001 Systolic blood pressure (mm Hg) 127 ± 15 131 ± 16 123 ± 12 0.001 Diastolic blood pressure (mm Hg) 80 ± 9 82 ± 9 77 ± 9 <0.001 Creatinine (μmol/L) 78 ± 12 85 ± 10 71 ± 10 <0.001 Bold means statistically significant difference between both groups. van GROOTEL et al. |  5 4.4 | Limitations This was a single-­center study including Dutch Caucasian subjects. Extrapolation to other ethnicities should be done with caution. We used QLAB for the strain analysis, though a recent study found no dif- ferences between vendors for LA measurements,29 comparison with other vendors should be done with caution. Also, subjects had no re- strictions regarding food intake prior to the echocardiographic examina- tion. This could influence tissue-­ and pulsed-­Doppler measurements.30 TA B LE 3 Left atrial echocardiographic volumes indexed for an allometric function of height2.7 Entire study 20–29 y 30–39 y 40–49 y 50–59 y 60–72 y r P-­value n = 147 n = 32 n = 28 n = 28 n = 31 n = 28 LA maximum volume (mL/m2.7) 12.2 ± 3.4 11.2 ± 2.5 11.7 ± 2.7 12.2 ± 4.4 12.6 ± 2.7 13.1 ± 4.4 0.202 0.018 LA minimum volume (mL/m2.7) 4.3 ± 1.7 3.5 ± 1.0 4.0 ± 1.1 4.5 ± 1.9 4.4 ± 1.3 5.2 ± 2.5 0.307 <0.001 LA pre-­a-­wave volume (mL/m2.7) 7.7 ± 2.6 5.9 ± 1.6 6.9 ± 1.5 7.9 ± 2.7 8.3 ± 1.9 9.5 ± 3.4 0.474 <0.001 Values are presented per age group and the correlation with age and corresponding P-­value are reported. Bold means statistically significant correlation with age as a continuous variable. Values are presented per age group and the correlation with age and corresponding P-­value are reported. Bold means statistically significant correlation with age as a continuous variable. Left ventricular diastolic dysfunction is closely related with LA function, and our results reflect that as well. E-­ and A-­wave velocity correlated well with LA conduit and pump function, regardless of the method used. An increase in LV stiffness leads to a reduction in LA conduit function, which is compensated by an increase in pump function. This can be witnessed by the E/A-­ratio, which inverses with age. This was seen for the LA myocardial function parameters. indexed using BSA. In our study, we no longer found differences between men and women after correcting for BSA but we did find relatively high values; a quarter of these volunteers had a LA max volume above the upper limit of normal.1 This might be explained by the fact that height and weight are not both as important for LA volume. The Dutch are the tallest people in the world15 which is why an additional analysis was done correcting for height as done previ- ously by Eshoo et al.16 We found no differences when comparing these results with the BSA corrected volumes. The only exception was that LA maximum volume became significantly but weakly cor- related with age (r: 0.202, P: 0.018). 4.3 | Effects of age and LV diastolic function on LA function Several studies have looked at possible age-­related effects on LA size and function, with mixed results.3–6,23 The idea that age influ- ences LA function is not new; Benjamin et al24 stated that E-­wave velocity decreases while A-­wave velocity increases with advanc- ing age. Our study demonstrates that age influences LA myocardial function. LA-­strain and LA-­Sre are lowest in older subjects while LA-­Sra is higher, which is as expected. This is partly in line with the study of Morris et al,19 who implicated as much for LA-­strain meas- urements. In our study, LA-­Sre and LA-­Sra also changed with age, though the values that we found for LA-­strain were slightly lower than reported earlier.19 This may be due to age differences between studies or intervendor differences, as a recent study showed that QLAB10 reports slightly lower values for GLS than other software packages.25 The study of Miglioranza et al,26 which looked at influ- ences due to age, showed similar effects, though the actual results cannot be compared as the P-­wave was used as onset. 4.5 | Clinical implications The results from this study may add to the foundation to formulate reference values regarding LA functional analysis, in preparation for studies to determine potential diagnostic and prognostic value which may eventually be used to assess patients in a clinical set- ting. In our experience, LA functional analysis, especially myocardial deformation, is easy and quick to perform. As expected, age plays an important role, which is why we propose age-­dependent refer- ence ranges. The fact that LA maximum volume did not correlate with age but LA-­strain did indicates that functional assessment is a more sensitive marker. Future studies should investigate the potential prognostic value of LA function and which technique, myocardial deformation or vol- umetric assessment, is most valuable. Currently, there is no consensus on how to assess LA phasic func- tion with STE. In this study, we used R-­wave as onset because that would allow extrapolation of our data to patients with atrial fibrillation. There are other recent studies that used either the R-­wave or the P-­ wave as onset showing that both these techniques are possible.19,26,27 We choose for strain rate to assess LA booster pump function instead of peak strain, as this was found to be superior.27,28 Pathan et al29 per- formed a meta-­analysis to formulate normal values for LA function. Reservoir function was 39.4% which corresponds very well with our findings, unfortunately for conduit and pump function, strain instead of strain rate was used, which makes it impossible to compare our findings. 4.2 | Factors influencing LA function There are a lot of factors that could influence LA volume and con- sequently function. We have assessed the LA through volumetric function with total emptying fraction, a sort of ejection fraction of the LA. It is well known that this is divided into a passive and active phase and that a portion will flow back into the pulmonary veins. Therefore, we also provided LA expansion index, which better de- scribes reservoir function. Instances that influence LA volumes are age, sex, height, and weight. To address these, LA volumes are often 6  | van GROOTEL et al. E 3 Left atrial echocardiographic volumes indexed for an allometric function of height2.7 5 | CONCLUSION Left atrial volumetric and myocardial function measurement is a viable option, and age-­dependent reference ranges for LA phasic function are presented. LA myocardial and volumetric function pa- rameters have proven to be age-­ but not sex-­dependent. Considering the high feasibility and clinical relevance of LA myocardial function |  7 van GROOTEL et al. an GROOTEL et al. 5 | CONCLUSION TA B LE 4 Left atrial function per age decade Feasibility (%) Entire study 20–29 y 30–39 y 40–49 y 50–59 y 60–72 y r P-­value n = 147 n = 32 n = 28 n = 28 n = 31 n = 28 LA volumetric function n = 136 (92.5%) LA reservoir function (%) Total emptying volume 18.7 ± 4.8 19.2 ± 4.7 18.7 ± 4.5 18.3 ± 6.3 19.0 ± 4.1 18.1 ± 4.7 ns ns Expansion index 201.2 ± 71.4 238.5 ± 83.5 206.2 ± 46.2 184.2 ± 70.8 199.4 ± 77.2 169.3 ± 51.8 −0.262 0.002 Total emptying fraction 65.9 ± 7.7 68.8 ± 7.3 66.6 ± 5.0 62.9 ± 8.5 64.8 ± 7.8 61.5 ± 7.4 −0.279 0.001 LA conduit function (%) Passive emptying volume 10.8 ± 4.2 13.3 ± 3.1 11.7 ± 4.0 10.3 ± 4.6 10.0 ± 3.6 8.1 ± 3.9 −0.399 <0.001 Passive emptying fraction 37.1 ± 11.3 47.9 ± 6.9 40.8 ± 9.4 34.7 ± 8.7 33.8 ± 9.4 26.6 ± 9.4 −0.613 <0.001 LA pump function (%) Active emptying volume 8.0 ± 2.9 5.9 ± 2.3 7.0 ± 1.8 8.0 ± 3.0 9.0 ± 2.6 10.0 ± 2.8 0.512 <0.001 Active emptying fraction 44.2 ± 10.0 40.3 ± 10.5 43.1 ± 7.5 43.3 ± 9.8 46.7 ± 10.2 47.1 ± 10.3 0.281 0.001 LA myocardial deformation analysis LA-­strain (%) n = 118 (80.3%) 39.6 ± 6.3 41.7 ± 6.5 40.4 ± 5.3 39.1 ± 5.8 38.7 ± 6.9 37.1 ± 6.3 −0.227 0.014 LA-­Sre (s−1) n = 115 (78.2%) −2.76 ± 0.63 −3.29 ± 0.54 −3.06 ± 0.32 −2.77 ± 0.38 −2.23 ± 0.45 −2.16 ± 0.45 −0.715 <0.001 LA-­Sra (s−1) n = 118 (80.3%) −2.57 ± 0.62 −2.33 ± 0.52 −2.35 ± 0.40 −2.65 ± 0.55 −2.83 ± 0.80 −2.81 ± 0.63 0.348 <0.001 LV function E-­wave (m/s) 0.69 ± 0.16 0.79 ± 0.15 0.75 ± 0.16 0.66 ± 0.15 0.65 ± 0.11 0.59 ± 0.13 −0.457 <0.001 A-­wave (m/s) 0.49 ± 0.15 0.38 ± 0.14 0.43 ± 0.09 0.47 ± 0.10 0.57 ± 0.11 0.62 ± 0.17 0.582 <0.001 E/A-­ratio 1.6 ± 0.7 2.3 ± 0.8 1.8 ± 0.4 1.4 ± 0.4 1.2 ± 0.3 1.0 ± 0.3 −0.68 <0.001 Deceleration time (ms) 190 ± 41 178 ± 28 181 ± 32 185 ± 29 195 ± 32 216 ± 64 0.313 <0.001 E′ (LV septum) (cm/s) 9.5 ± 2.6 12.5 ± 1.8 10.4 ± 1.6 9.2 ± 1.6 8.2 ± 1.8 6.9 ± 1.7 −0.756 <0.001 E/E′-­ratio 7.6 ± 1.9 6.5 ± 0.2 7.3 ± 1.5 7.3 ± 1.7 8.1 ± 1.4 9.1 ± 2.4 0.472 <0.001 LV ejection fraction (%) 60 ± 5 60 ± 3.6 61 ± 5 59 ± 5 62 ± 5 59 ± 5 ns ns The upper part of the table present volumetric assessment, followed by LA myocardial function. 5 | CONCLUSION Additionally, LV diastolic and systolic values are presented. Correlations with age and corresponding P-­values are given. Bold means statistically significant correlation with age as a continuous variable. 8  |     van GROOTEL et a FI G U R E 3 Correlations between left atrial (LA)-­strain, LA-­Sre and LA-­Sra and age. Each dot represents one individual’s measurement. The fitted lines and r2 values are given. All three variables were significantly correlated with age 8  | van GROOTEL et al. FI G U R E 3 Correlations between left atrial (LA)-­strain, LA-­Sre and LA-­Sra and age. Each dot represent The fitted lines and r2 values are given. All three variables were significantly correlated with age FI G U R E 3 Correlations between left atrial (LA)-­strain, LA-­Sre and LA-­Sra and age. Each dot represents one individual’s measurement. The fitted lines and r2 values are given. All three variables were significantly correlated with age FI G U R E 4 Three graphs showing left atrial myocardial function per sex for each age group FI G U R E 4 Three graphs showing left atrial myocardial function per sex for each age group TA B LE 5 Limits of normal for LA function assessed with volumetric and myocardial deformation Entire study 20–29 y 30–39 y 40–49 y 50–59 y 60–72 y LLN ULN LLN ULN LLN ULN LLN ULN LLN ULN LLN ULN LA volumetric function Total emptying volume (mL/m2) 9.1 28.3 9.8 28.6 9.7 27.7 5.7 30.9 10.8 27.2 8.7 27.5 Total emptying fraction (%) 50.5 81.3 54.2 83.4 56.6 76.6 45.9 79.9 49.2 80.4 46.7 76.3 Expansion index (%) 58.4 344 71.5 405.5 113.8 298.6 42.6 325.8 45 353.8 65.7 272.9 Passive emptying volume (mL/m2) 2.4 19.2 7.1 19.5 3.7 19.7 1.1 19.5 2.8 17.2 0.3 15.9 Passive emptying fraction (%) 14.5 59.7 34.1 61.7 22 59.6 17.3 52.1 15 52.6 7.8 45.4 Active emptying volume (mL/m2) 2.2 13.8 1.3 10.5 3.4 10.6 2 14 3.8 14.2 4.4 15.6 Active emptying fraction (%) 24.2 64.2 19.3 61.3 28.1 58.1 23.7 62.9 26.3 67.1 26.5 67.7 LA myocardial deformation analysis LA-­strain (%) 27 52.2 28.7 54.7 29.8 51 27.5 50.7 24.9 52.5 −49.7 −24.5 LA-­Sre (s−1) −4.02 −1.5 −4.37 −2.21 −3.7 −2.42 −3.53 −2.01 −3.13 −1.33 −3.06 −1.26 LA-­Sra (s−1) −3.81 −1.33 −3.37 −1.29 −3.15 −1.55 −3.75 −1.55 −4.43 −1.23 −4.07 −1.55 LLN = lower limit of normal; ULN = upper limit of normal. TA B LE 6 Table describing correlations between LA function (volumetric and myocardial) and baseline characteristics TA B LE 6 Table describing correlations between LA function (volumetric and myocardial) and baseline characteristics TA B LE 6 Table describing correlations between LA function (volumetric and myocardial) and baseline characteristics LA-­strain LA-­Sre LA-­Sra r r r Age −0.227* 0.715** −0.348** Height −0.045 0.011 −0.012 Weight −0.068 0.246* −0.153 Body mass index −0.043 0.307* −0.197* Body surface area −0.067 0.185* −0.119 Heart rate −0.052 0.076 −0.254* Systolic blood pressure −0.081 0.186* −0.275* Diastolic blood pressure −0.1 0.333* −0.295* E-­wave 0.331** −0.566** 0.182* A-­wave −0.004 0.422** −0.367** E′ 0.331** −0.697** 0.268* E/e′ −0.111 0.298* −0.128 Left atrial expansion index 0.468** −0.381** −0.257* Left atrial passive emptying fraction 0.354** −0.590** 0.249* Left atrial active emptying fraction 0.198* 0.115 −0.545** LA-­Sra −0.478** – – Bold mean statistically significant, *P-­value < 0.05, **P-­value < 0.001 6. Kou S, Caballero L, Dulgheru R, et al. Echocardiographic reference ranges for normal cardiac chamber size: results from the NORRE study. Eur Heart J Cardiovasc Imaging. 2014;15:680–690. 7. Cameli M, Caputo M, Mondillo S, et al. Feasibility and reference values of left atrial longitudinal strain imaging by two-­dimensional speckle tracking. Cardiovasc Ultrasound. 2009;7:6. 8. Vianna-Pinton R, Moreno CA, Baxter CM, et al. Two-­dimensional speckle-­tracking echocardiography of the left atrium: feasibility and regional contraction and relaxation differences in normal sub- jects. J Am Soc Echocardiogr. 2009;22:299–305. 9. Kim DG, Lee KJ, Lee S, et al. Feasibility of two-­dimensional global longitudinal strain and strain rate imaging for the assessment of left atrial function: a study in subjects with a low probability of car- diovascular disease and normal exercise capacity. Echocardiography. 2009;26:1179–1187. 10. Saraiva RM, Demirkol S, Buakhamsri A, et  al. Left atrial strain measured by two-­dimensional speckle tracking represents a new tool to evaluate left atrial function. J Am Soc Echocardiogr. 2010;23:172–180. 11. Sun JP, Yang Y, Guo R, et al. Left atrial regional phasic strain, strain rate and velocity by speckle-­tracking echocardiography: normal values and effects of aging in a large group of normal subjects. Int J Cardiol. 2013;168:3473–3479. 12. Xia J, Gao Y, Wang Q, et  al. Left atrial function examination of healthy individuals with 2D speckle-­tracking imaging. Exp Ther Med. 2013;5:243–246. 13. Menting ME, McGhie JS, Koopman LP, et  al. Normal myocar- dial strain values using 2D speckle tracking echocardiogra- phy in healthy adults aged 20 to 72  years. Echocardiography. 2016;33:1665–1675. 14. Rosner A, Barbosa D, Aarsaether E, et al. The influence of frame rate on two-­dimensional speckle-­tracking strain measurements: a study on silico-­simulated models and images recorded in patients. Eur Heart J Cardiovasc Imaging. 2015;16:1137–1147. measurements, these results can help integrate LA STE analysis into clinical practice. measurements, these results can help integrate LA STE analysis into clinical practice. 15. Collaboration NCDRF. A century of trends in adult human height. Elife. 2016;5:e13410. 16. Eshoo S, Ross DL, Thomas L. Impact of mild hypertension on left atrial size and function. Circ Cardiovasc Imaging. 2009;2:93–99. CONFLICT OF INTEREST 17. Nagueh SF, Smiseth OA, Appleton CP, et al. Recommendations for the evaluation of left ventricular diastolic function by echocardiog- raphy: an update from the American Society of Echocardiography and the European Association of Cardiovascular Imaging. Eur Heart J Cardiovasc Imaging. 2016;17:1321–1360. None declared. 5 | CONCLUSION TA B LE 5 Limits of normal for LA function assessed with volumetric and myocardial deformation 9 van GROOTEL et al. REFERENCES 18. Mor-Avi V, Lang RM, Badano LP, et al. Current and evolving echo- cardiographic techniques for the quantitative evaluation of cardiac mechanics: ASE/EAE consensus statement on methodology and indications endorsed by the Japanese Society of Echocardiography. Eur J Echocardiogr. 2011;12:167–205. 1. Lang RM, Badano LP, Mor-Avi V, et al. Recommendations for cardiac chamber quantification by echocardiography in adults: an update from the American Society of Echocardiography and the European Association of Cardiovascular Imaging. Eur Heart J Cardiovasc Imaging. 2015;16:233–270. 19. Morris DA, Takeuchi M, Krisper M, et al. Normal values and clin- ical relevance of left atrial myocardial function analysed by speckle-­tracking echocardiography: multicentre study. Eur Heart J Cardiovasc Imaging. 2015;16:364–372. 2. Appleton CP, Galloway JM, Gonzalez MS, et  al. Estimation of left ventricular filling pressures using two-­dimensional and Doppler echocardiography in adult patients with cardiac disease. Additional value of analyzing left atrial size, left atrial ejection fraction and the difference in duration of pulmonary venous and mitral flow velocity at atrial contraction. J Am Coll Cardiol 1993;22:1972–1982. 20. Bland JM, Altman DG. Statistical methods for assessing agree- ment between two methods of clinical measurement. Lancet. 1986;1:307–310. 21. D’Andrea A, Riegler L, Rucco MA, et  al. Left atrial volume index in healthy subjects: clinical and echocardiographic correlates. Echocardiography. 2013;30:1001–1007. 3. Okamatsu K, Takeuchi M, Nakai H, et al. Effects of aging on left atrial function assessed by two-­dimensional speckle tracking echo- cardiography. J Am Soc Echocardiogr. 2009;22:70–75. 22. van Grootel RWJ, Menting ME, McGhie J, et al. Echocardiographic chamber quantification in a healthy Dutch population. Neth Heart J. 2017;25(12):682–690. 4. Nikitin NP, Witte KK, Thackray SD, et al. Effect of age and sex on left atrial morphology and function. Eur J Echocardiogr. 2003;4:36–42. 4. Nikitin NP, Witte KK, Thackray SD, et al. Effect of age and sex on left atrial morphology and function. Eur J Echocardiogr. 2003;4:36–42. 23. Spencer KT, Mor-Avi V, Gorcsan J 3rd, et al. Effects of aging on left atrial reservoir, conduit, and booster pump func- tion: a multi-­institution acoustic quantification study. Heart. 2001;85:272–277. 5. Boyd AC, Schiller NB, Leung D, et al. Atrial dilation and altered func- tion are mediated by age and diastolic function but not before the eighth decade. JACC Cardiovasc Imaging. 2011;4:234–242. 5. Boyd AC, Schiller NB, Leung D, et al. Atrial dilation and altered func- tion are mediated by age and diastolic function but not before the eighth decade. JACC Cardiovasc Imaging. REFERENCES 2011;4:234–242. 10  | 10 van GROOTEL et al. 10  | 29. Pathan F, D’Elia N, Nolan MT, et  al. Normal ranges of left atrial strain by speckle-­tracking echocardiography: a systematic review and meta-­analysis. J Am Soc Echocardiogr. 2017;30:59–70. e58. 29. Pathan F, D’Elia N, Nolan MT, et  al. Normal ranges of left atrial strain by speckle-­tracking echocardiography: a systematic review and meta-­analysis. J Am Soc Echocardiogr. 2017;30:59–70. e58. 24. Benjamin EJ, Levy D, Anderson KM, et al. Determinants of Doppler indexes of left ventricular diastolic function in normal subjects (the Framingham Heart Study). Am J Cardiol. 1992;70:508–515. 30. Dencker M, Bjorgell O, Hlebowicz J. Effect of food intake on com- monly used pulsed Doppler and tissue Doppler measurements. Echocardiography. 2011;28:843–847. 30. Dencker M, Bjorgell O, Hlebowicz J. Effect of food intake on com- monly used pulsed Doppler and tissue Doppler measurements. Echocardiography. 2011;28:843–847. 25. Farsalinos KE, Daraban AM, Unlu S, et al. Head-­to-­head comparison of global longitudinal strain measurements among nine different vendors: the EACVI/ASE inter-­vendor comparison study. J Am Soc Echocardiogr. 2015;28:1171–1181, e1172. 26. Miglioranza MH, Badano LP, Mihaila S, et al. Physiologic determi- nants of left atrial longitudinal strain: a two-­dimensional speckle-­ tracking and three-­dimensional echocardiographic study in healthy volunteers. J Am Soc Echocardiogr. 2016;29:1023–1034. e1023. How to cite this article: van Grootel RWJ, Strachinaru M, Menting ME, McGhie J, Roos-Hesselink JW, van den Bosch AE. In-­depth echocardiographic analysis of left atrial function in healthy adults using speckle tracking echocardiography and volumetric analysis. Echocardiography. 2018;00:1–10. https://doi.org/10.1111/echo.14174 27. Rimbas RC, Mihaila S, Vinereanu D. Sources of variation in assess- ing left atrial functions by 2D speckle-­tracking echocardiography. Heart Vessels. 2016;31:370–381. 28. Hayashi S, Yamada H, Bando M, et al. Optimal analysis of left atrial strain by speckle tracking echocardiography: P-­wave versus R-­wave trigger. Echocardiography. 2015;32:1241–1249.
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Inkjet Printing of Functional Electronic Memory Cells: A Step Forward to Green Electronics
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Inkjet Printing of Functional Electronic Memory Cells: A Step Forward to Green Electronics Iulia Salaoru *, Salah Maswoud and Shashi Paul Emerging Technologies Research Centre, De Montfort University, Hawthorn Building, The Gateway, Leicester LE1 9BH, UK; P12049171@email.dmu.ac.uk (S.M.); spaul@dmu.ac.uk (S.P.) * Correspondence: iulia.salaoru@dmu.ac.uk; Tel.: +44-(0)116-250-6008 Iulia Salaoru *, Salah Maswoud and Shashi Received: 21 May 2019; Accepted: 18 June 2019; Published: 22 June 2019 Abstract: Nowadays, the environmental issues surrounding the production of electronics, from the perspectives of both the materials used and the manufacturing process, are of major concern. The usage, storage, disposal protocol and volume of waste material continue to increase the environmental footprint of our increasingly “throw away society”. Almost ironically, society is increasingly involved in pollution prevention, resource consumption issues and post-consumer waste management. Clearly, a dichotomy between environmentally aware usage and consumerism exists. The current technology used to manufacture functional materials and electronic devices requires high temperatures for material deposition processes, which results in the generation of harmful chemicals and radiation. With such issues in mind, it is imperative to explore new electronic functional materials and new manufacturing pathways. Here, we explore the potential of additive layer manufacturing, inkjet printing technology which provides an innovative manufacturing pathway for functional materials (metal nanoparticles and polymers), and explore a fully printed two terminal electronic memory cell. In this work, inkjetable materials (silver (Ag) and poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS)) were first printed by a piezoelectric Epson Stylus P50 inkjet printer as stand-alone layers, and secondly as part of a metal (Ag)/active layer (PEDOT:PSS)/metal (Ag) crossbar architecture. The quality of the individual multi-layers of the printed Ag and PEDOT:PSS was first evaluated via optical microscopy and scanning electron microscopy (SEM). Furthermore, an electrical characterisation of the printed memory elements was performed using an HP4140B picoammeter. Keywords: inkjet; printing; functional materials; silver; PEDOT:PSS; memory cells; green processes micromachines micromachines micromachines micromachines Article Inkjet Printing of Functional Electronic Memory Cells: A Step Forward to Green Electronics Iulia Salaoru *, Salah Maswoud and Shashi Paul Emerging Technologies Research Centre, De Montfort University, Hawthorn Building, The Gateway, Leicester LE1 9BH, UK; P12049171@email.dmu.ac.uk (S.M.); spaul@dmu.ac.uk (S.P.) * Correspondence: iulia.salaoru@dmu.ac.uk; Tel.: +44-(0)116-250-6008 Micromachines 2019, 10, 417; doi:10.3390/mi10060417 1. Introduction Inkjet printing technology is an additive manufacturing technique that works by generating small ink droplets and propelling those droplets onto a substrate. This digital printing technology consists of three main features: ink, printhead and substrate. First, from the ink perspective the chemical and physical properties of the solution play a crucial role, mainly in the formation and ejection of the ink. Secondly, the appropriate printhead (thermal and piezoelectric) and a suitable driving voltage waveform (the width and amplitude of the pulse) are essential for accurate, reliable and reproducible drop ejection. Furthermore, equally important in the printing process is the substrate, which has a strong impact on achieving high quality printed patterns. There has been immense and continuous interest in the digital printing technique, which can be attributed to its cost effectiveness, efficacy of material use, compatibility with a wide range of substrates, digital and additive deposition, maskless nature and suitability for small to large area deposition. Some of these advantages are presented in Figure 1. Micromachines 2019, 10, 417; doi:10.3390/mi10060417 www.mdpi.com/journal/micromachines 2 of 10 2 f 10 Micromachines 2019, 10, 417 Mi hi 1 10 Figure 1. Main features of digital manufacturing technologies. Figure 1. Main features of digital manufacturing technologies. Figure 1. Main features of digital manufacturing technologies. Figure 1. Main features of digital manufacturing technologies. In a nutshell, digital printing technology, which is defined as “the printing of things (PoTs)”, is capable of revolutionizing the whole system of manufacturing functional materials and electronic devices, therefore creating a “digital industrial revolution” or a pathway to large area and high throughput flexible electronics. As part of this digital revolution, both inorganic and organic polymers have been exploited. Printing conductive metal nanomaterial inks, such as copper (Cu), gold (Au), silver (Ag) and aluminium (Al) inks, is one of the directions that has been extensively investigated and the core findings have been presented in comprehensive review papers [1–3]. Copper [4–6] and aluminium [7] are highly abundant metals, but unfortunately suffer from rapid oxidation at room temperature in air. These metals are still being used in the electronics industry as contact materials, and the deposition is carried out in an inert environment. Thus, the interest in the use of such metals for digital printing is diminishing. As we know, gold [8–10] is a very good conductor and does not have an oxidation issue, but is rather expensive. 1. Introduction Due to the aforementioned problems, nanoparticle based silver ink [11–14] has attracted special attention, due to its stability, compatibility with the required ink additives, relatively high resistance to oxidation, high electrical conductivity and very competitive price. Hence, based on all of these factors we can safely conclude that silver is currently the best metal for printing conductive patterns. Such patterns can be used in flexible and large area electronics. Organic materials are also currently being studied as an alternative to metallic conductors for printing conductive paths, for example polypyrroles [15], graphene [16–19], polyanilines [19] and poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) PEDOT:PSS In a nutshell, digital printing technology, which is defined as “the printing of things (PoTs)”, is capable of revolutionizing the whole system of manufacturing functional materials and electronic devices, therefore creating a “digital industrial revolution” or a pathway to large area and high throughput flexible electronics. As part of this digital revolution, both inorganic and organic polymers have been exploited. Printing conductive metal nanomaterial inks, such as copper (Cu), gold (Au), silver (Ag) and aluminium (Al) inks, is one of the directions that has been extensively investigated and the core findings have been presented in comprehensive review papers [1–3]. Copper [4–6] and aluminium [7] are highly abundant metals, but unfortunately suffer from rapid oxidation at room temperature in air. These metals are still being used in the electronics industry as contact materials, and the deposition is carried out in an inert environment. Thus, the interest in the use of such metals for digital printing is diminishing. As we know, gold [8–10] is a very good conductor and does not have an oxidation issue, but is rather expensive. Due to the aforementioned problems, nanoparticle based silver ink [11–14] has attracted special attention, due to its stability, compatibility with the required ink additives, relatively high resistance to oxidation, high electrical conductivity and very competitive price. Hence, based on all of these factors we can safely conclude that silver is currently the best metal for printing conductive patterns. Such patterns can be used in flexible and large area electronics. Organic materials are also currently being studied as an alternative to metallic conductors for printing conductive paths, for example polypyrroles [15], graphene [16–19], polyanilines [19] and poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) PEDOT:PSS [20,21]. 1. Introduction [ 6 9], po ya i i es [ 9] a d po y(3, et y e edio yt iop e e) po y(sty e esu o ate) E O SS [20,21]. As we have discussed previously, digital printing can bring a number of benefits to the electronics industry. The printing of electronic memory is a thriving field that attracts the interest of not only the academic community, but industry as well. From the academic perspective, Hubber et al. [22] reported fully inkjet printed stand-alone resistive memory cells. In another report, Porro and Ricciardi [23] fabricated an asymmetric metal-insulator-metal (MIM) type memristor based on graphene oxide, in which only the active layer (graphene oxide) was deposited via inkjet printing and the top Al contact was deposited using a conventional thermal vacuum evaporation method. On the other hand, from an industrial perspective, a Norwegian company, Thinfilm, developed a flexible, rewritable, ferroelectric, polymer-based memory and recently this technology was transferred to As we have discussed previously, digital printing can bring a number of benefits to the electronics industry. The printing of electronic memory is a thriving field that attracts the interest of not only the academic community, but industry as well. From the academic perspective, Hubber et al. [22] reported fully inkjet printed stand-alone resistive memory cells. In another report, Porro and Ricciardi [23] fabricated an asymmetric metal-insulator-metal (MIM) type memristor based on graphene oxide, in which only the active layer (graphene oxide) was deposited via inkjet printing and the top Al contact was deposited using a conventional thermal vacuum evaporation method. On the other hand, from an industrial perspective, a Norwegian company, Thinfilm, developed a flexible, rewritable, ferroelectric, polymer-based memory and recently this technology was transferred to Xerox Corp for up-scaling and manufacturing. rewritable, ferroelectric, polymer based memory and recently this technology was transferred to Xerox Corp for up-scaling and manufacturing. In this study, all components (the electrodes and the active core of the two terminal devices) were fabricated using digital inkjet printing technology, and hence a fully printed crossbar memory array was achieved. To realise such a pathway, the main physical properties of the silver and PEDOT:PSS based inks, such as the viscosity, surface tension and pH, and their wettability on both rigid and flexible substrates were first investigated. 2. Experimental Section The silver and PEDOT:PSS inks were evaluated and deposited via inkjet printing. The silver nanoparticle (AgNP) ink (Drycure Ag-j) was a mixture of 8–22% silver by weight, 18–52% water by weight, 20–65% glycerol by weight and a small amount of alcohol. The PEDOT:PSS ink was purchased from Sigma-Aldrich (St. Louis, MO, USA), and was composed of 2% PEDOT:PSS in an ethylene glycol monobutyl ether:water (3:2) mixture. In order to validate that the inks were suitable for printing, their main properties such as the surface tension, viscosity and pH, were tested. The surface tension of the inks was measured using a torsion balance model “OS” (Weston-super-Mare, UK) and the viscosity was evaluated by a Brookfield DV2T viscometer (Brookfield, Toronto, ON, Canada). In addition, a 3520 pH meter was used to test the pH of the inks. Secondly, in order to ensure good adhesion of the ink to the substrate, the wetting behaviour of both inks on rigid and flexible substrates was evaluated by measuring the ink/substrate contact angle via the sessile drop analysis method (Attention Theta Optical Tensiometer, Biolin Scientific, Gothenburg, Sweden). A commercial desktop inkjet printer, the Epson Stylus P50, was employed to deposit Ag and PEDOT:PSS multi-layer patterns. The Epson Stylus P50 is a piezoelectric printer with a printhead that has 90 nozzles with a 65 µm nozzle diameter, 1.5 pL drop size and 360 dpi resolution. Both the printer and silver ink were purchased from Printed Electronics Limited (PEL) (Tamworth, UK). Moreover, PEL optimised the ink to match the requirements of the printer. Printing functional materials based ink. Both the Ag and PEDOT:PSS inks were kept in an ultrasonic bath for several hours before printing to ensure good homogeneity and to prevent sedimentation or aggregation of the particles. Then, the inks were filtered using a 5 µm filter to eliminate any large particles (Ag) or undissolved polymer (PEDOT:PSS) and hence avoid blocking the nozzles. Then, the cartridge was filled with ink and different numbers of layers were printed. In the case of the Ag ink, the printed patterns were cured at 120 ◦C for 5 min, and curing at 70 ◦C for 3 h was performed for the PEDOT:PSS ink. In this work, a ceramic (inorganic coating, 60 nm pore size) coated paper was used as a substrate and was purchased from PEL. 2. Experimental Section The quality and thickness of the inkjet printed silver and PEDOT:PSS stand-alone multi-layers were assessed using an optical microscope (LAOPHOT-2) fitted with a Nikon camera DS-Fi1 (Nikon, Tokyo, Japan) and scanning electron microscopy (SEM). Adhesive tape tests were performed in order to understand the adhesion properties of the Ag and PEDOT:PSS printed patterns to the selected substrates. Printing a full two terminal memory device. The memory cells fabricated and investigated in this work were deposited on ceramic coated paper. The conductive tracks of Ag (5 passes) were first printed on the paper to define the bottom electrode (BE) of the final devices. After printing the Ag conductive paths, curing took place at 120 ◦C for 5 min. Then, the PEDOT:PSS active layer (10 passes) was deposited onto a paper marked with Ag tracks and then cured (70 ◦C, 3 h). Finally, in order to achieve a crossbar architecture, the top electrode (TE)–Ag (5 passes) was printed. The current–voltage (I–V) characteristics and retention time tests for the two terminal memory cells were measured in a screened sample chamber in the dark at room temperature using a PC-driven HP4140B picoammeter. 1. Introduction Secondly, both Ag and PEDOT:PSS stand-alone multi-layers were printed using an Epson Stylus P50, a commonly used desktop printer (Epson, Suwa, Nagano, Japan) and the quality and surface thickness were evaluated by optical microscopy In this study, all components (the electrodes and the active core of the two terminal devices) were fabricated using digital inkjet printing technology, and hence a fully printed crossbar memory array was achieved. To realise such a pathway, the main physical properties of the silver and PEDOT:PSS based inks, such as the viscosity, surface tension and pH, and their wettability on both rigid and flexible substrates were first investigated. Secondly, both Ag and PEDOT:PSS stand-alone multi-layers were printed using an Epson Stylus P50, a commonly used desktop printer (Epson, Suwa, Nagano, Japan) and the quality and surface thickness were evaluated by optical microscopy and scanning electron microscopy (SEM). Furthermore, adhesive tape tests were performed in order to understand 3 of 10 Micromachines 2019, 10, 417 the adhesion properties of the printed patterns on the selected substrates. Finally, a two terminal Ag/PEDOT:PSS/Ag crossbar structure was prototyped using inkjet printing alone, and in-depth electrical characterisations (i.e., current–voltage characteristic and memory retention time tests) were performed using a HP4140B-pico-ammeter (Keysight, Santa Rosa, CA, USA). 3. Results and Discussion The contact angle can be easily influenced by the nature of the substrate, mainly the surface. In addition to ensuring surface wetting, (i.e., ink/substrate perfect match), the surface energy of the substrate should exceed the surface tension of the ink by 10–15 mN/m. The surface energy of the ceramic coated paper was reported as 45 mN/m [24] and corroborates with the surface tension values (Table 1). Both inks were compatible with the ceramic coated paper. Thus, this substrate was selected to be used in this work. Furthermore, one of the main features of this substrate is that the ceramic layer helps to absorb the solvent from the ink. More specifically, in the case of Ag ink, the incorporation of the nanoparticles into the ceramic coating results in the formation of ceramic/Ag d h In addition to ensuring surface wetting, (i.e., ink/substrate perfect match), the surface energy of the substrate should exceed the surface tension of the ink by 10–15 mN/m. The surface energy of the ceramic coated paper was reported as 45 mN/m [24] and corroborates with the surface tension values (Table 1). Both inks were compatible with the ceramic coated paper. Thus, this substrate was selected to be used in this work. Furthermore, one of the main features of this substrate is that the ceramic layer helps to absorb the solvent from the ink. More specifically, in the case of Ag ink, the incorporation of the nanoparticles into the ceramic coating results in the formation of ceramic/Ag composites during the sintering process. In addition to ensuring surface wetting, (i.e., ink/substrate perfect match), the surface energy of the substrate should exceed the surface tension of the ink by 10–15 mN/m. The surface energy of the ceramic coated paper was reported as 45 mN/m [24] and corroborates with the surface tension values (Table 1). Both inks were compatible with the ceramic coated paper. Thus, this substrate was selected to be used in this work. Furthermore, one of the main features of this substrate is that the ceramic layer helps to absorb the solvent from the ink. More specifically, in the case of Ag ink, the incorporation of the nanoparticles into the ceramic coating results in the formation of ceramic/Ag composites during the sintering process. s during the sintering process. Table 1. Measured parameters of the Ag and PEDOT:PSS inks. 3. Results and Discussion Wetting behaviour can be described as the interaction between the ink droplets and substrate. It should be highlighted that the printed quality is linked to the wettability of the ink and hence, the wettability of both inks on different substrates was investigated. In this study, four potential substrates 4 of 10 4 f 10 Micromachines 2019, 10, 417 were tested and the contact angle measurement results are presented in Figure 2. Two rigid (silicon and glass) and two flexible (paper and polyethylene terephthalate (PET)) substrates were studied. The paper substrate used in this work is ceramic coated (non-organic) and can be heated to 150 ◦C with minimal discolouration. i o a i e , , were studied. The paper substrate used in this work is ceramic coated (non-organic) and can be heated to 150 °C with minimal discolouration. were studied. The paper substrate used in this work is ceramic coated (non-organic) and can be heated to 150 °C with minimal discolouration. Figure 2. Contact angles measured via the sessile drop analysis method for the silver nanoparticles (AgNPs) and poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) inks and four potential substrates. The contact angle can be easily influenced by the nature of the substrate, mainly the surface Figure 2. Contact angles measured via the sessile drop analysis method for the silver nanoparticles (AgNPs) and poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) inks and four potential substrates. The contact angle can be easily influenced by the nature of the substrate, mainly the surface. Figure 2. Contact angles measured via the sessile drop analysis method for the silver nanoparticles (AgNPs) and poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) inks and four potential substrates. The contact angle can be easily influenced by the nature of the substrate, mainly the surface. Figure 2. Contact angles measured via the sessile drop analysis method for the silver nanoparticles (AgNPs) and poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) inks and four potential substrates. The contact angle can be easily influenced by the nature of the substrate, mainly th f Figure 2. Contact angles measured via the sessile drop analysis method for the silver nanoparticles (AgNPs) and poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) inks and four potential substrates. The contact angle can be easily influenced by the nature of the substrate, mainly the surface. Figure 2. Contact angles measured via the sessile drop analysis method for the silver nanoparticles (AgNPs) and poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) inks and four potential substrates. 3. Results and Discussion Parameters Silver Ink PEDOT:PSS Ink Surface tension (mN/m) 35 30 Viscosity (cP) 6 14 pH 9 2 9 Table 1. Measured parameters of the Ag and PEDOT:PSS inks. Parameters Silver Ink PEDOT:PSS Ink Surface tension (mN/m) 35 30 Viscosity (cP) 6 14 pH 9 2.9 Table 1. Measured parameters of the Ag and PEDOT:PSS inks. Parameters Silver Ink PEDOT:PSS Ink Surface tension (mN/m) 35 30 Viscosity (cP) 6 14 pH 9 2.9 e i e i g p o e Table 1. Measured parameters of the Ag and PEDOT:PSS inks. Table 1. Measured parameters of the Ag and PEDOT:PSS inks. We have further investigated the spreading behaviour of both the silver and PEDOT:PSS inks (i.e., the evolution of the contact angle with time). As can be seen in Figure 3, in the case of the Ag ink the de ea e of the o ta t a le take la e i t o te o e at 5 a d a othe at 10 We have further investigated the spreading behaviour of both the silver and PEDOT:PSS inks (i.e., the evolution of the contact angle with time). As can be seen in Figure 3, in the case of the Ag ink the decrease of the contact angle takes place in two steps, one at 5 s and another at 10 s. We have further investigated the spreading behaviour of both the silver and PEDOT:PSS inks (i.e., the evolution of the contact angle with time). As can be seen in Figure 3, in the case of the Ag ink the decrease of the contact angle takes place in two steps, one at 5 s and another at 10 s. We have further investigated the spreading behaviour of both the silver and PEDOT:PSS inks (i.e., the evolution of the contact angle with time). As can be seen in Figure 3, in the case of the Ag ink th d f th t t l t k l i t t t 5 d th t 10 We have further investigated the spreading behaviour of both the silver and PEDOT:PSS inks (i.e., the evolution of the contact angle with time). As can be seen in Figure 3, in the case of the Ag ink the decrease of the contact angle takes place in two steps, one at 5 s and another at 10 s. 3. Results and Discussion We have further investigated the spreading behaviour of both the silver and PEDOT:PSS inks (i.e., the evolution of the contact angle with time). As can be seen in Figure 3, in the case of the Ag ink the decrease of the contact angle takes place in two steps, one at 5 s and another at 10 s. We have further investigated the spreading behaviour of both the silver and PEDOT:PSS inks (i.e., the evolution of the contact angle with time). As can be seen in Figure 3, in the case of the Ag ink th d f th t t l t k l i t t t 5 d th t 10 We have further investigated the spreading behaviour of both the silver and PEDOT:PSS inks (i.e., the evolution of the contact angle with time). As can be seen in Figure 3, in the case of the Ag ink the decrease of the contact angle takes place in two steps, one at 5 s and another at 10 s. We have further investigated the spreading behaviour of both the silver and PEDOT:PSS inks (i.e., the evolution of the contact angle with time). As can be seen in Figure 3, in the case of the Ag ink the decrease of the contact angle takes place in two steps, one at 5 s and another at 10 s. g p p , (a) (b) Figure 3. Contact angle versus time for the (a) Ag ink and (b) PEDOT:PSS ink on paper. (a) (b) Figure 3. Contact angle versus time for the (a) Ag ink and (b) PEDOT:PSS ink on paper. Figure 3. Contact angle versus time for the (a) Ag ink and (b) PEDOT:PSS ink on paper. (b) (b) (a) (a) (a) (b) Figure 3. Contact angle versus time for the (a) Ag ink and (b) PEDOT:PSS ink on paper Figure 3. Contact angle versus time for the (a) Ag ink and (b) PEDOT:PSS ink on paper. Figure 3. Contact angle versus time for the (a) Ag ink and (b) PEDOT:PSS ink on paper. 5 of 10 5 of 10 Micromachines 2019, 10, 417 Micromachines 2019 10 x After 10 s of contact between the ink droplet and the substrate, the contact angle is quite constant with a value of 38◦for the Ag ink (Figure 4). 3. Results and Discussion Interestingly, for the PEDOT:PSS ink the evolution of the contact angle is smoother, and there is no large variation between the first drop and the drops immediately following it. The behaviour observed for both of the inks is quite different. These differences arise due to the different constituents of the inks, as was discussed in the experimental section. Furthermore, the drop–surface interaction is a complex process that is governed by different forces, such as inertial, capillary and gravitational forces, a comprehensive study of which was published by Derby [25]. After 10 s of contact between the ink droplet and the substrate, the contact angle is quite constant with a value of 38° for the Ag ink (Figure 4). Interestingly, for the PEDOT:PSS ink the evolution of the contact angle is smoother, and there is no large variation between the first drop and the drops immediately following it. The behaviour observed for both of the inks is quite different. These differences arise due to the different constituents of the inks, as was discussed in the experimental section. Furthermore, the drop–surface interaction is a complex process that is governed by different forces, such as inertial, capillary and gravitational forces, a comprehensive study of which was published by Derby [25]. (a) (b) Figure 4. Images of the (a) AgNP and (b) PEDOT:PSS ink droplets on ceramic coated paper after achieving equilibrium during the contact angle measurements. Figure 4. Images of the (a) AgNP and (b) PEDOT:PSS ink droplets on ceramic coated paper after achieving equilibrium during the contact angle measurements. (b) (b) (a) Figure 4. Images of the (a) AgNP and (b) PEDOT:PSS ink droplets on ceramic coated paper after achieving equilibrium during the contact angle measurements. Figure 4. Images of the (a) AgNP and (b) PEDOT:PSS ink droplets on ceramic coated paper after achieving equilibrium during the contact angle measurements. We suggest that the decrease in the contact angle over time may be associated with the rapid infiltration of solvent into the porous paper substrate controlled by capillary forces. This effect is more evident in the case of the PEDOT:PSS ink, which has only one solution phase and hence absorbs into the substrate more easily We suggest that the decrease in the contact angle over time may be associated with the rapid infiltration of solvent into the porous paper substrate controlled by capillary forces. 3. Results and Discussion This effect is more evident in the case of the PEDOT:PSS ink, which has only one solution phase and hence absorbs into the substrate more easily. into the substrate more easily. Ag Printing Pattern. In the case of a single printed Ag layer (one pass), a large number of disconnected particles can be seen in the optical microscopy image (Figure 5a). However, when more layers were printed, better connectivity or coverage is observed, as expected, as shown in Figure 5b. It is important to highlight that, along with the printability of the inks and the quality of the printed layers, another very important characteristic is the electrical behaviour of the printed patterns. Indeed, the continuity of the printed multi-layers has a crucial impact on the electrical properties (i.e., the conductivity of the printed-pattern). As expected, the patterns made by fewer passes were not electrically conductive, mainly due to the poor coverage or continuity of the silver particles, and hence were below the percolation threshold. However, in the case of five passes the coverage was much better and the resistivity was around 2.91 × 10−8 Ω·m, which is close to the values which have been reported previously [26] Ag Printing Pattern. In the case of a single printed Ag layer (one pass), a large number of disconnected particles can be seen in the optical microscopy image (Figure 5a). However, when more layers were printed, better connectivity or coverage is observed, as expected, as shown in Figure 5b. It is important to highlight that, along with the printability of the inks and the quality of the printed layers, another very important characteristic is the electrical behaviour of the printed patterns. Indeed, the continuity of the printed multi-layers has a crucial impact on the electrical properties (i.e., the conductivity of the printed-pattern). As expected, the patterns made by fewer passes were not electrically conductive, mainly due to the poor coverage or continuity of the silver particles, and hence were below the percolation threshold. However, in the case of five passes the coverage was much better and the resistivity was around 2.91 × 10−8 Ω·m, which is close to the values which have been reported previously [26]. been reported previously [26]. The thickness of the printed layers was evaluated by taking a cross-sectional optical image and was found to be in the range of 1.1 and 1.8 µm for five passes (Figure 5d). 3. Results and Discussion Interestingly, the SEM image revealed penetration of the solvent into the paper [27], and hence validated our statement relating to the fast decrease of the contact angle. Printing PEDOT:PSS. The correlation between the number of passes and the quality of the printed layers was evaluated by optical microscopy. 6 of 10 h have Micromachines 2019, 10, 417 much better and the re been reported previous Figure 5. Optical micrograph of the inkjet printed Ag pattern after (a) 1 pass and (b) 10 passes. (c) SEM image of 10 passes. (d) SEM cross-sectional image of the Ag printed pattern after 5 passes. romachines 2019, 10, x 6 of Figure 5. Optical micrograph of the inkjet printed Ag pattern after (a) 1 pass and (b) 10 passes. (c) SEM image of 10 passes. (d) SEM cross-sectional image of the Ag printed pattern after 5 passes. The thickness of the printed layers was evaluated by taking a cross-sectional optical image an s found to be in the range of 1.1 and 1.8 μm for five passes (Figure 5d). Interestingly, the SE age revealed penetration of the solvent into the paper [27], and hence validated our stateme ating to the fast decrease of the contact angle. Printing PEDOT:PSS. The correlation between the number of passes and the quality of t nted layers was evaluated by optical microscopy. 9, 10, x Figure 5. Optical micrograph of the inkjet printed Ag pattern after (a) 1 pass and (b) 10 passes. (c) SEM image of 10 passes. (d) SEM cross-sectional image of the Ag printed pattern after 5 passes. ing to the fast decrease of the contact angle. Printing PEDOT:PSS. The correlation between the number of passes and the quality of t ted layers was evaluated by optical microscopy. Both the optical microscopy and SEM images of the PEDOT:PSS ink revealed excellent coverage Figure 6 clearly shows the high quality of the PEDOT:PSS printed pattern, and we postulate that the observed results are completely determined by the nature of the functional material (i.e., the polymer-based solution). Thus, the ink is homogenous without any dispersion component and the wetting is therefore better when compared to ink containing particle dispersions (Ag). In addition, the value of the surface tension of the PEDOT:PSS ink is slightly smaller than that of the Ag based ink and hence, better wetting behaviour is observed. 3. Results and Discussion Both the optical microscopy and SEM images of the PEDOT:PSS ink revealed excellent coverage. Figure 6 clearly shows the high quality of the PEDOT:PSS printed pattern, and we postulate that the observed results are completely determined by the nature of the functional material (i.e., the polymer- based solution). Thus, the ink is homogenous without any dispersion component and the wetting is therefore better when compared to ink containing particle dispersions (Ag). In addition, the value of the surface tension of the PEDOT:PSS ink is slightly smaller than that of the Ag based ink and hence, better wetting behaviour is observed. Figure 6. Optical micrograph of the inkjet printed PEDOT:PSS pattern after (a) two passes and (b) five passes (c) SEM image of 5 passes of PEDOT:PSS ink pattern Figure 6. Optical micrograph of the inkjet printed PEDOT:PSS pattern after (a) two passes and (b) five passes. (c) SEM image of 5 passes of PEDOT:PSS ink pattern. Figure 6. Optical micrograph of the inkjet printed PEDOT:PSS pattern after (a) two passes and (b) five passes (c) SEM image of 5 passes of PEDOT:PSS ink pattern Figure 6. Optical micrograph of the inkjet printed PEDOT:PSS pattern after (a) two passes and (b) five passes. (c) SEM image of 5 passes of PEDOT:PSS ink pattern. Furthermore, the electrical properties of the PEDOT:PSS ink patterns after 5 and 10 passes were investigated. The printed patterns display high resistive behaviour with resistance values of 1 GΩ for 5 passes and 50 MΩ for 10 passes. It is quite clear that an increase in the number of printing passes Furthermore, the electrical properties of the PEDOT:PSS ink patterns after 5 and 10 passes were investigated. The printed patterns display high resistive behaviour with resistance values of 1 GΩfor 5 passes and 50 MΩfor 10 passes. It is quite clear that an increase in the number of printing passes results in a decrease in the electrical resistance. This effect has also been observed by Sankir [28]. results in a decrease in the electrical resistance. This effect has also been observed by Sankir [28]. Additionally, the adhesion behaviour of the printed patterns on a paper substrate was tested. Good adhesion between the printed patterns and the substrate is an essential requirement for achieving optimal performance and reliability in this technology, and hence for real potential exploitation of inkjet printing technology in flexible electronics. 3. Results and Discussion Secondly, the experimental results show that by increasing the number of printed layers the cohesive force between the substrate and the printed pattern decreases. Micromachines 2019, 10, x 7 of 10 Micromachines 2019, 10, x 7 of 10 Figure 7. Optical microscopy images of the PEDOT:PSS ink pattern after one pass (a) before and (b) after removal of adhesion tape, and after five passes (c) before and (b) after removal of the adhesive Figure 7. Optical microscopy images of the PEDOT:PSS ink pattern after one pass (a) before and (b) after removal of adhesion tape, and after five passes (c) before and (d) after removal of the adhesive tape. Figure 7. Optical microscopy images of the PEDOT:PSS ink pattern after one pass (a) before and (b) after removal of adhesion tape, and after five passes (c) before and (b) after removal of the adhesive tape. Figure 7. Optical microscopy images of the PEDOT:PSS ink pattern after one pass (a) before and (b) after removal of adhesion tape and after five passes (c) before and (b) after removal of the adhesive Figure 7. Optical microscopy images of the PEDOT:PSS ink pattern after one pass (a) before and (b) after removal of adhesion tape, and after five passes (c) before and (d) after removal of the adhesive tape. after removal of adhesion tape, and after five passes (c) before and (b) after removal of the adhesive tape. tape. Furthermore, no delamination was observed when the adhesion tape test was performed on the silver pattern (five passes), and images of the pattern before and after the test are presented in Figure 8a,b, respectively. Interestingly, as can be seen in Figure 8c, in this case the adhesive layer from the tape has been transferred and attached to the top of the printed Ag. In this situation, both the cohesion force between the silver layers and the adhesive force between the deposited layers and the solid substrate surface were very strong. Martínez-Sánchez et al. [29] demonstrated that the inclusion of silver nanoparticles in ceramic greatly enhances the mechanical properties, i.e., fracture toughness, while maintaining the levels of hardness and elasticity. We conclude that the high Furthermore, no delamination was observed when the adhesion tape test was performed on the silver pattern (five passes), and images of the pattern before and after the test are presented in Figure 8a,b, respectively. 3. Results and Discussion Interestingly, as can be seen in Figure 8c, in this case the adhesive layer from the tape has been transferred and attached to the top of the printed Ag. In this situation, both the cohesion force between the silver layers and the adhesive force between the deposited layers and the solid substrate surface were very strong. Martínez-Sánchez et al. [29] demonstrated that the inclusion of silver nanoparticles in ceramic greatly enhances the mechanical properties, i.e., fracture toughness, while maintaining the levels of hardness and elasticity. We conclude that the high adhesion strength is due to the formation of ceramic–silver composites during the sintering process. Furthermore, no delamination was observed when the adhesion tape test was performed on the silver pattern (five passes), and images of the pattern before and after the test are presented in Figure 8a,b, respectively. Interestingly, as can be seen in Figure 8c, in this case the adhesive layer from the tape has been transferred and attached to the top of the printed Ag. In this situation, both the cohesion force between the silver layers and the adhesive force between the deposited layers and the solid substrate surface were very strong. Martínez-Sánchez et al. [29] demonstrated that the inclusion of silver nanoparticles in ceramic greatly enhances the mechanical properties, i.e., fracture toughness, while maintaining the levels of hardness and elasticity. We conclude that the high adhesion strength is due to the formation of ceramic–silver composites during the sintering process. hesion strength is due to the formation of ceramic–silver composites during the sintering proce Figure 8. Optical microscopy images of printed Ag patterns after five passes (a) before and (b) after the removal of the adhesion tape (c) Photograph of the Ag surface where the adhesive part of the Figure 8. Optical microscopy images of printed Ag patterns after five passes (a) before and (b) after the removal of the adhesion tape. (c) Photograph of the Ag surface where the adhesive part of the tape was attached. Figure 8. Optical microscopy images of printed Ag patterns after five passes (a) before and (b) after the removal of the adhesion tape. (c) Photograph of the Ag surface where the adhesive part of the tape was attached. ceramic–silver composites during the sintering proc Figure 8. 3. Results and Discussion The adhesion tape test was performed for both PEDOT:PSS and silver ink patterns. In this test, an adhesive tape is applied to the surface and then pulled off. The patterns were evaluated in the same area before and after the tape was removed. First, the adhesion features of the PEDOT:PSS ink pattern after one pass were e aluated A a be ee i Fi u e 7a b o dela i atio of the i ted atte i ob e ed O the Additionally, the adhesion behaviour of the printed patterns on a paper substrate was tested. Good adhesion between the printed patterns and the substrate is an essential requirement for achieving optimal performance and reliability in this technology, and hence for real potential exploitation of inkjet printing technology in flexible electronics. The adhesion tape test was performed for both PEDOT:PSS and silver ink patterns. In this test, an adhesive tape is applied to the surface and then pulled off. The patterns were evaluated in the same area before and after the tape was removed. First, the adhesion features of the PEDOT:PSS ink pattern after one pass were evaluated. As can be seen in Figure 7a,b, no delamination of the printed pattern is observed. On the other hand, the pattern with five printed 7 of 10 Micromachines 2019, 10, 417 layers delaminates partially, as is illustrated in Figure 7c,d. Interestingly, the detached part is covered in paper, indicating that there is a strong cohesion among the PEDOT:PSS printed layers and weak adhesion between the paper and PEDOT:PSS, which could cause this failure. The strong cohesion among the printed PEDOT:PSS layers is very important for its applications to electronic devices, as it is acting as a single unit. Secondly, the experimental results show that by increasing the number of printed layers the cohesive force between the substrate and the printed pattern decreases. Micromachines 2019, 10, x 7 of 10 Micromachines 2019, 10, x 7 of 10 layers delaminates partially, as is illustrated in Figure 7c,d. Interestingly, the detached part is covered in paper, indicating that there is a strong cohesion among the PEDOT:PSS printed layers and weak adhesion between the paper and PEDOT:PSS, which could cause this failure. The strong cohesion among the printed PEDOT:PSS layers is very important for its applications to electronic devices, as it is acting as a single unit. C l i 4. Conclusions . Conclusions In this paper, we demonstrate that inkjet printing technology is capable of depositing full two erminal crossbar memory elements on a flexible substrate. Two functional materials, i.e., silver and PEDOT:PSS, as well as Ag/PEDOT:PSS/Ag structures were deposited by a commonplace Epson Sylus P50 desktop printer (Epson, Suwa, Nagano, Japan). The quality of the individual Ag and PEDOT:PSS printed patterns was investigated. It was found that in the case of the nanoparticulate ink the overage was improved by increasing the number of printed layers. However, for the polymer, i.e., PEDOT:PSS, based ink a good surface profile was achieved even for a low number of passes. The ross-sectional image of the printed layers indicated that the structure was continuously built, with no sign of a barrier between individual passes being observed. The electrical properties of both of the printed patterns were investigated and the expected conductive behaviour of silver and high esistance for PEDOT:PSS were observed. Furthermore, adhesion tests for both inks were conducted. The experimental results showed excellent adhesion between the silver patterns and the flexible paper substrate. This is an effect of the ceramic–nanoparticle composites formed during the sintering process. On the other hand, the adhesion between PEDOT:PSS and the substrate is not desirable, and urther work is required. Furthermore, a fully printed crossbar memory array was fabricated and the In this paper, we demonstrate that inkjet printing technology is capable of depositing full two terminal crossbar memory elements on a flexible substrate. Two functional materials, i.e., silver and PEDOT:PSS, as well as Ag/PEDOT:PSS/Ag structures were deposited by a commonplace Epson Stylus P50 desktop printer (Epson, Suwa, Nagano, Japan). The quality of the individual Ag and PEDOT:PSS printed patterns was investigated. It was found that in the case of the nanoparticulate ink the coverage was improved by increasing the number of printed layers. However, for the polymer, i.e., PEDOT:PSS, based ink a good surface profile was achieved even for a low number of passes. The cross-sectional image of the printed layers indicated that the structure was continuously built, with no sign of a barrier between individual passes being observed. The electrical properties of both of the printed patterns were investigated and the expected conductive behaviour of silver and high resistance for PEDOT:PSS were observed. Furthermore, adhesion tests for both inks were conducted. The experimental results showed excellent adhesion between the silver patterns and the flexible paper substrate. 3. Results and Discussion Optical microscopy images of printed Ag patterns after five passes (a) before and (b) after h l f h dh i ( ) Ph h f h A f h h dh i f h Figure 8. Optical microscopy images of printed Ag patterns after five passes (a) before and (b) after the removal of the adhesion tape. (c) Photograph of the Ag surface where the adhesive part of the tape was attached. Figure 8. Optical microscopy images of printed Ag patterns after five passes (a) before and (b) after the removal of the adhesion tape. (c) Photograph of the Ag surface where the adhesive part of the tape was attached. Micromachines 2019, 10, 417 8 of 10 Fully Printed Two Terminal Memory Devices. Two terminal crossbar structure memory elements were fully fabricated at room temperature on a flexible substrate using only a commonplace desktop inkjet printer. Figure 9a shows an optical microscopy image of the fabricated crossbar array. First, in order to validate that our printed devices exhibit memory behaviour, the current–voltage (I–V) characteristics were analysed. Typical I–V behaviour can be observed for five consecutive scans of the Ag/PEDOT:PSS/Ag memory cell, as can be seen in Figure 9b. The printed device shows hysteresis in the I–V behaviour, which is an indication of electrical bistability in these devices. Additionally, Vset, Vreset and Vread have been identified from the I–V curves, and these values were further used when the memory retention time test was performed. The low conductivity state was programmed by applying one pulse at +10 V with a 1 ms width. The state was then read by decreasing the voltage to 6 V, where it was held for 4000 pulses while the current was monitored. Then, by applying a −8 V pulse for 1 ms the device was switched to a high conductivity state and the state was then read at 6 V. The high and low conductivity states remained distinguishable, as can be seen from Figure 9c. Micromachines 2019, 10, x 8 of 10 n the I–V behaviour, which is an indication of electrical bistability in these devices. Additionally, Vset, Vreset and Vread have been identified from the I–V curves, and these values were further used when the memory retention time test was performed. The low conductivity state was programmed by applying one pulse at +10 V with a 1 ms width. 3. Results and Discussion The state was then read by decreasing the voltage o 6 V, where it was held for 4000 pulses while the current was monitored. Then, by applying a −8 V pulse for 1 ms the device was switched to a high conductivity state and the state was then read at V. The high and low conductivity states remained distinguishable, as can be seen from Figure 9c. Figure 9. (a) Optical microscopy image of the printed crossbar memory cells. (b) I–V characteristics of five consecutive runs of the Ag/PEDOT:PSS/Ag memory elements. (c) The memory retention time of the printed cells Figure 9. (a) Optical microscopy image of the printed crossbar memory cells. (b) I–V characteristics of five consecutive runs of the Ag/PEDOT:PSS/Ag memory elements. (c) The memory retention time of the printed cells. igure 9. (a) Optical microscopy image of the printed crossbar memory cells. (b) I–V characteristics of ve consecutive runs of the Ag/PEDOT:PSS/Ag memory elements. (c) The memory retention time of h i t d ll Figure 9. (a) Optical microscopy image of the printed crossbar memory cells. (b) I–V characteristics of five consecutive runs of the Ag/PEDOT:PSS/Ag memory elements. (c) The memory retention time of the printed cells. p In a nutshell, both the current–voltage and retention time tests validate that the fully printed devices are indeed exhibiting memory behaviour In a nutshell, both the current–voltage and retention time tests validate that the fully printed devices are indeed exhibiting memory behaviour. C l i 4. Conclusions This is an effect of the ceramic–nanoparticle composites formed during the sintering process. On the other hand, the adhesion between PEDOT:PSS and the substrate is not desirable, and further work is required. Furthermore, a fully printed crossbar memory array was fabricated and the electrical behaviour of these cells was investigated. q y p y y electrical behaviour of these cells was investigated. We envision that this study will provide a novel platform for the deposition of functional materials and electronic devices, which has the potential to gradually replace conventional b h l d k f d l g We envision that this study will provide a novel platform for the deposition of functional materials and electronic devices, which has the potential to gradually replace conventional subtractive technologies and make a step forward to greener electronics. Micromachines 2019, 10, 417 9 of 10 Author Contributions: I.S. conceived the experiments, I.S. and S.M. printed the functional materials and performed all the tests. All authors contributed in the analysis of the results and in writing the manuscript. Funding: This work was supported by the Higher Education Innovation Fund (HE00.11 and HE.0042.04) De Montfort University. Acknowledgments: S.M. likes to thank Libyan Cultural Bureau London for supporting his doctoral studies at De Montfort University. The authors also recognise and thank Neil Chilton and Clare Conboy of Printed Electronics Ltd. for their assistance. Acknowledgments: S.M. likes to thank Libyan Cultural Bureau London for supporting his doctoral studies at De Montfort University. The authors also recognise and thank Neil Chilton and Clare Conboy of Printed Electronics Ltd. for their assistance. Conflicts of Interest: The authors declare no conflict of interest. Conflicts of Interest: The authors declare no conflict of interest. Conflicts of Interest: The authors declare no conflict of interest. References 1. Naghdi, S.; Rhee, K.; Hui, D.; Park, J.S. A review of conductive nanomaterials as conductive, transparent, and flexible coatings, thin films, and conductive fillers: Different deposition methods and applications. Coatings 2018, 8, 278. [CrossRef] 1. Naghdi, S.; Rhee, K.; Hui, D.; Park, J.S. A review of conductive nanomaterials as conductive, transparent, and flexible coatings, thin films, and conductive fillers: Different deposition methods and applications. Coatings 2018, 8, 278. [CrossRef] 2. Kamyshny, A.; Magdassi, S. Conductive nanomaterials for printed electronics. Small 2014, 10, 3515. [CrossRef] [PubMed] 2. Kamyshny, A.; Magdassi, S. Conductive nanomaterials for printed electronics. Small 2014, 10, 3515. [CrossRef] [PubMed] 3. Huang, Q.; Zhu, Y. Printing conductive nanomaterials for flexible and stretchable electronics: A review of materials, processes, and applications. Adv. Mater. Technol. 2019, 4, 1800546. [CrossRef] 3. Huang, Q.; Zhu, Y. Printing conductive nanomaterials for flexible and stretchable electronics: A review of materials, processes, and applications. Adv. Mater. Technol. 2019, 4, 1800546. [CrossRef] p pp 4. Farraj, Y.; Grouchko, M.; Magdassi, S. Self-reduction of a copper complex MOD ink for inkjet printing conductive patterns on plastics. Chem. Commun. 2015, 51, 1587–1590. [CrossRef] 4. Farraj, Y.; Grouchko, M.; Magdassi, S. Self-reduction of a copper complex MOD ink for inkjet printing conductive patterns on plastics. Chem. Commun. 2015, 51, 1587–1590. [CrossRef] 5. Wang, B.Y.; Yoo, T.H.; Song, Y.W.; Lim, D.S.; Oh, Y. Facile preparation of monodisperse, impurity-free, and antioxidation copper nanoparticles on a large scale for application in conductive ink. ACS Appl. Mater. Interfaces 2013, 5, 4113–4119. [CrossRef] 5. Wang, B.Y.; Yoo, T.H.; Song, Y.W.; Lim, D.S.; Oh, Y. Facile preparation of monodisperse, impurity-free, and antioxidation copper nanoparticles on a large scale for application in conductive ink. ACS Appl. Mater. Interfaces 2013, 5, 4113–4119. [CrossRef] 6. Karthik, P.; Singh, S.P. Copper conductive inks: Synthesis and utilization in flexible electronics. RSC Adv. 2015, 5, 63985–64030. [CrossRef] 6. Karthik, P.; Singh, S.P. Copper conductive inks: Synthesis and utilization in flexible electronics. RSC Adv. 2015, 5, 63985–64030. [CrossRef] 7. Balucani, M.; Serenelli, L.; Kholostov, K.; Nenzi, P.; Miliciani, M.; Mura, F.; Izzi, M.; Tucci, M. Aluminum-silicon interdiffusion in screen printed metal contacts for silicon based solar cells applications. Energy Procedia 2013, 43, 100–110. [CrossRef] 7. Balucani, M.; Serenelli, L.; Kholostov, K.; Nenzi, P.; Miliciani, M.; Mura, F.; Izzi, M.; Tucci, M. Aluminum-silicon interdiffusion in screen printed metal contacts for silicon based solar cells applications. Energy Procedia 2013, 43, 100–110. [CrossRef] 8. References Maattanen, A.; Ihalainen, P.; Pulkkinen, P.; Wang, S.; Tenhu, H.; Peltonen, J. Inkjet-printed gold electrodes on paper: Characterization and functionalization. ACS Appl. Mater. Interfaces 2012, 4, 955–964. [CrossRef] 9. Hu, C.; Bai, X.; Wang, Y.; Jin, W.; Zhang, X.; Hu, S. Inkjet printing of nanoporous gold electrode arrays on cellulose membranes for high-sensitive paper-like electrochemical oxygen sensors using ionic liquid electrolytes. Anal. Chem. 2012, 84, 3745–3750. [CrossRef] y 10. Sau, T.K.; Rogach, A.L.; Jackel, F.; Klar, T.A.; Feldmann, J. Properties and applications of colloidal nonspherical noble metal nanoparticles. Adv. Mater. 2010, 22, 1805–1825. [CrossRef] 11. Joubert, T.; Bezuidenhout, P.H.; Chen, H.; Smith, S.; Land, K.J. Inkjet-printed silver tracks on different paper substrates. Mater. Today Proc. 2015, 2, 3891–3900. [CrossRef] 12. Fuller, S.B.; Wilhelm, E.J.; Jacobson, J.M. Ink-jet printed nanoparticle microelectromechanical systems. J. Microelectromech. Syst. 2002, 11, 54–60. [CrossRef] 13. Rajan, K.; Roppolo, I.; Chiappone, A.; Bocchini, S.; Perrone, D.; Chiolerio, A. Silver nanoparticle ink technology: State of the art. Nanotechnol. Sci. Appl. 2016, 9, 1–13. [CrossRef] [PubMed] 14. Lee, H.; Chou, K.; Huang, K. Inkjet printing of nanosized silver colloids. Nanotechnology 2005, 16, 2436. [CrossRef] [PubMed] 15. Koezuka, H.; Tsumura, A.; Fuchigami, H.; Kuramoto, K. Fully patterned all-organic thin film transistors. Appl. Phys. Lett. 1993, 62, 1794. [CrossRef] 6. Arapov, K.; Abbel, R.; de With, G.; Friedrich, H. Inkjet printing of graphene. Faraday Discuss. 2014, 323–336. [CrossRef] [PubMed] 17. Huang, S.; Shen, R.; Qian, B.; Li, L.; Wang, W.; Lin, G.; Zhang, X.; Li, P.; Xie, Y. Thermal bubble inkjet printing of water-based graphene oxide and graphene inkson heated substrate. J. Phys. D Appl. Phys. 2018, 51, 135302. [CrossRef] 18. Torrisi, F.; Hasan, T.; Wu, W.; Sun, Z.; Lombardo, A.; Kulmala, T.; Hshieh, G.W.; Jung, S.J.; Bonaccorso, F.; Paul, P.J.; et al. Ink-jet printed graphene electronics. ACS Nano 2012, 6, 2992–3006. [CrossRef] [PubMed] Micromachines 2019, 10, 417 10 of 10 10 of 10 19. Drury, J.; Mutsaers, C.M.J.; Hart, C.M.; Maters, M.; de Leeuw, D.M. Low-cost all-polymer integrated circuits. Appl. Phys. Lett. 1998, 73, 108. [CrossRef] 20. Halik, M.; Klauk, H.; Zschieschang, U.; Schmid, G.; Radlik, W.; Werner, W. Relationship between molecular structure and electrical performance of oligothiophene organic thin film transistors. Adv. Mater. 2002, 14, 1717. [CrossRef] 21. Sirringhaus, H.; Kawasem, T.; Friend, R.H.; Shimoda, T.; Inbasekaran, M.; Wu, W.; Woo, E.P. High-resolution inkjet printing of all-polymer transistor circuits. Science 2000, 290, 2123. [CrossRef] 22. References Huber, B.; Popp, P.B.; Kaiser, M.; Ruediger, A.; Schindler, C. Fully inkjet printed flexible resistive memory. Appl. Phys. Lett. 2017, 110, 143503. [CrossRef] 23. Porro, S.; Ricciardi, C. Memristive behaviour in inkjet printed graphene oxide thin layers. RSC Adv. 2015, 5, 68565. [CrossRef] 24. Salaoru, I.; Zhou, Z.; Morris, P.; Gibbons, G.J. Inkjet printing of polyvinyl alcohol multilayers for additive manufacturing applications. J. Appl. Polym. Sci. 2016, 133. [CrossRef] 25. Derby, B. Inkjet printing of functional and structural materials: Fluid property requirements, feature stability, and resolution. Annu. Rev. Mater. Res. 2010, 40, 395. [CrossRef] 26. Shen, W.; Zhang, X.; Huang, Q.; Xu, Q.; Song, W. Preparation of solid silver nanoparticles for inkjet printed flexible electronics with high conductivity. Nanoscale 2014, 6, 1622. [CrossRef] 27. Hsiao, W.; Hoath, S.; Martin, G.; Hutchings, I.; Chilton, N.; Jones, S. Imbibition dynamics of nano-particulate ink-jet drops on micro-porous media. In Proceedings of the Nanotech 2011 Conference, Boston, MA, USA, 13–16 June 2011. 28. Sankir, N.D. Selective deposition of PEDOT/PSS on to flexible substrates and tailoring the electrical resistivity by post treatment. Circuit World 2008, 34, 32–37. [CrossRef] 29. Rocha-Rangel, E.; Pérez-de la Fuente, A.; Rodríguez-García, J.A.; Estrada-Guel, I.; Martínez-Sánchez, R. Effect of silver nanoparticles on the microstructure and mechanical properties of alumina ceramics. Can. Metall. Q. 2017, 56, 332–339. [CrossRef] © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
https://openalex.org/W3012994333
https://jrpb.unram.ac.id/index.php/jrpb/article/download/122/107
Indonesian
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PENENTUAN TINGKAT BAHAYA EROSI DI WILAYAH DAS BEDADUNG KABUPATEN JEMBER
Jurnal Ilmiah Rekayasa Pertanian dan Biosistem
2,020
cc-by-sa
4,228
ABSTRACT The development conditions of Watershed (DAS) in Jember Regency currently need to be evaluated because the conditions have been damaged start from 1999. Thus causing natural disasters in the watershed area such as landslides, erosion and floods which claimed lives. The purpose of this study was to determine the level of erosion hazard which was influenced by several erosion parameter values using the Revised Universal Soil Loss Equation (RUSLE) method in Bedadung watershed. The input data used in this study were 2004 – 2014 rainfall, soil type maps, yearly RBI land use maps 2014, and Digital Elevation Model data (DEM) from ASTER-GDEM. The results showed that the erosivity parameters of rainfall (R) in Bedadung watershed was an average erosion value of 1708.70 MJ.cm/year. The parameters of soil erodibility (K) were dominated by latosol soil types with a K value of 0.26. The parameters of length and slope (LS) were dominated by a flat class which was with a slope of large 0-8%. The parameters of land cover vegetation and soil management (CP) were dominated by irrigated rice fields with a CP value of 0.02. The erosion rate of Bedadung watershed was 160.57 tons/ha.year, the erosion rate was included in the medium condition. The erosion hazard level in the Bedadung watershed was dominated at very low levels, i.e. the size of the erosion ranges from 0 – 15 (tons/ha.year) or 62.20% of the total area. Keywords: watershed, erosion rate, RUSLE, erosion hazard level Keywords: watershed, erosion rate, RUSLE, erosion hazard level JRPB, Vol. 8, No. 1, Maret 2020, Hal. 1-11 JRPB, Vol. 8, No. 1, Maret 2020, Hal. 1-11 DOI: 10.29303/jrpb.v8i1.122 ISSN 2301-8119, e-ISSN 2443-1354 Tersedia online di http://jrpb.unram.ac.id DOI: 10.29303/jrpb.v8i1.122 ISSN 2301-8119, e-ISSN 2443-1354 Tersedia online di http://jrpb.unram.ac.id Idah Andriyani*), Sri Wahyuningsih, Rosalina Sekar Arumsari Program Studi Teknik Pertanian Fakultas Teknologi Pertanian, Universitas Jember Kampus Tegal Boto, Jl. Kalimantan No. 37, Jember 68121, Indonesia Email*): idahandriyani32@gmail.com Email*): idahandriyani32@gmail.com Email*): idahandriyani32@gmail.com Diterima: Juli 2019 Disetujui: September 2019 Keywords: watershed, erosion rate, RUSLE, erosion hazard level PENDAHULUAN memiliki karakteristik mengalir dari tempat yang lebih tinggi ke tempat yang lebih rendah. ABSTRAK Kondisi perkembangan Daerah Aliran Sungai (DAS) di wilayah Kabupaten Jember untuk saat ini perlu dievaluasi karena kondisinya sudah rusak mulai dari tahun 1999. Hal ini dapat menimbulkan bencana alam di kawasan DAS seperti tanah longsor, erosi dan banjir yang memakan korban jiwa. Tujuan dari penelitian ini adalah mengetahui besarnya tingkat bahaya erosi yang dipengaruhi oleh beberapa nilai parameter erosi menggunakan metode Revised Universal Soil Loss Equation (RUSLE) di DAS Bedadung. Data input yang digunakan pada penelitian ini, yaitu curah hujan tahun 2004 – 2014, peta jenis tanah, peta penggunaan lahan RBI tahun 2014, dan data Digital Elevation Model (DEM) dari ASTER-GDEM. Hasil 1 JRPB, Vol. 8, No. 1, Maret 2020, Hal. 1-11 penelitian menunjukkan bahwa nilai parameter erosivitas hujan (R) DAS Bedadung rata-rata 1708,70 MJ.cm/tahun. Parameter erodibilitas tanah (K) didominasi jenis tanah latosol dengan nilai K sebesar 0,26. Parameter panjang dan kemiringan lereng (LS) didominasi kelas datar yaitu dengan besar kemiringan 0-8%. Parameter vegetasi penutupan lahan dan pengelolaan tanah (CP) didominasi sawah irigasi dengan nilai CP sebesar 0,02. Laju erosi DAS Bedadung sebesar 160,57 ton/ha.tahun, laju erosi ini termasuk pada kondisi sedang. Tingkat bahaya erosi pada DAS Bedadung didominasi pada tingkat sangat rendah, yaitu besar erosi berkisar 0 – 15 (ton/ha.tahun) atau 62,20% dari luas wilayahnya. Kata kunci: DAS, laju erosi, RUSLE, tingkat bahaya erosi Kata kunci: DAS, laju erosi, RUSLE, tingkat bahaya erosi Latar Belakang DAS Bedadung merupakan salah satu DAS terbesar di Kabupaten Jember (Santoso, dkk., 2013). DAS Bedadung dibedakan menjadi dua area antara lain: DAS Bedadung dengan panjang sungai 92.752 meter dengan melewati kali Sumber Pakem, kali Bunut, kali Kramat Agung, kali Mojo, dan kali Antirogo; serta DAS bedadung hilir dengan panjang sungai 69.680 meter dengan melewati kali Penggung, kali Besini, kali Glundengan, dan kali Bedadung (Badan Pusat Statistik, 2013). Erosi yang terjadi di DAS Bedadung rata-rata sebesar 1-3 ton/ha.tahun (Dinas Lingkungan Hidup Provinsi Jawa Timur, 2010). Erosi terjadi disebabkan intensitas curah hujan yang tinggi dan alih fungsi lahan. Erosi merupakan suatu proses hilangnya lapisan permukaan tanah bagian atas, yang disebabkan oleh pergerakan air maupun angin (Suripin, 2004). Erosi tanah dapat terjadi melalui dua proses, yaitu pertama proses penghancuran partikel tanah dan kedua proses pengangkutan partikel tanah yang telah dihancurkan. Kedua proses ini terjadi akibat hujan dan aliran permukaan yang dipengaruhi oleh berbagai parameter antara lain curah hujan (intensitas, diameter, lama, dan jumlah hujan), karakteristik tanah (sifat fisik), penutupan lahan, kemiringan lereng, panjang lereng dan sebagainya (Wischmeier dan Smith, 1978). Parameter- parameter yang dijelaskan oleh Wischmeier dan Smith (1978) tersebut satu sama lain akan bekerja secara simultan dalam mempengaruhi laju erosi (Banuwa, 2008). Dengan kondisi DAS Bedadung saat ini, perlu dilakukan penelitian tentang parameter-parameter yang mempengaruhi erosi dan memprediksi besarnya erosi serta tingkat bahaya erosi di wilayah DAS. Salah satu metode yang dapat digunakan untuk memprediksi besarnya erosi, yaitu metode RUSLE (Revised Universal Soil Loss Equation). Metode RUSLE merupakan suatu pemodelan erosi yang digunakan untuk memprediksi rata-rata besarnya laju erosi tahunan akibat percikan air hujan dan aliran permukaan dari suatu bentang lereng yang ada dengan tanaman dan pengolahan tertentu (Renard, dkk., 1997). Parameter erosivitas hujan (R), parameter erodibilitas tanah (K), parameter panjang dan kemiringan lereng (LS), serta parameter Menurut Peraturan Pemerintah Republik Indonesia No 37 (2012) Daerah Aliran Sungai adalah suatu wilayah daratan yang terdiri dari satu kesatuan ekosistem sungai dengan anak sungainya yang dibatasi oleh batas-batas topografi secara alami sedemikian rupa sehingga setiap air hujan yang jatuh dalam DAS tersebut akan mengalir melalui titik tertentu (titik pengukuran di sungai) dalam DAS tersebut. Apabila terdapat suatu kegiatan pada wilayah DAS mulai dari bagian hulu sampai hilir yang dapat mempengaruhi baik dari segi kualitas maupun kuantitas, maka akan menimbulkan dampak pada DAS. Erosi dapat mempengaruhi DAS karena air sebagai media pembawa butir-butir tanah 2 JRPB, Vol. 8, No. 1, Maret 2020, Hal. Metode Pengolahan Data Perhitungan laju erosi menggunakan metode RUSLE dengan menggunakan software GIS. Berikut tahapan pengolahan dan perhitungan menggunakan metode RUSLE dan software GIS: a. Parameter erosivitas hujan (R) Data curah hujan yang digunakan dalam penelitian, yaitu data curah hujan dari tahun 2004 – 2014. Data curah hujan yang digunakan pada DAS Bedadung terdiri dari 15 stasiun hujan. Data curah hujan harian diolah terlebih dahulu untuk mendapatkan nilai hujan maksimum 30 menit menggunakan metode mononobe, (Persamaan 1). I = (R24/24) (24/t)2/3 ................................ (1) I = (R24/24) (24/t)2/3 ................................ (1) . (1) Tujuan Tujuan dari penelitian ini adalah mengetahui besar laju erosi dan tingkat bahaya erosi yang dipengaruhi oleh beberapa nilai parameter erosi menggunakan metode Revised Soil Loss Equation (RUSLE) di DAS Bedadung. Latar Belakang 1-11 pengelolaan tanaman dan tindakan konservasi tanah (CP) merupakan parameter yang ada dalam perhitungan laju erosi menggunakan metode RUSLE. merupakan data sekunder. Peta diolah menggunakan aplikasi GIS yaitu ArcGIS 10. Selain itu, ArcGIS 10 digunakan untuk menghitung besar erosi dan tingkat bahaya erosi menggunakan metode RUSLE. Alat yang digunakan pada penelitian ini, yaitu laptop dilengkapi software GIS ArcMap 10.4.1. Waktu dan Tempat Penelitian Waktu dan Tempat Penelitian Penelitian ini terletak di daerah aliran sungai (DAS) Bedadung, Kabupaten Jember. Kegiatan penelitian ini dilaksanakan pada bulan Mei hingga bulan Juli 2018. DAS Bedadung adalah suatu DAS yang secara geografis terletak antara 113o38’24.45” sampai 114o01’97.00” BT dan 7o95’65.85” sampai 8o43’52.61” LS. DAS Bedadung memiliki luas sebesar 102.434,1 ha. Lokasi DAS Bedadung disajikan pada Gambar 1. f 1. Pengumpulan data dan interpretasi parameter erosi 1. Pengumpulan data dan interpretasi parameter erosi Alat dan Bahan Data yang digunakan dalam penelitian ini, yaitu data curah hujan durasi 10 tahun, peta tataguna lahan tahun 2014, peta jenis tanah, peta batas wilayah dan peta DEM di wilayah DAS Bedadung. Data tersebut Keterangan: g = Intensitas curah hujan mm/jam Gambar 1. Peta wilayah DAS Bedadung Gambar 1. Peta wilayah DAS Bedadung 3 3 JRPB, Vol. 8, No. 1, Maret 2020, Hal. 1-11 t = lamanya waktu hujan (menit) Tabel 1. Nilai K berdasarkan jenis tanah No. Jenis Tanah (Type of Soil) Nilai K (K Index) 1 Alluvial 0,29 2 Andosol 0,28 3 Brown Forest 0,28 4 Glei 0,29 5 Grumusol 0,16 6 Latosol 0,26 7 Litosol 0,13 8 Mediteran 0,16 9 Organosol 0,29 10 Podsolik merah 0,2 11 Regosol 0,31 Sumber: Bappenas (2012) Tabel 1. Nilai K berdasarkan jenis tanah Keterangan: EK = Energi kinetik (MJ/ha.cm hujan) I-30 = intensitas hujan maksimum 30 menit Parameter Indeks erosivitas hujan (R, EI-30) merupakan penjumlahan nilai-nilai indeks erosi hujan bulanan dan dihitung berdasarkan Persamaan 3 (Renard, dkk., 1997). parameter LS menggunakan ArcGIS memerlukan data Slope dan arah aliran (Flow Accumulation). Parameter panjang dan kemiringan dihitung menurut Persamaan 4 (Wischmeier dan Smith, 1978) untuk kemiringan kurang dari 9%. Untuk lahan dengan kemiringan di atas 9% menggunakan Persamaan 5. parameter LS menggunakan ArcGIS memerlukan data Slope dan arah aliran (Flow Accumulation). Parameter panjang dan kemiringan dihitung menurut Persamaan 4 (Wischmeier dan Smith, 1978) untuk kemiringan kurang dari 9%. Untuk lahan dengan kemiringan di atas 9% menggunakan Persamaan 5. EI-30 = EK x (I-30 x 10-2) ...................... (3) EI-30 = EK x (I-30 x 10-2) ...................... (3) Keterangan: EI-30 = Indeks erosivitas I-30 EK = Energi kinetik (MJ/ha.cm hujan) I-30 = intensitas hujan maksimum 30 menit (cm) Keterangan: EI-30 = Indeks erosivitas I-30 EK = Energi kinetik (MJ/ha.cm hujan) I-30 = intensitas hujan maksimum 30 menit (cm) LS = (X/22)0,50 (0,0138 + 0,00965S + 0,00138S2) ............................................ (4) LS = (X/22)0,50(S/9)1,35 .......................... (5) LS = (X/22)0,50 (0,0138 + 0,00965S + 0,00138S2) ............................................ (4) Nilai erosivitas hujan dari 15 stasiun hujan yang ada di wilayah DAS Bedadung kemudian diinput pada layer stasiun hujan menggunakan software ArcGIS. Untuk mengetahui daerah dengan nilai erosivitas berdasarkan luas wilayah menggunakan metode Poligon Theissen. Keterangan: X = panjang lereng (m) S = kecuraman lereng (%) b. Parameter erodibilitas tanah (K) b. Parameter erodibilitas tanah (K) d. Parameter vegetasi pengolahan lahan dan konservasi tanah (CP) d. Parameter vegetasi pengolahan lahan dan konservasi tanah (CP) Parameter erodibilitas tanah (K) adalah resistensi partikel tanah terhadap pengelupasan dan pengangkutan partikel- partikel tanah dari kekuatan air hujan. Nilai erodibilitas tanah dapat dilihat pada Tabel 1 berdasarkan Bappenas (2012). Pengelolaan vegetasi penutupan lahan dan konservasi tanah ini mempengaruhi erosi dengan mengubah pola aliran dan arah dari limpasan permukaan dengan mengurangi jumlah dan laju limpasan (Devatha, dkk., 2015). Peta tata guna lahan digunakan untuk mengetahui kondisi pemanfaatan lahan di wilayah penelitian. Adapun peta tata guna lahan dapat ditinjau dari peta Rupa Bumi Indonesia (RBI) pada tahun 2014 skala 1:25.000. Parameter CP dapat ditentukan berdasarkan penelitian di Jawa seperti Tabel 2 menurut Bappenas (2012). Nilai CP kemudian diinput pada c. Parameter panjang dan kemiringan lereng (LS) c. Parameter panjang dan kemiringan lereng (LS) c. Parameter panjang dan kemiringan lereng (LS) Parameter panjang dan kemiringan lereng (LS) merupakan dua unsur topografi yang berpengaruh besar terhadap aliran permukaan dan besarnya laju erosi. Analisis spasial LS memanfaatkan data DEM (Digital Elevation Model). Perhitungan 4 JRPB, Vol. 8, No. 1, Maret 2020, Hal. 1-11 interpretasi parameter erosi kemudian dihitung laju erosi menggunakan metode RUSLE dengan integrasi software GIS. Perhitungan laju erosi disajikan pada Persamaan (Wischmeier dan Smith, 1978). layer tata guna lahan menggunakan software GIS. Selanjutnya, dikonversi menggunakan tools “polygon to raster” pada software GIS. Sebagai standar penentuan parameter C dan P, berikut disajikan nilai faktor C dan P maupun CP (Tabel 2). p ( ) Tabel 2. Prakiraan parameter CP pada berbagai jenis penggunaan lahan No. Konservasi dan pengelolaan tanaman Nilai CP 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Kebun Tanah Kosong/Padang Rumput Ladang Hutan Sawah Irigasi Semak Belukar Sungai Pemukiman Sawah Tadah Hujan Empang Rawa/Hutan Rawa Danau/Bendungan Pasir Penggaraman Pabrik/Gedung Bandar Udara/ Pelabuhan 0,30 0,02 0,28 0,001 0,02 0,10 0,001 1 0,05 0,001 0,01 0,001 1 1 1 1 Sumber: Bappenas (2012) 2. Prediksi Laju Erosi Dari keseluruhan layer yang dihasilkan pada pengumpulan data dan Tabel 3. Nilai erosivitas hujan (R) pada Wilaya No Nama I-30 (cm/tahun) 1 Rambipuji 368 2 Rawatamtu 492,8 3 Curah Malang 460,8 4 Puger 278,4 5 Grenden 256 6 Gumelar Timur 310,4 7 Tamansari 464 8 Glundengan 339,2 9 Lojejer 342,4 10 Ampel 300,8 11 Sukowono 316,8 12 Sumberkalong 416 13 Sumberjambe 454,4 14 Cumedak 473,6 15 Kottok 531,2 Rata – rata 386,98 (6) 𝐴= 𝑅. 𝐾. 𝐿𝑆. 𝐶𝑃..................................... (6) Keterangan: A = Jumlah tanah yang tererosi (ton/ha.tahun) R = Parameter erosivitas curah hujan tahunan rata-rata (cm/tahun) K = Parameter erodibilitas tanah; LS = Parameter panjang dan kemiringan lereng (%) CP = Parameter vegetasi dan pengelolaan konservasi lahan 𝐴= 𝑅. 𝐾. 𝐿𝑆. 𝐶𝑃..................................... (6) Keterangan: A = Jumlah tanah yang tererosi (ton/ha.tahun) R = Parameter erosivitas curah hujan tahunan rata-rata (cm/tahun) K = Parameter erodibilitas tanah; LS = Parameter panjang dan kemiringan lereng (%) CP = Parameter vegetasi dan pengelolaan konservasi lahan Tabel 2. Prakiraan parameter CP pada berbagai jenis penggunaan lahan Keterangan: HASIL DAN PEMBAHASAN Parameter Erosivitas Hujan (R) Parameter Erosivitas Hujan (R) Stasiun hujan yang ada pada wilayah DAS Bedadung sebanyak 15 stasiun. Perhitungan data curah hujan yang digunakan untuk mengetahui sebaran nilai R di wilayah tersebut. Nilai erosivitas hujan pada wilayah DAS Bedadung disajikan pada Tabel 3 dan Gambar 2 memperlihatkan peta erovitas hujan di DAS Bedadung. Tabel 3. Nilai erosivitas hujan (R) pada Wilayah DAS Bedadung Tabel 3. Nilai erosivitas hujan (R) pada Wilayah DAS Bedadung No Nama I-30 (cm/tahun) Energi Kinetik (MJ/ha.cm) R (MJ.cm/ tahun) 1 Rambipuji 368 438,66 1614,27 2 Rawatamtu 492,8 449,95 2217,34 3 Curah Malang 460,8 447,35 2061,4 4 Puger 278,4 427,88 1191,21 5 Grenden 256 424,63 1087,06 6 Gumelar Timur 310,4 432,08 1341,18 7 Tamansari 464 447,62 2076,96 8 Glundengan 339,2 435,51 1477,25 9 Lojejer 342,4 435,87 1492,43 10 Ampel 300,8 430,87 1296,05 11 Sukowono 316,8 432,87 1371,33 12 Sumberkalong 416 443,4 1844,54 13 Sumberjambe 454,4 446,81 2030,31 14 Cumedak 473,6 448,41 2123,68 15 Kottok 531,2 452,85 2405,53 Rata – rata 386,98 439,65 1708,70 5 5 JRPB, Vol. 8, No. 1, Maret 2020, Hal. 1-11 Gambar 2. Peta erosivitas hujan (R) DAS Bedadung Gambar 2. Peta erosivitas hujan (R) DAS Bedadung dengan pertambahan waktu dan akumulasi intensitas hujan tersebut akan mendatangkan erosi (Kironoto, 2000 dalam Suripin, 2004). Nilai energi kinetik terendah pada wilayah DAS Bedadung, yaitu pada stasiun hujan Grenden sebesar 424,63 MJ/ha.cm, dengan nilai erosivitas hujan 1087,06 MJ.cm/tahun. Hal ini karena pada wilayah tersebut jarang terjadi hujan atau curah hujannya rendah. Sedangkan nilai energi kinetik tertinggi, yaitu pada stasiun hujan Kottok sebesar 452,85 MJ/ha.cm, dengan nilai erosivitas hujan 2405,53 MJ.cm/tahun. Hal ini karena pada wilayah tersebut sering terjadi hujan atau curah hujannya tinggi. Nilai erosivitas tergantung curah hujan bulanan rerata pada setiap stasiun hujan. Semakin tinggi curah hujan, maka semakin tinggi nilai erosivitas yang dihasilkan. Nilai erosivitas yang tinggi belum tentu menyebabkan terjadinya erosi yang tinggi pula, jika erosi terjadi pada tanah yang mempunyai nilai erodibilitas rendah, terletak pada daerah yang memiliki kemiringan lereng rendah (landai) serta pengelolaan lahan yang baik (Kartika, dkk., 2016). Dengan rata-rata erosivitas hujan selama 10 tahun, yaitu sebesar 1844,278 MJ.cm/ha, curah hujan yang jatuh secara langsung atau tidak langsung dapat mengikis permukaan tanah secara perlahan Gambar 3. Peta erodibilitas tanah (K) DAS Bedadung Gambar 3. Peta erodibilitas tanah (K) DAS Bedadung 6 JRPB, Vol. 8, No. 1, Maret 2020, Hal. 1-11 Tabel 4. Parameter Erosivitas Hujan (R) Sebaran jenis tanah dan tingkat erodibilitas tanah di wilayah DAS Bedadung No Jenis Tanah Nilai K (ton/Mj.c) Luas (ha) Luas (%) Tingkat Erodibilitas 1 Regosol 0,301 256316,4 25,03 Sedang 2 Andosol 0,28 159447,6 15,57 Sedang 3 Latosol 0,26 480700,8 46,94 Sedang 4 Aluvial 0,29 10712,7 1,05 Sedang 5 Glei 0,29 74962,8 7,32 Sedang 6 Mediteran 0,16 42016,5 4,10 Rendah Total 102.434,1 100 bel 4. Sebaran jenis tanah dan tingkat erodibilitas tanah di wilayah DAS Bedadung Parameter Erodibilitas Tanah (K) Parameter Erodibilitas Tanah (K) 74962,8 ha, andosol dengan nilai K sebesar 0,28 ton/MJ.cm dan luas 159447,6 ha, aluvial dengan nilai K sebesar 0,29 ton/MJ.cm dan luas 10712,7 ha, serta regosol dengan nilai K sebesar 0,31 ton/MJ.cm dan luas 256316,4 ha. Semakin besar nilai K, maka kepekaan tanah terhadap erosi semakin tinggi. Begitu juga sebaliknya, jika semakin kecil nilai K maka kepekaan tanah terhadap erosi semakin kecil pula. Menurut Arsyad (1989) berbagai jenis tanah memiliki tingkat kepekaan terhadap erosi yang berbeda-beda. Parameter Erodibilitas Tanah (K) Gambar 3 menyajikan Peta erodibilitas tanah (K) DAS Bedadung. Menurut Wischmeier dan Smith (1978), Parameter erodibilitas tanah (K) adalah resistensi partikel tanah terhadap pengelupasan dan pengangkutan partikel- partikel tanah dari kekuatan air hujan. Tanah akan semakin peka terhadap erosi jika curah hujan tinggi, karena curah hujan di Indonesia pada umumnya tinggi, berkisar dari 1500 – 3000 mm/tahun atau lebih setiap tahunnya, dengan intensitas yang juga tinggi (Dariah, dkk., 2004). 16777 Parameter Panjang dan Kemiringan Lereng (LS) Berdasarkan Tabel 4, jenis tanah yang memiliki tingkat erodibilitas rendah, yaitu mediteran dengan nilai K sebesar 0,16 ton/MJ.mm dan luas 42016,5 ha. Jenis tanah yang memiliki tingkat erodibilitas sedang, yaitu latosol dengan nilai K sebesar 0,26 ton/MJ.cm dan luas 480700,8 ha, glei dengan nilai K 0,29 ton/MJ.cm dan luas g Gambar 4 memperlihatkan Peta Parameter LS (Lenght Slope) DAS Bedadung. Berdasarkan Tabel 5, DAS Bedadung didominasi oleh nilai LS kelas 0 – 8 seluas 77208,40 ha atau 75,53% dengan deskripsi kemiringan lereng yang datar dari Gambar 4. Peta Parameter LS (Length Slope) DAS Bedadung Gambar 4. Peta Parameter LS (Length Slope) DAS Bedadung 7 JRPB, Vol. 8, No. 1, Maret 2020, Hal. 1-11 Gambar 5. Peta nilai CP Tahun 2014 DAS Bedadung Gambar 5. Peta nilai CP Tahun 2014 DAS Bedadung luas total DAS Bedadung. Sedangkan nilai LS pada kelas 8 – 15 seluas 8328,78 ha atau 8,148% dengan deskripsi kemiringan lereng yang landai. Nilai LS pada kelas 15-25 seluas 6252,39 ha atau 6,117% dengan deskripsi kemiringan lereng yang bergelombang. Nilai LS pada kelas 25-45 seluas 5658,038 ha atau 5,53% dengan deskripsi kemiringan lereng yang curam. aliran permukaan menjadi lebih tinggi kedalaman maupun kecepatannya. Parameter Vegetasi Penutupan Lahan dan Konservasi Tanah (CP) Dari hasil analisis peta RBI tahun 2014 di wilayah DAS Bedadung diperoleh 12 jenis penggunaan lahan. Nilai CP dan luas setiap penggunaan lahan pada wilayah DAS disajikan pada Gambar 5 dan Tabel 6 memperlihatkan peta nilai CP tahun 2014 DAS Bedadung. Tabel 5. Parameter LS pada DAS Bedadung No Kemiringan (%) Luas (Ha) Luas (%) Deskripsi 1 0 – 8 77208,40 75,533 Datar 2 8 – 15 8328,78 8,148 Landai 3 15 – 25 6252,39 6,117 Bergelombang 4 25 – 45 5658,03 5,535 Curam 5 > 45 4771,08 4,668 Sangat Curam Total 102.434,1 100,00 Tabel 5. Parameter LS pada DAS Bedadung Tabel 6. Penggunaan lahan tahun 2014 pada DAS Bedadung No Peruntukan Lahan Nilai CP Luas (ha) Luas (%) 1 Kebun 0,3 18701,6 18,26 2 Tanah Kosong 0,02 416,3 0,40 3 Ladang 0,28 10061,3 9,82 4 Hutan 0,001 20598,2 20,12 5 Sawah Irigasi 0,02 29084,6 28,41 6 Semak Belukar 0,1 4135,8 4,04 7 Sungai 0,001 263,7 0,25 8 Pemukiman 1 14269,8 13,94 9 Sawah Tadah Hujan 0,05 4742,1 4,63 10 Pasir 0,001 55,89 0,05 11 Danau/Bendungan 1 6,57 0,006 12 Tanah Campur 0,02 29,61 0,029 Jumlah 102434,1 100 Tabel 6. Penggunaan lahan tahun 2014 pada DAS Bedadung Nilai LS pada kelas > 45 seluas 4771,08 ha atau 4,66% dengan deskripsi kemiringan lereng yang sangat curam. Seperti yang dikatakan oleh Kartasapoetra, dkk., (2005), bahwa kemiringan dan panjang lereng yang besar pada tanah menyebabkan semakin besar pula kecepatan aliran air di permukaannya sehingga pengikisan terhadap bagian-bagian tanah juga semakin besar. Semakin panjang lereng suatu lahan menyebabkan semakin banyak air permukaan yang terakumulasi, sehingga 8 8 JRPB, Vol. 8, No. 1, Maret 2020, Hal. 1-11 Tabel 7. Hasil perhitungan laju erosi DAS Bedadung No Besar Erosi (ton/ha.thn) Luas (ha) Laju Erosi (ton/ha.tahun) Luas (%) TBE 1 0 – 15 63510 1,86 62,2 Sangat rendah 2 15 – 60 9542 31,40 9,35 Ringan 3 60 – 180 6169 110,22 6,04 Sedang 4 180 – 480 7799 315,80 7,64 Berat 5 > 480 15075 1966,33 14,7 Sangat berat Jumlah 102.434,1 2425,62 100 Rata-rata Laju Erosi (ton/ha.tahun) 160,57 Tabel 7. Hasil perhitungan laju erosi DAS Bedadung merupakan parameter yang ada dalam perhitungan laju erosi menggunakan metode RUSLE. Pemodelan RUSLE menggunakan software ArcGIS dilakukan dengan tool raster calculator. Perhitungan laju erosi menggunakan raster calculator dilakukan setelah semua peta parameter erosi telah menjadi format raster dan di-overlay (tumpang susun) antara parameter R, K, LS dan CP. Parameter Vegetasi Penutupan Lahan dan Konservasi Tanah (CP) Berdasarkan Tabel 6, penggunaan lahan 2014 di DAS Bedadung didominasi oleh sawah irigasi dengan luas 29084,58 ha atau 28,41% dari total luas wilayahnya. DAS Bedadung juga didominasi oleh kebun, hutan, dan pemukiman. Kebun pada DAS Bedadung memiliki luas sebesar 18701,6 ha. pemukiman memiliki luas sebesar 14269,8 ha, serta hutan memiliki luas sebesar 20598,2 ha. Apabila nilai parameter CP besar maka penggunaan lahan pada daerah tersebut akan besar, Oleh karena, itu besar potensinya untuk terjadi erosi karena tanah menjadi rusak akibat pengelolaan yang berlebihan dan tanah tidak tertutupi sepenuhnya oleh vegetasi. DAS Bedadung memiliki luas sebesar 102.434,1 ha; terdiri dari beberapa kecamatan memiki potensi erosi yang cukup besar. Laju erosi dihitung berdasarkan data hujan, data penggunaan lahan, data kemiringan lereng dan data jenis tanah. Besar laju erosi pada DAS Bedadung yang dihitung menggunakan persamaan metode RUSLE ditunjukkan pada Tabel 7. Adapun Gambar 6 memperlihatkan Peta laju erosi DAS Bedadung. Sedangkan untuk daerah dengan sedikit pengelolaan dari manusia dan terdapat vegetasi penutup lahan maka akan memiliki nilai parameter CP yang kecil. Seperti yang disampaikan Devatha, dkk., (2015), jika pada suatu daerah terdapat banyak kegiatan pengelolaan lahan yang mengurangi vegetasi penutup lahan, maka air hujan akan langsung jatuh ke tanah, sehingga besar kemungkinan terjadinya erosi. Besar rata-rata laju erosi pada wilayah DAS Bedadung pertahunnya sebesar 160,57 ton/ha.tahun. Wilayah DAS Bedadung didominasi pada tingkat bahaya erosi sangat rendah, yaitu besar erosi berkisar 0-15 (ton/ha.tahun). Besar laju erosi pertahunnya berkisar 1,86 ton/ha.tahun atau 62,20% dari luas wilayahnya. Pada tingkat bahaya erosi ringan laju erosinya, yaitu 31,40 ton/ha.tahun atau 9,35% dari luas wilayah yang ada. Pada tingkat bahaya erosi sedang laju erosinya, yaitu 110,22 ton/ha.tahun atau 6,04% dari luas wilayah yang ada. Pada tingkat bahaya erosi berat laju erosinya, yaitu 315,80 ton/ha.tahun atau 7,64% dari luas wilayah yang ada. Pada tingkat bahaya erosi sangat berat laju erosinya, yaitu UCAPAN TERIMA KASIH 1966,33 ton/ha.tahn atau 14,76% dari luas wilayah yang ada. 1966,33 ton/ha.tahn atau 14,76% dari luas wilayah yang ada. Ucapan terima kasih terutama ditujukan kepada pemberi dana penelitian atau donatur (Hibah Keris Batch 1 tahun 2018) dan kepada pihak-pihak yang membantu pelaksanaan penelitian. Laju Erosi dan Tingkat Bahaya Erosi (TBE) Laju Erosi dan Tingkat Bahaya Erosi (TBE) Pendugaan laju erosi pada penelitian ini menggunakan metode RUSLE dengan menggunakan software ArcGIS. Nilai laju erosi dipengaruhi oleh parameter-parameter penyebab erosi. Parameter erosivitas hujan (R), parameter erodibilitas tanah (K), parameter panjang dan kemiringan lereng (LS), serta parameter pengelolaan tanaman dan tindakan konservasi tanah (CP) 9 9 JRPB, Vol. 8, No. 1, Maret 2020, Hal. 1-11 Gambar 6. Peta laju erosi DAS Bedadung Gambar 6. Peta laju erosi DAS Bedadung Kesimpulan Berdasarkan pembahasan yang telah dijelaskan di atas, dapat disimpulkan bahwa besar laju erosi DAS Bedadung sebesar 160,57 ton/ha.tahun. Tingkat bahaya erosi pada DAS Bedadung didominasi oleh kelas 1, yaitu 0 – 15 ton/ha.tahun sebesar 62,2% dari total wilayah luas DAS. Pada tingkat bahaya erosi ringan 15-60 ton/ha.tahun sebesar 9,35%, tingkat bahaya erosi sedang 60-180 ton/ha.tahun sebesar 6,04% dari luas wilayah yang ada. Pada tingkat bahaya erosi berat 180-480 ton/ha.tahun sebesar 7,64%, tingkat bahaya erosi sangat berat laju erosinya, yaitu > 480 ton/ha.tahun sebesar 14,76% dari luas wilayah yang ada. DAFTAR REFERENSI Arsyad, S. (1989). Konservasi Tanah dan Air. Bogor: IPB Press. Badan Pusat Statistik. (2013). Jember Dalam Angka. Jember: BPS. Banuwa, I.S. (2008). Erosi. Jakarta: Kencana Prenada Media Group. Bappenas. (2012). Analisa Perubahan Penggunaan Lahan di Ekosistem DAS dalam Menunjang Ketahanan Air dan Ketahanan Pangan. E-book. Jakarta: Direktorat Kehutanan dan Konservasi Sumber Daya Air. Saran Data hasil penelitian yang telah dilakukan sebaiknya perlu dilakukan perhitungan langsung terkait nilai laju erosi untuk membandingkan dengan hasil pendugaan erosi menggunakan Sistem Informasi Geografis (SIG). Dariah, A., Rachman, A., & Kurnia, U. (2004). Erosi dan Degradasi Lahan Kering di Indonesia, dalam: Teknologi Konservasi Tanah pada Lahan Kering Berlereng. Bogor: Puslittanah, BP3 Deptan. 10 JRPB, Vol. 8, No. 1, Maret 2020, Hal. 1-11 Devatha, P.C., Deshpande, V., & Renukaprasad, M.S. (2015). Estimation of Soil loss using USLE model for Kulhan Watershed, Chattisgarh- A case study. International Conference On Water Resources, Coastal and Ocean Engineering (ICWRCOE 2015). Aquatic Procedia, 4, 1429-1436. tentang Pengelolaan Daerah Aliran Sungai. Diakses 4 April 2018, dari http://www.bphn.go.id/data/document s /12pp037.pdf. Renard, K.G., Foster, G.R., Weesies, G.A., McCool, D.K., & Yoder, D.C. (1997). Predicting Soil Erosion by Water: A Guide to Conservation Planning with the Revised Universal Soil Loss Equation (RUSLE). USDA Agriculture Handbook No. 703. Dinas Lingkungan Hidup Provinsi Jawa Timur. (2010). Informasi Kinerja Pengelolaan Lingkungan Hidup Daerah Provinsi Jawa Timur Tahun 2010. Surabaya: DIKPLHD. Santoso, B., Hendrijanto, K., Rahmawati, A., Jannah, R., & Tyas, M.R. (2013). Model Intervensi Pengelolaan Daerah Aliran Sungai (DAS) (Community Based Action Research pada Masyarakat di Daerah Aliran Sungai Bedadung Kabupaten Jember). Jember: Program Studi Sosiologi FISIP Universitas Jember. Kartasapoetra, G., Kartasapoetra, A.G., & Sutedjo, M.M. (2005). Teknologi Konservasi Tanah dan Air. Jakarta: Rineka Cipta. Kartika, I., Indarto, Muharjo, P., & Hamid, A. (2016). Pemetaan Tingkat Bahaya Erosi Pada Level Sub-DAS: Studi pada Dua DAS Identik. Jurnal Agroteknologi, 10(01), 117-128. Suripin. (2004). Drainase Perkotaan yang Berkelanjutan. Yogyakarta: ANDI OFFSET. Pemerintah Republik Indonesia. (2012). Peraturan Pemerintah Republik Indonesia Nomor 37 Tahun 2012 Wischmeier, W.H., & Smith, D.D. (1978). Predicting Rainfall Erosion Losses. USDA Agriculture Handbook. 11
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https://revistes.ub.edu/index.php/RED/article/download/37695/36987, https://dialnet.unirioja.es/descarga/articulo/8215066.pdf
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Hacia el desarrollo sostenible: La educación en derechos humanos en la formación de especialistas en Derecho Penal
Revista de educación y derecho
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REVISTA EDUCACIÓN Y DERECHO. I NÚMERO EXTRAORDINARIO Hacia el desarrollo sostenible: La educación en derechos humanos en la formación de especialistas en Derecho Penal Towards Sustainable Development: Human Rights Education in the Training of Criminal Law Specialists Darina Ortega León Profesora Titular de Derecho Procesal Penal y Criminología 145 145 Facultad de Derecho Universidad de Oriente (Cuba) E-mail: darina@uo.edu.cu María Elvira Batista Ojeda Profesora Titular de Derecho Procesal Penal Facultad de Derecho Universidad de Oriente (Cuba) E-mail: melvira@uo.edu.cu Resumen: La educación como derecho humano y su dimensionamiento dentro de los objetivos para el desarrollo sostenible, han encontrado un punto de convergencia dentro de la educación en valores en lo que se ha denominado la educación en derechos. Desde esta idea, se promueve el desarrollo de una cultura de respeto a los derechos humanos a la que se debe contribuir desde todos los niveles de formación, incluyendo el posgrado. Como parte de estas aspiraciones adquiere especial significación la formación de REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW I NÚMERO EXTRAORDINARIO OCTUBRE 2021 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… especialistas en Derecho penal, al ser en este ámbito donde más comprometidos se pueden ver los derechos humanos. De ahí la necesidad de formar no sólo profesionales con vastos conocimientos, sino también, sujetos de derecho que promuevan el respeto a la dignidad humana desde su actuación. Desde estas premisas nos acercamos a la experiencia desarrollada por el Programa de Formación de Especialistas en Derecho penal de la Facultad de Derecho de la Universidad de Oriente de Cuba con el objetivo de valorar si su concepción y ejecución responde a la educación en derechos humanos como expresión de la educación en valores y la transferencia de los objetivos de desarrollo sostenible a la sociedad civil, profesional y académica. Palabras clave: Derechos humanos, educación, derecho penal, desarrollo sostenible. Abstract: Education as human right, and its dimension within the sustainable development objectives, have found a convergent point in education in values, in what has been denominated education in rights. From this idea, it is promoted a human right respect culture, to which it ought be a contribution from all the education levels, including post degree. As a part of this aims, the post degree formation in criminal law specialization has a special significance, for the criminal law may be considered the area of most human right jeopardy. Therefore, is needed to form a well and vast knowledge professional, but also acting subjects of rights who promotes human dignity respect. Form this assumptions, we approach to the experience of the Criminal Law Specialists program of degree, developed in the Faculty Law of the University off the Oriente in Cuba, to evaluate if its conception and execution responds to education in human rights, as an expression of the education in values, and the transference of sustainable development objectives into the academic, professional and civil society. Keywords: Human rights, education, criminal law, development sustainable. Sumario: 1. Derechos humanos, educación y desarrollo sostenible: Fundamentos teóricos para definir su convergencia. 2. La educación en derechos humanos en la formación de posgrado. 3. La formación de la educación en derechos humamos para especialistas en Derecho penal: Una experiencia. 4. Conclusiones. 5. Bibliografía. REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 146 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… 1. Derechos humanos, educación y desarrollo sostenible: Fundamentos teóricos para definir su convergencia Las luchas por la defensa de los derechos humanos y su consagración en los instrumentos jurídicos internacionales que hoy sirven como fundamento y referente a los ordenamientos jurídicos, ha sido una de las más importantes conquistas de la humanidad en pos de preservar la dignidad humana. Así se refiere en la Declaración Universal de los Derechos Humanos la necesidad de que todos los pueblos y naciones promuevan mediante la enseñanza y la educación el respeto a los derechos humanos. Un hito importante lo marcó la Conferencia Mundial de Derechos Humanos de Viena de 1993, espacio en el que se declaró la indivisibilidad, interdependencia e interconexión de todos los derechos humanos. Como un pilar esencial no sólo para el reconocimiento sino también para el control de las garantías de estos derechos, se definió la igualdad desde una dimensión asociada a la dignidad, configurándose a posteriori como principio, derecho y garantía, no sólo en la doctrina sino también en los ordenamientos jurídicos. Es la igualdad uno de los fundamentos a partir del cual se estructuran los denominados derechos de carácter colectivo de segunda generación. Derechos en los que el Estado está compelido a asumir un papel activo con la consecuente obligación de crear las condiciones necesarias para la satisfacción de las necesidades sociales, culturales y económicas de todas las personas por igual. De lo que se trata es, de reivindicar los derechos económicos, sociales y culturales. Ello implica un proceso social, político y legal en el que se pretende comprometer al Estado en el cumplimiento de sus responsabilidades. Dentro de los derechos que el Estado debe garantizar se encuentra el derecho a la educación. El reconocimiento de este derecho y su efectiva realización, ha sido, una constante en el esfuerzo de la Naciones Unidas para conseguir una educación sostenible y de calidad para todos los seres humanos. Ejemplo de ello es como en la Declaración Universal de los Derechos Humanos de 1948, en su artículo 26, se señala que toda persona tiene derecho a la educación y que esta tendrá como objeto el pleno desarrollo de la personalidad humana y el fortalecimiento y respeto de los derechos humanos. REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 147 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… En el reconocimiento y protección jurídica internacional del derecho a la educación se reconocen varios hitos importantes: la Convención de los Derechos del Niño (1989) y la Conferencia Mundial sobre la Educación para Todos (EPT)77 celebrada en Jomtien (1990). Como resultado de esta última, se promueve la Declaración Mundial sobre Educación para Todos, contentiva de una declaración de buenos principios; y en la que se establecen diez artículos que promueven la eficacia de la cooperación para la obtención de una educación universal sostenible. En su plan de acción, se señalan las pautas, los objetivos y los recursos a invertir por los gobiernos para la mejora de las necesidades básicas de aprendizaje a nivel global. Otros referentes se encuentran en el Foro Mundial sobre Educación (2000), a través del cual se adoptó el: Marco de Acción de Dakar como compromiso de acción conjunto para proponer soluciones concretas a las carencias de la educación. En el mismo año 2000, en septiembre, en la 55th sesión de la Asamblea General de las Naciones Unidas se suscribió, por parte de todos los gobiernos participantes, la Declaración del Milenio. Con esta Declaración, se establecieron ocho Objetivos de Desarrollo del Milenio (ODM), los que se convirtieron en un marco de referencia para la comunidad internacional, el segundo de ellos dedicado a la educación. La Cumbre Mundial sobre Desarrollo Sostenible, celebrada en Johannesburgo en el 2002, fue de suma importancia para reforzar el desarrollo sostenible, tanto a nivel local como mundial. Fue en este espacio donde se promovió la idea de crear un Decenio para la Educación con miras al Desarrollo Sostenible78. En diciembre de este propio año, siguiendo las pautas de lo acontecido en Johannesburgo, la Asamblea General de las Naciones Unidas proclamó el Decenio de las Naciones Unidas de la Educación para el Desarrollo Sostenible (DEDS), y nombró a la Unesco como el organismo rector de la 77 Esta conferencia dio un impulso significativo para promocionar una enseñanza primaria universal y erradicar el analfabetismo en el mundo. Durante el tiempo que duró la cumbre, los/as representantes de 155 Estados se reunieron para detectar y analizar los obstáculos que impedían el avance en la consecución de la educación en todo el planeta, y se establecieron medidas y acciones para que todas las personas pudieran favorecerse de una educación que les permitiera un mayor progreso personal y social. 78 El uso generalizado del término «Desarrollo Sostenible», tal y como afirma GUTIÉRREZ, es un concepto que ha sido impulsado y acuñado por primera vez en la Conferencia de las Naciones Unidas para el Medio Ambiente y el Desarrollo, celebrada en 1992 en Rio de Janeiro (GUTIÉRREZ et al. 2006). Pero también es cierto que ya desde 1987 las Naciones Unidas comienzan a utilizar este vocablo (Informe Brundtland). Se define “desarrollo sostenible” por primera vez en Oxford en el Informe Brundtland: “el desarrollo que satisface las necesidades actuales de las personas sin comprometer la capacidad de las futuras generaciones para satisfacer las suyas” (Naciones Unidas, 1987). REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 148 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… promoción del Decenio y el encargado de elaborar un plan, con la finalidad de subrayar y enfatizar el papel de la educación como motor fundamental para promover el desarrollo sostenible. El objetivo prioritario de este decenio 2005-2014 fue integrar los principios y valores del desarrollo sostenible en todos los aspectos de la educación y el aprendizaje, con el fin de conseguir cambios de comportamiento que garantizaran la integridad del medio ambiente y la viabilidad del planeta. La educación, desde esta perspectiva, se considera, uno de los fundamentos de la sociedad, es decir, una herramienta sin la cual no es posible ni el desarrollo de los pueblos, ni la sostenibilidad del planeta. En este devenir no podemos perder de vista la relación existente entre los DEDS, los ODM y los EPT. En los Objetivos de Desarrollo del Milenio, se reconoce la educación como un indicador mensurable de gran importancia para la erradicación de la pobreza. Por su parte, la EPT, se centra en buscar vías para lograr oportunidades de educación de calidad; y el DEDS promueve una serie de valores y comportamientos que deben estar presentes en el aprendizaje de todos los seres humanos. 149 En septiembre de 2015, 150 jefes de Estado se reunieron en la Cumbre de Desarrollo Sostenible para aprobar la Agenda 2030, también llamada la agenda Post- 2015, como sucesora de la Agenda del Milenio. Su objetivo fundamental fue conseguir aquellas metas que no fueron logradas con los ODM. Esta nueva agenda contó con 17 Objetivos de Desarrollo Sostenible (ODS) que debían cumplirse para el año 2030, compuestos por 169 metas y por, aproximadamente, 300 indicadores para su cumplimiento. La Agenda 2030, en su objetivo 4, plantea la importancia de promover una educación y aprendizaje inclusivo y de calidad para todos y todas. En su meta 4.7 proclama la necesidad de promover el desarrollo sostenible mediante la educación y la promoción de una cultura de paz, la ciudadanía mundial y la contribución de la cultura al desarrollo sostenible. Este objetivo transversaliza todo el documento, y se pueden constatar referencias a él en otros ODS. Para su consecución se proponen 7 metas de vital importancia que deben cumplirse al llegar al 2030. Entre ellos se establece el acceso igualitario de todos los hombres y las mujeres a una formación, incluida la enseñanza REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… universitaria y que los/as alumnos/as se formen en la promoción del desarrollo sostenible y la justicia. Estos pronunciamientos fundamentan una educación inclusiva, equitativa y de calidad para dimensionar la igualdad de oportunidades de aprendizaje durante toda la vida, para todas las personas. Así mismo, ha quedado asentada como una pauta importante, la idea de que para obtener el desarrollo sostenible, debemos estar conscientes de que hay cambios que deben producirse, tanto en los estilos de vida y de desarrollo, como en los estilos de pensamiento y conocimiento. Cambios que sólo serán dables, como se ha sostenido: “…desde procesos educativos que promuevan la concientización pública, la participación ciudadana bien informada y el desarrollo de capacidades para que la gente sepa tomar decisiones en todos aquellos asuntos que afecten su calidad de vida”. (GONZÁLEZ, 2003,1). La visión de la educación dentro de estas aspiraciones rebasa las concepciones tradicionales de la instrucción. Se aboga por una nueva dimensión en la que como afirma Ramos, se define a la educación como un proceso social que tiene que responder a las características de la sociedad en la que está inscrita y a través de la cual las soluciones no tienen que ser sólo técnicas sino que tienen una dimensión ética porque está en juego el destino del hombre. Este autor afirma además que: “La dimensión ética implica que los individuos necesitan un grupo de valores que orienten su comportamiento social en un mundo cambiante, enfrentar los problemas con sentido ciudadano, con autonomía personal, conciencia de sus deberes y derechos y sentimiento positivo de vínculos con todo ser humano comprometido en la búsqueda de una sociedad más justa y solidaria” (RAMOS, 2000, 121-122). A partir de las pautas enunciadas la relación: Derechos humanos - Educación – Desarrollo Sostenible, no supone una suerte o mera conjugación de palabras, sino una concepción holística y humanista. Es el resultado de comprender la imbricación de cada uno de sus contenidos como parte de objetivos y metas comunes, y que se ha articulado dentro de lo que se ha denominado: la educación en derechos humanos. Este concepto se ha estructurado y reconocido como parte de la denominada educación en valores. Educar en valores no es sólo un compromiso, de lo que se trata es de REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 150 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… dimensionar y llevar a vías de hecho un proyecto humano de transformación de aquellas condiciones sociales, culturales, políticas y pedagógicas que se estiman como deseables e ideales para el logro de una sociedad inclusiva y de formas de vida basadas en la felicidad, la justicia, la libertad y la dignidad humana. GARZA y PATIÑO al definir la educación en valores se refieren a: “… un replanteamiento cuya finalidad esencial es humanizar la educación. Coincidimos con estos autores en que una educación en valores es necesaria para ayudarnos a ser mejores personas en lo individual y mejores integrantes de los espacios sociales en los que nos desarrollamos” (GARZA y PATIÑO, 2000, 25). Desde esta perspectiva, la formación en valores se estructura sobre la base de cuatro aspectos fundamentales:”… la persona, las relaciones humanas, la realidad y la espiritualidad” (JUÁREZ y MORENO, 2000, 47). Como parte de esta concepción, el rol del educador, es conducir al educando para desarrollar sus potencialidades bajo una dimensión moral y ética, en el marco de su realidad social, de manera que pueda interpretarla, asumir la responsabilidad de sus actos y participar proactivamente. En este sentido, se ha concebido, desde el año 2004, un Programa mundial para la educación en derechos humanos de la ONU, a través del cual se reconoce que la educación en derechos humanos tiene por objeto fomentar el entendimiento de que cada persona comparte la responsabilidad de lograr que los derechos humanos sean una realidad en cada comunidad y en la sociedad en su conjunto. Pretensiones que contribuyen a la promoción de la igualdad y devienen congruentes con los ODS. Como parte de esta construcción, el derecho a la educación, viene a definir el pleno desarrollo de la personalidad humana, el sentido de la dignidad y como consecuencia de ello, fortalece el respeto por los derechos humanos. Si bien toda persona tiene derecho a una educación de calidad, integral, permanente y en igualdad de condiciones y oportunidades; la educación que recibe debe ser capaz de capacitarla para participar en la sociedad y favorecer su comprensión y tolerancia. De lo que se trata es de fomentar una cultura del respeto a la dignidad. Una cultura sustentada en tres pilares fundamentales: el derecho a la integridad personal, a la libertad de expresión y a no sufrir discriminación. REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 151 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… El fomento de esta cultura a través de la educación debe estructurarse a través del desarrollo de las capacidades éticas creando los espacios en ello a los valores, es decir, dimensionar la denominada educación en valores dentro del contexto del desarrollo sostenible. Suscribimos la idea de que la educación así concebida hace referencia a los valores y principios éticos y cívicos que se intenta inculcar a las personas para la construcción de una ciudadanía crítica, que sea capaz de analizar y reflexionar sobre los cambios acontecidos y liderar un cambio que mejore nuestro mundo y lo haga viable y sostenible. De manera que no basta con reconocer jurídicamente los derechos humanos, sino de necesario crear las condiciones para sus garantías, enseñarlos y crear una cultura de y para los derechos humanos que se internalice por las personas y se exprese en su hacer diario en aras de una convivencia social de justicia y humanismo. 2. La educación en derechos humanos en la formación de posgrado La meta 4.4 de los ODS está referida a las competencias técnicas y vocacionales; y plantea que hasta el 2030, se debe incrementar sustancialmente el número de jóvenes y adultos que posean las competencias necesarias, en particular técnicas y profesionales, para acceder al empleo, el trabajo decente y el emprendimiento. Por su parte, la meta 4.7, se refiere a una formación de calidad, tanto teórica como práctica encaminada a garantizar que todos los alumnos adquieran los conocimientos teóricos y prácticos necesarios mediante la educación, la adopción de estilos de vida sostenibles, el respeto a los derechos humanos y la igualdad de género, la promoción de una cultura de paz y no violencia, la valoración de la diversidad cultural y la contribución de la cultura al desarrollo sostenible. Se nos plantea así, un paradigma que propone propiciar nuevos modos de reflexión y de pensamiento, con el propósito de crear un movimiento crítico, capaz de influenciar en las decisiones a todos los niveles. Y en este proceso, si bien todos los niveles de enseñanza devienen en importantes, el papel de la Universidad es crucial como organismo encargado de formar a personas en el liderazgo social. Para el logro de la formación de un profesional REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 152 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… participativo, responsable y respetuoso de los derechos humanos que contribuya a transformar la sociedad, la Agenda 2030, define a la Universidad como actor relevante. En este sentido, se reafirma la Declaración Mundial sobre la Educación Superior de la Unesco al establecer, que se ha de prestar especial atención a las funciones de la educación superior al servicio de la sociedad, y más concretamente a las actividades encaminadas a eliminar la pobreza, la intolerancia, la violencia, el analfabetismo, el hambre, el deterioro del medio ambiente y las enfermedades, y a las actividades enfocadas en el fomento de la paz, mediante un planteamiento interdisciplinario y transdisciplinario. Se trata de garantizar una formación universitaria que prevea la adquisición de los conocimientos teóricos y prácticos necesarios para promover el desarrollo sostenible, la adopción de estilos de vida sostenibles, el respeto a los derechos humanos, la igualdad de género y la promoción de una cultura de paz y no violencia. Desde esta visión integral se plantea que la formación en la Universidad, no sólo debe diseñarse en función de la incorporación del sujeto a la vida productiva a través del empleo, sino a partir de una formación profesional que desarrolle habilidades, conocimientos, actitudes, aptitudes y valores en función de lograr un papel proactivo del sujeto en su contexto en función del cambio, la transformación y el respecto a los derechos humanos. Un papel importante para el logro de tales propósitos, lo viene a desempeñar la proyección del Ministerio de Educación Superior en Cuba, pues se ha abocado en los últimos años a perfeccionar los planes de estudios. En el caso de la formación del profesional del Derecho, ha implementado el Plan E, en el que se postula que un profesional del Derecho debe formarse no solo desde el punto de vista técnico, sino también, en los valores esenciales de nuestra sociedad como paradigma conductual para ejercer las funciones propias de la profesión. Por lo que a través de este plan de estudio se deben educar juristas dotados de un alto sentido humanista y de sensibilidad social, conscientes de su papel transformador de la realidad en la que se desenvuelven y de la importancia de la investigación para el desarrollo del conocimiento jurídico. En esta concepción juega un rol fundamental la denominada formación continua, definida por la Red Universitaria de Educación Continua como la actividad docente universitaria REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 153 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… cuya misión es vincularse con el medio a través de programas de formación y capacitación que posibiliten educar de por vida a las personas (licenciados, profesionales, no profesionales) que desean o requieran profundizar, mantenerse al día en los conocimientos, habilidades, actitudes y destrezas que caracterizan a su disciplina, o bien requieran extender su conocimiento hacia áreas complementarias, acceder al manejo de nuevos procedimientos y/o tecnologías que les permitan lograr un mejor desempeño o posición laboral o bien crecer en su desarrollo personal o espiritual. Este tipo de formación, asumida por el sistema de educación superior cubano, de forma intencionada y coherentemente estructurada desde la relación universidad – sociedad, procura también la referida sostenibilidad. Dentro de este diseño, desde cada una de las áreas del conocimiento científico, se habrá de dimensionar, no sólo la adquisición de las herramientas teórico prácticas para un mejor desempeño una vez egresados de la enseñanza superior, sino también, potenciar una cultura de respeto a los derechos humanos, con la convicción de que no son privativos de las ciencias humanísticas, independientemente que estas los potencien y visualicen con mayor claridad. De manera que el reto, desde el prisma que hemos planteado, es incorporar las competencias propias de la especialización desde una concepción en la que se conjuguen la sostenibilidad, la responsabilidad y el compromiso social. Con ella se aspira no sólo a satisfacer los intereses formativos de la entidad en pos de un profesional competente desde su saber y su campo de acción, sino también, dotarlo de una visión encaminada hacia el debate público y abierto en torno al desarrollo sostenible. En esta concepción, no debemos perder de vista, que la competencia es algo más que una habilidad, es el dominio de procesos y métodos para aprender de la práctica, la experiencia y la intersubjetividad. Vistas así, las competencias permiten adquirir una capacidad, donde se combina la pericia con el comportamiento social79; y suponen, como se ha reconocido en el ámbito de la pedagogía, cultivar también cualidades humanas para 79 Por ejemplo, se puede considerar competencia la aptitud para trabajar en equipo, la capacidad de iniciativa y la de asumir riesgos. Las competencias no sólo se aprenden en la escuela, resultan también del empeño y el desempeño del trabajador que, por sus cualidades innatas o subjetivas adquiridas, combina los conocimientos teóricos y los prácticos que lo llevan a adquirir la capacidad de comunicarse, de trabajar con los demás, de afrontar y de solucionar problemas y de mejorar la aptitud para las relaciones interpersonales. REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 154 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… obtener la capacidad de establecer y mantener relaciones estables y eficaces entre las personas. Para nuestros análisis merece una especial referencia las denominadas competencias específicas, definidas como la base particular del ejercicio profesional, y vinculadas a condiciones específicas de ejecución. En este sentido, a través de la educación de posgrado, se debe cumplir el importante reto de desarrollar la capacidad para relacionar los saberes teóricos, prácticos y valorativos. Estos últimos, vienen a desplegar las actitudes que se relacionan con la predisposición y motivación para el autoaprendizaje, y el saber convivir. De manera que devienen en esenciales, no sólo para que el profesional pueda establecer y desarrollar relaciones sociales; sino también, para convertirse en un sujeto garante desde su actuar del respeto a los derechos humanos. Es importante distinguir dentro de este diseño: la calidad y la cualidad. De ahí que en el proceso de formación posgraduada no sólo se dimensione la calidad del conocimiento para el desempeño, sino también, las cualidades que se aprecian desde la actuación del profesional y de este para con los otros actores sociales. Son estos aspectos los que deben tenerse en cuenta a la hora de determinar los niveles de desempeño y los criterios para su evaluación. Resulta así necesario promover una formación posgraduada a través de situaciones problemáticas que le permitan el perfeccionamiento de sus competencias desde la educación en derechos humanos. Para la formación en derechos humanos en la formación posgraduada se necesita una educación donde el profesorado adquiera un compromiso social y ético. Este ha de colaborar con los educandos, para facilitarles la creación y el desarrollo de capacidades que intervengan en el juicio y la acción moral, de manera que se posibilite la formación de actitudes, la integración, la aplicación y la valoración crítica de las normas que rigen en una sociedad. Dentro de esta concepción cobran especial significación, las estrategias didácticas como herramientas individuales o grupales que facilitan la sistematización de la organización y el procesamiento de los aspectos cognoscitivos, afectivos y motores, implicados en los objetivos propuestos. REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 155 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… Para desarrollar estas competencias, se debe lograr que el profesional, a partir de las habilidades adquiridas en la formación de pre grado, y el desempeño en su campo y modo de actuación, perfeccione aquellas y encuentren para su vida un conjunto significativo de comportamientos, que sea capaz de llevar a vías de hecho en el ámbito laboral. Es formar sujetos de derecho desde una perspectiva en la que se deben poseer los conocimientos de los cuerpos normativos relativos a los derechos humanos, y utilizarlos como fundamento para aplicarlos en la promoción y defensa de sus derechos y de los del resto de los actores sociales. Por ello los programas de formación posgraduada deben identificar los conocimientos, habilidades, aptitudes y valores que promuevan la formación de un sujeto de derecho de manera que responda a una educación en derechos humanos. Así mismo, definir su formación con la finalidad de que adquieran las competencias y contribuya a expandir sus capacidades y posibilidades de acción; y en consecuencia, incrementar el poder de actuar en el contexto social donde se desenvuelven. El reto en la educación de posgrado, es lograr a través de una metodología vivencial operativa, un desempeño que estimule no sólo la adquisición de conocimientos sino también de comportamientos. Ello favorece el desarrollo de la capacidad de empatía y capacidades operativas para la promoción, defensa y ejercicio de los derechos humanos. Es formar a un profesional que sea capaz de actuar con argumentos fundamentados e informados, con un discurso asertivo, articulado y racionalmente convincente; en el que, sin incumplir con la legalidad, se manifieste su esencia humanista y el respeto a la justicia. Coincidimos con la idea de que no es sólo fortalecer las habilidades comunicativas. Se trata de desarrollar un pensamiento autónomo estructurado reflexivamente y con disposición a la crítica y al dialogo, y sobre todo, de respeto y aceptación de los puntos de vista divergentes, apreciando el aporte de estas actitudes para la formación personal. Este tipo de formación, le va a conferir la posibilidad de formular afirmaciones y juicios así como, ampliar sus posibilidades de actuar no sólo desde la égida de la norma, sino también, lograr que la argumentación se convierta en una herramienta para convencer razonadamente y persuadir efectivamente a los demás acerca de la validez de sus afirmaciones, con el pleno respeto de la dignidad humana. REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 156 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… Estas ideas dentro de la formación de posgrado no pueden quedar en un discurso. Se deben establecer los estándares que posibiliten evaluar si el aprendizaje refleja la relación: conocimientos- competencias- actitudes en correspondencia con la defensa de los derechos humanos. Por lo que se ha de formar y evaluar a través del programa que cursa: el conocimiento de los derechos humanos, y que sus actitudes reflejen valores de derechos humanos como la igualdad, la no discriminación, la inclusión, la participación en la sociedad, el respeto y la compasión hacia los demás (especialmente hacia las personas más vulnerables y marginadas), es decir, la vocación por la justicia. De lo que se trata es que sean capaces de promover los derechos y analizar el propio entorno usando una perspectiva de derechos humanos así como trabajar colectivamente para abordar problemas. Para ello se deben concebir dentro de los programas de formación posgraduada: métodos de enseñanza participativos, el debate abierto, el aprendizaje colaborativo así como la utilización de casos y técnicas de simulación y los materiales audiovisuales que reflejen situaciones de la vida real del personal encargado de hacer cumplir la ley. En este sentido, el rendimiento relativo a la educación en derechos humanos se monitorea como parte de evaluaciones continuas de rendimiento. Como parte del programa se deben articular evaluaciones coordinadas con los empleadores que posibiliten constatar que la formación adquirida eleva la calidad de su desempeño desde el respeto a la dignidad humana. 3. La formación de la educación en derechos humamos para especialistas en Derecho penal: Una experiencia La enseñanza en derechos humanos en las Universidades españolas ha sido acusada de graves insuficiencias desde principios del siglo XXI, pese al compromiso teórico de España de desarrollarla tras apoyar todas las iniciativas internacionales vistas anteriormente. Desde la perspectiva planteada, si bien en el escenario actual deviene en esencial el desarrollo de competencias, no se debe renunciar al trabajo sistemático durante el proceso formativo en el posgrado de la educación en valores, prestando especial atención a aquellos cuya incidencia recae sobre el respeto a los derechos humanos. Para el profesional que se desempeña en el campo del Derecho penal, rama del ordenamiento REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 157 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… jurídico cuyos efectos se hacen sentir sobre las personas titulares de los referidos derechos, una cultura encaminada a su preservación y respeto se muestra como primordial, pues se trata del ámbito en el que con mayor frecuencia son susceptibles de ser vulnerados. No se puede asumir que por el hecho de ser graduado del Derecho, el egresado lleva implícita en su formación una educación en derechos humanos. Si bien es cierto, que conoce de derechos y sus instrumentos jurídicos internacionales, su reconocimiento y la importancia de sus garantías; el primer debate que se le plantea consiste en eliminar la jerarquización de los derechos e internalizar que todos son derechos humanos. Otras veces en el ejercicio de la profesión, determinadas prácticas, asumidas y asentadas e incorporadas a los recién graduados por aquellos que los guían y orientan en sus primeros pasos como profesionales, abren una brecha cada vez más acentuada para lograr una educación en derechos humanos. Asimilar esta concepción trasciende a la forma de actuar del profesional y de percibir cuándo se ha vulnerado un derecho y cuándo las garantías previstas son insuficientes dentro del diseño de justicia y, más allá de lo que prevé la norma, comprender que es necesario perfeccionar y transformar su modo de hacer. Se trata de conjugar en la formación de competencias de los profesionales del Derecho, y en particular, de aquellos que se desempeñan en el campo penal, la idea de VALLAEYS: “… establecer de qué modo la enseñanza superior puede dar respuesta a la sociedad y contribuir así a un mundo más justo y sostenible” (VALLAEYS, 2008, 191220). Ello implica que los profesionales que ejercen el Derecho penal, reciban una formación a través de los programas de especialización, que le permita no sólo contribuir al perfeccionamiento de su actuación, sino también, que los convierta de forma efectiva en un actor con conocimientos, y una visión del Derecho penal que no sólo queda saldada con la comprensión de lo que significa la condición de última ratio de este, sino también, respetuoso y garante de los derechos humanos en todos los momentos de su actuación respecto a todas las personas. Pensar en cómo se han de implementar las ideas enunciadas nos direccionó hacia un programa de especialización teniendo en cuenta que en Cuba los programas de Especialidad tienen como finalidad la actualización, profundización, perfeccionamiento o ampliación de la competencia laboral para el desempeño profesional especializado y la REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 158 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… innovación en los escenarios inherentes, que requiere de un puesto de trabajo o familia de estos, la solución de problemas específicos de la profesión en correspondencia con las necesidades de la producción y los servicios, así como del desarrollo económico, social, tecnológico y cultural del país. En la Facultad de Derecho de la Universidad de Oriente, en Santiago de Cuba, desde el año 1999 se desarrolla la formación posgraduada de Especialistas en Derecho penal. Durante este período se han formado un total de 599 fiscales, abogados defensores, jueces, investigadores penales y profesores, incorporados a un total de 20 ediciones concluidas. En la fundamentación del programa se plantea como meta: desempeñar una eficaz contribución a la progresiva elevación teórica y práctica para los profesionales que lo cursan, así como coadyuvar, de modo concreto al perfeccionamiento de la práctica jurídica en la esfera de la justicia penal. La justicia penal constituye un amplio y coherente sistema de concepciones teóricas y de regulaciones normativas, en el que se hallan asociadas, de manera estrecha, materias pertenecientes a diversos campos de las ciencias penales. A ello adiciona la pertinencia del programa teniendo en cuenta que el sistema integral de la justicia penal cubano ha alcanzado, en la actualidad, un relevante desarrollo e importancia. Ello exige, como necesidad impostergable, la adopción de medidas de índole diversa, entre ellas las dirigidas a la permanente, apropiada y activa elevación de los conocimientos y a la adquisición de nuevas y consecuentes competencias de los profesionales relacionados, precisamente, con la justicia penal, o sea, jueces, fiscales, abogados, instructores penales, profesores universitarios y especialistas del sistema del Ministerio de Justicia que tramitan los procesos de revisión en materia penal, que constituyen, los destinatarios de este programa de Especialidad de Postgrado. El objetivo general se encamina a proporcionar una amplia y profunda preparación en el campo de las ciencias penales que califique y capacite teórica y prácticamente a los egresados para el ejercicio de la esfera de esta rama jurídica, afianzar los elementos metodológicos fundamentales en el terreno de las investigaciones relacionadas con las ciencias penales, así como desarrollar en los egresados modos de actuación que se REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 159 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… correspondan con los avances alcanzados en el campo de la justicia penal y con las exigencias que demanda el nivel de las actuales necesidades de la justicia penal. Ubicar a los profesionales que ejercen el Derecho penal en las complejidades con que han de desarrollar sus competencias profesionales constituye un objetivo esencial del programa. Es esta una rama del ordenamiento jurídico cubano, que no por haber sido considerada por algunos como la vedette del Derecho, esa de la que todos quieren saber o al menos opinar; se encuentra hoy carente de profundos debates y complejidades, muchos de los cuales, pueden trascender a los derechos humanos que han de ser respetados y protegidos. De ahí, la necesidad de que los graduados de este programa requieran además de conocimientos, de un buen trabajo en equipo, iniciativas que se fundamenten en el principio de legalidad e igualdad y asumir conscientemente los riesgos que puedan derivar de sus actos, ninguno de los cuales puede sustentarse en la oportunidad de lesionar un derecho humano. Para el logro de los objetivos propuestos se desarrollan un total de 6 Módulos, que abarcan 16 cursos, cuyos contenidos esenciales versan sobre: Las teorías sobre el Derecho penal en general y las manifestaciones actuales en algunas figuras delictivas como son las que afectan la economía nacional, las contribuciones de la ciencia criminalística y la medicina legal al esclarecimiento de los hechos delictivos con el aporte que a ellas ofrecen las nuevas tecnologías de la investigación criminal, la criminología y sus tendencias, y dentro de estas la delincuencia organizada y los debates sobre ella en el contexto cubano. Se destaca en su concepción un Módulo: Constitución, Derecho penal y derechos humanos, expresión de la significación y el alcance que la temática de los derechos humanos adquiere para los profesionales que han de egresar de este programa teniendo en cuenta su relevancia para el campo del Derecho penal. El contenido esencial de los cursos que componen cada uno de los módulos del programa, de la Especialidad en Derecho penal desarrollado por la Facultad de Derecho de la Universidad de Oriente de Cuba, no deja lugar a dudas de la presencia de la educación en derechos humanos. Así, todos los cursos están direccionados, no sólo a adquirir los conocimientos que debe tener un profesional del Derecho penal competente, sino también a promover una cultura de respeto a los derechos humanos, particular que es objeto de constatación por los miembros del claustro en la evaluación de los tres componentes REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 160 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… esenciales que lo integran: a saber, el componente académico, el componente laboral y el componente investigativo. Se ha concebido un sistema de evaluación que se lleva a cabo mediante la periódica realización de exámenes, seminarios-debates, solución de complejos problemas prácticos, elaboración de trabajos prácticos sobre los temas concretos abordados durante el curso, la realización de mesas redondas, talleres de aplicación práctica así como otras modalidades evaluativas, que colocan al cursista ante las actuales complejidades del ejercicio del Derecho penal. A través de estas formas evaluativas se conjugan los conocimientos teóricos y jurídicos con su experiencia profesional con la finalidad de desplegar sus iniciativas para la solución de un complejo y polémico asunto de la práctica jurídica, y dar las soluciones al mismo, las que se debaten de manera colectiva para el logro del trabajo en equipo, socializar los conocimientos y promover el debate reflexivo. Una de las formas evaluativas más frecuente son los talleres. Es esta una forma organizativa del proceso docente en la enseñanza posgraduada, que posibilita el debate a partir de las teorías, estudios comparados e investigaciones realizadas, así como el análisis del desempeño en la práctica del cursista. Para ello se orienta con antelación la selección de las sentencias o casos para que a través de una valoración crítica de su propio desempeño, sean capaces de analizar las instituciones teóricas que se utilizaron en el caso, las tendencias en el ámbito del derecho comparado que solucionan este tipo de situación jurídica; y las afectaciones a los derechos humanos y garantías de estos que se producen a través de su actuación. Interesante resulta para el desarrollo de los talleres, la experiencia del claustro, pues el 100 % de sus miembros cuenta con experiencia práctica en el ejercicio del Derecho penal. Ello permite enriquecer los debates que se originan entre los cursistas como resultado de las especificidades de su modo de actuación; bien como fiscal, como abogado defensor, como juez o como investigador criminal. Valoraciones en las que se ubica como centro, los límites que deben de existir como garantía para la afectación de los derechos humanos de otros en su actuación profesional. Los talleres también pueden realizarse también a través de los comentarios de sentencias. Para ello se les indica la selección de la sentencia conforme a la institución que se analiza, REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 161 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… el análisis teórico, el análisis de otras sentencias emitidas por órganos judiciales internacionales, referentes del derecho comparado y sus valoraciones, las que van indicando a los profesionales el camino que como tendencia siguen las interpretaciones del órgano superior de justicia en Cuba y su visión frente a la afectación de los derechos humanos así como desde los estándares que se han delimitado en el ámbito internacional. Ofrece este ejercicio la posibilidad de promover el análisis y respeto a los instrumentos jurídicos internacionales en materia de derechos humanos y de otros pronunciamientos, que formando parte de la política penal guían el respeto a estos derechos. Un ejercicio importante dentro de las actividades evaluativas para el desarrollo de una cultura en derechos humanos se logra a través del intercambio de roles en la solución de casos. Ello le posibilita al cursista responder a una situación jurídica desde otro modo de actuación que no es desde el cual se desempeña en su ejercicio profesional. Es decir, se le entrega un caso y se le pide, por ejemplo, si es fiscal, que lo solucione como abogado defensor, si es juez como fiscal, y si es abogado como juez. Luego, se intercambian los roles, siempre evitando que le corresponda desde el rol que desempeña en el ejercicio profesional. Este tipo de actividad posibilita el análisis no sólo de las instituciones en el orden teórico y normativo, sino también, desarrolla la empatía, la justicia social y el humanismo en los cursistas. Estos se verán compelidos a abordar sus soluciones desde el respeto a los derechos y garantías de los demás sujetos intervinientes en el proceso penal. Se trata de lograr que el cursista no sólo se interese porque se le respete su verdad, sino que valore, hasta donde es respetable la verdad de otro que puede ser su contrario en la relación jurídica. Un momento importante para la educación en derechos humanos dentro del programa lo constituye la evaluación del componente laboral. En el componente laboral del programa define en su objetivo: Perfeccionar las competencias del ejercicio profesional como jueces, fiscales, abogados, instructores penales o especialistas del sistema del Ministerio de Justicia que tramitan los procedimientos de revisión en materia penal y dotarlos de las técnicas y métodos para la ampliación de sus conocimientos en las respectivas funciones, con la finalidad de que éstas se desenvuelvan con elevada profesionalidad, de manera que se alcance una creciente elevación de la calidad en la esfera de la justicia penal. REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 162 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… El cursista frente a un tribunal, presenta y discute a través de casos previamente seleccionados, su desempeño conforme a las competencias que forma el programa. Pensemos en algo básico dentro del ámbito del Derecho penal como lo es la determinación de la medida de la pena, en la que subyacen importantes manifestaciones de humanismo para las partes involucradas en los hechos, incluida la sociedad, frente a la oportunidad de una pena que afecta el derecho a la libertad en determinada medida y la posibilidad de la búsqueda de otras satisfacciones para los perjudicados que pueden privilegiar el sentido sobre la justicia y dimensionar los valores de esos sujetos en materia de derechos humanos. El trabajo final constituye otro momento de constatación de la forma en que los futuros Especialistas en Derecho Penal se han apropiado como parte de sus competencias de la educación en derechos humanos. Los métodos para las investigaciones socio jurídicas resultan de utilidad para el desarrollo por los cursistas de los trabajos finales correspondientes al componente investigativo del programa y el estudio de las particularidades con que se desarrolla el proceso penal cubano en los tiempos actuales. Este ejercicio está dirigido, en lo fundamental, a resolver una problemática de la práctica profesional. El tema deberá ser examinado no solo desde un punto de vista práctico, sino también teórico, por lo que deberán conjugarse la teoría con la práctica. Así mismo, la cuestión tratada en el trabajo final concluye ofreciendo soluciones que contribuyen al perfeccionamiento de la justicia penal cubana y al cumplimiento de las exigencias demandadas por el desarrollo social, económico y político del país. No pueden por supuesto las soluciones ofrecidas por el optante al título de Especialista en Derecho penal encontrarse alejadas del sistema de valores propios del etos de la profesión y especialmente de aquellos que son expresión de los derechos humanos. 4. Conclusiones El reconocimiento del derecho a la educación en todos sus niveles y su efectiva realización como contribución a los esfuerzos de las Naciones Unidas en este campo, constituye un elemento esencial en la calidad de vida de los seres humanos, especialmente dimensionada en la educación posgraduada, a la que se ha prestado por los Estados especial atención en el orden político, normativo y a través de espacios de reflexión y REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 163 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… análisis internacionales y nacionales dedicados a este tema tan sensible para el logro de un desarrollo sostenible. Es la formación de cuarto nivel, a la que corresponde cerrar el ciclo por el que se visualicen los derechos humanos como transversalizadores en todas las relaciones que se establecen entre las universidades y la sociedad en las complejas y diversas áreas del conocimiento humano. A través del desarrollo de su objeto social, ha de llevar un importante mensaje: los derechos humanos y la educación en derechos humanos no son temas privativos de las ciencias sociales y humanísticas, aún y cuando, pueda ser en ellas en las que por razones de sus objetos de estudio, se hagan más ostensibles. El Derecho, ciencia humanística en su esencia, tiene en el Derecho penal la rama del ordenamiento jurídico su rama más sensible frente al tema de los derechos humanos. Pues hace recaer sus efectos, tanto los positivos como los negativos, fundamentalmente, sobre los seres humanos. Razones que justifican que como parte de la superación posgraduada, se incluya el dimensionamiento de la educación en derechos humanos de manera que trascienda al desempeño de los profesionales que se desempeñan en este capo del Derecho. De lo que se trata es que el profesional del Derecho penal adquiera una formación posgraduada encaminada no solo al desarrollo de sus competencias sino también al respeto de los más elementales derechos humanos en cada actuación. Las experiencias que exponemos forman parte, como se ha referido, de las que desarrolla el Claustro del programa de Especialidad en Derecho penal que se imparte por la Facultad de Derecho de la Universidad de Oriente en Santiago de Cuba, República de Cuba. Los resultados obtenidos en este tipo de formación fueron evaluados por la Junta de Acreditación Nacional de la República de Cuba en el año 2019 con la finalidad de a través de la validación de un patrón de calidad, medir esta, tomando como referente los resultados obtenidos en los mismos, vistos a través de su claustro, de sus egresados, de sus beneficiarios y de los cursistas en formación al momento de aplicar el referido patrón de calidad. Se pudo constatar a través entrevistas con egresados de la Especialidad, Empleadores, profesionales que cursaban el programa en el momento de la evaluación y docentes del claustro el alto nivel del programa para la formación de competencias profesionales; y se REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 164 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… destaca, dentro de los elementos aportados por los entrevistados, la contribución del programa a la formación de un profesional del Derecho penal competente y comprometido con la justicia social y más humanista. Dentro de los egresados del programa se logró corroborar los elevados niveles de satisfacción de los egresados del programa con la calidad de su proceso formativo y una valoración positiva sobre la repercusión de los mismos en la calidad de su desempeño profesional, criterio que fue corroborado además por los empleadores de los referidos egresados. Estos aspectos, unido a otros que fueron analizados, trajo como resultado que el programa fuera evaluado con la categoría de Excelencia. Este resultado no sólo habla de su pertinencia, demostrada por la cantidad de ediciones que se han desarrollado y concluido con altos niveles de eficiencia, veinte ya concluidas y por los intereses que hoy se extienden hasta el territorio centro oriental del país, sino por el reconocimiento de sus resultados dentro del Ministerio de Educación Superior cubano y de los organismos del sector jurídico que son sus principales beneficiarios. 165 Como valor añadido, desde el año 2020 hasta la fecha, en Cuba se desarrolla un intenso programa legislativo en el cual participa activamente los egresados del programa y cursistas. Este programa legislativo está encaminado a lograr, tal y como plantea el texto Constitucional cubano aprobado en febrero del 2019, en su artículo 40 que la dignidad humana se constituya en el valor supremo que sustente el reconocimiento y ejercicio de los derechos y deberes consagrados en la Constitución, los tratados y las leyes. Así mismo, se realza, como fundamento jurídico, contenido en el artículo 41 de la ley de leyes cubana la responsabilidad del Estado en el reconocimiento y garantía a las personas del goce y ejercicio irrenunciable, imprescriptible, indivisible, universal e interdependiente de los derechos humanos, en correspondencia con los principios de progresividad, igualdad y no discriminación. Su respeto y garantía es de obligatorio cumplimiento para todos. Como colofón a ello en el artículo 42 se plantea que todas las personas son iguales ante la ley, reciben la misma protección y trato de las autoridades y gozan de los mismos derechos, libertades y oportunidades, sin ninguna discriminación. El establecimiento de las garantías jurídicas y su particularización para el proceso penal REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… como garantías para el debido proceso, es otro de los importantes contenidos de la norma constitucional, al que hacen referencia sus artículos 94 y 95 y que indudablemente ofrecen vialidad al cumplimiento de todos y cada uno de los derechos humanos a que desde el mandato constitucional se les ofrece protección. Estos fundamentos jurídicos, si bien han marcado tradicionalmente la formación de nuestro programa de formación de Especialistas en Derecho penal, hoy se dimensionan y presuponen importantes transformaciones en el diseño de justicia penal cubano. Se impone así, que en aras de proteger cada vez más las garantías de los derechos humanos y ser consecuentes con la educación en derechos humanos que suscribimos en correspondencia con las metas trazadas por los ODS, se perfeccione la contribución que se realiza hoy desde el programa de referencia, a través de su constante perfeccionamiento como lo viene realizando el claustro que lo imparte. Es la participación activa a través de nuestro programa y nuestro compromiso lograr un jurista comprometido con los cambios y transformaciones a que se aspiran en el diseño cubano, en función de la preservación y cumplimiento de las garantías de los derechos humanos. Se nos avizoran nuevos tiempos en los que la educación en derechos humanos habrá de constituir, sin lugar a dudas, el eje transverzalizador de la formación de los especialistas en Derecho penal. Este es sin lugar a dudas el aporte de este programa a las aspiraciones planteadas por los ODS, en la construcción de un mundo de derechos humanos y para los derechos humanos. 5. Bibliografía GARZA, T. J. y PATIÑO, G. S. (2000). Educación en Valores. México Editorial Trillas. GONZÁLEZ GUDIANO. E. (2003). Hacia un Decenio de la Educación para el Desarrollo Sustentable, México, Agua y Desarrollo Sustentable. https://antigo.mma.gov.br/estruturas/educamb/_arquivos/20_11122008091528.pdf. GUTIÉRREZ. J., BENAYAS. J., y CALVO, S. (2006). Educación para el desarrollo sostenible: evaluación de retos y oportunidades del decenio 2005-2014, Revista Ibeoramericana De Educación, 40, 25-69. DOI: https://doi.org/10.35362/rie400781 REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021 166 DARINA ORTEGA LEÓN Y MARÍA ELVIRA BATISTA OJEDA. Hacia el desarrollo sostenible: La… JUÁREZ, J. F, MORENO, M. A (2000). Una Nueva Propuesta para la Educación en Valores. Guía Teórica – Práctica. Colección Valores para Vivir, Caracas (Venezuela). RAMOS, M. G. (2000). Para Educar en Valores. Teoría y Práctica. Valencia-Venezuela. Editorial El Viaje del Pez. Dirección de Medios y Publicaciones. Universidad de Carabobo. VALLAEYS, F. (2008). Responsabilidad Social Universitaria: una nueva filosofía de gestión Ética e Inteligente para las Universidades. Revista Educación Superior y Sociedad, 13 (2), 191-220. 167 REVISTA DE EDUCACIÓN Y DERECHO. EDUCATION AND LAW REVIEW FECHA DE ENTRADA: 16-04-2021 I NÚMERO EXTRAORDINARIO OCTUBRE 2021 FECHA DE ACEPTACIÓN: 15-09-2021
https://openalex.org/W2809151631
https://europepmc.org/articles/pmc6015082?pdf=render
English
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LINC complex-Lis1 interplay controls MT1-MMP matrix digest-on-demand response for confined tumor cell migration
Nature communications
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15,778
ARTICLE ARTICLE ARTICLE With decreasing matrix pore size, cancer cell invasion critically depends on MT1-MMP surface expression to enlarge matrix pores2,11. Inhibition of MT1-MMP function impairs confined cell movement and correlates with increased nuclear deformation, nuclear envelope (NE) rupture and DNA damage2,15,17. Physical features of the matrix and cellular parameters can affect cancer cell motility such as matrix porosity and nuclear stiffness, respectively1–4. We explored potential relations between these parameters and MT1-MMP-dependent pericellular collage- nolysis. Matrix pore size was increased by reducing collagen polymerization temperature to 20 °C instead of 37 °C, the condition used so far, while keeping collagen concentration constant (2.0 mg/ml); this led to a ~2-fold increase in the distance between fibrils (Supplementary Fig. 1d, e)2,21. GM treatment did not result in a significant increase of nuclear deformation in cells invading through the gel of higher porosity (Fig. 1d). In addition, invasion speed in the large pore size gel was not affected by GM treatment contrasting with inhibition observed in the smaller pore size gel (Fig. 1e). These data indicated that in a permissive large pore size collagen environment causing reduced nuclear constriction, MT1-MMP was dispensable for invasion, in agreement with previous observation2. Strikingly, we found that invasion through the higher porosity gel correlated with a ~60% reduction of pericellular collagenolysis as compared to the small pore size collagen network and a lack of proteolysis anterior of the nucleus (Fig. 1b, c, f and Supplementary Fig. 1b). Similarly, pore size enlargement correlated with a significant decrease of collagenolysis by HT-1080 fibrosarcoma cells, while invasion speed was similar in large and small pore size gels (Supplemen- tary Fig. 1f–h). These data indicated that modulation of cell confinement correlated with changes in MT1-MMP-dependent pericellular proteolysis of constricting collagen fibrils. g Cancer cells adjust their levels of surface-exposed MT1-MMP through trafficking from late endosomal/lysosomal storage com- partments18. Whether and how matrix porosity and cell con- finement influence MT1-MMP surface localization remain unexplored. To address these outstanding questions, we used live cell imaging of breast carcinoma and fibrosarcoma cells invading through 3D collagen gels of controlled porosity. We report that invasion through small pore size collagen meshwork triggers an adaptive response with polarized centrosome-centered distribu- tion of MT1-MMP-positive storage endosomes ahead of the nucleus and enhanced MT1-MMP-based pericellular proteolysis of confining collagen fibrils. In contrast, endosome polarization is lost and collagenolysis decreases in cells invading through a permissive large pore size collagen environment. ARTICLE ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 R e n n degradation in front of the nucleus and cleared collagen from the cell path probably through the action of collagenases, consistent with previous observations20. Importantly, when fluorescence intensity of cleaved collagen was measured along the long cell axis of several invasive cells and averaged, a robust pericellular col- lagenolysis in association with the bulky part of the cell anterior to the nucleus was observed, while collagen degradation was minimal at the cell front (Fig. 1b). In agreement with previous findings2,3,17, we observed that 28 ± 2.9% of invasive cells in the 3D collagen gel presented various degrees of nuclear deformation as the nucleus moved through constricting spaces (Fig. 1d and Supplementary Fig. 1a). Moreover, inhibition of MMP activity upon GM6001 (GM) treatment, which reduced invasion speed in 3D collagen by ~2-fold and interfered with pericellular col- lagenolysis (Fig. 1e, f and Supplementary Fig. 1b), correlated with a strong enhancement of nuclear deformation (~55–60% deformed nuclei, see Fig. 1d and Supplementary Fig. 1c). Simi- larly, MT1-MMP silencing using small interfering (si)RNA led to a robust inhibition of pericellular collagenolysis and increased nuclear deformation (Fig. 1d, g and Supplementary Fig. 1b). Altogether, these findings indicated that surface-exposed MT1- MMP enabled efficient cell movement in confinement by med- iating proteolysis anterior of the nucleus. R ecent studies revealed that limited deformability of the nucleus prevents constricted cell movement and that nuclear stiffness is a critical element for the ability of normal and cancer cells to migrate through confined extracellular matrix (ECM) environments1–4. Nuclear rigidity depends on lamin A (LMNA) levels, component of the nuclear lamina acting as a rigid and protective shell underneath the inner nuclear membrane5,6. Down-modulation of LMNA in cancer cells cor- relates with increased nuclear deformability and enhanced cell migration in confined environments by facilitating nucleus squeezing through ECM pores1–4,7–9. q g g p Also critical for metastasis is the capacity of cancer cells to remodel ECM barriers10. Invasion by carcinoma cells is potentiated by pericellular matrix proteolysis, executed by trans- membrane membrane-type 1 matrix metalloproteinase (MT1-MMP)11,12. MT1-MMP is up-regulated during tumor progression and its up-regulation predicts the invasive potential of cancerous breast lesions13,14. In 3D type I collagen network, pericellular ECM proteolysis is associated with the invasive cell protrusion ahead of the nucleus, and is reduced at the cell leading edge, involved in cell-matrix adhesion to support 3D migra- tion15,16. ARTICLE Importantly, modulating LMNA levels with known consequences on nuclear stiffness impinges on MT1-MMP-positive endosome polarity and collagenolysis. We provide evidence that endosome polarization and MT1-MMP-dependent collagenolysis require integrity of the linker of nucleoskeleton and cytoskeleton (LINC) complex that connects the nuclear lamina to cytoskeletal elements in the cytoplasm and the dynein regulator Lis1 involved in nucleus- microtubule cytoskeleton linkage19. Our data support a model whereby focal MT1-MMP-mediated ECM proteolysis response is engaged by mechanical signals during confined migration to facilitate nuclear movement and promote tumor cell invasion. p p y g g Next, the influence of lamin A expression levels, with well described relationship with nuclear stiffness and deformability was tested on MT1-MMP-dependent response. Nuclei from GFPLMNA-overexpressing cells slowed down or even stalled within the 2.5 μm-diameter constrictions of microfabricated channels as compared to GFPH2B-expressing cell nuclei that crossed the constriction in 1–2 h (Supplementary Fig. 2a–d). These findings are in agreement with increased nuclear stiffness induced by elevated LMNA levels1,5. GFPLMNA overexpression did not affect MT1-MMP level nor association of LINC complex components Nesprin-1 and SUN1 to the NE (Supplementary Fig. 2a and e, f). Invasion speed of MDA-MB-231 cells in 20 °C polymerized collagen gel (large pore size) was not affected by overexpression of GFPLMNA as compared to GFPH2B (Fig. 1h). However, contrasting with the reduction of collagenolysis by MDA-MB-231 cells in the permissive large pore size collagen gel LINC complex-Lis1 interplay controls MT1-MMP matrix digest-on-demand response for confined tumor cell migration Elvira Infante1, Alessia Castagnino1, Robin Ferrari1, Pedro Monteiro1, Sonia Agüera Perrine Paul-Gilloteaux 1,2, Mélanie J. Domingues1, Paolo Maiuri 3, Matthew Raa Alexandre Baffet1, Matthieu Piel 1, Edgar R. Gomes 5 & Philippe Chavrier 1 Elvira Infante1, Alessia Castagnino1, Robin Ferrari1, Pedro Monteiro1, Sonia Agüera-González1, Perrine Paul-Gilloteaux 1,2, Mélanie J. Domingues1, Paolo Maiuri 3, Matthew Raab1, Catherine M. Shanahan4, Alexandre Baffet1, Matthieu Piel 1, Edgar R. Gomes 5 & Philippe Chavrier 1 Cancer cells’ ability to migrate through constricting pores in the tissue matrix is limited by nuclear stiffness. MT1-MMP contributes to metastasis by widening matrix pores, facilitating confined migration. Here, we show that modulation of matrix pore size or of lamin A expression known to modulate nuclear stiffness directly impinges on levels of MT1-MMP- mediated pericellular collagenolysis by cancer cells. A component of this adaptive response is the centrosome-centered distribution of MT1-MMP intracellular storage compartments ahead of the nucleus. We further show that this response, including invadopodia formation in association with confining matrix fibrils, requires an intact connection between the nucleus and the centrosome via the linker of nucleoskeleton and cytoskeleton (LINC) complex protein nesprin-2 and dynein adaptor Lis1. Our results uncover a digest-on-demand strategy for nuclear translocation through constricted spaces whereby confined migration triggers polarization of MT1-MMP storage compartments and matrix proteolysis in front of the nucleus depending on nucleus-microtubule linkage. 1 Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d’Ulm, F-75005 Paris, France. 2 Institut Curie, Cell and Tissue Imaging Facility (PICT-IBiSA), 26 rue d’Ulm, F-75005 Paris, France. 3 IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy. 4 BHF Centre of Research Excellence, Cardiovascular Division, King’s College, 125 Coldharbour Lane, SE5 9NU London, UK. 5 Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal. These authors contributed equally: Elvira Infante, Alessia Castagnino, Robin Ferrari, Pedro Monteiro. Correspondence and requests for materials should be addressed to E.I. (email: elvira.infante@kcl.ac.uk) or to P.C. (email: philippe.chavrier@curie.fr) 1 NATURE COMMUNICATIONS | (2018) 9:2443 | DOI: 10.1038/s41467-018-04865-7 | www.nature.com/naturecommunications NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 ARTICLE (Fig. 1f), collagenolysis levels of GFPLMNA-overexpressing cells remained elevated in large, as compared to small, pore size collagen environment (Fig. 1i and Supplementary Fig. 2g). These observations revealed a relationship between LMNA overexpression, known to increase nuclear stiffness and elevated levels of MT1-MMP-mediated ECM proteolysis during 3D invasion. Reciprocally, reduction of LMNA levels has been shown to increase nuclear deformability4,22,23. Results C fi Confinement and nuclear stiffness regulate collagenolysis. The morphology and collagenolysis activity of invasive MDA-MB-231 cells embedded in the 3D fibrillar type I collagen network were analyzed by staining for microtubules and a cleaved collagen neoepitope. After a short 2.5 hrs incubation, different cell morphologies were observed (Fig. 1a): (i) pre-invasive rounded cells with collagen degradation surrounding the cell edge, (ii) cells that initiated invasion as exemplified by limited collagen degra- dation track behind the cell and at the basis of the nascent pro- trusion ahead of the nucleus, (iii) fully invasive cells showing typical elongated mesenchymal organization with collagen NATURE COMMUNICATIONS | (2018) 9:2443 | DOI: 10.1038/s41467-018-04865-7 | www.nature.com/naturecommunications 2 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 Collectively, these findings suggested that endosome polarization in front of the nucleus is part of the response to adjust pericellular collagenolysis and widen constricting pores in the matrix. Polarization of MT1-MMP endosomes during confined migration. In order to identify the mechanism underlying increased collagenolysis during constricted migration, we looked at the dynamic distribution of MT1-MMP-positive storage endosomes in MDA-MB-231 cells invading in 3D collagen by automated endosome tracking over time. In cells invading through the small pore size collagen gel, MT1-MMP-containing endosomes clustered in a region anterior to the nucleus relative to the direction of movement (Fig. 2a and Supplementary Movie 1); The centrosome is positioned ahead of the nucleus. We observed that the centrosome was located in front of the nucleus in cells invading through the 3D small pore size collagen gel and noticed that the centrosome was often located in the vicinity of maximal nuclear constriction when invasion was impaired upon MMP inhibition (Fig. 3a, b). MT1-MMP endosome positioning and clustering around the centrosome are controlled by interac- tions with the microtubule network and dynein and kinesin motor activity24. Thus, nucleus-centrosome linkage and Fig. 1 MT1-MMP-dependent pericellular collagenolysis is an adaptive response to matrix porosity. a MDA-MB-231 cells were embedded in 2.0 mg/ml fluorescent type I collagen (cyan) and polymerization was induced at neutral pH at 37 °C. Cells were fixed after 2.5 hrs and stained for cleaved collagen neoepitope (Col1-3⁄4C antibody, red), α-tubulin (green) and DAPI (blue). Dashed box indicates the region used for line-scan analysis in panel b with yellow, orange and pink dots indicating nucleus center, posterior and anterior limits of regions used for line-scan analysis. Dashed lines indicate initial cell position (thick) and cell rear (thin), respectively. Inset shows nucleus and cleaved collagen signal and arrowheads point to nucleo-anterior collagenolysis. b Averaged maximal fluorescence intensity profiles of cleaved collagen in 37 °C (orange curve) or 20 °C (purple curve) polymerized collagen±SD (left Y- axis) and DAPI (right Y-axis) along cell axis. n, number of cells used to calculate averaged intensity profiles from three independent experiments; “0” on X-axis corresponds to nucleus center. c MDA-MB-231 cells embedded in 20 °C polymerized gel analyzed as in a. d Morphological analysis of DAPI-stained nuclei (see Supplementary Fig. 1a for nucleus shape scoring criteria) in MDA-MB-231 cells in 3D collagen matrix under indicated experimental conditions. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 Data are mean % ± SEM from three independent experiments (except Ctrl at [37 °C], N = 2 and siNT, N = 6); (n), number of cells analyzed. P-values of Kruskal–Wallis test as compared to control condition in each dataset. e MDA-MB-231 cells expressing H2BGFP were embedded in 3D 37 °C or 20 °C polymerized gels. Cells were treated with ethanol (Ctrl) or GM as indicated. Nuclei were automatically tracked from time-lapse sequences obtained from three independent experiments and plot shows the distribution of nuclei speed. n, number of cells analyzed from three independent experiments. Data were transformed using the log transformation y = log(y) to make data conform to normality and analyzed using one-way ANOVA test. f, g Pericellular collagenolysis by MDA-MB-231 cells treated with GM (f) or silenced for MT1-MMP (g) in 37 °C or 20 °C polymerized gels measured as mean intensity of Col1-3⁄4C signal per cell (see Supplementary Fig. 1b for representative images). Values for vehicle-treated (panel f) or siNT-treated cells in 37 °C polymerized gel (g) were set to 100%. n, number of cells analyzed from three to five independent experiments (except experiments in 20 °C polymerized gel, N = 2); Kruskal–Wallis (f) and Mann-Whitney (g) tests. h MDA-MB-231 cells expressing H2BGFP or GFPLMNA were embedded in 3D collagen gel polymerized at 20 °C and invasion speed was analyzed as in e. n number of cells analyzed from three independent experiments. Unpaired t-test. i Pericellular collagenolysis by MDA-MB-231 cells expressing GFPLMNA in 37 °C (set to 100%) or 20 °C polymerized gels (see Supplementary Fig. 2g for representative images). n, number of cells analyzed from three independent experiments; Mann-Whitney test. j Analysis of nuclear deformation in MDA- MB-231 cells knocked down for LMNA in 37 °C polymerized gel as in d. Data are mean % ± SEM from three independent experiments (except siNT, N = 6); (n), number of cells analyzed. P-values of One-way ANOVA test as compared to control condition. k Pericellular collagenolysis by MDA-MB-231 cells knocked down for LMNA in 37 °C polymerized gel normalized to mean intensity of siNT-treated cells ± SEM (see Supplementary Fig. 3c for representative images); n number of cells analyzed from three independent experiments; Kruskal–Wallis test. l Relative invasion of cells penetrating 3D collagen to depths ≥30 μm (see Supplementary Fig. 3d for representative images). NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 3a, b). Reduced LMNA levels correlated with increased nuclear deformation in 3D collagen gel polymerized at 37 °C (55–65% deformed nuclei including 25% polymorphic lobulated nuclei, Fig. 1j) and in cells plated on a thick fibrous collagen layer (Supplementary Fig. 3b). In addition, LMNA KD correlated with increased migration speed of GFPH2B-expressing cells in microchannels (Supplementary Fig. 2c, d). Collectively these data indicated that LMNA-depleted cells had more deformable nuclei and retained full migratory capacity. Remarkably, MT1-MMP-dependent collagenolytic activity in the small pore size collagen gel decreased by ~2-fold upon LMNA KD (Fig. 1k and Supplementary Fig. 3c). Despite reduced collagenolysis, silencing of LMNA correlated with a 1.5–1.7-fold increase of invasion (Fig. 1l and Supplementary Fig. 3d). Thus, reduced LMNA expression enhanced the invasive potential of breast tumor cells by increasing nucleus deformability and its capacity to squeeze through constricted spaces, while MT1-MMP response was lowered down. All together, these findings indicated that MT1-MMP-mediated pericellular collage- nolysis is an adaptive response that is switched on during confined migration in the dense ECM environment, suggesting a relationship between environment, nuclear biomechanics and modulation of active MT1-MMP at the cell surface. ~50% of MT1-MMP-positive endosomes polarized in a 90° quadrant in front of the nucleus relative to movement with a non- uniform distribution as demonstrated by Rao’s Spacing test (P < 0.001, Fig. 2b). In contrast, we observed a striking uniform endosome distribution in MDA-MB-231 cells invading in the large pore size collagen gel polymerized at 20 °C (P > 0.1, Fig. 2d, e and Supplementary Movie 2). Relationship between MT1-MMP endosome polarity and collagen gel porosity was similarly observed in HT-1080 cells (Fig. 2c, f). Then, we examined the consequences of modulating LMNA levels, nuclear deformability and gel porosity on endosome polarization in MDA-MB-231 cells. In the permissive gel polymerized at 20 °C, decreased nuclear deformability upon LMNAGFP overexpression correlated with a remarkable polarization of MT1-MMP endo- somes in front of the nucleus (Fig. 2g, h, compare to Fig. 2d, e, and see Supplementary Movie 3). Conversely, silencing of LMNA correlated with a loss of endosome polarization in front of the nucleus in cells invading through the confining gel polymerized at 37 °C and instead a bimodal endosome distribution was obser- ved (Fig. 2i, j, compare to 2a, b, and see Supplementary Movie 4). NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 LMNA was silenced to ≤5% of endogenous levels using two independent siRNAs with no p xpression, known to increase nuclear stiffness and elevated y of endogenous levels using two independent siRNAs with Invasion speed (μm/min) e Ctrl GM Ctrl GM 0 0.2 0.4 0.6 0.8 **** ns ns n=12 20 21 10 [37 °C] [20 °C] (iii) Invasive a 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 –0.1 –0.2 –0.3 –0.4 –0.5 –0.6 –0.7 –0.8 –0.9 Mean DAPI intensity (a.u.) 0 50 100 150 200 [37 °C] n=24 [20 °C] n=24 Distance to nucleus center (a.u.) 25 50 125 150 Mean collagen degradation (a.u.) 100 75 REAR FRONT b 0 Collagen I [37°C]/Col1-3/4C/α-tubulin/DAPI (i) Pre-invasive (ii) Early invasive Collagen I [20 °C] c Ctrl GM Ctrl GM [37 °C] [20 °C] Collagen degradation (% ctrl) 0 100 50 f 0 50 100 150 n= 1191 909 **** siNT siMT1-MMPS Collagen degradation (% siNT) [37 °C] g **** ns n= 2152 2095 849 830 100 20 60 Ctrl GM Ctrl GM [37 °C] [20°C] [20 °C] siNT siMT1-MMPS [37 °C] Deformed nuclei (%) *** *** ns n= 221 281 611 312 330 274 d 0 GFPLMNA H2BGFP Invasion speed (μm/min) 0 0.2 0.4 0.6 0.8 n=10 n=10 ns h [20°C] [20 °C] 0 50 100 150 Collagen degradation (% [37 °C]) MDA-MB-231 GFPLMNA ns 1153 n = 872 i [37°C] [20°C] [20°C] 100 20 60 0 siNT siLMNA_02 siLMNA_01 j Deformed nuclei (%) n= 611 329 239 [37 °C] **** **** 0 50 100 150 1191 575 n = 948 *** *** siNT siLMNA_02 siLMNA_01 Collagen degradation (% siNT) k [37 °C] 0 50 100 150 200 n = 111 43 51 siNT siLMNA_01 siLMNA_02 3D invasion (% siNT) **** ** l 250 [37 °C] E COMMUNICATIONS | (2018) 9:2443 | DOI: 10.1038/s41467-018-04865-7 | www.nature.com/naturecommunications 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 –0.1 –0.2 –0.3 –0.4 –0.5 –0.6 –0.7 –0.8 –0.9 Mean DAPI intensity (a.u.) 0 50 100 150 200 [37 °C] n=24 [20 °C] n=24 Distance to nucleus center (a.u.) 25 50 125 150 Mean collagen degradation (a.u.) 100 75 REAR FRONT b 0 (iii) Invasive a Collagen I [37°C]/Col1-3/4C/α-tubulin/DAPI (i) Pre-invasive (ii) Early invasive b a c ( ) Collagen I [20 °C] c Ctrl GM Ctrl GM Collagen degradation (% ctrl) 0 100 50 f **** ns n= 2152 2095 849 830 Invasion speed (μm/min) e Ctrl GM Ctrl GM 0 0.2 0.4 0.6 0.8 **** ns ns n=12 20 21 10 100 20 60 Ctrl GM Ctrl GM siNT -MMPS Deformed nuclei (%) *** *** ns n= 221 281 611 312 330 274 d 0 f f d e g 0 50 100 150 n= 1191 909 **** siNT 1-MMPS Collagen degradation (% siNT) g Collagen degradation (% siNT) Deformed nuclei (%) si siMT1-MM [37 °C] l [37 °C] [20°C] [20 °C] s siMT1-MM [37 °C] h i [37 °C] [37 °C] h 100 20 60 0 siNT siLMNA_02 siLMNA_01 j Deformed nuclei (%) n= 611 329 239 [37 °C] **** **** [ GFPLMNA H2BGFP Invasion speed (μm/min) 0 0.2 0.4 0.6 0.8 n=10 n=10 ns h [20°C] [20 °C] i l j i h k 0 50 100 150 200 n = 111 43 51 siNT iLMNA_01 iLMNA_02 3D invasion (% siNT) **** ** 250 Collagen degradation (% siNT) 3D invasion (% siNT) NATURE COMMUNICATIONS | (2018) 9:2443 | DOI: 10.1038/s41467-018-04865-7 | www.nature.com/naturecommunications 3 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 change in MT1-MMP expression nor visible alteration in cytoskeletal organization (Supplementary Fig. Fig. 1 MT1-MMP-dependent pericellular collagenolysis is an adaptive response to matrix porosity. a MDA-MB-231 cells were embedded in 2.0 mg/ml fluorescent type I collagen (cyan) and polymerization was induced at neutral pH at 37 °C. Cells were fixed after 2.5 hrs and stained for cleaved collagen neoepitope (Col1-3⁄4C antibody, red), α-tubulin (green) and DAPI (blue). Dashed box indicates the region used for line-scan analysis in panel b with yellow, orange and pink dots indicating nucleus center, posterior and anterior limits of regions used for line-scan analysis. Dashed lines indicate initial cell position (thick) and cell rear (thin), respectively. Inset shows nucleus and cleaved collagen signal and arrowheads point to nucleo-anterior collagenolysis. b Averaged maximal fluorescence intensity profiles of cleaved collagen in 37 °C (orange curve) or 20 °C (purple curve) polymerized collagen±SD (left Y- axis) and DAPI (right Y-axis) along cell axis. n, number of cells used to calculate averaged intensity profiles from three independent experiments; “0” on X-axis corresponds to nucleus center. c MDA-MB-231 cells embedded in 20 °C polymerized gel analyzed as in a. d Morphological analysis of DAPI-stained nuclei (see Supplementary Fig. 1a for nucleus shape scoring criteria) in MDA-MB-231 cells in 3D collagen matrix under indicated experimental conditions. Data are mean % ± SEM from three independent experiments (except Ctrl at [37 °C], N = 2 and siNT, N = 6); (n), number of cells analyzed. P-values of Kruskal–Wallis test as compared to control condition in each dataset. e MDA-MB-231 cells expressing H2BGFP were embedded in 3D 37 °C or 20 °C polymerized gels. Cells were treated with ethanol (Ctrl) or GM as indicated. Nuclei were automatically tracked from time-lapse sequences obtained from three independent experiments and plot shows the distribution of nuclei speed. n, number of cells analyzed from three independent experiments. Data were transformed using the log transformation y = log(y) to make data conform to normality and analyzed using one-way ANOVA test. f, g Pericellular collagenolysis by MDA-MB-231 cells treated with GM (f) or silenced for MT1-MMP (g) in 37 °C or 20 °C polymerized gels measured as mean intensity of Col1-3⁄4C signal per cell (see Supplementary Fig. 1b for representative images). Values for vehicle-treated (panel f) or siNT-treated cells in 37 °C polymerized gel (g) were set to 100%. n, number of cells analyzed from three to five independent experiments (except experiments in 20 °C polymerized gel, N = 2); Kruskal–Wallis (f) and Mann-Whitney (g) tests. h MDA-MB-231 cells expressing H2BGFP or GFPLMNA were embedded in 3D collagen gel polymerized at 20 °C and invasion speed was analyzed as in e. n number of cells analyzed from three independent experiments. Unpaired t-test. i Pericellular collagenolysis by MDA-MB-231 cells expressing GFPLMNA in 37 °C (set to 100%) or 20 °C polymerized gels (see Supplementary Fig. 2g for representative images). n, number of cells analyzed from three independent experiments; Mann-Whitney test. j Analysis of nuclear deformation in MDA- MB-231 cells knocked down for LMNA in 37 °C polymerized gel as in d. Data are mean % ± SEM from three independent experiments (except siNT, N = 6); (n), number of cells analyzed. P-values of One-way ANOVA test as compared to control condition. k Pericellular collagenolysis by MDA-MB-231 cells knocked down for LMNA in 37 °C polymerized gel normalized to mean intensity of siNT-treated cells ± SEM (see Supplementary Fig. 3c for representative images); n number of cells analyzed from three independent experiments; Kruskal–Wallis test. l Relative invasion of cells penetrating 3D collagen to depths ≥30 μm (see Supplementary Fig. 3d for representative images). Data represent mean ± SEM normalized to invasion of control cells from three independent experiments. n number of cells analyzed from three independent experiments; Kruskal-Wallis test. **P < 0.01; ***P < 0.001; ****P < 0.0001; ns, not significant. Scale bar=10 μm NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 05:10 0° 180° 90° 270° 5 10 c: 12 e: 5031 MDA-MB-231/H2BGFP/ MT1-MMP mCh/siLMNA_01 j Collagen [37 °C] 0.001<P<0.01 i 00:00 00:20 01:00 Collagen [37 °C] MDA-MB-231/siLMNA_01 H2BGFP/MT1-MMPmCh 0° 180° 90° 270° 5 10 15 c: 11 e: 3041 MDA-MB-231/ GFPLMNA/MT1-MMPmCh h Collagen [20 °C] 01:49 03:29 04:00 05:20 Collagen [20 °C] 05:49 GFPLMNA/MT1-MMPmCh g MDA-MB-231/ GFPLMNA/MT1-MMPmCh d Collagen [20 °C] 03:21 04:43 07:28 09:22 09:32 H2BGFP/MT1-MMPmCh MDA-MB-231-H2BGFP/MT1-MMPmCh 5 10 15 HT-1080 H2BGFP/MT1-MMPmCh c: 14 e: 2056 c 0° 90° 270° 180° P<0.001 5 10 0° 180° 90° 270° c: 15 e: 2174 f HT-1080 H2B GFP/MT1-MMP mCh P>0.1 0° 180° 90° 270° 5 10 15 c: 18 e: 4538 e Collagen [20 °C] P >0.1 MDA-MB-231 H2BGFP/MT1-MMPmCh 5 10 15 0° 180° 90° 270° c: 17 e: 4067 b Collagen [37 °C] P<0.001 MDA-MB-231 H2BGFP/MT1-MMPmCh a 00:40 Collagen [37 °C] 01:25 02:05 03:45 H2BGFP/MT1-MMPmCh MDA-MB-231-H2BGFP/MT1-MMPmCh 0.001<P<0.01 MT1-MMPmCh endosome angular distribution olarization of MT1-MMP endosomes is part of the adaptive MT1-MMP-dependent collagenolysis response during confined invasion. a expressing MT1-MMPmCh (red) and H2BGFP (green) were embedded in the 3D small pore size collagen gel and analyzed by time-lap -disk microscopy (see Supplementary Movie 1). The gallery shows representative non-consecutive frames from a representative mov ee independent experiments (time in h:min). Arrows show the direction of migration. b, c Rose plots showing the percentage of MT mes in 15° segments relative to the direction of nucleus movement (0°) scored from time-lapse sequences of MDA-MB-231 T-1080 (c) cells. c number of cells, e number of endosomes analyzed from three independent experiments. P-values for circular unifo test are provided. d Representative frames from a time-lapse sequence of MDA-MB-231 cells invading in the large pore size collage mentary Movie 2). e, f Angular distribution of MT1-MMP endosomes relative to the direction of nuclear movement as in b, c. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 Data represent mean ± SEM normalized to invasion of control cells from three independent experiments. n number of cells analyzed from three independent experiments; Kruskal-Wallis test. **P < 0.01; ***P < 0.001; ****P < 0.0001; ns, not significant. Scale bar=10 μm NATURE COMMUNICATIONS | (2018) 9:2443 | DOI: 10.1038/s41467-018-04865-7 | www.nature.com/naturecommunications 4 4 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 g Galle ntative time-lapse sequence of MDA-MB-231 cells expressing MT1-MMPmCh (red) and GFPLMNA (green) embedded in the large po pplementary Movie 3) h Rose plot of MT1 MMP endosome angular distribution from three independent experiments i Representative a 00:40 Collagen [37 °C] 01:25 02:05 03:45 H2BGFP/MT1-MMPmCh MDA-MB-231-H2BGFP/MT1-MMPmCh 5 10 15 HT-1080 H2BGFP/MT1-MMPmCh c: 14 e: 2056 c 0° 90° 270° 180° P<0.001 f 5 10 15 0° 180° 90° 270° c: 17 e: 4067 b Collagen [37 °C] P<0.001 MDA-MB-231 H2BGFP/MT1-MMPmCh MT1-MMPmCh endosome angular distribution 5 10 15 0° 180° 90° 2 c: 17 e: 4067 b C P< MDA-MB-231 H2BGFP/MT1-MMPmCh MT1 MMP endos 5 10 15 HT-1080 H2BGFP/MT1-MMPmCh c: 14 e: 2056 c 0° 90° 270° 180° P<0.001 0° lagen [37 °C] .001 b a d Collagen [20 °C] 03:21 04:43 07:28 09:22 09:32 H2BGFP/MT1-MMPmCh MDA-MB-231-H2BGFP/MT1-MMPmCh f 5 10 0° 180° 90° 270° c: 15 e: 2174 f HT-1080 H2B GFP/MT1-MMP mCh P>0.1 0° lagen [20 °C] .1 e d h 0° 180° 90° 2 5 10 15 c: 18 e: 4538 e Co P > MDA-MB-231 H2BGFP/MT1-MMPmCh h 5 10 0° 180° 90° 270° c: 15 e: 2174 f HT-1080 H2B GFP/MT1-MMP mCh P>0.1 0° 180° 90° 270° 5 10 15 c: 18 e: 4538 e Collagen [20 °C] P >0.1 MDA-MB-231 H2BGFP/MT1-MMPmCh MDA-MB-231 H2BGFP/MT1-MMPmCh 90° 15 i 00:00 00:20 01:00 Collagen [37 °C] MDA-MB-231/siLMNA_01 H2BGFP/MT1-MMPmCh 01:49 03:29 04:00 05:20 Collagen [20 °C] 05:49 GFPLMNA/MT1-MMPmCh g MDA-MB-231/ GFPLMNA/MT1-MMPmCh i 01:49 03:29 04:00 05:20 Collagen [20 °C] 05:49 GFPLMNA/MT1-MMPmCh g MDA-MB-231/ GFPLMNA/MT1-MMPmCh 180° h 180° 180° g MD 0° 180° 90° 270° 5 10 15 c: 11 e: 3041 MDA-MB-231/ GFPLMNA/MT1-MMPmCh Collagen [20 °C] 0.001<P<0.01 90° 15 i 180° i 00:00 00:20 01:00 Collagen [37 °C] MDA-MB-231/siLMNA_01 H2BGFP/MT1-MMPmCh 01:00 2BGFP/MT1-MMPmCh j 05:10 0° 180° 90° 270° 5 10 c: 12 e: 5031 MDA-MB-231/H2BGFP/ MT1-MMP mCh/siLMNA_01 Collagen [37 °C] 0.001<P<0.01 180° Fig. 2 Polarization of MT1-MMP endosomes is part of the adaptive MT1-MMP-dependent collagenolysis response during confined invasion. a MDA-MB- 231 cells expressing MT1-MMPmCh (red) and H2BGFP (green) were embedded in the 3D small pore size collagen gel and analyzed by time-lapse confocal spinning-disk microscopy (see Supplementary Movie 1). The gallery shows representative non-consecutive frames from a representative movie obtained from three independent experiments (time in h:min). Arrows show the direction of migration. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 b, c Rose plots showing the percentage of MT1-MMP endosomes in 15° segments relative to the direction of nucleus movement (0°) scored from time-lapse sequences of MDA-MB-231 (b) or HT-1080 (c) cells. c number of cells, e number of endosomes analyzed from three independent experiments. P-values for circular uniformity Rao’s Spacing test are provided. d Representative frames from a time-lapse sequence of MDA-MB-231 cells invading in the large pore size collagen gel (see Supplementary Movie 2). e, f Angular distribution of MT1-MMP endosomes relative to the direction of nuclear movement as in b, c. g Gallery from a representative time-lapse sequence of MDA-MB-231 cells expressing MT1-MMPmCh (red) and GFPLMNA (green) embedded in the large pore size gel (see Supplementary Movie 3). h Rose plot of MT1-MMP endosome angular distribution from three independent experiments. i Representative frames of a movie of MDA-MB-231 cells treated with siRNA against LMNA invading through 37 °C polymerized gel (see time-lapse in Supplementary Movie 4). j Rose plot of MT1-MMP endosome angular distribution from three independent experiments. Scale bars=10 μm (b) or HT-1080 (c) cells. c number of cells, e number of endosomes analyzed from three independent experiments. P-values for circular uniformity Rao’s Spacing test are provided. d Representative frames from a time-lapse sequence of MDA-MB-231 cells invading in the large pore size collagen gel (see Supplementary Movie 2). e, f Angular distribution of MT1-MMP endosomes relative to the direction of nuclear movement as in b, c. g Gallery from a representative time-lapse sequence of MDA-MB-231 cells expressing MT1-MMPmCh (red) and GFPLMNA (green) embedded in the large pore size gel (see Supplementary Movie 3). h Rose plot of MT1-MMP endosome angular distribution from three independent experiments. i Representative frames of a movie of MDA-MB-231 cells treated with siRNA against LMNA invading through 37 °C polymerized gel (see time-lapse in Supplementary Movie 4). j Rose plot of MT1-MMP endosome angular distribution from three independent experiments. Scale bars=10 μm centrosome positioning in front of the nucleus could underlie polarization of MT1-MMP endosomes during constricted migration. Anchoring of the nucleus to the centrosome involves LINC complex components SUN and nesprins, which interact with cytoskeletal elements including microtubules25–28. We used overexpression of the dominant negative KASH domain of nesprin-2 (GFPDN-KASH) known to antagonize SUN-nesprin interactions, which displaced nesprin-1 and -2 from the NE of with cytoskeletal elements including microtubules25–28. TURE COMMUNICATIONS | (2018) 9:2443 | DOI: 10.1038/s41467-018-04865-7 | www.nature.com/naturecommunications NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 We used overexpression of the dominant negative KASH domain of nesprin-2 (GFPDN-KASH) known to antagonize SUN-nesprin interactions, which displaced nesprin-1 and -2 from the NE of NATURE COMMUNICATIONS | (2018) 9:2443 | DOI: 10.1038/s41467-018-04865-7 | www.nature.com/naturecommunications 5 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 Scale bars=10 µm H2BmCherry/GFPCentrin 10 0 50 100 200 300 Ctrl GM Time (min) b DAPI/α-tubulin/Pericentrin GM Ctrl a b 4 00:00 00:20 00:59 d Collagen [37 °C] H2BGFP + GFPDN-KASH/MT1-MMPmCh GFPDN-KASH H2BmCherry/GFPCentrin 10 0 50 100 200 300 Ctrl GM Time (min) b Deformed nuclei (%) 0 20 60 100 Ctrl GM Ctrl GM Ctrl GM GFPKASHext GFPDN-KASH GFP c **** n= 256 166 304 192 223 164 ns ns ns ** Deformed nuclei (%) c 00:00 00:20 00:59 d Collagen [37 °C] H2BGFP + GFPDN-KASH/MT1-MMPmCh GFPDN-KASH d c 0 50 100 150 576 460 n= f ** GFPDN-KASH GFPKASHext Collagen degradation (% GFPKASHext) 0° 90° 270° e Collagen [37 °C] H2BGFP/GFPDN-KASH c: 22 e: 13151 10 5 0.01<P<0.05 G 0 50 100 150 45 43 n= g **** GFPDN-KASH GFPKASHext 3D invasion (% GFPKASHext) g e Fig. 3 Nucleus-centrosome linkage through LINC complex is involved in MT1-MMP endosome polarization and collagenolysis-based invasion. a MDA-MB- 231 cells in 3D collagen I polymerized at 37 °C treated or not with GM MMP inhibitor and stained for α-tubulin (green), centrosomal pericentrin (red) and nucleus (blue). b Galleries from representative time-lapse sequences of MDA-MB-231 cells expressing H2BmCherry (magenta) and GFPCentrin-1 (yellow) invading through type I collagen gel as in a. c Morphological analysis of DAPI-stained nuclei as in Fig. 1d. Data are mean % ± SEM from three independent experiments. (n), number of cells analyzed. P-values of Kruskal–Wallis test as compared to non-treated GFP-expressing cells. d Representative frames of a movie of MDA-MB-231 cells expressing MT1-MMPmCh (red) and H2BGFP together with GFPDN-KASH (green) invading through the small pore size collagen gel polymerized at 37 °C (see time-lapse sequence in Supplementary Movie 5). e Rose plots of endosome angular distribution from three independent experiments as in Fig. 2b. P-value for circular uniformity Rao’s Spacing test is provided. f Pericellular collagenolysis by MDA-MB-231 cells expressing GFPDN-KASH in 37 °C polymerized gel normalized to mean intensity of GFPKASHext-expressing cells ± SEM (see Supplementary Fig. 4e for representative images); n, number of cells analyzed from three independent experiments; Mann–Whitney test. g 3D invasion of GFPDN-KASH-expressing cells in the small pore size gel normalized to invasion of GFPKASHext-expressing cells ± SEM from three independent experiments as in Fig. 1l. n number of cells analyzed from three independent experiments (see Supplementary Fig. 4f for representative images); Mann–Whitney test. **P < 0.01; ****P < 0.0001; ns non significant. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 0° 90° 270° e Collagen [37 °C] H2BGFP/GFPDN-KASH c: 22 e: 13151 10 5 0.01<P<0.05 Deformed nuclei (%) 0 20 60 100 Ctrl GM Ctrl GM Ctrl GM GFPKASHext GFPDN-KASH GFP c **** n= 256 166 304 192 223 164 ns ns ns ** 0 50 100 150 45 43 n= g **** 0 50 100 150 576 460 n= f ** GFPDN-KASH GFPKASHext GFPDN-KASH GFPKASHext Collagen degradation (% GFPKASHext) 3D invasion (% GFPKASHext) 00:00 00:20 00:59 d Collagen [37 °C] H2BGFP + GFPDN-KASH/MT1-MMPmCh GFPDN-KASH DAPI/α-tubulin/Pericentrin GM Ctrl a H2BmCherry/GFPCentrin 10 0 50 100 200 300 Ctrl GM Time (min) b Fig. 3 Nucleus-centrosome linkage through LINC complex is involved in MT1-MMP endosome polarization and collagenolysis-based invasion. a MDA-MB- 231 cells in 3D collagen I polymerized at 37 °C treated or not with GM MMP inhibitor and stained for α-tubulin (green), centrosomal pericentrin (red) and nucleus (blue). b Galleries from representative time-lapse sequences of MDA-MB-231 cells expressing H2BmCherry (magenta) and GFPCentrin-1 (yellow) invading through type I collagen gel as in a. c Morphological analysis of DAPI-stained nuclei as in Fig. 1d. Data are mean % ± SEM from three independent experiments. (n), number of cells analyzed. P-values of Kruskal–Wallis test as compared to non-treated GFP-expressing cells. d Representative frames of a movie of MDA-MB-231 cells expressing MT1-MMPmCh (red) and H2BGFP together with GFPDN-KASH (green) invading through the small pore size collagen gel polymerized at 37 °C (see time-lapse sequence in Supplementary Movie 5). e Rose plots of endosome angular distribution from three independent experiments as in Fig. 2b. P-value for circular uniformity Rao’s Spacing test is provided. f Pericellular collagenolysis by MDA-MB-231 cells expressing GFPDN-KASH in 37 °C polymerized gel normalized to mean intensity of GFPKASHext-expressing cells ± SEM (see Supplementary Fig. 4e for representative images); n, number of cells analyzed from three independent experiments; Mann–Whitney test. g 3D invasion of GFPDN-KASH-expressing cells in the small pore size gel normalized to invasion of GFPKASHext-expressing cells ± SEM from three independent experiments as in Fig. 1l. n number of cells analyzed from three independent experiments (see Supplementary Fig. 4f for representative images); Mann–Whitney test. **P < 0.01; ****P < 0.0001; ns non significant. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 Centrosome displacement was measured before (pre) and after Laser beam Pre Pre Post –0.2 0.0 0.2 0.4 0.6 1.4 1.6 Centrosome displacement (μm) n=18 a *** Post Centrosome position Microchannel Nucleus a c Lis1 Lis1/Nesprin-2 0 50 –50 0 50 –50 Time (s) Laser ablation Laser ablation Laser ablation 2 μm 20 μm 30 μm 0 50 –50 b H2BmCh/siR-Tubulin Pre Pre Pre Post Post Post b Centrosome displacement (μm) d Lis1 LMNA siNT siNesprin2 #10 Lis1 LMNA d siNT siLis1 #06 siLis1 #07 0 1 2 Centrosome-nucleus (μm) ** 123 107 123 f n= 3 siNesprin-2 #09 siNesprin-2 #10 * ** **** 103 107 siNT siNesp2 #09 siNesp2 #10 siLis1 #06 siLis1 #07 Pericentrin DAPI siNT siLis1 #06 siLis1 #07 0 1 2 Centrosome-nucleus (μm) ** 123 107 123 f n= 3 siNesprin-2 #09 siNesprin-2 #10 * ** **** 103 107 e Pre Post siNT siNesp2 #09 siNesp2 #10 siLis1 #06 siLis1 #07 Pericentrin DAPI 0 20 40 60 80 100 Lis1 localization (% of cells) siNT n=165 163 175 **** **** GFPKASHext GFPDN-KASH NE + cytoplasm Cytoplasm 140 145 **** siNesprin-2 #09 siNesprin-2 #10 siNT siLis1 #06 siLis1 #07 0 1 2 Centrosome-nucleus (μm) ** 123 107 123 f n= 3 siNesprin-2 #09 siNesprin-2 #10 * ** **** 103 107 e Pr Pos Nucleus Ce A + g siNT siNesp2 #09 siNesp2 #10 siLis1 #06 siLis1 #07 Pericentrin DAPI 0 20 40 60 80 100 iNT is1S % of frames with centrosome ahead of nucleus n=55 n=7 *** 0 20 40 60 80 100 Lis1 localization (% of cells) siNT n=165 163 175 **** **** GFPKASHext GFPDN-KASH NE + cytoplasm Cytoplasm 140 145 **** siNesprin-2 #09 siNesprin-2 #10 e P Po 0 20 40 60 80 100 Lis1 localization (% of cells) siNT n=165 163 175 **** **** GFPKASHext GFPDN-KASH NE + cytoplasm Cytoplasm 140 145 **** siNesprin-2 #09 siNesprin-2 #10 e e Nucleus Centrosome Ahead + g g Lis1 localization (% of cells) Centrosome-nucleus (μm) 0 20 40 60 80 100 siNT siLis1S % of frames with centrosome ahead of nucleus n=55 n=77 **** Fig. 4 Lis1 contributes to nucleus-centrosome linkage in MDA-MB-231 cells. a Schematic representation of MDA-MB-231 cell expressing H2BmCherry and with SiR-tubulin-labeled microtubules migrating through the microfabricated channel. Centrosome displacement was measured before (pre) and after (post) irradiation with the laser beam (blue dots) focused between the nucleus and the centrosome. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 siNT siLis1 #06 siLis1 #07 0 1 2 Centrosome-nucleus (μm) ** 123 107 123 f n= 3 siNesprin-2 #09 siNesprin-2 #10 * ** **** 103 107 Lis1 LMNA siNT siNesprin2 #10 Lis1 Lis1 Lis1 LMNA c Lis1 Lis1/Nesprin-2 e Laser beam Pre Pre Post –0.2 0.0 0.2 0.4 0.6 1.4 1.6 Centrosome displacement (μm) n=18 a *** 0 50 –50 0 50 –50 Time (s) Laser ablation Laser ablation Laser ablation 2 μm 20 μm 30 μm 0 50 –50 b H2BmCh/siR-Tubulin Post Centrosome position Microchannel Nucleus Nucleus Centrosome Ahead + g d siNT siNesp2 #09 siNesp2 #10 siLis1 #06 siLis1 #07 Pericentrin DAPI 0 20 40 60 80 100 siNT siLis1S % of frames with centrosome ahead of nucleus n=55 n=77 **** 0 20 40 60 80 100 Lis1 localization (% of cells) siNT n=165 163 175 **** **** GFPKASHext GFPDN-KASH NE + cytoplasm Cytoplasm 140 145 **** siNesprin-2 #09 siNesprin-2 #10 Pre Pre Pre Post Post Post Fig. 4 Lis1 contributes to nucleus-centrosome linkage in MDA-MB-231 cells. a Schematic representation of MDA-MB-231 cell expressing H2BmCherry and with SiR-tubulin-labeled microtubules migrating through the microfabricated channel. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 Scale bars=10 µm MDA-MB-231 cells (Supplementary Fig. 4a–c), and correlated with a ~10-fold increase in centrosome-nucleus distance (Sup- plementary Fig. 4d)29,30. In contrast, GFPKASHext with a C- terminal extension preventing binding to SUN did not affect nesprin association to the NE nor nucleus-centrosome linkage (Supplementary Fig. 4a–d). Increase in nuclear deformation during 3D invasion in the 37 °C polymerized gel upon MT1- MMP inhibition was suppressed when nucleus-centrosome linkage was loosened by GFPDN-KASH expression but not by GFPKASHext (Fig. 3c). Moreover, front polarization of MT1- MMP-positive endosomes was lost upon GFPDN-KASH over- expression in MDA-MB-231 cells in the small pore size collagen gel (Fig. 3d, e and Supplementary Movie 5). These effects were accompanied by a ~50% reduction of pericellular collagenolysis and invasive potential upon GFPDN-KASH overexpression as compared to GFPKASHext (Fig. 3f, g and Supplementary Fig. 4e, f). To rule out some global cytoskeletal defects due to perturba- tion of nucleus-cytoskeletal linkage induced upon DN-KASH expression, we compared cytoskeletal changes induced by constitutively active Rac1 in cells expressing GFPDN-KASH or not. Expression of activated MycRac1L61 in MDA-MB-231 cells induced the archetypical cortactin-positive lamellipodial exten- sion and cell spreading phenotype (Supplementary Fig. 4g, h). DN-KASH, like the inactive KASHext construct, did not interfere with Rac1L61-induced effects (Supplementary Fig. 4g, h). Thus we concluded that interfering with LINC complex function did not prevent actin filament assembly induced by Rac1 activation at the cell cortex. All together, these findings suggested that NATURE COMMUNICATIONS | (2018) 9:2443 | DOI: 10.1038/s41467-018-04865-7 | www.nature.com/naturecommunications 6 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 counterbalancing forces are exerted on the centrosome through cortically anchored microtubules31–33. We used laser ablation to probe forces in the nucleus-centrosome axis during confined migration of MDA-MB-231 cells in microfabricated channels (Fig. 4a). Centrosome movement was recorded by time-lapse imaging, revealing low-amplitude oscillatory movement (Fig. 4a, b, pre). NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 Dashed green circles, positions of the centrosome before laser irradiation; green dot, centrosome position after irradiation. For each cell analyzed (n = 18), the graph shows paired mean centrosome displacements (in μm) before (pre) and after (post) irradiation; Wilcoxon signed rank test. b Kymographs showing elastic recoil of the centrosome after laser irradiation (time 0). H2BmCherry-labeled nucleus is shown in red, SiR-tubulin-labeled microtubules and the centrosome are in green. c Lis1 and Nesprin-2 immunostaining in MDA-MB-231 cells treated with nocodazole. d MDA-MB-231 cells treated or not with nesprin-2 siRNA were treated with nocodazole and immunostained for Lis1 and LMNA. Insets in c and d represent Lis1 signal of the boxed regions. Arrowheads point at regions of Lis1 association with the NE. e Percentage of cells with Lis1 association with the NE was scored in cells treated with indicated siRNA. n, number of cells analyzed from three independent experiments; Fisher exact test. f Pericentrin and DAPI immunostaining. Scale bars=5 μm. Mean centrosome-nucleus distance (μm) in MDA-MB-231 cells in 3D collagen under indicated conditions ± SEM; n, number of cells analyzed from three (siLis1 and siNesprin-2) or two (siLMNA) independent experiments; Kruskal–Wallis test. g Centrosome position related to the nucleus was scored as schematized from time-lapse sequences of MDA-MB-231 cells expressing GFPcentrin-1 and H2BmCherry and treated with Lis1 siRNA or with control siNT during invasion through the small pore size collagen gel. The graph represents the percentage of frames with the centrosome ahead of the front edge of the nucleus for each cell analyzed and the corresponding Box-and-whisker plot. n, number of cells analyzed from three independent experiments; Mann-–Whitney test. *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001. Scale bars=10 μm perturbation of LINC complex function and nucleus-centrosome linkage interfered with front polarization of MT1-MMP storage compartments and with pericellular collagenolysis during con- fined migration in 3D. perturbation of LINC complex function and nucleus-centrosome linkage interfered with front polarization of MT1-MMP storage compartments and with pericellular collagenolysis during con- fined migration in 3D. Nesprin-2 and Lis1 mediate nucleo-centrosome attachment. Current models in neuronal cells suggest that nucleus-centrosome linkage involves interaction of cytoplasmic dynein anchored at the NE with centrosome-anchored microtubules, while 7 NATURE COMMUNICATIONS | (2018) 9:2443 | DOI: 10.1038/s41467-018-04865-7 | www.nature.com/naturecommunications 7 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 In addition, when centrosome position was scored relative to the nucleus based on movies of MDA-MB-231 cells invading through the small pore size collagen gel polymerized at 37 °C, we found that the centrosome was at ~50% of the time positioned ahead of the nucleus in control cells in agreement with data described above (Fig. 4g). Conversely, the centrosome was only at ~15% of the time positioned in front of the nucleus in cells knocked down for Lis1 (Fig. 4g). Based on these observations we concluded that interfering with Lis1 function affected centrosome positioning in front of the nucleus during confined migration in the collagen matrix, suggesting a role for Lis1 in nucleus- centrosome linkage in MDA-MB-231 cells. g Collagen degradation is mediated by F-actin, Tks5-positive invadopodia forming at the cell cortex in association with collagen fibrils, where MT1-MMP accumulates43–47. MDA-MB-231 cells embedded in a small pore size 3D collagen network formed typical Tks5-positive structures in association with nucleus-constricting fibrils and with collagenolysis (Fig. 5d, e, siNT). In contrast, cells knocked down for nesprin-2 or Lis1 showed reduced accumula- tion of Tks5 and collagen degradation in front of the nucleus (Fig. 5e), in agreement with global decrease in collagenolysis (Fig. 5b). Cortactin- and Tks5-positive structures were also visible at the ventral surface of MDA-MB-231 cells in contact with a ~5–10 µm thick (2.5D) layer of fibrous collagen polymerized at 37 °C allowing quantification of invadopodia formation (Fig. 5f)46,47. Silencing of Lis1 in MDA-MB-231 or HT-1080 cells resulted in a strong inhibition of the formation of Tks5-positive structures (Fig. 5f, g). Total level of Tks5 or MT1-MMP proteins were not affected by Lis1 silencing (Supplementary Fig. 5e). Endogenous Lis1 protein was silenced and Lis1 levels were restored by transfection with a cDNA encoding a siRNA-resistant variant of Lis1GFP (Lis1R#06/GFP, Supplementary Fig. 5f, g). Lis1R#06/GFP rescued assembly of Tks5-positive structures in knocked down cells similar to control levels arguing for a specific effect of Lis1 depletion (Supplementary Fig. 5h). Silencing of Nesprin-2 similarly interfered with formation of Tks5 structures (Fig. 5g), as did disruption of LINC complex function by DN- KASH (Fig. 5h). Altogether, our findings indicated that interfering with LINC complex and Lis1 function in nucleus-centrosome attachment affects pericellular collagenoysis in association with cortical cell-matrix contact sites (see model in Fig. 6). Nesprin-2 and Lis1 regulate nucleo-anterior collagenolysis. The consequences of Lis1 silencing on MT1-MMP-based invasion were analyzed. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 5b). In addition, we found that Lis1 depletion interfered with MT1-MMP endosome polarization ahead of the nucleus during confined migration in the small pore size collagen gel (Fig. 5c and Supplementary Movie 6). Endosome polarization was lost in the large pore size gel irrespective of Lis1 expression (Fig. 5c). Of note, silencing of Lis1 in MDA-MB-231 cells did not alter the overall distribution of MT1-MMP endosomes (Supple- mentary Fig. 5d). In contrast, overexpression of the p50Glued/ dynamitin subunit known to disrupt dynactin complex function led to a dramatic redistribution of MT1-MMP endosomes to the cell periphery (Supplementary Fig. 5d)24,42. Therefore, we con- cluded that Lis1 was unlikely to play a significant role in microtubule-based traffic of MT1-MMP-containing endosomes and that it mainly contributed to MT1-MMP-dependent invasion through the regulation of nucleus/centrosome linkage and cen- trosome positioning. advancing cell protrusion (Fig. 4a, b, post). All together, these data supported the existence of tension forces in the nucleus-centrosome axis during confined migration of MDA-MB-231 cells. Dynein motor and its regulator Lis1, which is essential for high-load dynein functions, have been implicated in nucleus- centrosome linkage during neuronal migration34–37. The prevail- ing model is that SUN-nesprin1/2 complexes mediate nucleo- centrosome attachment by providing anchors to cytoplasmic dynein/Lis1 complexes to pull the nucleus toward the centro- some38. Strong enrichment of Lis1 at the NE has been reported in different cell types upon nocodazole treatment39–41. Using similar conditions, we observed partial co-localization of Lis1 and Nesprin-2 at the NE in MDA-MB-231 cells (Fig. 4c). Lis1 was also associated with cytoplasmic vesicles (Fig. 4c, d). Interestingly, Nesprin-2 KD or GFPDN-KASH expression correlated with a significant reduction of Lis1 association with the NE (Fig. 4d, e). Collectively, these data suggested a contribution of nesprin-2 and LINC complex to Lis1 association with the NE. These observa- tions also highlighted a possible function for Lis1 at the NE. Silencing of Lis1 in MDA-MB-231 cells (85-90% depletion by two independent siRNAs, Supplementary Fig. 5a, b) resulted in a significant 3-4-fold increase of centrosome-nucleus distance (Fig. 4f), similar to findings in Lis1-deficient neurons19,34,35. Silencing of Nesprin-2 (Supplementary Fig. 5c) also increased centrosome-nucleus distance (Fig. 4f), although to a lesser extent as compared to DN-KASH overexpression (Supplementary Fig. 4d). NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 Microtubules located between the nucleus and the centrosome were then ablated by UV laser irradiation; the centrosome under- went elastic recoil towards the cell leading edge probably due to unbalanced pulling forces exerted from cortical sites in the g y p p g 0 Fluorescence (a.u.) Distance (px) 0 10 50 100 Fluorescence DAPI (a.u.) 200 250 300 350 50 100 200 siNesprin-2 #09 1 0 50 100 200 Fluorescence (a.u.) Distance (px) 10 50 100 150 0 10 50 100 Fluorescence DAPI (a.u.) siLIS1 #06 1 0 100 200 3D collagen - Tks5GFP/Col1-3/4C/DAPI Fluorescence (a.u.) Distance (px) 50 10 50 100 0 10 50 100 Fluorescence DAPI (a.u.) siNT 1 siNT siLIS1 #06 1 136 siNesprin-2 #09 1 155 350 1 e 355 siLIS1 #06 Tks5/Coll I Cortactin/Tks5 Tks5/Coll I Cortactin/Tks5 siNT 2.5D collagen - Cortactin/Tks5/Collagen I/DAPI f 1 2 3 1 2 3 3D collagen [37 °C] - Tks5GFP/Col1-3/4C/Coll I [37 °C]/DAPI d Col1-3/4C/Collagen I Tks5/Collagen I Tks5/Col1-3/4C 1 2 2 2 2 siNT siLis1 #06 siLis1 #07 siNesprin-2 #09 siNesprin-2 #10 0 50 100 150 **** **** **** **** **** **** **** **** MDA-MB-231 Tks5+ invadopodia (% of siNT) HT-1080 200 110 94 109 88 100 107 110 111 96 n= g ** GFPKASHext GFPDN-KASH 0 50 100 150 Tks5+ invadopodia (% of GFPKASHext) h 50 n= 41 50 100 150 HT-1080 siNT siLis1 #06 siLis1 #07 0 50 100 150 Collagen degradation (% of siNT) MDA-MB-231 3272 2372 1547 1797 b n= 2453 1324 siNesprin-2 #09 siNesprin-2 #10 1333 1382 1551 921 *** *** *** *** *** *** *** * Invasion speed (μm/min) ns 0 0.5 1.0 1.5 siNT siLis1S n=28 53 25 28 [37 °C] [20 °C] siNT siLis1S MDA-MB-231 H2BGFP *** a 0° 180° 90° 270° 5 10 c: 30 e: 16730 Collagen [37 °C] 0° 180° 90° 270° 5 10 c: 74 e: 44137 0° 180° 90° 270° 5 10 c: 31 e: 16378 Collagen [20 °C] 0° 180° 90° 270° 5 10 c: 28 e: 12259 P<0.001 siNT siNT siLis1S siLis1S P<0.001 P>0.1 P>0.05 MDA-MB-231/H2BGFP/MT1-MMPmCh c 1 [37 °C] [20 °C] NATURE COMMUNICATIONS | (2018) 9:2443 | DOI: 10.1038/s41467-018-04865-7 | www.nature.com/naturecommunications 3D collagen [37 d Invasion speed (μm/min) ns 0 0.5 1.0 1.5 siNT siLis1S n=28 53 25 28 [37 °C] [20 °C] siNT siLis1S MDA-MB-231 H2BGFP *** a [37 °C] [20 °C] 0° 180° 90° 270° 5 10 c: 30 e: 16730 Collagen [37 °C] 0° 180° 90° 270° 5 10 c: 74 e: 44137 0° 180° 90° 270° 5 10 c: 31 e: 16378 Collagen [20 °C] 0° 180° 90° 270° 5 10 c: 28 e: 12259 P<0.001 siNT siNT siLis1S siLis1S P<0.001 P>0.1 P>0.05 MDA-MB-231/H2BGFP/MT1-MMPmCh c 0° 180° 90° 27 5 10 c: 30 e: 16730 Collagen [37 °C] 0° 180° 90° 27 5 10 c: 74 e: 44137 P<0.001 siNT siLis1S P<0.001 MDA-MB-231/H c a c HT-1080 siNT siLis1 #06 siLis1 #07 0 50 100 150 Collagen degradation (% of siNT) MDA-MB-231 3272 2372 1547 1797 b n= 2453 1324 siNesprin-2 #09 siNesprin-2 #10 1333 1382 1551 921 *** *** *** *** *** *** *** * Invasion speed (μm/min) ns 0 0.5 1.0 1.5 siNT siLis1S n=28 53 25 28 [37 °C] [20 °C] siNT siLis1S MDA-MB-231 H2BGFP *** a [37 °C] [20 °C] 70° 70° 0° 180° 90° 270° 5 10 c: 31 e: 16378 Collagen [20 °C] 0° 180° 90° 270° 5 10 c: 28 e: 12259 1 siNT siLis1S 1 P>0.1 P>0.05 H2BGFP/MT1-MMPmCh HT-1080 siNT siLis1 #06 siLis1 #07 0 50 100 150 Collagen degradation (% of siNT) MDA-MB-231 3272 2372 1547 1797 b n= 2453 1324 siNesprin-2 #09 siNesprin-2 #10 1333 1382 1551 921 *** *** *** *** *** *** *** * b P>0.1 Collagen degradation (% of siNT) 0° 0° 180° 90° 270° 5 10 c: 28 e: 12259 siLis1S P>0.05 0° siLis1S c: 28 e: 12259 siLIS1 #06 Tks5/Coll I Cortactin/Tks5 Tks5/Coll I Cortactin/Tks5 siNT 2.5D collagen - Cortactin/Tks5/Collagen I/DAPI f 1 2 3 1 2 3 f 3D collagen [37 °C] - Tks5GFP/Col1-3/4C/Coll I [37 °C]/DAPI d Col1-3/4C/Collagen I Tks5/Collagen I Tks5/Col1-3/4C 1 2 2 2 2 1 d f 0 Fluorescence (a.u.) Distance (px) 0 10 50 100 Fluorescence DAPI (a.u.) 200 250 300 350 50 100 200 siNesprin-2 #09 1 0 50 100 200 Fluorescence (a.u.) Distance (px) 10 50 100 150 0 10 50 100 Fluorescence DAPI (a.u.) siLIS1 #06 1 0 100 200 3D collagen - Tks5GFP/Col1-3/4C/DAPI Fluorescence (a.u.) Distance (px) 50 10 50 100 0 10 50 100 Fluorescence DAPI (a.u.) siNT 1 NT LIS1 #06 1 136 Nesprin-2 09 1 155 350 1 355 Cortactin/Tks5 Cortactin/Tks5 3 2 2 2 siNT siLis1 #06 siLis1 #07 siNesprin-2 #09 siNesprin-2 #10 0 50 100 150 **** **** **** **** **** **** **** **** MDA-MB-231 Tks5+ invadopodia (% of siNT) HT-1080 200 110 94 109 88 100 107 110 111 96 n= g Tks5+ invadopodia (% of GFPKASHext) h 50 100 150 0 Fluorescence (a.u.) Distance (px) 0 10 50 100 Fluorescence DAPI (a.u.) 200 250 300 350 50 100 200 siNesprin-2 #09 1 0 50 100 200 Fluorescence (a.u.) Distance (px) 10 50 100 150 0 10 50 100 Fluorescence DAPI (a.u.) siLIS1 #06 1 0 100 200 3D collagen - Tks5GFP/Col1-3/4C/DAPI Fluorescence (a.u.) Distance (px) 50 10 50 100 0 10 50 100 Fluorescence DAPI (a.u.) siNT 1 1 1 350 355 50 100 150 e siNT siLis1 #06 siLis1 #07 siNesprin-2 #09 siNesprin-2 #10 0 50 100 150 **** **** **** **** **** **** **** **** MDA-MB-231 Tks5+ invadopodia (% of siNT) HT-1080 200 110 94 109 88 100 107 110 111 96 n= g *** GFPKASHext GFPDN-KASH 0 50 100 150 Tks5+ invadopodia (% of GFPKASHext) h 50 n= 41 *** GFPKASHext GFPDN-KASH 0 50 100 150 Tks5+ invadopodia (% of GFPKASHext) h 50 n= 41 h g Tks5+ invadopodia (% of siNT) NATURE COMMUNICATIONS | (2018) 9:2443 | DOI: 10.1038/s41467-018-04865-7 | www.nature.com/naturecommunications 8 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 MDA-MB-231 and HT-1080 cells in the confining collagen environment similar to silencing of LINC complex component Nesprin-2 (Fig. Fig. 5 Lis1 and LINC complex function is required for invadopodia assembly and activity. a Effect of Lis1 KD on invasion speed of MDA-MB-231 cells expressing H2BGFP in 3D collagen gels polymerized at 37 °C or 20 °C (as in Fig. 1e). n, number of cells analyzed from three independent experiments. Data were transformed using the log transformation y = log(y) to make data conform to normality and analyzed using one-way ANOVA test. b Pericellular collagenolysis (mean Col1-3⁄4C signal per cell normalized to mean intensity of siNT-treated cells ± SEM) by MDA-MB-231 and HT-1080 cells silenced for Lis1 or Nesprin-2 in collagen polymerized at 37 °C (as in Fig. 1k). n, number of cells analyzed from three independent experiments. Kruskal–Wallis test as compared to siNT. c Angular distribution of MT1-MMPmCh endosomes in Lis1-depleted cells in 37 °C or 20 °C polymerized collagen gel (as in Fig. 2b). See Supplementary Movie 6. d Maximal projection of a series of sixteen confocal sections (7.5 μm width) of MDA-MB-231 cells expressing Tks5GFP (green) in 3D collagen gel polymerized at 37 °C (Cyan) stained for cleaved collagen (red) and nucleus (blue). Scale bars, 10 μm. Bottom row, two-by-two channel combinations corresponding to boxed region #2. Scale bar=5 μm. e MDA-MB-231 cells silenced for Lis1 or nesprin-2 embedded in 3D collagen as in d, stained for Tks5GFP (green) and cleaved collagen (red). Right row shows intensity profiles of Tks5GFP, Col1-3⁄4C and DAPI maximum intensities along the long-cell axis (dotted line-enclosed regions). f MDA-MB-231 cells silenced for Lis1 were incubated on a thick fibrous type I collagen layer (cyan). Invadopodia in association with collagen fibrils are labeled for cortactin (green) and Tks5 (red). Insets, two-by-two channel combinations of boxed regions. Tks5 is excluded from cortactin-positive lamellipodia (inset #2). Scale bars=10 μm. g Quantification of Tks5 signal in MDA-MB-231 and HT-1080 cells treated with indicated siRNAs plated on a thick layer of type I collagen. Y-axis indicates ratio of Tks5 area to total cell area normalized to mean value in siNT-treated cells (as percentage) ± SEM. n, number of cells analyzed from three independent experiments. Kruskal–Wallis test. h Quantification of Tks5 signal in MDA-MB-231 expressing GFPKASHext or GFPDN-KASH as in panel g from two independent experiments; Mann–Whitney test. *P < 0.05; ***P < 0.001; ****P < 0.0001 Discussion S l physical constraints and confinement. Noticeably, a previous study reported no effect of SUN1 or nesprin-2 KD on invado- podia formation and function in a melanoma cell line55. This discrepancy with our data may be related to difference in matrix environment, i.e., 2D non-fibrillar denatured collagen (gelatin) vs. fibrous native type I collagen in our study with distinct collagenic receptors contributing to invadopodia formation55–59. Several converging studies revealed that nuclear stiffness and nuclear deformability are critical factors that limit confined cell migration through adjacent tissue and basement membrane transmigration by carcinoma cells1–4,7. In addition, recent reports have shown that confinement can generate mechanical stress on the nucleus as exemplified by nuclear deformations and loss of NE integrity and DNA damage3,17,48,49. Increased nucleus deformability as a consequence of LMNA down-modulation can facilitate the migration of cancer cells through small constrictions in reconstituted 3D matrix environments2–4,8,9. Nucleus migra- tion through constricted spaces is also central to several devel- opmental processes50. g Additional mechanisms of tumor cells have been described that lead to nuclear deformation through formation of perinuclear actin- and actomyosin-based structures in association with LINC complex components including nesprin-family proteins. These mechanisms enable nucleus squeezing through narrow spaces and correlate with increased invasiveness and metastatic potential60– 63. In addition, a nuclear piston mechanism based on actomyosin contractility has been described, which generates high pressure within the anterior cytoplasmic compartment and enables migration through the 3D confining matrix64. This mechanism was recently reported to represent a strategy for nuclear forward movement through confining 3D environments that could com- pensate for low MMP activity65. The adaptive MT1-MMP-based collagenolysis response to confinement that we described here and the nuclear piston mechanism may represent different molecular systems consequential to nuclear stiffness and nuclear forward movement during confined migration. An intriguing possibility is whether the nuclear piston mechanism may con- tribute to nucleo-anterior polarization of MT1-MMP compart- ments. More work will be needed to determine the contribution and integration of these mechanisms to the metastatic program to tumor cell plasticity. Future studies should also unravel how these mechanisms are integrated with and possibly control invadopodia formation and targeted delivery of MT1-MMP to the cell surface for dissolution of confining ECM fibrils. p p Our findings reveal a novel mechanism in which tumor cells adapt to the 3D matrix environment based on a digest-on- demand response to support confined migration in the tissue matrix. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 Nucleus-microtubule cytoskeleton linkage through LINC complex and dynein heavy load factor Lis1 and cortical anchoring of microtubules is required for centrosome and MT1-MMP endosome positioning and for targeted delivery of MT1-MMP to invadopodia. Nucleus movement is facilitated by localized invadopodia-based pericellular proteolysis of confining fibrils ahead of the nucleus. Open arrows represent nuclear pulling force and counteracting forces from the matrix. Inset, scheme of nucleus- cytoskeletal linkage through LINC complex components nesprin and SUN in association with lamins. Lis1, probably in complex with dynein associates to the NE depending on Nesprin-2 and is involved in nucleus-microtubule linkage Discussion S l This mechanism depends on LINC complex-mediated linkage of the nucleus to the microtubule-centrosome network and to high-load dynein adaptor Lis1 (see Fig. 6). It is known that mechanical coupling of the nucleus to the cell cortex through cytoskeletal elements enables force transmission to the nucleus in a LINC complex-dependent manner30,51. Our data suggest a model whereby anchoring of dynein and its regulator Lis1 to the NE mediated by the LINC complex is involved in generation of forward nucleus pulling force on the microtubule-centrosome system19,26,35,52–54. We hypothesize that nucleus forward-pulling forces generate nuclear deformation due to the resistance opposed by constricting matrix fibrils during confined cell migration and that nucleo-cortex linkage may contribute to the assembly of invadopodial structures at plasma membrane-matrix contact sites resulting in focal degradation of confining fibrils (Fig. 6). It may seem paradoxical that interfering with LINC complex or Lis1 function affects invadopodia formation in cells cultured on top of a 2D collagen layer (see Fig. 5f–h). However, under these con- ditions we observed some pulling and pushing activities of cells on the surrounding collagen fibrils, and cells also squeezed through fibrils, all situations that may lead to some level of NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 Lis1 KD significantly reduced the invasion speed of MDA-MB-231 cells in the small pore size gel, while it did not affect invasion in the permissive 20 °C polymerized collagen environment (Fig. 5a). Correlating with the reduction of invasive potential in the small pore size collagen gel, depletion of Lis1 resulted in a strong reduction of pericellular collagenolysis by NATURE COMMUNICATIONS | (2018) 9:2443 | DOI: 10.1038/s41467-018-04865-7 | www.nature.com/naturecommunications 9 9 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 Nucleus Nucleus SUN LMNA Nesprin (KASH) Dynein/Lis1 Dynein/Lis1 Endosome MT1-MMP+ Invadopodia Microtubules Centrosome Cleaved fibrils ECM fibrils Fig. 6 Model of LINC complex-, Lis1-dependent nucleus-centrosome linkage control of MT1-MMP matrix digest-on-demand response. Confined migration of tumor cells through dense 3D collagen network results in nucleus confinement by constricting collagen fibrils. Nucleus-microtubule cytoskeleton linkage through LINC complex and dynein heavy load factor Lis1 and cortical anchoring of microtubules is required for centrosome and MT1-MMP endosome positioning and for targeted delivery of MT1-MMP to invadopodia. Nucleus movement is facilitated by localized invadopodia-based pericellular proteolysis of confining fibrils ahead of the nucleus. Open arrows represent nuclear pulling force and counteracting forces from the matrix. Inset, scheme of nucleus- cytoskeletal linkage through LINC complex components nesprin and SUN in association with lamins. Lis1, probably in complex with dynein associates to the NE depending on Nesprin-2 and is involved in nucleus-microtubule linkage Nucleus Nucleus SUN LMNA Dynein/Lis1 Endosome MT1-MMP+ Invadopodia Microtubules Centrosome Cleaved fibrils ECM fibrils Fig. 6 Model of LINC complex-, Lis1-dependent nucleus-centrosome linkage control of MT1-MMP matrix digest-on-demand response. Confined migration of tumor cells through dense 3D collagen network results in nucleus confinement by constricting collagen fibrils. Nucleus-microtubule cytoskeleton linkage through LINC complex and dynein heavy load factor Lis1 and cortical anchoring of microtubules is required for centrosome and MT1-MMP endosome positioning and for targeted delivery of MT1-MMP to invadopodia. Nucleus movement is facilitated by localized invadopodia-based pericellular proteolysis of confining fibrils ahead of the nucleus. Open arrows represent nuclear pulling force and counteracting forces from the matrix. Inset, scheme of nucleus- cytoskeletal linkage through LINC complex components nesprin and SUN in association with lamins. Lis1, probably in complex with dynein associates to the NE depending on Nesprin-2 and is involved in nucleus-microtubule linkage Fig. 6 Model of LINC complex-, Lis1-dependent nucleus-centrosome linkage control of MT1-MMP matrix digest-on-demand response. Confined migration of tumor cells through dense 3D collagen network results in nucleus confinement by constricting collagen fibrils. Methods Plasmid constructs. Construct expressing Tks5GFP was a kind gift of Dr S. Courtneidge (OHSU, Portland, OR). Retroviral vector encoding H2BGFP and GFPLMNA were provided by F. A. Dick (UWO, London, ON, Canada) and T. ARTICLE For transient expression, MDA-MB-231 cells or HT-1080 cells were transfected with plasmid constructs using AMAXA nucleofection (Lonza). Cells were analyzed by live cell imaging 24–48 h after transfection. For knockdown, MDA-MB-231 cells were treated with the indicated siRNA (50 nM, Dharmacon) using Lullaby (OZ Biosciences, France) and analyzed after 72 h of transfection. The following siRNAs were used: siNT (Non Targeting), siLMNA-01: 5′-GGUGGUGACGAUC UGGGCU-3′; siLMNA-02: 5′-CUGGGCAGGUGGUGACGAU-3′; siMT1-MMPS (Smartpool): 5′-GGAUGGACACGGAGAAUUU-3′; 5′-GGAAACAAGUACUAC 3D type I collagen invasion assay. 200 μl of 2.0 mg/ml Collagen I was allowed to polymerize in transwell inserts (Corning) for 2 h at 37 °C as above. Cells were seeded on top of the collagen gel in complete medium and 20 ng/ml HGF was added to the medium in the bottom chamber of the transwell as chemoattractant. After 48 h of seeding, cells were fixed and stained with DAPI and visualized by confocal microscopy with serial optical sections captured at 10-µm intervals with a ×10 objective on a Zeiss LSM510 confocal microscope. Invasion was measured by dividing the sum of DAPI signal intensity of all slides beyond 30 μm (invading cells) by the sum of the intensity of all slides (total cells). Antibodies and reagents. The source and working dilution of commercial anti- bodies used for this study are listed in Supplementary Table 1. Monoclonal anti- body against Nesprin-2A has been previously described66,67. Nocodazole (Sigma) was diluted in DMSO and used at a concentration of 10 μM. GM6001 (Millipore) diluted in ethanol was used at a concentration of 40 μM. Hepatocyte growth factor (HGF) was purchased from PeproTech Inc. and used at 20 ng/ml. Live-cell imaging in 3D type I collagen. For Inter-fibril distance estimation, a 50 µl drop of 2.0 mg/ml fluorescently-labeled Collagen I was allowed to polymerize for 2 h at 37 °C or 20 °C as described above. Distances between collagen fibrils were measured from stacks of 30 optical sections acquired at 0.5 μm-interval with a SP8 Leica laser confocal microscope in the xy, xz, and yz planes (15 µm depth) using a 63 × 1.4NA oil objective, 4 detection channels (2 PMTs and 2 hybrid Detectors) and 405, 488, 561 and 633 nm laser lines. The system was steered by Leica Application Suite (LAS-X) software. ARTICLE For live cell imaging, glass bottom dishes (MatTek Corporation) were layered with 10 µl of a solution of 5 mg/ml unlabeled type I collagen mixed with 1/20-40 volume of Alexa Fluor 647-labeled collagen. Polymerization was induced at 37 °C or 20 °C for 3 min as described above, and the bottom collagen layer was washed gently in PBS and 1 ml of cell suspension (1.5–2.5 × 105 cells/ml) in complete medium was added. Cultures were incubated for 30 min at 37 °C, then medium was gently removed and two drops of a mix of Alexa Fluor 647-labeled type I collagen/unlabeled type I collagen at 2.0 mg/ml final concentration were added on top of the cells (top layer). After polymerization at 37 °C or 20 °C for 90 min as described above, 1 ml of medium containing 20 ng/ml HGF was added to the cultures. z-staks of images were acquired every 5 min (150 ms exposure time) during 16 h by confocal spinning disk microscopy (Roper Scientific) using a CSU22 Yokogawa head mounted on the lateral port of an inverted TE-2000U Nikon microscope equipped with a 40 × 1.4NA Plan-Apo objective lens and a dual-output laser launch, which included 491 nm and 561 nm 50 mW DPSS lasers (Roper Scientific). Images were acquired with a CoolSNAP HQ2 CCD camera (Roper Scientific). The system was steered by Metamorph 7 software. Western blot analysis. Cells were lysed in SDS sample buffer, separated by SDS-PAGE, and detected by immunoblotting analysis with the indicated anti- bodies. Antibodies were visualized using the ECL detection system (GE Healthcare) Indirect immunofluorescence microscopy. Samples were fixed with 4% paraf- ormaldehyde, permeabilized with 0.1% Triton X-100, and then incubated with indicated antibodies. For alpha-tubulin staining samples were fixed with 4% par- aformaldehyde at 37 °C for 30 min. For better visualization of Lis1 association with the NE, cells were incubated for 1 h in nocodazole (10 μM) prior to fixation35,39– 41,68. The analysis of MT1-MMPmCh endosome position relative to the cell center/ cell periphery axis was performed, as described in ref. 24. Invadopodia formation assay. Coverslips were layered with 200 µl of ice-cold 2.0 mg/ml acidic extracted collagen I solution (Corning) in 1 × MEM mixed with Alexa Fluor 647-conjugated type I collagen (5% final). The collagen solution was adjusted to pH7.5 using 0.34 N NaOH and Hepes was added to 25 µM final concentration. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 Misteli (Addgene #17662), respectively. Lentiviral vector encoding H2BmCh was from M. Mercola (Addgene #21217). The GFPCentrin-1 plasmid was obtained from M. Bornens (Institut Curie, Paris, France). pRK5mycRac1L61 was a kind gift of Dr S. Etienne-Manneville (Institut Pasteur, Paris, France). GFPDN-KASH and GFPKASHext were generated by inserting the C-terminal domain of Nesprin-2 (corresponding to the last 331 amino acids) into the XhoI–BamHI site of pECFP- C1 (Takara Bio Inc.). KASHext was derived from the DN-KASH construct by adding a C-terminal VDGTAGPGSTGSR amino acid extension29. For Lis1 rescue experiment, LIS1GFP construct was mutagenized to make it resistant to siLIS1#06 siRNA using the QuikChange Primer Design kit (Agilent) using: forward primer; 5′-CTCTGCTTCcGAGGATGCTACTATcAAaGTtTGGGAcTACGAGAC TGGAGATTTTGAA-3′; reverse primer: 5′-AAAATCTCCAGTCTCGTAgTCCC AaACtTTgATAGTAGCATCCTCgGAAGCAGAG-3′. Quantification of pericellular collagenolysis. Cells treated with indicated siRNAs and expressing indicated GFP-tagged constructs were trypsinized and resuspended (2.5 × 105 cells/ml) in 0.2 ml of ice-cold ( ) 2.0 mg/ml acidic extracted collagen I solution in 1 × MEM, pH 7.5 buffer. The pH of the collagen solution was raised to 7.5 using 0.34 N NaOH and Hepes was added to 25 µM final concentration. 40 µl of the cell suspension in collagen was added on to 25 µM final concentration. 40 µl of the cell suspension in collagen was added on a 18 mm-diameter glass coverslip and collagen polymerization was induced by incubation for 90 min at 20 °C or 30 min at 37 °C. After polymerization, complete medium was added and collagen-embedded cells were incubated for 16 h at 37 °C. After fixation in 4% paraformaldehyde in PBS at 37 °C for 30 min, samples were incubated with anti–Col1-3/4C antibodies (2.5 µg/ml) for 2 h at 4 °C, washed extensively with PBS and counterstained with Cy3-conjugated anti-rabbit IgG antibodies and with Phalloïdin-Alexa488 to visualize cell shape and with DAPI. Image acquisition was performed with an A1r Nikon confocal microscope with a 40 × NA 1.3 oil objective using high-sensitivity GaASP PMT detector and a 595 ± 50 nm band-pass filter. Quantification of degradation spots was performed as previously described47. Briefly, maximal projection of 10 optical sections with 2 μm interval from confocal microscope z-stacks (20 µm depth) were preprocessed by a laplacian of Gaussian filter using a homemade ImageJ macro (available as sup- plementary information in47). Detected spots were then counted and saved for visual verification. No manual correction was done. ARTICLE Degradation index was the number of degradation spots divided by the number of cells present in the field, normalized to the degradation index of control cells set to 100. Nuclear defor- mation was visually and qualitatively assessed from maximal projection of 10 optical sections of DAPI signal from confocal microscope z-stacks (20 µm depth) by scoring nuclei as “normal” or “deformed” using criteria as described in Sup- plementary Fig. 1a. µ µ p g a 18 mm-diameter glass coverslip and collagen polymerization was induced by incubation for 90 min at 20 °C or 30 min at 37 °C. After polymerization, complete medium was added and collagen-embedded cells were incubated for 16 h at 37 °C. After fixation in 4% paraformaldehyde in PBS at 37 °C for 30 min, samples were 3/4 Cell culture, stable and transient transfection and siRNA treatment. MDA- MB-231 cells (ATCC HTB-26) were grown in L15 medium supplemented with 15% foetal calf serum and 2 mM glutamine at 37 °C in 1% CO2. HT-1080 fibro- sarcoma cells (ATCC CCL-121) were grown in DMEM GlutaMAX supplemented with 10% foetal calf serum. Cell lines were obtained from ATCC and were routinely tested for mycoplasma contamination. MDA-MB-231 cells stably expressing H2BGFP/mCh, MT1-MMPmCh or GFPLMNA and MT1-MMPmCh or HT-1080 cells stably expressing MT1-MMPmCh were generated by lentiviral transduction. For transient expression, MDA-MB-231 cells or HT-1080 cells were transfected with plasmid constructs using AMAXA nucleofection (Lonza). Cells were analyzed by live cell imaging 24–48 h after transfection. For knockdown, MDA-MB-231 cells were treated with the indicated siRNA (50 nM, Dharmacon) using Lullaby (OZ Biosciences, France) and analyzed after 72 h of transfection. The following siRNAs were used: siNT (Non Targeting), siLMNA-01: 5′-GGUGGUGACGAUC UGGGCU-3′; siLMNA-02: 5′-CUGGGCAGGUGGUGACGAU-3′; siMT1-MMPS (Smartpool): 5′-GGAUGGACACGGAGAAUUU-3′; 5′-GGAAACAAGUACUAC CGUU-3′; 5′-GGUCUCAAAUGGCAACAUA-3′; 5′-GAUCAAGGCCAAUGUU CGA-3′; siLis1S (Smartpool): 5′-CAAUUAAGGUGUGGGAUUA-3′ (siLis1#06); 5′-UGAACUAAAUCGAGCUAUA-3′ (siLis1#07); 5′-GGAGUGCCGUUGAUUG UGU-3′; 5′-UGACAAGACCCUACGCGUA-3′; siNesprin-2S (Smartpool): 5′AGG AAUUUCUGCAAACCGA-3′ (siNesprin-2#09); 5′GGUAGAACGUCAACCUCA A-3′ (siNesprin-2#10); 5′CCUAGAGUGUCGGAGGGAA-3′; 5′CACAGGAGCU UCACAAUAA-3′. Cell culture, stable and transient transfection and siRNA treatment. MDA- MB-231 cells (ATCC HTB-26) were grown in L15 medium supplemented with 15% foetal calf serum and 2 mM glutamine at 37 °C in 1% CO2. HT-1080 fibro- sarcoma cells (ATCC CCL-121) were grown in DMEM GlutaMAX supplemented with 10% foetal calf serum. Cell lines were obtained from ATCC and were routinely tested for mycoplasma contamination. MDA-MB-231 cells stably expressing H2BGFP/mCh, MT1-MMPmCh or GFPLMNA and MT1-MMPmCh or HT-1080 cells stably expressing MT1-MMPmCh were generated by lentiviral transduction. Methods Plasmid constructs. Construct expressing Tks5GFP was a kind gift of Dr S. Courtneidge (OHSU, Portland, OR). Retroviral vector encoding H2BGFP and GFPLMNA were provided by F. A. Dick (UWO, London, ON, Canada) and T. NATURE COMMUNICATIONS | (2018) 9:2443 | DOI: 10.1038/s41467-018-04865-7 | www.nature.com/naturecommunications 10 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 2. Wolf, K. et al. Physical limits of cell migration: control by ECM space and nuclear deformation and tuning by proteolysis and traction force. J. Cell. Biol. 201, 1069–1084 (2013). were then converted to this nucleus velocity-dependent coordinate system. Endosomes exactly in front of the nucleus in the direction of movement are then at 0° and endosomes exactly at the rear of the displacement vector are at 180°. All data created for endosomes for all processed nuclei and all movies for one condition were then pooled to create a polar histogram (radar plot), showing the distribution of endosomes relative to the direction of nuclear movement. 3. Harada, T. et al. Nuclear lamin stiffness is a barrier to 3D migration, but softness can limit survival. J. Cell. Biol. 204, 669–682 (2014). 4. Davidson, P. M., Denais, C., Bakshi, M. C. & Lammerding, J. Nuclear deformability constitutes a rate-limiting step during cell migration in 3-D environments. Cell Mol. Bioeng. 7, 293–306 (2014). Averaged Col1-3/4C intensity profiles. Col1-3/4C neoepitope (collagen degra- dation) and DAPI (nucleus) intensity profiles were obtained using the line-scan function (maximal intensity) of Metamorph analyzing the back-to-front cell region including the nucleus for both signals (see Fig. 1a, c). Then, we used a homemade Matlab program (available on demand) to normalize line-scans to correct for line- scan length difference. Briefly, three reference points were manually defined based on the DAPI signal profile; the nucleus center and the back and front of the cell, respectively. These reference points were used to define a linear transformation such that they became 0, −1, and 1 coordinates, respectively on the normalized curves, allowing direct comparison of different profiles. 5. Lammerding, J. et al. Lamins A and C but not lamin B1 regulate nuclear mechanics. J. Biol. Chem. 281, 25768–25780 (2006). 6. Swift, J. et al. Nuclear lamin-A scales with tissue stiffness and enhances matrix-directed differentiation. Science 341, 1240104 (2013). 7. Fu, Y., Chin, L. K., Bourouina, T., Liu, A. Q. & VanDongen, A. M. Nuclear deformation during breast cancer cell transmigration. Lab Chip 12, 3774–3778 (2012). 8. Bell, E. S. & Lammerding, J. Causes and consequences of nuclear envelope alterations in tumour progression. Eur. J. Cell Biol. 95, 449–464 (2016). ( ) 9. Irianto, J., Pfeifer, C. R., Ivanovska, I. L., Swift, J. & Discher, D. E. Nuclear lamins in cancer. Cell Mol. Bioeng. 9, 258–267 (2016). ARTICLE Centrosome-nucleus distance measurement. Cells were embedded in 2.0 mg/ml type I collagen polymerized at 37 °C as above. After 16 h, cultures were fixed with 4% paraformaldehyde and stained using polyclonal rabbit anti-pericentrin anti- bodies. Detection was performed with fluorescently-labeled anti-rabbit antibody. DNA was stained with DAPI. Centrosome-to-nucleus distance was determined by overlaying pericentrin and DAPI images and extending a line from the centrosome (center of pericentrin staining) to the nearest point of the nucleus rim; length of this line was measured using ImageJ software tools. 10. Rowe, R. G. & Weiss, S. J. Breaching the basement membrane: who, when and how? Trends Cell Biol. 18, 560–574 (2008). 11. Sabeh, F., Shimizu-Hirota, R. & Weiss, S. J. Protease-dependent versus -independent cancer cell invasion programs: three-dimensional amoeboid movement revisited. J. Cell. Biol. 185, 11–19 (2009). 12. Kessenbrock, K., Plaks, V. & Werb, Z. Matrix metalloproteinases: regulators of the tumor microenvironment. Cell 141, 52–67 (2010). 13. Perentes, J. Y. et al. Cancer cell-associated MT1-MMP promotes blood vessel invasion and distant metastasis in triple-negative mammary tumors. Cancer Res. 71, 4527–4538 (2011). Microfabrication of microchannels. Micro-channels were prepared as previously described69. Briefly, polydimethylsiloxane (PDMS) (GE Silicones, 10/1 w/w PDMS A/crosslinker B) was used to prepare 7 µm-wide micro-channels with 2.5 µm constrictions from a self-made mold. Channels with constrictions were washed with PBS at least three times and incubated with complete medium for at least 5 h before adding the cells. 14. Lodillinsky, C. et al. p63/MT1-MMP axis is required for in situ to invasive transition in basal-like breast cancer. Oncogene 35, 344–357 (2016). 15. Wolf, K. et al. Multi-step pericellular proteolysis controls the transition from individual to collective cancer cell invasion. Nat. Cell Biol. 9, 893–904 (2007). 16. Doyle, A. D. & Yamada, K. M. Mechanosensing via cell-matrix adhesions in 3D microenvironments. Exp. Cell Res. 343, 60–66 (2016). Laser ablation. MDA-MB-231 cells expressing H2BmCh migrating in PDMS channels were labeled with 50 mM SiR-tubulin-Cy5 (Spirochrome) in medium containing 20 ng/ml HGF during 3 hrs at 37 °C. Cells with the nucleus passing through the constrictions were selected. Z stacks (4 images, 0.5 µm z-step) images were acquired at 5 s interval during 75 s (pre-ablation). For photoablation, the 355 nm laser beam was focused to a region of interest selected between the nucleus and SiR-tubulin-labeled centrosome during a 40–80 ms pulse at 50–80% laser power. ARTICLE The conditions of ablation were monitored by the absence of recovery of SiR- tubulin signal. Z stacks were acquired as above for 25 s (post-ablation). The cen- trosome displacement was measured before and after laser ablation over 25 s periods of time and scored as positive in the direction of cell movement or negative otherwise. Pre- and post-ablation displacements are measured in the same cell and paired in the statistical analysis. 17. Denais, C. M. et al. Nuclear envelope rupture and repair during cancer cell migration. Science 352, 353–358 (2016). g 18. Castro-Castro, A. et al. Cellular and molecular mechanisms of MT1-MMP- dependent cancer cell invasion. Annu. Rev. Cell. Dev. Biol. 32, 555–576 (2016). 19. Tsai, J. W., Bremner, K. H. & Vallee, R. B. Dual subcellular roles for LIS1 and dynein in radial neuronal migration in live brain tissue. Nat. Neurosci. 10, 970–979 (2007). 20. Wolf, K. & Friedl, P. Mapping proteolytic cancer cell-extracellular matrix interfaces. Clin. Exp. Metastas. 26, 289–298 (2009). p 21. Raub, C. B. et al. Noninvasive assessment of collagen gel microstructure and mechanics using multiphoton microscopy. Biophys. J. 92, 2212–2222 (2007). 22. Lammerding, J. et al. Lamin A/C deficiency causes defective nuclear mechanics and mechanotransduction. J. Clin. Invest. 113, 370–378 (2004). Statistics and reproducibility. All results are presented as the mean ± SEM of three independent experiments except for collagen degradation in 20 °C poly- merized gel Fig. 1f (N = 2), centrosome-nucleus distance analysis in siLMNA- treated cells in Fig. 3e (N = 2) and Tks5 recruitment analysis in Fig. 5h (N = 2). GraphPad Prism (GraphPad Software) was used for statistical analysis. Statistical significance was defined as *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001; ns, not significant. Data were tested for normal distribution using the D’Agostino- Pearson normality test and nonparametric tests were applied otherwise. One-way ANOVA, Kruskal–Wallis, Mann–Whitney or Wilcoxon signed rank tests were applied as indicated in the figure legends. Radial distributions of endosome loca- lization with respect to instantaneous direction of nuclear movement were plotted and analyzed using the “circular” R package70,71. Circular uniformity Rao’s Spacing test was employed to test if angle distributions were significantly different from a uniform distribution (significant difference between data and a uniform distribu- tion when P < 0.05). 23. Pajerowski, J. D., Dahl, K. N., Zhong, F. L., Sammak, P. J. & Discher, D. E. Received: 16 March 2017 Accepted: 9 May 2018 Received: 16 March 2017 Accepted: 9 May 2018 Received: 16 March 2017 Accepted: 9 May 2018 31. Tsai, L. H. & Gleeson, J. G. Nucleokinesis in neuronal migration. Neuron 46, 383–388 (2005). 32. McKenney, R. J., Weil, S. J., Scherer, J. & Vallee, R. B. Mutually exclusive cytoplasmic dynein regulation by NudE-Lis1 and dynactin. J. Biol. Chem. 286, 39615–39622 (2011). 33. Gundersen, G. G. & Worman, H. J. Nuclear positioning. Cell 152, 1376–1389 (2013). 1. Rowat, A. C. et al. Nuclear envelope composition determines the ability of neutrophil-type cells to passage through micron-scale constrictions. J. Biol. Chem. 288, 8610–8618 (2013). ARTICLE After 3 min of polymerization at 37 °C, the collagen layer was washed gently in PBS and 1 ml of the cell suspension in L15 medium with 15% FCS (105 cells/ml) was added. Cells were incubated for 90 min at 37 °C in 1% CO2 before fixation. Cells were pre-extracted with 0.5% Triton X-100 in 4% paraformaldehyde in PBS during 90 s and then fixed in 4% paraformaldehyde in PBS for 20 min and stained for immunofluorescence microscopy with Tks5 and Cortactin antibodies. Images were acquired with a wide-field microscope (Eclipse 90i Upright; Nikon) using a 100 × Plan Apo VC 1.4 oil objective and a highly sensitive cooled interlined charge- coupled device (CCD) camera (CoolSnap HQ2; Roper Scientific). A z-dimension series of images was taken every 0.2 µm by means of a piezoelectric motor (Physik Instrumente). For quantification of Tks5 associated with curvilinear invadopodia in cells plated on collagen fibers, five consecutive z-planes corresponding to the plasma membrane in contact with collagen fibers were projected and surface covered by Tks5 signal was determined using the thresholding command of ImageJ excluding regions <8 pixels to avoid non-invadopodial structures. Surface covered by Tks5 was normalized to the total cell surface and values normalized to control cells. Automated tracking of endosome angular distribution. A homemade Matlab program (available on demand) was developed to track nuclei based on nuclear staining and create a velocity-dependent coordinate system to analyze MT1-MMP endosomes relative to the direction of displacement of the nucleus. Nuclei were automatically segmented from maximal z-stack projection of sequential time frames (see previous section) based on smoothing and thresholding and then were tracked based on the distance from their previous position. From the trajectory of each nucleus, speed (μm/min) and directionality (persistence) were computed for each consecutive pair of frames. A new polar coordinate system was defined such that the gravity center of the nucleus becomes the position (0,0) for all time points and that the velocity direction had an angle of 0°. This coordinate system was then changing for each time point and was different for each nucleus. Endosomes around each nucleus were automatically segmented by laplacian of gaussian spot enhancement and marker-control watershed segmentation based on regional maxima. The coordinates of the positions of the center of gravity of all endosomes 11 NATURE COMMUNICATIONS | (2018) 9:2443 | DOI: 10.1038/s41467-018-04865-7 | www.nature.com/naturecommunications ARTICLE Physical plasticity of the nucleus in stem cell differentiation. Proc. Natl Acad. Sci. USA 104, 15619–15624 (2007). 24. Marchesin, V. et al. ARF6-JIP3/4 regulate endosomal tubules for MT1-MMP exocytosis in cancer invasion. J. Cell. Biol. 211, 339–358 (2015). 25. Crisp, M. et al. Coupling of the nucleus and cytoplasm: role of the LINC complex. J. Cell. Biol. 172, 41–53 (2006). complex. J. Cell. Biol. 172, 41–53 (2006). 26. Lee, J. S. et al. Nuclear lamin A/C deficiency induces defects in cell mechanics, polarization, and migration. Biophys. J. 93, 2542–2552 (2007). 27. Luxton, G. W., Gomes, E. R., Folker, E. S., Vintinner, E. & Gundersen, G. G. Linear arrays of nuclear envelope proteins harness retrograde actin flow for nuclear movement. Science 329, 956–959 (2010). 28. Ketema, M. & Sonnenberg, A. Nesprin-3: a versatile connector between the nucleus and the cytoskeleton. Biochem. Soc. Trans. 39, 1719–1724 (2011). 29. Stewart-Hutchinson, P. J., Hale, C. M., Wirtz, D. & Hodzic, D. Structural requirements for the assembly of LINC complexes and their function in cellular mechanical stiffness. Exp. Cell Res. 314, 1892–1905 (2008). Data availability. All data are available within the Article and Supplementary Files, or available from the authors upon request. 30. Lombardi, M. L. et al. The interaction between nesprins and sun proteins at the nuclear envelope is critical for force transmission between the nucleus and cytoskeleton. J. Biol. Chem. 286, 26743–26753 (2011). Author contributions 50. Bone, C. R. & Starr, D. A. Nuclear migration events throughout development. J. Cell. Sci. 129, 1951–1961 (2016). E.I, A.C., R.F., and P.M were equally involved in experimental design, experiments and data analysis; S.A.G. designed and performed microfabricated channel experiments with help from M.R. and M.P.; M.J.D. performed experiments and analyzed data; P.P.G. generated software for automated tracking analysis and contributed to data analysis; Pa.M. performed circular statisticar tests; E.R.G. and A.B. suggested and contributed to designing experiments based on nucleus-cytoskeleton coupling; C.M.S. provided critical reagents and P.C. and E.I. conceived the study and wrote the manuscript. 51. Maniotis, A. J., Chen, C. S. & Ingber, D. E. Demonstration of mechanical connections between integrins, cytoskeletal filaments, and nucleoplasm that stabilize nuclear structure. Proc. Natl Acad. Sci. USA 94, 849–854 (1997). 52. Fridolfsson, H. N. & Starr, D. A. Kinesin-1 and dynein at the nuclear envelope mediate the bidirectional migrations of nuclei. J. Cell. Biol. 191, 115–128 (2010). 53. Starr, D. A. & Fridolfsson, H. N. Interactions between nuclei and the cytoskeleton are mediated by SUN-KASH nuclear-envelope bridges. Annu. Rev. Cell. Dev. Biol. 26, 421–444 (2010). Acknowledgements 41. Baffet, A. D., Hu, D. J. & Vallee, R. B. Cdk1 activates pre-mitotic nuclear envelope dynein recruitment and apical nuclear migration in neural stem cells. Dev. Cell. 33, 703–716 (2015). g We thank the Nikon Imaging Centre @ Institut Curie-CNRS and Cell and Tissue Imaging Facility of Institut Curie, member of the France Bio Imaging national research infrastructure (ANR-10-INBS-04) for help with image acquisition, Drs M. Bornens, S. Courtneidge, S. Etienne-Manneville, A-M Lennon-Duménil, F. Perez, M. Mercola, T. Mistelli, Q. Zhang and R. Vallee for providing reagents for this study and Dr I. Brito for help with statistical analysis. E.I. was supported by a postdoctoral fellowship from Ligue Nationale contre le Cancer, P.M. by a fellowship from Fondation ARC pour la Recherche contre le Cancer, R.F. by a fellowship from Ministère de l’Education Nationale, de l’Enseignement supérieur et de la Recherche, A.C. by a grant from Worldwide Cancer Research (Grant 16-1235 to P.C.) and S.A.G. by a grant provided by the program «Investissements d’Avenir» launched by the French Government and implemented by Agence Nationale pour la Recherche (ANR) with the reference ANR-10-LBX-0038 (Labex CelTisPhyBio) part of the IDEX PSL (ANR-10-IDEX-0001-02 PSL). Funding for this work was provided by the program «Investissements d’Avenir» launched by the French Government and implemented by Agence Nationale pour la Recherche (ANR) with the reference ANR-10-LBX-0038 (Labex CelTisPhyBio) part of the IDEX PSL (ANR-10-IDEX-0001-02 PSL) and by grants from Ligue Nationale contre le Cancer (Equipe labellisée 2015) and from Worldwide Cancer Research (Grant 16-1235) to P.C. and by core funding from Institut Curie and Centre National pour la Recherche Sci- entifique (CNRS). 42. Burkhardt, J. K., Echeverri, C. J., Nilsson, T. & Vallee, R. B. Overexpression of the dynamitin (p50) subunit of the dynactin complex disrupts dynein- dependent maintenance of membrane organelle distribution. J. Cell. Biol. 139, 469–484 (1997). 43. Seals, D. F. et al. The adaptor protein Tks5/Fish is required for podosome formation and function, and for the protease-driven invasion of cancer cells. Cancer Cell. 7, 155–165 (2005). 44. Linder, S., Wiesner, C. & Himmel, M. Degrading devices: invadosomes in proteolytic cell invasion. Annu. Rev. Cell. Dev. Biol. 27, 185–211 (2011). 45. Murphy, D. A. & Courtneidge, S. A. The ‘ins’ and ‘outs’ of podosomes and invadopodia: characteristics, formation and function. Nat. Rev. Mol. Cell Biol. 12, 413–426 (2011). 46. Juin, A. et al. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04865-7 66. Randles, K. N. et al. Nesprins, but not sun proteins, switch isoforms at the nuclear envelope during muscle development. Dev. Dyn. 239, 998–1009 (2010). 35. Tanaka, T. et al. Lis1 and doublecortin function with dynein to mediate coupling of the nucleus to the centrosome in neuronal migration. J. Cell. Biol. 165, 709–721 (2004). 67. Duong, N. T. et al. Nesprins: tissue-specific expression of epsilon and other short isoforms. PLoS ONE 9, e94380 (2014). 36. Kardon, J. R. & Vale, R. D. Regulators of the cytoplasmic dynein motor. Nat. Rev. Mol. Cell Biol. 10, 854–865 (2009). 37. McKenney, R. J., Vershinin, M., Kunwar, A., Vallee, R. B. & Gross, S. P. LIS1 and NudE induce a persistent dynein force-producing state. Cell 141, 304–314 (2010). 68. Hebbar, S. et al. Lis1 and Ndel1 influence the timing of nuclear envelope breakdown in neural stem cells. J. Cell. Biol. 182, 1063–1071 (2008). 69. Heuze, M. L., Collin, O., Terriac, E., Lennon-Dumenil, A. M. & Piel, M. Cell migration in confinement: a micro-channel-based assay. Methods Mol. Biol. 769, 415–434 (2011). 38. Zhang, X. et al. SUN1/2 and Syne/Nesprin-1/2 complexes connect centrosome to the nucleus during neurogenesis and neuronal migration in mice. Neuron 64, 173–187 (2009). 70. R Core Team. R: A Language and Environment for Statistical Computing http://www.r-project.org/ (2014). 39. Smith, D. S. et al. Regulation of cytoplasmic dynein behaviour and microtubule organization by mammalian Lis1. Nat. Cell Biol. 2, 767–775 (2000). 71. C. Agostinelli and U. Lund R package ‘circular’: Circular Statistics (version 0.4-7). https://r-forge.r-project.org/projects/circular/ (2013). 40. Coquelle, F. M. et al. LIS1, CLIP-170’s key to the dynein/dynactin pathway. Mol. Cell. Biol. 22, 3089–3102 (2002). Acknowledgements Physiological type I collagen organization induces the formation of a novel class of linear invadosomes. Mol. Biol. Cell. 23, 297–309 (2012). 47. Monteiro, P. et al. Endosomal WASH and exocyst complexes control exocytosis of MT1-MMP at invadopodia. J. Cell. Biol. 203, 1063–1079 (2013). y p 48. Raab, M. et al. ESCRT III repairs nuclear envelope ruptures during cell migration to limit DNA damage and cell death. Science 352, 359–362 (2016). 49. Irianto, J. et al. Nuclear constriction segregates mobile nuclear proteins away from chromatin. Mol. Biol. Cell. 27, 4011–4020 (2016). Additional information Rev. Cell. Dev. Biol. 26, 421 444 (2010). 54. Bone, C. R., Chang, Y. T., Cain, N. E., Murphy, S. P. & Starr, D. A. Nuclei migrate through constricted spaces using microtubule motors and actin networks in C. elegans hypodermal cells. Development 143, 4193–4202 (2016). 55. Revach, O. Y. et al. Mechanical interplay between invadopodia and the nucleus in cultured cancer cells. Sci. Rep. 5, 9466 (2015). 54. Bone, C. R., Chang, Y. T., Cain, N. E., Murphy, S. P. & Starr, D. A. Nuclei migrate through constricted spaces using microtubule motors and actin networks in C. elegans hypodermal cells. Development 143, 4193–4202 (2016). Supplementary Information accompanies this paper at https://doi.org/10.1038/s41467- 018-04865-7. g yp p 55. Revach, O. Y. et al. Mechanical interplay between invadopodia and the nucleus in cultured cancer cells. Sci. Rep. 5, 9466 (2015). Competing interests: The authors declare no competing interests p ( ) 56. Mueller, S. C. et al. A novel protease-docking function of integrin at invadopodia. J. Biol. Chem. 274, 24947–24952 (1999). Reprints and permission information is available online at http://npg.nature.com/ reprintsandpermissions/ 57. Destaing, O. et al. beta1A integrin is a master regulator of invadosome organization and function. Mol. Biol. Cell. 21, 4108–4119 (2010). Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. g 58. Juin, A. et al. Discoidin domain receptor 1 controls linear invadosome formation via a Cdc42-Tuba pathway. J. Cell. Biol. 207, 517–533 (2014). 59. Artym, V. V. et al. Dense fibrillar collagen is a potent inducer of invadopodia via a specific signaling network. J. Cell. Biol. 208, 331–350 (2015). Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/ licenses/by/4.0/. 60. Khatau, S. ARTICLE ARTICLE ARTICLE References 1. Rowat, A. C. et al. Nuclear envelope composition determines the ability of neutrophil-type cells to passage through micron-scale constrictions. J. Biol. Chem. 288, 8610–8618 (2013). 34. Shu, T. et al. Ndel1 operates in a common pathway with LIS1 and cytoplasmic dynein to regulate cortical neuronal positioning. Neuron 44, 263–277 (2004). 12 NATURE COMMUNICATIONS | (2018) 9:2443 | DOI: 10.1038/s41467-018-04865-7 | www.nature.com/naturecommunications Additional information B. et al. The distinct roles of the nucleus and nucleus-cytoskeleton connections in three-dimensional cell migration. Sci. Rep. 2, 488 (2012). connections in three-dimensional cell migration. Sci. Rep. 2, 488 (2012). 61. Thomas, D. G. et al. Non-muscle myosin IIB is critical for nuclear translocation during 3D invasion. J. Cell. Biol. 210, 583–594 (2015). 62. Thiam, H. R. et al. Perinuclear Arp2/3-driven actin polymerization enables nuclear deformation to facilitate cell migration through complex g p , ( ) 61. Thomas, D. G. et al. Non-muscle myosin IIB is critical for nuclear translocation during 3D invasion. J. Cell. Biol. 210, 583–594 (2015). 62. Thiam, H. R. et al. Perinuclear Arp2/3-driven actin polymerization enables nuclear deformation to facilitate cell migration through complex environments. Nat. Commun. 7, 10997 (2016). 61. Thomas, D. G. et al. Non-muscle myosin IIB is critical for nuclear translocation during 3D invasion. J. Cell. Biol. 210, 583–594 (2015). 62. Thiam, H. R. et al. Perinuclear Arp2/3-driven actin polymerization enables nuclear deformation to facilitate cell migration through complex environments. Nat. Commun. 7, 10997 (2016). 63. Jayo, A. et al. Fascin regulates nuclear movement and deformation in migrating cells. Dev. Cell 38, 371–383 (2016). g g 64. Petrie, R. J., Koo, H. & Yamada, K. M. Generation of compartmentalized pressure by a nuclear piston governs cell motility in a 3D matrix. Science 345, 1062–1065 (2014). 65. Petrie, R. J., Harlin, H. M., Korsak, L. I. & Yamada, K. M. Activating the nuclear piston mechanism of 3D migration in tumor cells. J. Cell. Biol. 216, 93–100 (2017). © The Author(s) 2018 13 NATURE COMMUNICATIONS | (2018) 9:2443 | DOI: 10.1038/s41467-018-04865-7 | www.nature.com/naturecommunications
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USO DO MÉTODO ELECTRE III PARA ESCOLHA DE UMA ESTRATÉGIA DE NAVEGAÇÃO DE BARCOS DE APOIO ÀS UNIDADES MARÍTIMAS
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USO DO MÉTODO ELECTRE III PARA ESCOLHA DE UMA ESTRATÉGIA DE NAVEGAÇÃO DE BARCOS DE APOIO ÀS UNIDADES MARÍTIMAS Pablo Tentempo Steiner Programa de Engenharia de Produção/Coppe – UFRJ -Rio de Janeiro -RJ Av. Horácio Macedo, 2030 - Cidade Universitária pablo.stb@gmail.com Ayala Liberato Braga Programa de Engenharia de Produção/Coppe – UFRJ -Rio de Janeiro -RJ Av. Horácio Macedo, 2030 - Cidade Universitária ayala.braga@gmail.com Alexandre Portela de Abreu Programa de Engenharia de Produção/Coppe – UFRJ -Rio de Janeiro -RJ Av. Horácio Macedo, 2030 - Cidade Universitária Alexandre30portela@gmail.com Igor Girão Peres Vianna Programa de Engenharia de Produção/Coppe – UFRJ -Rio de Janeiro -RJ Av. Horácio Macedo, 2030 - Cidade Universitária igor_gpv@poli.ufrj.br Tharcisio Cotta Fontainha Programa de Engenharia de Produção/Coppe – UFRJ -Rio de Janeiro -RJ Av. Horácio Macedo, 2030 - Cidade Universitária tharcisio.fontainha@gmail.com Tharcisio Cotta Fontainha Programa de Engenharia de Produção/Coppe – UFRJ -Rio de Janeiro -RJ Av. Horácio Macedo, 2030 - Cidade Universitária tharcisio.fontainha@gmail.com Como Citar: STEINER, P.T.; BRAGA, A.L.; DE ABREU, A.P., VIANNA, I.G.P.; FONTAINHA, T.C. Uso do método electre iii para escolha de uma estratégia de navegação de barcos de apoio às unidades marítimas. In: SIMPÓSIO DE PESQUISA OPERACIONAL E LOGÍSTICA DA MARINHA, 19., 2019, Rio de Janeiro, RJ. Anais […]. Rio de Janeiro: Centro de Análises de Sistemas Navais, 2019. Palavra-chave: ELECTRE III; Logística; Multicritério; Unidades Marítimas; Simulação. Palavra-chave: ELECTRE III; Logística; Multicritério; Unidades Marítimas; Simulação. alavra-chave: ELECTRE III; Logística; Multicritério; Unidades Marítimas; Simulação. ABSTRACT With the growth of the oil sector in the world and Brazil, activities in the offshore environment show that there is a range of difficulties in logistics operations in this production environment. Given a large number of variables and data used in the activities that integrate the entire operational chain in the offshore area, operational research models can be used to find optimized solutions. For these cases, it is necessary to use a multicriteria analysis, which can then be considered economic factors, sustainable factors among others. Thus, this work seeks to contribute to the scheduling of three strategies of the selection of the navigation speed of the fleet of PSVs (Platform Supply Vessels), boats that supply the demands of the Maritime Units, based on economic, environmental and crew welfare, analyzed by a multicriteria model. To achieve this goal, a decision support tool called APOLO was used, which combines a discrete event simulator with a PSVs heuristic for cargo and marine units allocation. The ELECTRE III model was selected for the multicriteria analysis, then the relevant indicators for the problem were defined. As a result, we obtained the third strategy as the winner, presenting the agreement indices and the preference relations between the navigation strategies. Thus, the results obtained by the model can contribute to take decisions. The multicriteria method was relevant and applicable to decision-making processes that involve subjective and quantitative variables. Keywords: ELECTRE III; Logistic; Multicriteria; Maritime Units; Simulation. RESUMO Com o crescimento do setor de petróleo no mundo e no Brasil as atividades em ambiente offshore mostram que existe uma gama de dificuldades nas operações logísticas neste meio produtivo. Dada a grande quantidade de variáveis e de dados utilizados nas atividades que integram toda a cadeia operacional na área offshore podem ser utilizados modelos de pesquisa operacional a fim de encontrar soluções otimizadas. Para estes casos se faz necessária o uso de uma análise multicritério, podendo então ser considerados fatores econômicos, fatores sustentáveis dentre outros. Assim, o trabalho busca contribuir no ordenamento de três estratégias de seleção da velocidade de navegação da frota de PSVs (Plataform Supply Vessels) que são barcos que suprem as demandas das Unidades Marítimas (UMs), baseando-se em critérios econômicos, ambientais e de bem-estar da tripulação, analisados por um modelo multicritério. Para alcançar este objetivo, foi utilizada uma ferramenta de apoio à decisão denominada APOLO, que combina um simulador de eventos discretos com uma heurística de alocação dos PSVs às cargas e às unidades marítimas. Foi selecionado o modelo ELECTRE III para a realização da análise multicritério e depois foram definidos os indicadores relevantes para o problema. Como resultado obteve-se a terceira estratégia como vencedora, apresentando os índices de concordância e as relações de preferência entre as estratégias de navegação. Deste modo, as informações obtidas pelo modelo podem contribuir para a tomada de decisão e que realçam a viabilidade do emprego do método para análise de tal problema. O método multicritério se mostrou relevante e aplicável a processos de tomada de decisão que envolvam variáveis de caráter subjetivo e 1 quantitativo. recursos e infraestrutura logísticos, que são áreas fundamentais para a sua continuidade operacional, podendo causar, por exemplo, paradas de produção e atraso no cronograma de perfuração de determinado poço (ARES, 2013). Nesse contexto, a logística de apoio offshore, ou apenas logística offshore pode ser dividida em três grandes tipos de operações: logística de cargas, logística de passageiros e serviços. Para as operações de transporte e abastecimento, que se encontram dentro da logística de cargas, realizadas para as unidades marítimas (UMs), são utilizadas embarcações supridoras, chamadas de barcos de apoio ou de PSVs (Plataform Supply Vessels), sendo um dos elementos mais custosos de cadeia logística offshore. O aumento das operações offshore se não for planejado e bem coordenado, pode gerar inúmeros problemas econômicos e também sustentáveis como: atrasos nas entregas dos produtos; maior consumo de combustível por parte da frota e consequentemente maior emissão de gases poluentes; maiores períodos embarcados da tripulação; dentre outros. Muitos desses problemas são impactados diretamente pela velocidade de navegação do PSV. Dada a importância do setor de E&P, a grande quantidade de variáveis e de dados utilizados e as atividades que integram toda a cadeia operacional na área offshore, o planejamento pode se tornar extremamente complexo, sendo necessária a utilização de modelos de pesquisa operacional a fim de encontrar soluções otimizadas para o empreendimento. Esta abordagem se faz ainda mais necessária quando se visa avaliar indicadores, que, a priori, não poderiam ser analisados em conjunto. Para estes casos se faz necessário o uso de uma análise multicritério de avaliação, podendo então considerar fatores econômicos e fatores sustentáveis ao mesmo tempo. A principal contribuição deste trabalho é o ordenamento de diferentes estratégias de seleção da velocidade de navegação da frota, baseando-se em critérios econômicos, ambientais e de bem-estar, analisados por um modelo multicritério. Para alcançar este objetivo, cabe identificar primeiramente o método de apoio à decisão mais adequando. Watrobski et al. (2019) discute a existência de diversos métodos, tais como AHP, ELECTRE I, ELECTRE II, ELECTRE III, PROMETHEE I, PROMETHEE II, etc, e que sua utilização é indicada de acordo com características do problema, de precisão/incerteza das variáveis envolvidas, etc. A partir das características do problema, verifica-se como adequada a utilização uma ferramenta de apoio à decisão, denominada APOLO e apresentada em Vianna (2019), que combina um simulador de eventos discretos com uma heurística de alocação dos PSVs às cargas e às unidades marítimas. No que tange o método de apoio à decisão, é selecionado o modelo ELECTRE III para a realização da análise multicritério, depois são definidos os indicadores relevantes para o problema, um para cada um dos critérios propostos. Então são definidas três estratégias de determinação da velocidade de navegação do PSV. Na sequência deste artigo é apresentada uma revisão sobre a logística offshore e métodos multicritérios, seguida pela definição do problema estudado. Na seção 4 são apresentados os experimentos computacionais conduzidos. Encerra o artigo as conclusões e sugestões de trabalhos futuros. 1. INTRODUÇÃO O setor de petróleo vem crescendo continuamente no mundo e no Brasil, com um crescimento de 3,2% na comparação anual. Porém, com o passar dos anos as reservas de mais fácil exploração foram se esgotando. No atual cenário brasileiro, a grande maioria da produção atual, 94% do total, e das futuras reservas se encontra em ambiente offshore, sendo o pré-sal responsável por 40,6% da produção nacional, que é um dos mais complicados de serem explorados devido as grandes profundidades a serem perfuradas e aos efeitos do mar na corrosão de equipamentos e tubos e na instabilidade ocasionada pelas ondas (ANP,2017). Além de todos os complicadores mencionados, ainda há uma gama de dificuldades na logística de operação em grande escala nesse ambiente. Dessa forma, as atividades de Exploração e Produção de Óleo e Gás (E&P) no setor offshore têm imposto grandes desafios relacionados à área de planejamento e operação de 2 geral (peças de reposição, equipamentos, tubos, etc.), óleo diesel e outros. O suporte marítimo destaca-se como um elo importante na cadeia logística que garante o nível de serviço desejado nas operações de suprimento Di Luccio e Dores (2016), sendo vital o planejamento eficiente da logística para suprimento de material para a exploração e produção Arpini e Rosa (2015), no qual atrasos ou falhas nas entregas podem acarretar enormes prejuízos financeiros e ambientais (BRAGA, 2017). Assim, essa logística de apoio vem se tornando uma nova área de conhecimento no segmento de Óleo e Gás (O&G), onde cada vez mais as empresas de E&P de petróleo demandam elevados níveis de serviço nas atividades de suporte à operação de exploração e produção (COSTA, 2015). Para atender essa demanda, Almeida (2002) demonstra que métodos multicritérios de apoio à decisão se adequam às situações em que nem todos os dados de um determinado problema prático podem ser facilmente quantificados, por medição ou estimativa e, onde tais situações frequentes nos processos decisórios das empresas e são geralmente complexos. A aplicação de métodos Múltiplos Critérios é pertinente em situações em que se necessita da análise de múltiplos (dois ou mais) critérios, ou múltiplos atributos (MARTINS e COELHO, 2012). Visando entregar esses elevados níveis de serviços se faz necessário também a utilização de simuladores de eventos para minimizar os erros. Dessa forma, Silva et al. (2015) compararam várias políticas de transporte marítimo, empregando a simulação de eventos discretos para estimar o dimensionamento da frota e a infraestrutura necessárias para suprir a demanda de carga. De acordo com Pinto et al. (2015), grandes distâncias no deslocamento e o alto custo envolvido nessas operações demonstram a importância de se trabalhar com a otimização do dimensionamento de barcos de apoio marítimo e do roteamento desta frota, melhorando o nível de serviço. Assim, eles propõem um modelo matemático baseado no Problema de Roteamento de Veículos Periódicos (PRVP) para elaboração de viagens diárias de barcos às plataformas offshore, bem como a definição de tamanho e composição da frota para atender a demanda. Silva et al. (2015) comparam várias políticas de transporte marítimo, empregando a simulação de eventos discretos para estimar o dimensionamento da frota e a infraestrutura necessárias para suprir a demanda de carga. Moreira (2017) mostra como é possível unir frotas de navios e carga geral, sem deteriorar o nível de serviço. Vários cenários são avaliados utilizando-se a simulação de eventos discretos. 2. REVISÃO BIBLIOGRÁFICA Aguiar (2013) apresenta as atividades de apoio offshore como as atividades de transporte e armazenagem de cargas realizadas por embarcações de apoio para realizar serviços de E&P nas plataformas offshore. Segundo Almeida (2009), as atividades de E&P offshore de petróleo e gás demandam uma logística muito complexa no suprimento de alimentação, água, cargas em 3 3.1. DEFINIÇÃO CONCEITUAL As UMs são responsáveis pelas operações de E&P da indústria de petróleo e necessitam de uma gama grande e variada de cargas, denominadas de carga geral, que apresentam datas de entrega definidas, elas também produzem cargas que precisam ser retornadas para terra, as cargas de backload. Além disso, as UMs apresentam demandas por diesel para combustível e água para suas operações internas, sendo possível que algumas delas sejam capazes de produzir uma parte da água utilizada para consumo. As demandas e necessidades das UMs são sanadas por uma frota heterogênea de PSVs, responsável pelo transporte de todas as cargas. Para que seja possível o abastecimento dos PSVs, é necessário que um porto faça parte da cadeia. O porto apresenta uma limitação física no número de berços disponíveis para uso e um conjunto de horários restritos, chamado de cronogramas, nos quais os PSVs podem atracar no porto e realizar suas operações. Devido ao grande número de UMs e às grandes distâncias até a costa, se faz necessário que mais de uma UM seja atendida em cada viagem. Em decorrência desse fato, as UMs são separadas em clusters, sendo a clusterização e o roteamento do sistema pré- definidos. A frota de PSVs é a maior responsável pelas emissões de poluentes, como o dióxido de carbono, óxido de nitrogênio, óxido de enxofre e partículas, de todo o setor upstream de petróleo (NORLUND et al., 2015). Estas emissões são provenientes do consumo de combustível e das condições dos equipamentos. O principal fator que impacta no consumo de combustível de uma embarcação é a velocidade de navegação, outros fatores que também têm influência nesse consumo são as condições meteorológicas, o tipo de embarcação e o peso de navegação. Para este trabalho é considerado apenas o impacto da velocidade no consumo de diesel. O consumo de combustível e a sua relação com a velocidade de navegação podem ser aproximados pela relação〖con〗_ij=(B+A*v_ij^n )*t_ij, onde〖con〗_ij é a quantidade de combustível consumido para fazer o trajeto de i até j, v_ij é a velocidade de navegação do ponto i ao ponto j, t_ij é o tempo do decorrido para ir do ponto i até o ponto j e B, A e n parâmetros que dependem do tipo de embarcação e das condições de operação, sendo sempre B ≥ 0, A > 0 e n ≥ 3, segundo (PSARAFTIS e KONTOVAS 2013). Kisialiou et al. (2018) visam minimizar o número de embarcações e o gasto com combustíveis ao mesmo tempo que mantém um nível mínimo de serviço. Vianna (2019) analisa diferentes estratégias, entre heurísticas gulosas e modelo de otimização, de alocação de PSVs às cargas e às unidades marítimas com o auxílio de simulação de eventos discretos baseados nas operações da Petrobras no litoral do Rio de Janeiro e de Espírito Santo. Como resultado, uma notável redução dos custos é observada, graças ao significante corte na frota original de PSVs estimada pelo trabalho. Em Norlund et al. (2015) é analisado como a otimização da velocidade das embarcações pode reduzir o consumo de combustível e emissões de CO2. Em um trabalho posterior, Norlund e Gribkovskaia (2017) estendem essa análise em como a programação do porto pode ser construída visando diminuir o consumo de combustível baseado em diferentes técnicas de otimização de velocidade das embarcações. Em ambos os trabalhos, a condições meteorológicas é levada em conta na simulação. Eskandari e Mahmoodi (2016) também utilizam um simulador de eventos discretos que leva em conta condições ambientais e uma estratégia de otimização baseada em simulação para achar a composição da frota que minimize o custo total mantendo um nível de serviço mínimo. Norstad et al. (2017) apresentam um estudo feito para o mar do ártico onde são simulados vários formatos dos navios e composições de frota respeitando alguns requerimentos de segurança, preparações emergenciais e indicadores ambientais levando em conta o impacto do clima nos tempos de navegação e no consumo de combustíveis. 4 4 3. DEFINIÇÃO DO PROBLEMA Para uma melhor definição do problema, ele é dividido em três partes principa Para uma melhor definição do problema, ele é dividido em três partes principais: a) Definição conceitual: é apresentada uma definição geral do problema e das etapas propostas para a solução do mesmo; a) Definição conceitual: é apresentada uma definição geral do problema e das etapas propostas para a solução do mesmo; p p p ç ; b) Modelagem da operação offshore: explicita as operações relevantes para este trabalho; b) Modelagem da operação offshore: explicita as operações relevantes para este trabalho; c) Modelo multicritério: É apresentado o modelo multicritério a ser utilizado. c) Modelo multicritério: É apresentado o modelo multicritério a ser utilizado. comumente utilizadas, com B = 0 e n = 3 e não dependência do peso da carga. É utilizado o valor de A = 0,75, como meio de validar o consumo do modelo com os valores reais de consumo de combustível da frota analisada. A importância cada vez maior de buscar reduções nas emissões de poluentes nas operações, ao mesmo tempo em que não haja prejuízo no nível do serviço prestado e levando em conta o bem-estar da tripulação das embarcações, leva a uma necessidade de conciliar esses três aspectos muito distintos e de difícil comparação. Para que seja possível a avaliação conjunta destes fatores, é necessária a utilização de ferramentas multicritérios, que sejam capazes de avaliar todos os indicadores com suas devidas importâncias. Assim, são abordadas três diferentes estratégias para determinar a velocidade de gação dos PSVs: ç • Estratégia 1: a velocidade utilizada segue o padrão observado nas operações da • Estratégia 1: a velocidade utilizada segue o padrão observado nas operações da Petrobras nas Bacias de Campos e Espírito Santo; • Estratégia 1: a velocidade utilizada segue o padrão obse Petrobras nas Bacias de Campos e Espírito Santo; Petrobras nas Bacias de Campos e Espírito Santo; Petrobras nas Bacias de Campos e Espírito Santo; p p • Estratégia 2: a velocidade de navegação é reduzida em relação a Estratégia 1; e • Estratégia 3: a velocidade de navegação é aumentada em relação a Estratégia 1. Ao se definir um grupo de estratégias que se quer comparar, é necessário definir os meios que permitiram que estas comparações sejam realizadas. São utilizados dois métodos considerados adequados para realizar a comparação: o primeiro é a utilização de um simulador de eventos discretos, conhecido como APOLO de Vianna (2019), que permite a implementação de detalhes pormenorizados da operação, embutindo por meios de distribuições de probabilidade as incertezas inerentes a operação e que são conhecidas; e o segundo é a utilização do modelo ELECTRE III, que é responsável pela análise multicritério da operação. Para possibilitar a comparação entre as diferentes estratégias de determinação da velocidade de embarcação, é necessária a utilização de indicadores que retratem os três aspectos aqui abordados e que devem ser avaliados pelo método multicritério: Fator econômico: é representado pelo nível de serviço de entrega de carga geral, que consiste na proporção de pedidos entregues no prazo pelo total de pedidos entregues (no prazo mais atrasados). Este indicador é de suma importância econômica, pois atrasos nas entregas dos pedidos podem acarretar paralização das operações nas unidades marítimas, gerando grandes prejuízos para as empresas envolvidas; Fator sustentável: é caracterizado pelo total de combustível consumido pela frota de PSVs, já que o mesmo tem ligação direta com a quantidade de poluentes emitidos; e Fator sustentável: é caracterizado pelo total de combustível consumido pela frota de PSVs, já que o mesmo tem ligação direta com a quantidade de poluentes emitidos; e Fator de bem-estar: é representado pelo tempo total de viagem, ou seja, quanto tempo é gasto do momento que o PSV sai do fundeio para o porto até o momento que ele volta para o fundeio. Este período pode ser considerado como sendo de trabalho ininterrupto da tripulação do PSV, longos períodos de trabalho isolado podem apresentar malefícios para a tripulação. 3.1. DEFINIÇÃO CONCEITUAL Psaraftis e Kontovas (2013) ainda dizem que a maioria dos artigos na literatura assumem uma função cúbica, por ser uma boa aproximação para o consumo de PSVs nas velocidades operacionais 5 • Velocidade do PSV: Para o cálculo da velocidade de navegação em cada uma das etapas da viagem, é levado em conta uma distância crítica, ou seja, quando a viagem tiver uma distância maior que a crítica, é sorteada a velocidade de 3.3. MODELO MULTICRITÉRIO Na literatura da decisão, um sistema é muitas vezes definido em termos das interações existentes entre os elementos que o formam. Segundo Tomlinson e Kiss (1984), um processo de apoio à tomada de decisão é um sistema aberto. Para adaptar-se a complexidade do mundo real, é necessária uma simplificação a um modelo quantificável. Assim, a teoria da decisão é a convergência entre as escolhas, as alternativas e as respostas, referentes a diversos contextos de análise. A análise de problemas multicritério para o processo decisório passa pela consideração dos modelos referentes às qualidades dos operadores/atores diretamente envolvidos. Essas qualidades se referem a transdisciplinaridade e a multidisciplinaridade. Dentre os modelos de apoio a tomada de decisão destacam-se os ELECTRE. Os modelos ELECTRE (Elimination et Choix Traduisant la Réalité) são um agrupado de métodos pertencentes à área de Auxílio Multicritério à Tomada de Decisão (AMD). O modelo ELECTRE III é desenvolvido por Roy (1978). Este modelo incorpora a natureza imprecisa e incerta na ordenação de alternativas de melhor para pior, utilizando os limiares de indiferença e preferência. Este modelo é o mais indicado para integrar diferentes variáveis linguísticas dentro de diferentes alternativas e, ainda, classificar e selecionar a melhor dentre tais alternativas. navegação a partir de uma determinada distribuição e, por outro lado, quando a distância for menor que a crítica é sorteada uma velocidade de navegação a partir de outra distribuição. Para ambas as velocidades há um limite superior e inferior, que se forem alcançados a velocidade é sorteada novamente; • Consumo de combustível do PSV: Para cada uma das atividades que o PSV realizou, há um consumo de combustível relacionado ao tempo que ele realizou essa tarefa. Os consumos são divididos entre: fundeio; berço; atravessando o canal; navegando, único caso que o consumo não é fixo, sendo dependente da velocidade de navegação; e na UM, que engloba o tempo que ele espera na fila para atracar, o tempo de espera para o começo das operações e o tempo de operação na UM. Não se considera que o PSV esteja consumindo combustível enquanto estiver em inoperância. • Consumo de combustível do PSV: Para cada uma das atividades que o PSV realizou, há um consumo de combustível relacionado ao tempo que ele realizou essa tarefa. Os consumos são divididos entre: fundeio; berço; atravessando o canal; navegando, único caso que o consumo não é fixo, sendo dependente da velocidade de navegação; e na UM, que engloba o tempo que ele espera na fila para atracar, o tempo de espera para o começo das operações e o tempo de operação na UM. Não se considera que o PSV esteja consumindo combustível enquanto estiver em inoperância. 3.2. MODELAGEM DA OPERAÇÃO OFFSHORE A operação offshore é composta por uma grande quantidade de etapas, que podem ser vistas em pormenores em Vianna (2019). Porém, apenas dois destes aspectos da modelagem são de maior relevância para este trabalho e devem ser detalhados: • Velocidade do PSV: Para o cálculo da velocidade de navegação em cada uma das etapas da viagem, é levado em conta uma distância crítica, ou seja, quando a viagem tiver uma distância maior que a crítica, é sorteada a velocidade de • Velocidade do PSV: Para o cálculo da velocidade de navegação em cada uma das etapas da viagem, é levado em conta uma distância crítica, ou seja, quando a viagem tiver uma distância maior que a crítica, é sorteada a velocidade de 6 6 cj(a,b)= =]0,1[,se gj (a)+ q j [gj (a)]< gj (b)< gj (a)+ p j [gj (a)] (1) = 1, se gj (a) + q j [gj (a)]  gj (b) cj(a,b)= =]0,1[,se gj (a)+ q j [gj (a)]< gj (b)< gj (a)+ p j [gj (a)] (1) -Índices de concordância global c(a, b): que expressam a concordância que existe em se afirmar que a subordinada b, à luz de todos os critérios. kj é o peso associado a cada critério, obtendo assim a equação (2):        m j j j m j j k b a c k b a c 1 1 )) , ( . ( , (2)        m j j j m j j k b a c k b a c 1 1 )) , ( . ( , (2) A partir dos índices Gc(a, b), constrói-se uma sucessão de relações de subordinação. Utilizam-se planos de corte k  [0,1] e um limite de discriminação s() = ’ ’ k. A fim de impedir a utilização inadequada da função s() os valores recomendados para os parâmetros ’ e ’ são, respectivamente, 0 e 0 (o decisor experiente pode alterá-los, se desejar ). Se D0 o conjunto das melhores alternativas de A. No primeiro passo k=0: (3) Se D0 o conjunto das melhores alternativas de A. No primeiro passo k=0: (3) (3) (4) Obtém-se a primeira relação a 1 0  D S b se e apenas: Obtém-se a primeira relação a 1 0  D S b se e apenas: Gc(a,b)1 e Gc(a,b)  Gc(b,a) + ’  ’Gc(a,b) Gc(a,b)1 e Gc(a,b)  Gc(b,a) + ’  ’Gc(a,b) (5) (5) 3.3.1. Breve Descrição do Método ELECTRE III Em relação um conjunto A = {a1, a2, ..., am} de alternativas avaliadas em relação a uma família de critérios F= {g1, ..., gn}, o método ELECTRE III de Roy (1985) se propõe a estabelecer uma ordenação de preferência de alternativas. Neste método, a atribuição relativa dos pesos (importância) dos critérios é considerada de fundamental importância na modelagem. O método é estruturado em duas etapas: para cada par de alternativas (a, b), estas relações expressam a intensidade com que se pode afirmar que a subordinada b (intensidade com que a é ao menos tão boa quanto b). Se gj (a) é o valor de desempenho da alternativa a à luz do critério j, então calculam-se: - Índices de concordância parcial cj (a, b): que expressam a intensidade com que se pode afirmar que, sob o critério j, a é ao menos tão boa quanto b. cj (a, b) pode assumir os valores da equação (1): =0, se gj (a) +p j [gj (a)]  gj (b) 7 7 divididas em 23 clusters, o porto possui 6 berços com um total de 46 cronogramas disponíveis por semana. A Tabela 1 apresenta os resultados dos indicadores para as três estratégias de velocidade adotadas. Tabela 1 - Resultados das três estratégias. Estratégia Nível de serviço Consumo de diesel (m3) Tampo de viagem (dias) 1 86,35% 33673 4,304 2 75,00% 24247 4,629 3 88,20% 39725 4,175 Fonte: Os autores Fonte: Os autores Para a construção dos cenários considera-se os pesos dos critérios econômico, ambiental e bem-estar da tripulação. As estratégias são as apresentadas em Vianna (2019). A Tabela 2 apresenta os resultados da matriz de concordância dos cenários um, dois, três e quatro. No primeiro cenário é dada igualdade de importância aos critérios econômico, ambiental e bem-estar da tripulação. No segundo cenário é dada maior importância ao critério econômico. No terceiro cenário é dada maior importância ao critério ambiental. Já no quarto cenário, é dada maior importância ao critério bem-estar. Para a matriz de concordância não é possível dizer a preferências dentre as estratégias propostas, pois os índices de concordância são distintos. Neste caso, os valores muito diferentes entre as duas matrizes revelam forte influência dos índices de discordância, enfraquecendo a noção de concordância da preferência entre as alternativas. Tabela 2 – Matriz de concordância dos cenários 1, 2, 3 e 4. CENÁRIO 1 ECONÔMICO AMBIENTAL BEM-ESTAR ESTRATÉGIA 1 1,0 0,6 0,3 ESTRATÉGIA 2 0,3 1,0 0,3 ESTRATÉGIA 3 0,6 0,6 1,0 CENÁRIO 2 ECONÔMICO AMBIENTAL BEM-ESTAR ESTRATÉGIA 1 1,0 0,6 0,3 ESTRATÉGIA 2 0,3 1,0 0,3 ESTRATÉGIA 3 0,6 0,6 1,0 CENÁRIO 3 ECONÔMICO AMBIENTAL BEM-ESTAR ESTRATÉGIA 1 1,0 0,6 0,4 ESTRATÉGIA 2 0,4 1,0 0,4 ESTRATÉGIA 3 0,6 0,6 1,0 CENÁRIO 4 ECONÔMICO AMBIENTAL BEM-ESTAR ESTRATÉGIA 1 1.0 0,5 0,5 ESTRATÉGIA 2 0,5 1,0 0,5 ESTRATÉGIA 3 0,5 0,5 1 Fonte: Os autores Tabela 2 – Matriz de concordância dos cenários 1, 2, 3 e 4. CENÁRIO 1 Tabela 2 – Matriz de concordância dos cenários 1, 2, 3 e 4. CENÁRIO 1 A Tabela 3 apresenta os resultados da matriz de preferência dos cenários um, dois, três e quatro. No cenário 1, a estratégia vencedora é a estratégia 3 tendo preferência de utilizando os critérios ambiental e bem-estar. No cenário 2, a estratégia vencedora é a estratégia 3. 4. RESULTADOS A partir da matriz de subordinação, calculam-se: a eficácia de a (nº de alternativas que a subordinada), a fraqueza de a (nº de alternativas que subordinam a) e a qualificação de a (a eficácia de a – a fraqueza de a). Após a qualificação, selecionam-se a(s) melhor(es) seleção(ões) descendente ou a(s) pior(es) seleção(ões) ascendente, das quais extraem-se as alternativas restantes. Todos os testes realizados nessa etapa são executados em uma máquina equipada com Windows Server® Intel® Xeon® CPU E5-2620 v4 @ 2.10GHz com 2 processadores e 256 GB de memória RAM. É utilizado o Python 3.6 para a utilização do simulador APOLO. Para obtenção dos resultados utilizando o ELECTRE III, utiliza-se o software RStudio versão 3.5.3. Para os resultados iniciais são simuladas no APOLO as três estratégias apresentadas previamente, com a Estratégia 2 apresentando valores de velocidade 20% menores e a Estratégia 3 com valores 20% maiores, comparadas a Estratégia 1. O cenário utilizado foi retirado de Vianna (2019), sendo o cenário base das operações e dos testes feitos, sendo utilizada a Estratégia 3B de alocação com um total de 32 PSVs na frota. Para todas as estratégias de seleção de velocidade, foram realizadas 30 replicações com duração de 180 dias de simulação com 90 dias de aquecimento. Neste cenário o espaço reservado no PSV para o primeiro backload é de 10 unidades, com um total de 90 UMs 8 5. CONCLUSÃO O presente trabalho contextualiza o crescimento do setor de petróleo no mundo e no Brasil, indicando que as atividades em ambiente offshore possuem uma gama de dificuldades nas operações logísticas neste meio produtivo. Dada a grande quantidade de variáveis e de dados utilizados, nas atividades que integram toda a cadeia operacional na área offshore podem ser utilizar utilizados modelos de pesquisa operacional a fim de encontrar soluções otimizadas. Para estes casos se faz necessária o uso de uma análise multicritério, podendo então serem considerados fatores econômicos, fatores sustentáveis dentre outros. Tabela 3 – Matriz de Preferência dos cenários 1,2, 3 e 4. CENÁRIO 1 ESTRATÉGIA 1 ESTRATÉGIA 2 ESTRATÉGIA 3 ESTRATÉGIA 1 I P P ESTRATÉGIA 2 NP I P ESTRATÉGIA 3 NP NP I CENÁRIO 2 ESTRATÉGIA 1 ESTRATÉGIA 2 ESTRATÉGIA 3 ESTRATÉGIA 1 I P P ESTRATÉGIA 2 NP I P ESTRATÉGIA 3 NP NP I CENÁRIO 3 ESTRATÉGIA 1 ESTRATÉGIA 2 ESTRATÉGIA 3 ESTRATÉGIA 1 I I I ESTRATÉGIA 2 I I I ESTRATÉGIA 3 I I I CENÁRIO 4 ESTRATÉGIA 1 ESTRATÉGIA 2 ESTRATÉGIA 3 ESTRATÉGIA 1 I I I ESTRATÉGIA 2 I I I ESTRATÉGIA 3 I I I Fonte: Os autores Tabela 3 – Matriz de Preferência dos cenários 1,2, 3 e 4. CENÁRIO 1 Tabela 3 – Matriz de Preferência dos cenários 1,2, 3 e 4. Á Fonte: Os autores Assim, o trabalho busca contribuir no ordenamento de três estratégias de seleção da velocidade de navegação da frota de PSVs (Plataform Supply Vessels) que são barcos que suprem as demandas das Unidades Marítimas (UMs), baseando-se em critérios econômicos, ambientais e de bem-estar da tripulação, analisados por um modelo multicritério. Para alcançar este objetivo, é utilizada uma ferramenta de apoio à decisão, denominada APOLO, que combina um simulador de eventos discretos com uma heurística de alocação dos PSVs às cargas e às unidades marítimas. É selecionado o modelo ELECTRE III para a realização da análise multicritério, depois são definidos os indicadores relevantes para o problema. Como resultado, obtém-se a terceira estratégia como vencedora, apresentando os índices de concordância e as relações de preferência entre as estratégias de navegação. Deste modo, as informações obtidas pelo modelo podem contribuir para a tomada de decisão e que realçam a viabilidade do emprego do método para análise de tal problema. Já para os cenários 3 e 4, não há como determinar qual estratégia será utilizada pois há indiferença de utilização das três estratégias para os cenários propostos. 9 A seleção de uma estratégia de movimentação de embarcações tipo PSV envolve muitos critérios, o que normalmente faz com que o decisor tenha dificuldades neste processo. Deste modo, a presente pesquisa utilizou o Método ELECTRE III para estabelecer um critério de escolha à luz de um conjunto de critérios (econômico, ambiental e bem-estar). São apresentados, os índices de concordância e as relações de preferência entre as estratégias de navegação, informações que podem contribuir para a tomada de decisão e que realçam a viabilidade do emprego do método para análise de tal problema. 1. REFERÊNCIAS [1] AGUIAR, R. A. Estudo do Impacto da Ampliação de Berço e de Área de Pátio no Aumento da Capacidade Operacional de uma Base de Apoio Offshore. Dissertação (Mestrado em Engenharia Civil) – Programa de Pós-Graduação em Engenharia Civil. Universidade Federal do Espírito Santo, Vitória, 2013. [2] ALMEIDA, M. R. de. Algoritmos Genéticos Aplicados a Programação de Embarcações de Apoio às Operações “Offshore”. Anais do XLI Simpósio Brasileiro de Pesquisa Operacional (SBPO), Bahia, 2009. [3] ALMEIDA, P. P. de. Aplicação do método AHP - Processo Analítico Hierárquico - à seleção de helicópteros para apoio logístico à exploração e produção de petróleo "offshore". Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro Tecnológico. Programa de Pós-Graduação em Engenharia de Produção. 2002. [4] AGÊNCIA NACIONAL DO PETRÓLEO - ANP. Anuário Estatístico 2017. 2017. Rio de Janeiro. Disponível em: <http://www.anp.gov.br/wwwanp/images/publicacoes/ anuario-estatistico/2017/ anuário {_} 2017.pdf.>. Acessado em 15 de abr de 2019. [5] ARES, G. Logística de apoio offshore - integração e sincronização da cadeia de atendimento às unidades marítimas. 2013. Disponível em: <http://www.ilos.com.br/ web/logistica-de-apoio-offshore-integracao-e-sincronizacao-da-cadeia-de- atendimento-as-unidades-maritimas/.eferência>. Acessado em 15 de abr de 2019. [6] ARPINI, B. P.; ROSA, R. DE A. Planejamento da logística de suprimento de plataformas Offshore por meio de um modelo matemático 2L-CVRP com frota heterogênea e equilíbrio náutico. Transportes, v. 23, n.4, p. 67-78. 2015. [7] BRAGA, A. A. Uma análise de um sistema de transporte de passageiros para plataformas offshore. Monografia apresentada na Graduação em Engenharia Naval e Oceânica da Escola Politécnica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 2017. [8] COSTA, P. F. F da. Otimização da logística de operação de navios aliviadores de petróleo usando programação matemática. Dissertação de mestrado do Departamento de Engenharia Industrial, Pontifícia Universidade Católica do Rio de Janeiro, 2015. [9] DI LUCCIO, F.B.; DORES, P.B.DAS. O mercado de apoio offshore: panorama e perspectivas. BNDES Setorial, Rio de Janeiro, n.43, p. 295-323, março, 2016. [10] ESKANDARI, H.; MAHMOODI, E. A simulation-based multi-Objective optimization study of the fleet sizing problem in the offshore industry. Maritime Economics and Logistics, v.18, p.436–457, 2016. [11] KISIALIOU, Y.; GRIBKOVSKAIA, I.; LAPORTE, G. Robust supply vessel routing and scheduling. Transportation Research Part C: Emerging Technologies, v.90, p.366–378, 2018. [12] MARTINS, F.G.; COELHO L.S. Aplicação do método de análise hierárquica do processo para o planejamento de ordens de manutenção em dutovias. Revista GRPOS, Gestão da Produção, Operações e Sistemas, v. 7, n. 1, p. 65-80, 2012. [13] MOREIRA, P. 5. CONCLUSÃO O método multicritério se mostra relevante e aplicável a processos de tomada de decisão que envolvam variáveis de caráter subjetivo e quantitativo 10 1. REFERÊNCIAS C. M. Análise de aumento da eficiência do sistema marítimo offshore de transporte de carga por meio de simulação probabilística. Dissertação 11 As Referências Bibliográficas devem seguir as normas da ABNT/NBR 6023. de Mestrado no Programa de Engenharia de Transportes, Universidade Federal do Rio de Janeiro, 2017. de Mestrado no Programa de Engenharia de Transportes, Universidade Federal do Rio de Janeiro, 2017. de Mestrado no Programa de Engenharia de Transportes, Universidade Federal do Rio de Janeiro, 2017. [14] NORLUND, E.K.; GRIBKOVSKAIA, I.; LAPORTE, G. Supply vessel planning under cost, environment and robustness considerations. Omega, v. 57, p. 271–281, 2015. [15] NORLUND, E.K.; GRIBKOVSKAIA, I. Environmental performance of speed optimization strategies in offshore supply vessel planning under weather uncertainty. Transportation Research Part D: Transport and Environment, v. 57, p.10–22, 2017. [16] NORSTAD, I.; GRIBKOVSKAIA, V.; JOHNSEN, T.; LINDSTAD, H.E.; UTHAUG, E. Simulation-Based Evaluation of Upstream Logistics System Concepts for Offshore Operations in Remote Areas. ASME 2017 36th International Conference on Ocean, Offshore and Arctic Engineering, p. V008T07A003, 2017. [17] PSARAFTIS, H.N.; KONTOVAS, C.A. Speed models for energy-efficient maritime transportation: a taxonomy and survey. Transportation Research Part C: Emerging Technologies, v. 26, p. 331–351, 2013. [18] PINTO, A.P.; ROSA, R. DA A.; ROSA, A.L. DA S. Modelo matemático para planejamento tático das rotas dos barcos para suprimento das plataformas offshore de exploração de petróleo. Logística, Modelagem em Transportes e Logística, v.31, p. 630-641, 2015. [19] SILVA, V. A.; LIANG, D. A.; YUBA, D. G. T.; ROSSETTO, R.; KOVALSKI, S. Logistics Planning for Critical Cargos Related to Hydrogen Sulfide Removal Processes in Pre-Salt Basin Fields. Offshore Technology Conference, Rio de Janeiro, Brazil, Oct., 2015. [20] ROY, B. ELECTRE III: Algorithme de Classement Base Sur Une Représentation Floue des Préférences en Présence des Critères Multiples. Cahiers du CERO, v. 20, n.1, p. 3-24, 1978. [21] ROY, B. Méthodologie multicritère d’aide à la décision. Paris: Economica. 1985. [22] TOMLINSON, R.; KISS, I. Rethinking the Process of Operational Research and Systems Analysis. United Kingdom: Pergamon Press, 1984. [23] VIANNA, I. G. P. Análise da alocação de embarcações de apoio offshore com o uso de heurísticas e simulação de eventos discretos. Dissertação de Mestrado do Programa de Engenharia de Produção, Universidade Federal do Rio de Janeiro, 2019. [24] WATROBSKI, J.; JANKOWSKI, J.; ZIEMBA, P.; KARCZMARCZYK, A.; ZIOLO, M. Generalised framework for multi-criteria method selection. Omega, v.86, p. 107- 124, 2019. 12 12
https://openalex.org/W2012730834
https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0029306&type=printable
English
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Conditional Gene Expression in Mycobacterium abscessus
PloS one
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cc-by
8,676
Abstract The authors gratefully acknowledge Conseil Re´gional d’Ile de France and INSERM for funding this project. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: jean-louis.herrmann@rpc.aphp.fr increased pathogenicity in various in vitro and in vivo models [13,14,15,16]. With the recent availability of its complete genome sequence [17], M. abscessus is now a particularly relevant model for studying pathogenic mechanisms of mycobacterial disease [10]. However, research molecular microbiology and pathophysiology of diseases caused by M. abscessus has been hampered by the lack of genetic tools working on this agent, and the absence of knock-out mutants, with only one described so far from an S isotype [18]. Several genetic tools for mutagenesis by homologous recombina- tion and conditional gene expression have been extensively modified and engineered for use in mycobacteria. Two thermo- sensitive systems [19,20] and a plasmid encoding phage-recombi- nases [21] were used for homologous recombination. Several regulated expression systems were developed to control gene expression in mycobacteria. The first described expression system was based on the acetamide-inducible promoter of M. smegmatis [22]. Other systems used for modulating gene expression in M. tuberculosis were based on the TetR repressor [23,24,25] and revTetR [26,27]. Alternate systems included the Streptomyces coelicolor pristinamycin I repressor Pip [28], the Rhodococcus rhodochrous nitrilase repressor NitR [29] and the recently described TetR/PipOFF double repressor system [30]. Conditional Gene Expression in Mycobacterium abscessus Me´lanie Cortes1,2, Anil Kumar Singh1,2, Jean-Marc Reyrat1,2{, Jean-Louis Gaillard3, Xavier Nassif1,2, Jean- Louis Herrmann3* 1 Universite´ Paris Descartes, Faculte´ de me´decine, Paris, France, 2 INSERM (U-1002), Paris, France, 3 EA 3647 Physiopathologie et diagnostic des infections microbiennes, Universite´ Versailles St Quentin, and Laboratoire de Microbiologie, Hoˆpital Raymond Poincare´, AP-HP, Garches, France Abstract Mycobacterium abscessus is an emerging human pathogen responsible for lung infections, skin and soft-tissue infections and disseminated infections in immunocompromised patients. It may exist either as a smooth (S) or rough (R) morphotype, the latter being associated with increased pathogenicity in various models. Genetic tools for homologous recombination and conditional gene expression are desperately needed to allow the study of M. abscessus virulence. However, descriptions of knock-out (KO) mutants in M. abscessus are rare, with only one KO mutant from an S strain described so far. Moreover, of the three major tools developed for homologous recombination in mycobacteria, only the one based on expression of phage recombinases is working. Several conditional gene expression tools have recently been engineered for Mycobacterium tuberculosis and Mycobacterium smegmatis, but none have been tested yet in M. abscessus. Based on previous experience with genetic tools allowing homologous recombination and their failure in M. abscessus, we evaluated the potential interest of a conditional gene expression approach using a system derived from the two repressors system, TetR/PipOFF. After several steps necessary to adapt TetR/PipOFF for M. abscessus, we have shown the efficiency of this system for conditional expression of an essential mycobacterial gene, fadD32. Inhibition of fadD32 was demonstrated for both the S and R isotypes, with marginally better efficiency for the R isotype. Conditional gene expression using the dedicated TetR/PipOFF system vectors developed here is effective in S and R M. abscessus, and may constitute an interesting approach for future genetic studies in this pathogen. Citation: Cortes M, Singh AK, Reyrat J-M, Gaillard J-L, Nassif X, et al. (2011) Conditional Gene Expression in Mycobacterium abscessus. PLoS ONE 6(12): e29306. doi:10.1371/journal.pone.0029306 Editor: Olivier Neyrolles, Institut de Pharmacologie et de Biologie Structurale, France Editor: Olivier Neyrolles, Institut de Pharmacologie et de Biologie Structurale, France Received September 12, 2011; Accepted November 24, 2011; Published December 15, 2011 Received September 12, 2011; Accepted November 24, 2011; Published December 15, 2011 Copyright:  2011 Cortes et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and rep duction in any medium, provided the original author and source are credited. ro Funding: MC is funded by a postdoctoral grant from DIM Malinf. AKS was funded by Marie-Curie IIF fellowship. This work was supported by grants from Re´gion Ile-de-France. PLoS ONE | www.plosone.org Citation: Cortes M, Singh AK, Reyrat J-M, Gaillard J-L, Nassif X, et al. (2011) Conditional Gene Expression in Mycobacterium abscessus. PLoS ONE 6(12): e29306. doi:10.1371/journal.pone.0029306 Functionality of the TetR/PipOFF constructs in M. abscessus S isotype y Once the functionality of pMC30A and pMC30B were confirmed in M. smegmatis as compared to pFRA42A, pMC30A and pMC30B plasmids were then electroporated in M. abscessus strain CIP 104536T (S isotype), in addition to pMVlac as a positive control. b-galactosidase activity was expressed as the ratio of the activity observed in presence of ATc (100, 200 and 300 ng/ml) to the activity obtained in the absence of ATc. Such ATc concentrations were well below tetracycline MIC described towards M. abscessus (range 8 to 128 mg/ml) [31]. This activity was measured and expressed as a percentage at 24, 48 and 72 h. M. abscessus S strain had no b-galactosidase activity. b-galactosidase activity in M. abscessus - pMC30A S isotype was decreased by 52% at 24 h, 62% at 48 h and nearly 67% at 72 h in the presence of 100 ng/ml of ATc as compared to the b-galactosidase activity measured in absence of ATc. Increasing ATc concentrations had only a slight negative effect on the b-galactosidase activity in M. abscessus S isotype. b- galactosidase activity in M. abscessus - pMC30A S isotype was decreased by 60% fold at 24 h, 72% fold at 48 h and at 72 h at a concentration of 200 ng/ml of ATc as compared to the b- galactosidase activity in the absence of ATc. Similar results were obtained at 300 ng/ml of ATc compared to 200 ng/ml. M. abscessus - pMVlac S isotype demonstrate of a b-galactosidase activity 8 times higher compared to M. abscessus - pMC30A S isotype in the absence of ATc (data not shown), and kept this activity throughout the experiment (data not shown). Similar results were obtained with both integrative plasmids pMC30A and pMC30B (Figure 3A). Therefore research into M. abscessus, an emerging virulent pathogen, is still hampered by the lack of effective genetic tools. For this reason, we have considered the key role of regulated expression systems for studying mycobacteria pathogenesis, as we felt it was of outmost importance to test and adapt one of the last described repressor system in this mycobacterium. Previous experiments performed on tools for homologous recombination in our laboratory required us to modify the existing TetR/PipOFF system and to clone the different promoters in integrative vectors known to work in M. abscessus. We then studied the efficiency of the adapted TetR/PipOFF system firstly by controlling lacZ expression in M. Functionality of the TetR/PipOFF constructs in M. smegmatis pMC30A, pMC30B, pMVlac plasmids, and the pFRA42A (kindly provided by Boldrin et al.) [30] were electroporated into M. smegmatis mc2155 strain, to demonstrate their respective function- ality (Figure S1). As a negative control, M. smegmatis mc2155 strain was shown to have no b-galactosidase activity (Figure 2). By comparison, b-galactosidase activity was obtained in each transformant, with activity ranging from 123, 67 and 71 Miller units without ATc respectively for mc2155-pFRA42A and mc2155-pMC30A or -pMC30B respectively (Figure 2). By comparison, b-galactosidase activity was high in mc2155-pMVlac, with 8396228 Miller units in absence of ATc (Figure 2). Similarly, b-galactosidase activity decreased by 12 and 10-fold respectively in mc2155-pMC30A and mc2155-pMC30B after 24 h and 42 h of incubation in presence of ATc (Figure 2). By comparison, the presence of ATc had no impact on the b-galactosidase activity of Introduction Mycobacterium abscessus is an emerging, rapidly growing mycobac- terium (RGM) that causes a wide spectrum of disease in humans, including chronic lung disease, skin and soft tissue disease, meningitis, meningoencephalitis, and disseminated disease in patients receiving immunosuppressive therapy [1,2,3]. M. abscessus lung disease is highly prevalent in patients with cystic fibrosis (CF) and is becoming a major issue for most CF centres worldwide [4,5,6]. M. abscessus is also a leading cause of sporadic and epidemic cases of skin and soft-tissue infections after surgery or following the use of contaminated syringes and needles [7,8], with reports of several large outbreaks associated with injection of adrenal cortex extract, abdominoplasty, laparo- scopic surgeries, mesotherapy, tattooing and piercing [9]. M. abscessus is one of the most antibiotic-resistant RGM species: it is naturally resistant to conventional anti-tuberculous drugs and only very few drugs are potentially active [1,10]. Although a rapid grower, M. abscessus has the ability to induce a chronic disease associated with granuloma formation and on occasion caseous lesions [11,12,13]. Moreover, this species may exist in the form of a smooth (S) or rough (R) isotype, the latter being associated with more severe disease [4,12], and with 1 December 2011 | Volume 6 | Issue 12 | e29306 PLoS ONE | www.plosone.org Conditional Gene Expression in M. abscessus mc2155-pMVlac, with 781695 Miller units and 864689 Miller units after 24 h and 42 h of incubation (Figure 2). These genetics tools working on Mycobacterium tuberculosis, Mycobacterium bovis strain BCG or M. smegmatis are generally considered to be able to work in virtually all mycobacteria. However, this was recently found not to be the case for M. abscessus for the tools devoted to mutagenesis by homologous recombina- tion. Indeed poor results were obtained with the thermosensitive counterselectable plasmid based on sucrose sensitivity [19] and the thermosensitive mycobacteriophage [20]. Only the most recently developed mycobacterial recombinase-based system [21] was used successfully in M. abscessus [18]. Despite this, the percentage of recombinants by homologous recombination with a double crossing-over was very low as compared to M. smegmatis, which still renders this tool cumbersome for the development of M. abscessus knock-outs [18]. Functionality of the TetR/PipOFF constructs in M. abscessus S isotype abscessus, and secondly by characterizing its role as an essential gene of fadD32 in M. abscessus. Our results have shown the difficulties encountered in adapting existing mycobac- terial tools for M. abscessus, and we describe for the first time its success in this mycobacterium and confirmed the efficacy of the plasmid encoding phage – recombinases in creating recombinant by single cross-over in M. abscessus. Construction of TetR/PipOFF system vectors for M. abscessus The same series of experiments were performed using a well- documented R isotype from M. abscessus CIP 104536T [15]. b- galactosidase activity in the presence of 100 ng/ml of ATc in M. abscessus - pMC30A R isotype was decreased by 54% at 24 h, and 76% at 48 h and at 72 h which closely corresponded to b- galactosidase values obtained for the isotype S in the presence of 200 ng/ml of ATc (Figure 3B). In fact, the inhibition of the b- galactosidase activity in M. abscessus R isotype was slightly more efficient at low ATc concentrations as compared to the S isotype (Figure 3B). Increasing the ATc concentrations also increased the inhibition of b-galactosidase activity as shown by decreased values observed in the presence of 200 ng/ml or 300 ng/ml of ATc (Figure 3B). b-galactosidase activity in M. abscessus - pMC30A R isotype was decreased by nearly 64% at 24 h and 82% at 48 h and at 72 h respectively as compared to the b-galactosidase activity in the absence of ATc. Similar results were obtained with both integrative plasmids pMC30A and pMC30B (Figures 3A and 3B). Future described experiments will be performed using plasmid pMC30A and an ATc concentration of 200 ng/ml, where we have obtained satisfactory gene repression. The TetR/PipOFF repressible system was cloned into the vector pMV306, which is an integrative vector coding for the kanamycin resistance, and which has demonstrated of its efficiency in M. abscessus. Two integrative constructs were prepared and inserted in the M. abscessus genome: pMC30A (lacZ(R);tetR(r); pip(r)) and pMC30B (lacZ(R);tetR(R);pip(r)) (Table 1 and Figure 1). To control the potential effect the integrative plasmid had by itself we also inserted the integrative vector pMVlac (pMV306 with Pptr-lacZ) described above (Table 1 and Figure 1). Results Construction of TetR/PipOFF system vectors for M. abscessus Construction of fadD32 conditional mutants (fad32c) in M. abscessus S and R isotypes The results presented above demonstrated that the regulated TetR/PipOFF system works in M. abscessus S and R isotypes, with a marginally better efficiency in the R isotype. These results prompted us to test the ability of the TetR/PipOFF system to unravel essential genes by creating conditional mutants. fadD32, a gene involved in fatty acid biosynthesis, was chosen as a test- PLoS ONE | www.plosone.org PLoS ONE | www.plosone.org December 2011 | Volume 6 | Issue 12 | e29306 2 Conditional Gene Expression in M. abscessus Table 1. Strains and plasmids used in this study. Strains or plasmid Relevant characteristics or sequence Reference or source E. coli DH5a Invitrogen (Paisley, UK) M. smegmatis mc2155 [38] M. abscessus S CIP 104536T ( = ATCC19977T), Smooth [15] M. abscessus R CIP 104536T ( = ATCC19977T), Rough [15] M. abscessus S fadD32C S Pptr-fadD32 This study M. abscessus R fadD32C R Pptr-fadD32 This study pJV53 chec9 genes gp60_61 under the control of the acetamidase promoter [21] pBSKIISK (+) Cloning vector; AmpR Stratagene pLYG204.Zeo Plasmid encoding a ZeoR cassette [45] pMV306 KnR, int, attP integrates at attB site on mycobacterial chromosome [46] pMVlac pMV306 containing lacZ under Pptr promoter This study pMC30A pMVlac containing PfurA102tetO-pip and Psmyc-tetR in the same sense This study pMC30B pMVlac containing PfurA102tetO-pip and Psmyc-tetR in the opposite sense This study pFRA42A Psmyc-tetR; PfurA102tetO-pip; Pptr-lacZ; int; SmR [30] pFRA61 Psmyc-tetR; PfurA102tetO-pip (Sm) From R. Manganelli pFRA50 pSM240 derivative; Pptr; (Hyg) [30] pMC14 pFRA50 with ZeoR cassette This study pMC18 pMC14 with Pptr-first 953 bp of M. abscessus fadD32 This study AmpR, ampicillin resistance; HygR, Hygromycin resistance; KnR, kanamycin resistance; ZeoR, zeocin resistance; SmR, Streptomycin resistance. doi:10.1371/journal.pone.0029306.t001 Relevant characteristics or sequence mpicillin resistance; HygR, Hygromycin resistance; KnR, kanamycin resistance; ZeoR, zeocin resistance; SmR, Streptomycin resistance. 371/journal.pone.0029306.t001 and fadV (Table 2) giving the expected fragment of 1700 bp. This PCR was negative in the wild type strain and on plasmid pMC18 (see Figure 4B lanes 1–4). Replacements were performed in both S and R isotypes giving strains S fadD32C and R fadD32C. gene, as it has been reported to be essential in mycobacteria [28,32]. The fadD32 gene of M. tuberculosis (Rv3801c) has orthologs in M. smegmatis (MSMEG_6393, Blastp: 76% identities and 87 % positives) and M. abscessus (MAB_0179, BlastP: 66% identities and 81 % positives). Genomic organization in the fad32 region was similar in all three mycobacterial species. fadD32C growth characteristics in presence of ATc To create the conditional fadD32 mutant in M. abscessus, we cloned the 59 region of fadD32 under the control of Pptr giving plasmid pMC18 (Figure 4A). After electroporation and zeocin selection, we checked for recombinants with a single cross-over in all the clones growing in the presence of zeocin. Such single cross-over allows replacement of the wild-type gene under the control of its own promoter by the 59 truncated part of fadD32 under the control of Pptr (Figure 4A). Conditional mutants were searched for by PCR using primers MC77 After transformation of plasmid pMC30A or pMVlac in fadD32C S and R strains, growth analysis was performed in the presence or absence of 200 ng/ml of ATc by spotting 5 ml of the liquid cultures of each conditional mutant and wild type strain (Figure 5A). The growth of wild type M. abscessus strain (S and R isotype) was similar with or without ATc (Figure 5A, lane 1 and 5). For S fadD32C and R fadD32C strains containing the plasmid pMVlac or not, their growth was unchanged in the presence of Figure 1. Schematic representation of plasmids pMVlac, pMC30A and pMC30B. Plasmids are derivative of the empty vector pMV306. In pMVlac, the Pptr promoter and lacZ was cloned in pMV306. In pMC30A or pMC30B, Psmyc-tetR and PfurA102tetO-pip were cloned in pMVlac in the same or opposite direction. int: gene coding for an integrase; knR: kanamycin resistance gene; oriE: replication origin in E.coli; attP: site-specific recombination; lacZ: gene coding for b-galactosidase; pip: gene coding for the protein Pip, a repressor of the Pptr promoter; tetR: gene coding for TetR, a repressor of the PfurA102tetO promoter in absence of ATc; Psmyc: constitutive promoter; PfurA102tetO: promoter repress by TetR; Pptr: promoter repress by the protein Pip. doi:10.1371/journal.pone.0029306.g001 Figure 1. Schematic representation of plasmids pMVlac, pMC30A and pMC30B. Plasmids are derivative of the empty vector pMV306. In pMVlac, the Pptr promoter and lacZ was cloned in pMV306. In pMC30A or pMC30B, Psmyc-tetR and PfurA102tetO-pip were cloned in pMVlac in the same or opposite direction. fadD32C growth characteristics in presence of ATc int: gene coding for an integrase; knR: kanamycin resistance gene; oriE: replication origin in E.coli; attP: site-specific recombination; lacZ: gene coding for b-galactosidase; pip: gene coding for the protein Pip, a repressor of the Pptr promoter; tetR: gene coding for TetR, a repressor of the PfurA102tetO promoter in absence of ATc; Psmyc: constitutive promoter; PfurA102tetO: promoter repress by TetR; Pptr: promoter repress by the protein Pip. doi:10.1371/journal.pone.0029306.g001 December 2011 | Volume 6 | Issue 12 | e29306 PLoS ONE | www.plosone.org 3 Conditional Gene Expression in M. abscessus Figure 2. Assays with vectors pMC30A and pMC30B containing TetR/Pip OFF system in M. smegmatis. mc2155 and mc2155- pMVlac, - pFRA42A, -pMC30A and pMC30B were cultured in Luria-Bertani broth, and their respective b-Galactosidase activity was measured at 0 h, 24 h and 42 h in presence of 50 ng/ml ATc. Results were expressed in Miller units. mc2155 with or without pFRA42A serve as negative and positive control respectively. doi:10.1371/journal.pone.0029306.g002 Conditional Gene Expression in M. abscessus Figure 2. Assays with vectors pMC30A and pMC30B containing TetR/Pip OFF system in M. smegmatis. mc2155 and mc2155- pMVlac, - pFRA42A, -pMC30A and pMC30B were cultured in Luria-Bertani broth, and their respective b-Galactosidase activity was measured at 0 h, 24 h and 42 h in presence of 50 ng/ml ATc. Results were expressed in Miller units. mc2155 with or without pFRA42A serve as negative and positive control respectively. doi:10.1371/journal.pone.0029306.g002 200 ng/ml ATc, demonstrating the correct control of fadD32 by the Pptr promoter (Figure 5A, lane 2, 3, 6 and 7). own promoter. When the TetR/PipOFF system was introduced (via pMC30A) into this construct, the expression of fadD32 was decreased but was still higher than in the wild type strain. In the presence of 200 ng/ml of ATc, qRT-PCR confirmed the total absence of fadD32 mRNA and by so the inhibitory activity linked to the TetR/PipOFF system. Similar results were obtained in the R strain (Figure 6B). p Strains S fadD32C-pMC30A and R fadD32C-pMC30A growth were similar as the wild type strain growth in absence of ATc. Reduction of growth was observed in presence of 200 ng/ml ATc for the S fadD32C-pMC30A as shown by the absence of colonies after spotting 5 ml at dilutions 1022 and 1023 respectively (Figure 5A, lane 4). fadD32C growth characteristics in presence of ATc The absence of growth was observed for the R fadD32C-pMC30A, as shown by the non-existence of any colonies from pure and 1021 dilution (figure 5A, lane 8). Such results confirmed the inhibitory role of Pip towards Pptr promoter in presence of ATc. These experiments demonstrate the inability of M. abscessus fad32C to grow in the presence of ATc, demonstrating its essential role in M. abscessus. In conclusion, these experiments have demonstrated for the first time the functionality of the TetR/PipOFF regulated system in M. abscessus on lacZ and fadD32 genes. We have confirmed that fadD32 is also an essential gene in M. abscessus. PLoS ONE | www.plosone.org Conditional Gene Expression in M. abscessus December 2011 | Volume 6 | Issue 12 | e29306 Discussion Ever since the recognition recently in 1992 of M. abscessus as a species, the number of clinical reports of infections due to M. abscessus has increased annually, mainly but not exclusively affecting subjects with predisposing conditions (e.g., Cystic Fibrosis, or those receiving immunosuppressive therapy). Aside from its role as an emerging pathogen, M. abscessus may function as a suitable surrogate host for the study of mycobacterial infections in general. Like M. smegmatis, it grows rapidly on conventional culture media and is a level 2 pathogen. However, it shares a number of traits with slow-growing mycobacterial pathogens, such as the formation of caseous lesions [13] and the ability to persist silently for decades in the human host [10]. Several relevant in vivo and ex vivo models of infections have already been developed [13,14,15,33] and its complete genome sequence is now available [17]. Growth with or without ATc was also controlled in liquid culture. Diluted liquid culture aliquots of S fadD32C-pMC30A and R fadD32C-pMC30A were separated into two cultures: one without ATc and one with 200 ng/ml ATc. After 48 h, OD600nm was measured and CFU counts were numbered on LB agar plates (Figure 5B). CFU counts showed that S fadD32C-pMC30A and R fadD32C-pMC30A growths were decreased, in the presence of ATc, by 93 and 99% of the values of the initial inocula respectively (Figure 5B). Optical density values at 600 nm were similar, with or without ATc, for both S/R fadD32C-pMC30A variants (data not shown). These results were in agreement with data obtained on solid medium. To confirm these results, the expression level of fadD32 was measured by quantitative RT-PCR (qRT-PCR) in both fadD32C strains after 48 h with or without 200 ng/ml ATc. As shown in figure 6A, when fadD32 was positioned under the Pptr promoter (strain S fadD32C), its expression was 5-fold higher than with its However, a true understanding of the genetics of M. abscessus is still in its infancy with only one KO mutant described so far [18]. M. abscessus is indeed one of the most resistant of the mycobacteria, December 2011 | Volume 6 | Issue 12 | e29306 December 2011 | Volume 6 | Issue 12 | e29306 4 Conditional Gene Expression in M. abscessus Conditional Gene Expression in M. Discussion abscessus was associated with the loss of a surface molecule named glycopeptidolipid (GPL) [13,15,33,37]. The difference between the S and R strains of M. abscessus might thus be due to changes of surface properties and the degree of permeability from the loss of GPL. However, nothing is known regarding comparative MICs towards ATc for both isotypes. In addition, the induction of efflux systems was demonstrated to be responsible for the lower efficiency of ATc used at high concentrations [25]. Having taken into account all of these mycobacterial properties, we decided to test the recently developed TetR/PipOFF system, which has previously proven to be extremely useful in the detection and study of conditional mutants in M. tuberculosis and M. smegmatis [30,35]. The TetR/PipOFF system allows repression to be achieved by the addition of ATc rather than its removal from the culture medium. The ATc based induction of the Pip-encoding gene permits a tight repression of the gene under investigation [30]. Several steps were necessary to adapt the TetR/PipOFF system to M. abscessus. Firstly, it was necessary to use different and integrative vectors coding for the zeocin resistance. This resistance marker was shown to be more efficient than the kanamycin resistance marker, by selecting far fewer spontaneous antibiotic- resistant mutants [18], and was used at a concentration of less than 50 mg/ml. The second step was to achieve a recombination event, by single cross-over. We firstly electroporated the recently developed mycobacterial recombinase-based system pJV53 [21] in M. abscessus S and R isotypes. Plasmid pMC18 was then electroporated in both S and R isotypes – pJV53 and integration by single cross-over was checked by amplification. The success of Several leads might enable us to improve the adapted TetR/ PipOFF system, for example by isolating highly efficient M. abscessus strains for electroporation, as described several years ago for M. smegmatis with the isolation of the mc2155 strain [38]. R strains form aggregates and tend to stick to plastic surfaces, which hampered electroporation efficiency. The other improvement Figure 4. Construction of conditional mutants. (A) Schematic representation of the recombination event used to get the conditional mutant fadD32C after a single crossover. The size of PCR product using primers MC77 and fadV is 1700 bp. (B) PCR analysis of construction obtaining for conditional mutant. Lane 1, 2, 3 and 4: PCR with primer MC77 and fadV. Discussion abscessus does not grow above 39uC (the temperature for its optimal growth being 28uC), rendering the 40uC counterselection impossible. Finally, its S to R switch may modify the permeability of the outer layer, and the presence of a DNA degradation locus [34], a full plasmid and a complete phage [17] might restrict the efficiency of foreign DNA integration and/or recombination into the chromosome, either by DNA degradation or incompatibility. with a high frequency of spontaneous antibiotic-resistant clones when selecting for recombinants, which has hampered the use of common resistance markers. In addition, its metabolism and the optimal temperature for growth may differ between M. abscessus and other mycobacterial species. For example, the absence of a sucrose import system in M. abscessus would explain the lack of toxicity in the presence of sucrose; even if the sacB gene is expressed. This makes the thermosensitive counterselectable plasmid based on sucrose sensitivity inefficient [19]. In addition, M. abscessus does not grow above 39uC (the temperature for its optimal growth being 28uC), rendering the 40uC counterselection impossible. Finally, its S to R switch may modify the permeability of the outer layer, and the presence of a DNA degradation locus [34], a full plasmid and a complete phage [17] might restrict the efficiency of foreign DNA integration and/or recombination into the chromosome, either by DNA degradation or incompatibility. However if gene expression can be dramatically reduced in M. smegmatis and M. tuberculosis with 50 ng/ml and 200 ng/ml of ATc respectively ([30] and our study), we were unable to obtain a similar reduction in M. abscessus, even at the highest concentration of ATc (200 ng/ml). Previous studies have shown that the MIC for tetracycline is low in M. smegmatis, but higher in M. tuberculosis, thus explaining the use of a higher ATc concentration to induce the TetR repression in M. tuberculosis [25]. Less is known about resistance of M. abscessus towards tetracycline. Several studies have previously shown that M. abscessus possesses a number of resistance determinants, which makes this bacterium more resistant than M. smegmatis or M. tuberculosis towards ATc [36]. We have also identified a difference between S and R strains, the R isotype showing a higher level of lacZ repression for similar ATc concentrations, compared to S strain. A number of recent studies have shown that the S/R switch in M. Discussion absces PLoS ONE | www.plosone.org 5 December 2011 | Volume 6 | Issue 12 | e293 PLoS ONE | www.plosone.org 5 December 2011 | Volume 6 | Issue 12 | e2 December 2011 | Volume 6 | Issue 12 | e29306 PLoS ONE | www.plosone.org PLoS ONE | www.plosone.org Conditional Gene Expression in M. abscessus Conditional Gene Expression in M. abscessus Figure 3. Characterization of the TetR/Pip OFF system in M. abscessus. M. abscessus S (A) and R (B) strains with pMC30A or pMC30B were grown in Luria-Bertani broth and b-Galactosidase activity was measured in absence or in presence of 100, 200 or 300 ng/ml ATc at three time points (24, 48 and 72 h). b-Galactosidase activity was expressed as the percentage of the residual activity in presence of ATc to the normal activity observed in absence of ATc. Black bars 24 h; grey bars: 48 h; white bars: 72 h. doi:10.1371/journal.pone.0029306.g003 Figure 3. Characterization of the TetR/Pip OFF system in M. abscessus. M. abscessus S (A) and R (B) strains with pMC30A or pMC30B were grown in Luria-Bertani broth and b-Galactosidase activity was measured in absence or in presence of 100, 200 or 300 ng/ml ATc at three time points (24, 48 and 72 h). b-Galactosidase activity was expressed as the percentage of the residual activity in presence of ATc to the normal activity observed in absence of ATc. Black bars 24 h; grey bars: 48 h; white bars: 72 h. doi:10.1371/journal.pone.0029306.g003 this gene replacement, which represents only the second published description so far in M. abscessus, has allowed us to demonstrate, once again, the efficacy of pJV53 and its recombinases in both isotypes. Finally, lacZ as a simple marker of expression, and fadD32 as an example of an essential gene have confirmed the functionality of the adapted TetR/PipOFF in M. abscessus. with a high frequency of spontaneous antibiotic-resistant clones when selecting for recombinants, which has hampered the use of common resistance markers. In addition, its metabolism and the optimal temperature for growth may differ between M. abscessus and other mycobacterial species. For example, the absence of a sucrose import system in M. abscessus would explain the lack of toxicity in the presence of sucrose; even if the sacB gene is expressed. This makes the thermosensitive counterselectable plasmid based on sucrose sensitivity inefficient [19]. In addition, M. Plasmids construction Restriction endonucleases and modification enzymes (phospha- tase and Klenow fragment) (New England Biolabs, Ipswich, UK) were used according to the manufacturer’s instructions. PCRs were performed using 1 U DyNazyme DNA polymerase (Finn- zymes, Espoo, Finland) in 1X buffer, 200 mM concentration of each deoxynucleoside triphosphate (MP biomedicals, Illkirch, France), 0.8 mM concentration of each primer (Eurogentec, Seraing, Belgium), and 10 ng of chromosomal DNA in a 50-ml reaction volume. Cycling conditions were as follows: 1 cycle of 5 min at 94uC; 30 cycles of 20 s at 94uC, 20 s at 55uC, and 40 s/ kb at 72uC; with a final extension of 10 min at 72uC. PCR products were separated in 1% agarose gels for 1 h at 10 V/cm of gel. DNA fragments were purified from agarose gel by use of a WizardH SV gel and PCR Clean-Up system (Promega, Madison, WI, USA). E. coli DH5a strain (Invitrogen, Paisley, UK) was used for cloning experiments. doi:10.1371/journal.pone.0029306.t002 might be the counter selective marker. One recently developed antibiotic, Nourtheothricin (http://www.webioage.com/) (Jun- Rong Wei and Eric Rubin, personal communication) was shown to be active against M. abscessus, and might represent only the second efficient counterselective agent to be developed for use as a genetic tool for M. abscessus. This further demonstrates the difficulties encountered when working on M. abscessus, and henceforth might impede the development of genetic tools dedicated to this species. Plasmid pMVlac was constructed starting with the restriction of pMV306 plasmid by EcoRV followed by the ligation with the PCR product Pptr-lacZ purified after amplification using primers MC77 and lacZ-3 using plasmid pFRA42A as target (Figure 1 and S2 and Table 1 and 2). Plasmid pMC30A (Figure 1 and S2) was constructed as a derivative of pMVlac after restriction by NcoI followed by ligation of the restricted fragments PfurA102tetO-pip and Psmyc-tetR both purified after SphI-EcoRI digestion of pFRA61 plasmid (Table 1). Plasmid pMC30B (Figure 1 and S2) represents the opposite of pMC30A with PfurA102tetO-pip and Psmyc-tetR ligated in opposite orientation in the NcoI site of pMV306 plasmid (Table 1). Using the TetR/PipOFF system, we have demonstrated the essential role of the fadD32 in M. abscessus. Although predictable - fadD32 does plays an important role in the formation of the outer membrane and in cell-wall permeability [39] making it essential for M. tuberculosis and M. Construction of conditional mutants in M. abscessus Plasmid pMC18 (Table 1), which contains the first 953 bases of fadD32 (MAB_0179) under the control of the Pptr promoter, was electroporated into M. abscessus strain bearing pJV53 (Table 1). After a single cross-over event, pMC18 was integrated into the chromosome giving the entire fad32 gene under the control of Pptr promoter and a deleted part of fad32 gene under the control its own promoter (strain fadD32C, see Table 1). M. abscessus recombinants were isolated afterwards on LB agar plates after zeocin selection (50 mg/ml). Plasmid pMC18 integration by single cross-over was checked by amplification using primers MC77 (on Pptr promoter) and fadV (on 39end of fadD32) (Table 2). After elimination of plasmid pJV53, plasmids pMC30A and pMC30B (Table 1) were electroporated to obtain the final conditional mutant fad32. After kanamycin (50 mg/ml) and X-gal (50 mg/ml) selection on LB agar, strains S or R fadD32C-pMC30A or – pMC30B were obtained. Transformation with pMVlac (Table 1) was performed (strains S or R fadD32C-pMVlac) to control for functionality of the plasmid without the two regulatory genes pip and tetR. Conditional Gene Expression in M. abscessus Conditional Gene Expression in M. abscessus Table 2. Primers used in this study. Primer Name Sequence fadF cgatgcatgcgttcgacaacccgttc fadR cgatgcatattgatgatcgagtggatgt fadV cggtgtattcgatgtcttg lacZ-3 ttattattatttttgacaccagac MC77 cgcatatgagatctccatcctgacgg ZeoF ccgctagctcgagcac ZeoR cgactagtgatccccgggaattc MC82 agcgtgagctgctacaggac MC83 tggatttccagcaccttctc MC84 acatcgaatacaccgcacaa MC85 ggattgtcgaaaaccacctg doi:10.1371/journal.pone.0029306.t002 abscessus. This plasmid is used to induce the crossing-over as described previously [10]. After several sub-cultures in the absence of a selective marker, the pJV53 plasmid can be lost by the strain, as checked by kanamycin sensitivity. Table 2. Primers used in this study. Materials and Methods Bacterial strains, transformation condition and growth conditions Plasmids construction smegmatis [32] - this result nonetheless proves the functionality of the adapted TetR/PipOFF system in M. abscessus. This will permit further investigation of candidate genes, such as those identified recently using a transcriptomic approach to unravel the molecular mechanisms of the S/R switch (Herrmann et al., unpublished, and [16]). Indeed, while we know that the S/R switch is essential for M. abscessus to modulate the innate immune response of the host [13,16], nothing is currently known about the precise mechanisms involved. The development of the TetR/PipOFF system may also allow the characterization of the respective roles of candidate virulence genes recently identified in the M. abscessus genome [17]. Zeocin, as a selective marker, was inserted by amplification with primers ZeoF and ZeoR from the plasmid pLYG204-Zeo, then restricted by SpeI and ligated into the plasmid pFRA50 previously restricted by SpeI and purified, to create pMC14 (Table 1). 953 bp of the 59 end of fadD32 (MAB_0179) was amplified using primers fadF and fadR (Table 2) and then cloned into the NsiI site of pMC14 which is located downstream of the Pptr promoter giving plasmid pMC18 (Table 1 and Figure S1). Discussion Lane 1: CIP-S fadD32C; lane 2: CIP-R fadD32C; lane 3: CIP-S; lane 4: pMC18; lane MW: molecular size standard. doi:10.1371/journal.pone.0029306.g004 Figure 4. Construction of conditional mutants. (A) Schematic representation of the recombination event used to get the conditional mutant fadD32C after a single crossover. The size of PCR product using primers MC77 and fadV is 1700 bp. (B) PCR analysis of construction obtaining for conditional mutant. Lane 1, 2, 3 and 4: PCR with primer MC77 and fadV. Lane 1: CIP-S fadD32C; lane 2: CIP-R fadD32C; lane 3: CIP-S; lane 4: pMC18; lane MW: molecular size standard. doi:10.1371/journal.pone.0029306.g004 December 2011 | Volume 6 | Issue 12 | e29306 December 2011 | Volume 6 | Issue 12 | e29306 PLoS ONE | www.plosone.org 6 Figure 5. Characterization of growth for conditional mutants in M. abscessus. (A) Bacteria were grown to exponential phase and 5 ml of 10- fold serial dilutions were spotted onto LB agar medium supplemented or not with ATc 200 ng/ml. Plates were incubated at 37uC. Pictures were taken after five days. Arrows indicate the difference of growth in presence or absence of ATc. (B) Diluted liquid culture of S fadD32C-pMC30A and R fadD32C- pMC30A were separated in two cultures (one without ATc and one with 200 ng/ml ATc). After 48 h, cfu was numbered on LB agar plates. Results are expressed in percentage of growth in comparison with the same strain culture without ATc. doi:10.1371/journal.pone.0029306.g005 Figure 5. Characterization of growth for conditional mutants in M. abscessus. (A) Bacteria were grown to exponential phase and 5 ml of 10- fold serial dilutions were spotted onto LB agar medium supplemented or not with ATc 200 ng/ml. Plates were incubated at 37uC. Pictures were taken after five days. Arrows indicate the difference of growth in presence or absence of ATc. (B) Diluted liquid culture of S fadD32C-pMC30A and R fadD32C- pMC30A were separated in two cultures (one without ATc and one with 200 ng/ml ATc). After 48 h, cfu was numbered on LB agar plates. Results are expressed in percentage of growth in comparison with the same strain culture without ATc. doi:10.1371/journal.pone.0029306.g005 Bacterial strains, transformation condition and growth conditions Bacterial strains and plasmids are described in table 1 and on figure 1. Bacteria were grown in Luria-Bertani (LB) broth at 37uC with agitation. Ampicillin (100 mg/ml, Sigma, Saint-Louis, MO, USA), kanamycin (50 mg/ml, Sigma, Saint-Louis, MO, USA), zeocin (25 mg/ml for E. coli; 50 mg/ml for mycobacteria, Invitrogen, Paisley, UK), hygromycin (200 mg/ml, Roche Diag- nostics, Mannheim, Germany), streptomycin (50 mg/ml, Sigma, Saint-Louis, MO, USA) and X-gal (50 mg/ml, MP biomedicals, Illkirch, France) were added when necessary. ATc (Sigma, Saint- Louis, MO, USA) was added as required at concentrations starting at 0 and up to 300 ng/ml. Preparation of electrocompetent cells, electroporation and preparation of mycobacterial genomic DNA were performed as previously described [40,41]. The plasmid pJV53, which express recombinases [21], was electroporated in M. PLoS ONE | www.plosone.org December 2011 | Volume 6 | Issue 12 | e29306 7 Conditional Gene Expression in M. abscessus b-galactosidase activity assay percentage of Miller unit for the tested strain at a give time versus Figure 5. Characterization of growth for conditional mutants in M. abscessus. (A) Bacteria were grown to exponential phase and 5 ml of 10- fold serial dilutions were spotted onto LB agar medium supplemented or not with ATc 200 ng/ml. Plates were incubated at 37uC. Pictures were taken after five days. Arrows indicate the difference of growth in presence or absence of ATc. (B) Diluted liquid culture of S fadD32C-pMC30A and R fadD32C- pMC30A were separated in two cultures (one without ATc and one with 200 ng/ml ATc). After 48 h, cfu was numbered on LB agar plates. Results are expressed in percentage of growth in comparison with the same strain culture without ATc. doi:10.1371/journal.pone.0029306.g005 PLoS ONE | www.plosone.org 2. Talati NJ, Rouphael N, Kuppalli K, Franco-Paredes C (2008) Spectrum of CNS disease caused by rapidly growing mycobacteria. Lancet Infect Dis 8: 390–398. Growth analysis 10-fold serial dilutions were made from exponentially grown cultures (37uC with agitation) in the absence of ATc, and 5 ml of Conditional Gene Expression in M. abscessus Growth analysis 10-fold serial dilutions were made from exponentially grown cultures (37uC with agitation) in the absence of ATc, and 5 ml of Figure 6. Quantification of fadD32 expression in conditional mutant. Expression of fadD32 was measured by quantitative real-time PCR as described in Materials and Methods, using sigA gene as a housekeeping gene standard. Results are relative expression ratios compared to expression in wild type strain (S or R). Expression was measured in wild type strain, fadD32C strains and fadD32C pMC30A strains with or without 200 ng/ml ATc after 48 h culture. (A) results in S fadD32C derivative strains; (B) results in R fadD32C derivative strains. doi:10.1371/journal.pone.0029306.g006 each dilution was plated on LB agar in the presence or absence of ATc (200 ng/ml). After five days, the presence of growth was checked for each condition and comparison was performed between plate with or without ATc. Each assay was performed in triplicate. Supporting Information Figure S1 TetR/Pip OFF system mechanism and function of plasmids used in this system. (TIF) Figure S2 Construction of pMC18, pMVlac, pMC30A and pMC30B. (TIF) Figure S2 Construction of pMC18, pMVlac, pMC30A and pMC30B. Figure 6. Quantification of fadD32 expression in conditional mutant. Expression of fadD32 was measured by quantitative real-time PCR as described in Materials and Methods, using sigA gene as a housekeeping gene standard. Results are relative expression ratios compared to expression in wild type strain (S or R). Expression was measured in wild type strain, fadD32C strains and fadD32C pMC30A strains with or without 200 ng/ml ATc after 48 h culture. (A) results in S fadD32C derivative strains; (B) results in R fadD32C derivative strains. doi:10.1371/journal.pone.0029306.g006 Acknowledgments We greatly acknowledge Dr Ben Marshall (Southampton University Hospitals Trust, UK) for careful review of the manuscript. We thank Francesca Boldrin and Riccardo Manganelli for providing us with plasmid pFRA42A and pFRA61. Author Contributions Conceived and designed the experiments: MC AKS J-MR . Performed the experiments: MC AKS. Analyzed the data: MC J-LG XN J-LH. Contributed reagents/materials/analysis tools: MC J-MR. Wrote the paper: MC J-LG XN J-LH. Conceived and designed the experiments: MC AKS J-MR . Performed the experiments: MC AKS. Analyzed the data: MC J-LG XN J-LH. Contributed reagents/materials/analysis tools: MC J-MR. Wrote the paper: MC J-LG XN J-LH. 1. Brown-Elliott BA, Wallace RJ, Jr. (2002) Clinical and taxonomic status of pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria. Clin Microbiol Rev 15: 716–746. RNA extraction Total RNA was extracted from 10 ml of bacteria in liquid culture (with or without ATc at 200 ng/ml). Pellet of bacteria was mixed with 1 ml of Trizol (Invitrogen, Paisley, UK) and placed in lysing matrix B tubes (MP Biomedicals, Illkirch, France). Bacteria were lysed by shaking in a Fastprep FP120 apparatus (MP Biomedicals, Illkirch, France). Two hundred microliters of 1-bromo-3-chloro- propane were added and tubes were centrifuged for 10 min at 10 000 g. The aqueous phase was recovered, and RNAs were precipitated with 500 ml of isopropyl alcohol and washed with ethanol 75%. RNAs were then resuspended in 50 ml of water, treated with DNase I, and purified on RNeasy minicolumns (Qiagen). The quantity and the quality of the RNAs were verified spectrophotometrically (Nanodrop ND-1000) and on agarose gels. qRT-PCR Reverse transcriptase PCR (RT-PCR) was performed with Superscript RT II (Invitrogen) using gene specific primer (MC83 and MC85, Table 2). The primer sequences were designed with Primer3Plus online software [43]. Samples without RT were prepared concurrently and analysed for the absence of contaminating genomic DNA. Real-time quantitative PCR analysis was performed using FastStart SYBR Green Master (Roche Diagnostics, Mannheim, Germany). cDNAs obtained as described above were diluted ten-fold in nuclease-free water before qPCR. The PCR program consisted of 35 amplifications/quantification cycles of 95uC for 15s and 60uC for 1 min, with signal acquisition at the end of each cycle. MC82 and MC83 were used to amplify sigA and MC84 and MC85 to amplify fadD32 (Table 2). Equation 1 from Pfaffl [44] was used to analyse the statistical significance of the data, using sigA as a reference gene standard. Each assay was performed in duplicate and repeated at least twice. b-galactosidase activity assay percentage of Miller unit for the tested strain at a give time versus Miller unit for the tested strain in the absence of ATc. percentage of Miller unit for the tested strain at a give time versus Miller unit for the tested strain in the absence of ATc. Assays on M. smegmatis mc2155 derivative strains were performed on culture prepared like described by Boldrin et al. [30]. Briefly, cultures in liquid medium were grown 18 h with or without ATc (50 ng/ml). After, culture without ATc was diluted in new culture +/2 ATc (50 ng/ml), and culture with ATc was diluted in same condition (with ATc). After 24 h, enzymatic activity of b-galactosidase was measured. Each assay was performed in triplicate. b-galactosidase activity assay was performed as previously described and enzymatic activity expressed in Miller units [42]. For M. abscessus R strains, OD600 nm was taken after sonication to represent a homogenous suspension. Exponentially growing culture cultivated at 37uC with agitation were diluted in new media in the presence of 0, 100, 200, or 300 ng/ml of ATc and incubated in similar conditions. At 24, 48 and 72 h, an aliquot was taken to perform b-galactosidase activity assay. Each assay was performed in triplicate. Results were expressed as the relative Assays on M. smegmatis mc2155 derivative strains were performed on culture prepared like described by Boldrin et al. [30]. Briefly, cultures in liquid medium were grown 18 h with or without ATc (50 ng/ml). After, culture without ATc was diluted in new culture +/2 ATc (50 ng/ml), and culture with ATc was diluted in same condition (with ATc). After 24 h, enzymatic activity of b-galactosidase was measured. Each assay was performed in triplicate. PLoS ONE | www.plosone.org December 2011 | Volume 6 | Issue 12 | e29306 8 Conditional Gene Expression in M. abscessus Conditional Gene Expression in M. abscessus 3. Wallace RG, Jr., Silcox V, Brown BA (1994) Taxonomy of rapidly growing mycobacteria. Clin Infect Dis 18: 121–122. 25. Ehrt S, Guo XV, Hickey CM, Ryou M, Monteleone M, et al. (2005) Controlling gene expression in mycobacteria with anhydrotetracycline and Tet repressor. Nucleic Acids Res 33: e21. y 4. Jo¨nsson BE, Gilljam M, Lindblad A, Ridell M, Wold AE, et al. (2007) Molecular epidemiology of Mycobacterium abscessus, with focus on cystic fibrosis. J Clin Microbiol 45: 1497–1504. 26. Guo XV, Monteleone M, Klotzsche M, Kamionka A, Hillen W, et al. (2007) Silencing Mycobacterium smegmatis by using tetracycline repressors. J Bacteriol 189: 4614–4623. 5. Roux AL, Catherinot E, Ripoll F, Soismier N, Macheras E, et al. (2009) Multicenter study of prevalence of nontuberculous mycobacteria in patients with cystic fibrosis in france. J Clin Microbiol 47: 4124–4128. 27. Klotzsche M, Ehrt S, Schnappinger D (2009) Improved tetracycline repressors for gene silencing in mycobacteria. Nucleic Acids Res 37: 1778–1788. cystic fibrosis in france. J Clin Microbiol 47: 4124–4128. 6. Sermet-Gaudelus I, Le Bourgeois M, Pierre-Audigier C, Offredo C, Guillemot D, et al. (2003) Mycobacterium abscessus and children with cystic fibrosis. Emerg Infect Dis 9: 1587–1591. 28. Forti F, Crosta A, Ghisotti D (2009) Pristinamycin-inducible gene regulation in mycobacteria. J Biotechnol 140: 270–277. 29. Pandey AK, Raman S, Proff R, Joshi S, Kang CM, et al. (2009) Nitrile-inducible gene expression in mycobacteria. Tuberculosis (Edinb) 89: 12–16. 7. Feldman EM, Ellsworth W, Yuksel E, Allen S (2009) Mycobacterium abscessus infection after breast augmentation: a case of contaminated implants? J Plast Reconstr Aesthet Surg 62: e330–332. 30. Boldrin F, Casonato S, Dainese E, Sala C, Dhar N, et al. (2010) Development of a repressible mycobacterial promoter system based on two transcriptional repressors. Nucleic Acids Res 38: e134. 8. Newman MI, Camberos AE, Clynes ND, Ascherman JA (2005) Outbreak of atypical mycobacteria infections in U.S. Patients traveling abroad for cosmetic surgery. Plast Reconstr Surg 115: 964–965. 31. Brown BA, Wallace RJ, Jr., Onyi G (1996) Activities of the glycylcyclines N,N- dimethylglycylamido-minocycline and N,N-dimethylglycylamido-6-demethyl-6- deoxytetracycline against Nocardia spp. and tetracycline-resistant isolates of rapidly growing mycobacteria. Antimicrob Agents Chemother 40: 874–878. g y g 9. Garcia-Navarro X, Barnadas MA, Dalmau J, Coll P, Gurgui M, et al. (2008) Mycobacterium abscessus infection secondary to mesotherapy. Clin Exp Dermatol 33: 658–659. p y g g y g 32. Conditional Gene Expression in M. abscessus Portevin D, de Sousa-D’Auria C, Montrozier H, Houssin C, Stella A, et al. (2005) The acyl-AMP ligase FadD32 and AccD4-containing acyl-CoA carboxylase are required for the synthesis of mycolic acids and essential for mycobacterial growth: identification of the carboxylation product and determination of the acyl-CoA carboxylase components. J Biol Chem 280: 8862–8874. 10. Medjahed H, Gaillard JL, Reyrat JM (2010) Mycobacterium abscessus: a new player in the mycobacterial field. Trends Microbiol. 11. Cullen AR, Cannon CL, Mark EJ, Colin AA (2000) Mycobacterium abscessus infection in cystic fibrosis. Colonization or infection? Am J Respir Crit Care Med 161: 641–645. 12. Catherinot E, Roux AL, Macheras E, Hubert D, Matmar M, et al. (2009) Acute respiratory failure involving an R variant of Mycobacterium abscessus. J Clin Microbiol 47: 271–274. 33. Ordway D, Henao-Tamayo M, Smith E, Shanley C, Harton M, et al. (2008) Animal model of Mycobacterium abscessus lung infection. J Leukoc Biol 83: 1502–1511. 34. Zhang Y, Yakrus MA, Graviss EA, Williams-Bouyer N, Turenne C, et al. (2004) Pulsed-field gel electrophoresis study of Mycobacterium abscessus isolates previously affected by DNA degradation. J Clin Microbiol 42: 5582–5587. 13. Rottman M, Catherinot E, Hochedez P, Emile JF, Casanova JL, et al. (2007) Importance of T cells, gamma interferon, and tumor necrosis factor in immune control of the rapid grower Mycobacterium abscessus in C57BL/6 mice. Infect Immun 75: 5898–5907. affected by DNA degradation. J Clin Microbiol 42: 5582–5587. 35. Serafini A, Boldrin F, Palu G, Manganelli R (2009) Characterization of a Mycobacterium tuberculosis ESX-3 conditional mutant: essentiality and rescue by iron and zinc. J Bacteriol 191: 6340–6344. 14. Byrd TF, Lyons CR (1999) Preliminary characterization of a Mycobacterium abscessus mutant in human and murine models of infection. Infect Immun 67: 4700–4707. 36. Wallace RJ, Jr., Brown-Elliott BA, Crist CJ, Mann L, Wilson RW (2002) Comparison of the in vitro activity of the glycylcycline tigecycline (formerly GAR-936) with those of tetracycline, minocycline, and doxycycline against isolates of nontuberculous mycobacteria. Antimicrob Agents Chemother 46: 3164–3167. 15. Catherinot E, Clarissou J, Etienne G, Ripoll F, Emile JF, et al. (2007) Hypervirulence of a rough variant of the Mycobacterium abscessus type strain. Infect Immun 75: 1055–1058. 16. Roux AL, Ray A, Pawlik A, Medjahed H, Etienne G, et al. (2010) Overexpression of proinflammatory TLR-2-signalling lipoproteins in hypervir- ulent mycobacterial variants. Cell Microbiol. 37. Ripoll F, Deshayes C, Pasek S, Laval F, Beretti JL, et al. Conditional Gene Expression in M. abscessus (2007) Genomics of glycopeptidolipid biosynthesis in Mycobacterium abscessus and M. chelonae. BMC Genomics 8: 114. 17. Ripoll F, Pasek S, Schenowitz C, Dossat C, Barbe V, et al. (2009) Non mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus. PLoS One 4: e5660. 38. Snapper SB, Melton RE, Mustafa S, Kieser T, Jacobs WR, Jr. (1990) Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis. Mol Microbiol 4: 1911–1919. 18. Medjahed H, Reyrat JM (2009) Construction of Mycobacterium abscessus defined glycopeptidolipid mutants: comparison of genetic tools. Appl Environ Microbiol 75: 1331–1338. 39. Daffe´ M, Draper P (1998) The envelope layers of mycobacteria with reference to their pathogenicity. Adv Microb Physiol 39: 131–203. 19. Pelicic V, Jackson M, Reyrat JM, Jacobs WR, Jr., Gicquel B, et al. (1997) Efficient allelic exchange and transposon mutagenesis in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 94: 10955–10960. 40. Cortes MA, Nessar R, Singh AK (2010) Laboratory maintenance of Mycobacterium abscessus. Curr Protoc Microbiol Chapter 10: Unit 10D 11. 41. Medjahed H, Singh AK (2010) Genetic manipulation of Mycobacterium abscessus. Curr Protoc Microbiol Chapter 10: Unit 10D 12. 20. Bardarov S, Kriakov J, Carriere C, Yu S, Vaamonde C, et al. (1997) Conditionally replicating mycobacteriophages: a system for transposon delivery to Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 94: 10961–10966. 42. Miller JH (1992) A short course in bacterial genetics: a laboratory manual and handbook for Escherichia coli and related bacteria. Press CSHL, editor. New York. 876 p. y 21. van Kessel JC, Hatfull GF (2007) Recombineering in Mycobacterium tuberculosis. Nat Methods 4: 147–152. p 43. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, et al. (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35: W71–74. 22. Parish T, Mahenthiralingam E, Draper P, Davis EO, Colston MJ (1997) Regulation of the inducible acetamidase gene of Mycobacterium smegmatis. Microbiology 143 ( Pt 7): 2267–2276. 44. Pfaffl MW (2001) A new mathematical model for relative quantification in real- time RT-PCR. Nucleic Acids Res 29: e45. gy ( ) 23. Blokpoel MC, Murphy HN, O’Toole R, Wiles S, Runn ES, et al. (2005) Tetracycline-inducible gene regulation in mycobacteria. Nucleic Acids Res 33: e22. 45. Gao LY, Groger R, Cox JS, Beverley SM, Lawson EH, et al. (2003) Transposon mutagenesis of Mycobacterium marinum identifies a locus linking pigmentation and intracellular survival. Infect Immun 71: 922–929. References 1. Brown-Elliott BA, Wallace RJ, Jr. (2002) Clinical and taxonomic status of pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria. Clin Microbiol Rev 15: 716–746. PLoS ONE | www.plosone.org December 2011 | Volume 6 | Issue 12 | e29306 9 Conditional Gene Expression in M. abscessus 24. Carroll P, Muttucumaru DG, Parish T (2005) Use of a tetracycline-inducible system for conditional expression in Mycobacterium tuberculosis and Mycobacterium smegmatis. Appl Environ Microbiol 71: 3077–3084. 46. Stover CK, de la Cruz VF, Fuerst TR, Burlein JE, Benson LA, et al. (1991) New use of BCG for recombinant vaccines. Nature 351: 456–460. PLoS ONE | www.plosone.org December 2011 | Volume 6 | Issue 12 | e29306 10
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THE CONTRIBUTION OF INFORMATION TECHNOLOGIES TO THE PROTECTION OF WORLD CULTURAL AND NATURAL HERITAGE MONUMENTS "THE CASE OF ANCIENT PHILIPPI, GREECE"
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Received: 23/12/2021 Accepted: 23/03/2022 Received: 23/12/2021 Accepted: 23/03/2022 Corresponding author:K.Kravari ( kkravari@ihu.gr) SCIENTIFIC CULTURE, Vol. 8, No. 3, (2022), pp. 169-178 Open Access. Online & Print SCIENTIFIC CULTURE, Vol. 8, No. 3, (2022), pp. 169-178 Open Access. Online & Print THE CONTRIBUTION OF INFORMATION TECHNOLOGIES TO THE PROTECTION OF WORLD CULTURAL AND NATURAL HERITAGE MONUMENTS “THE CASE OF ANCIENT PHILIPPI, GREECE” 1*Kalliopi Kravari, 1Dimitrios Emmanouloudis, 2Elena Korka & 3Aglaia Vlachopoulou 1UNESCO Chair on Conservation and Ecotourism of Riparian and Deltaic Ecosystems, International Hellenic University, Greece 2 Hellenic Committee of the Blue Shield, 29 Archimidous Str., Athens 116 36, Greece 3International Hellenic University, Greece 1UNESCO Chair on Conservation and Ecotourism of Riparian and Deltaic Ecosystems, International Hellenic University, Greece 2 Hellenic Committee of the Blue Shield, 29 Archimidous Str., Athens 116 36, Greece 3International Hellenic University, Greece Received: 23/12/2021 Accepted: 23/03/2022 2. THE INBO APPROACH The INBO approach, developed by members of this team, brings forward a holistic and easily adaptable methodology that combines edge technology with risk assessment techniques. The main purpose of INBO is to prevent potential damage to the Cultural and Natural heritage sites by enabling the right prog- nosis leading to timely and smart decisions. Follow- ing this methodology, first responders, heritage stakeholders, as well as visitors will be able to im- prove the way, in which they react and handle the provided information. The current work designs, develops and presents the first steps of INBO, a methodology that brings to- gether artificial intelligence, risk assessment tech- niques and even stakeholders. The proposed smart awareness and management solution, based on accu- rate information and the right knowledge, will be able to automatically make or propose the right actions and decisions. More specifically, the article clarifies the added value of the approach focusing on augment reality and the intelligent agent technology that acts as a virtual alter ego of our world without the limita- tions of the human factor. INBO is a three-stage methodology that includes an INDEX and an IT Booklet, (INDEX + BOOKLET = INBO) which allows both monument monitoring and real-time emergency response. Fig. 1 depicts the main stages of the methodology. The first stage aims at the monument studying. The second stage reproduces the site purposes of public awareness. The third stage monitors and manages the site using Artificial Intelli- gence (AI) technologies, such as the Intelligent Agents and the Internet of Things (IoT) (Kravari & Bassili- ades, 2019). This holistic smart awareness and man- agement approach will be able to automatically make or propose the right actions and decisions, supporting managers and stakeholders. The first stage of the methodology includes the de- velopment of an INDEX for each monument and its potential hazard levels, including monument features such as marshlands in the ancient city of Philippi, and potential types of hazards such as floods. The risks will be classified and prioritized, customizing the protection actions. The next stage involves the devel- opment of the IT Booklet, where initially with the use of augmented and virtual reality the monument will be reproduced, providing awareness to the public and visitors. This part will demonstrate risky loca- tions while evacuation plans will be provided. ABSTRACT Natural and man-made disasters are happening more and more often, leading to hundreds of casualties and significant catastrophic consequences. Unfortunately, they are affecting not only urban centers, outdoor set- tlements, and infrastructure, but also world cultural and natural heritage sites. Many of these monuments, which are included in the UNESCO World Heritage List, are at risk due to even moderate natural or man- made hazards, given the structural vulnerability created over the course of their hundreds or even millennia of existence. In this context, for several years, the issue of the risks of World Heritage sites has been of concern to UNESCO and in particular the World Heritage Center. Following this effort, the present work aims to enrich methods and techniques with the help of advanced information technologies and in particular a combination of Artificial Intelligence (AI), Virtual and Augmented Reality, and the Internet of Things (IoT). The article presents the first steps towards a holistic and easily adaptable methodology, forming the so-called INBO (IN- DEX + BOOKLET = INBO), a novel combination of INDEX (catalogue) and IT Booklet, which will allow both monument monitoring and real-time emergency response. This methodology will improve the way in which first responders and monument managers, even visitors, react and handle the information provided. INBO will allow the right prognosis to be achieved by leading to timely and smart decisions that will help prevent potential damage to the cultural heritage. The Ancient City of Philippi will serve as a pilot study for the ap- proach. The archaeological site of Philippi, located in Northern Greece, is one of the heritage sites, listed on the UNESCO World Heritage List. DS: Artificial Intelligence, Risk Assessment, Heritage Protection, INDEX, UNESCO, Monument Copyright: © 2022. This is an open-access article distributed under the terms of the Creative Commons Attribution License. (https://cre- ativecommons.org/licenses/by/4.0/). K. KRAVARI et al 170 1. INTRODUCTION and software. This pert will include the appropriate IoT equipment, collecting and reasoning on data, smart real-time control applications, as well as AI techniques for stakeholders. In recent decades the number of disastrous natural phenomena (floods, fires, earthquakes and others) as well as man-made disasters has increased, causing both social and economic problems and adverse ef- fects on cultural heritage, affecting world Cultural and Natural heritage sites. Many of these Monuments are at risk due to even moderate natural or man-made hazards, given the structural vulnerability created over the course of their hundreds or even millennia of existence. To this end, novel approaches that could as- sist on protecting them is undoubtedly imperative. In this context, for several years, the issue of the risks of World Heritage sites has been of concern to UNESCO and in particular the World Heritage Center. The re- sult of the effort was the compilation of a manual guide, written with the help of experts. This guide lists the hazards, their special features and their im- pact on cultural monuments and people. Following this effort, the present work aims to enrich methods and techniques with the help of advanced infor- mation technologies and in particular a combination of Artificial Intelligence (AI), Virtual and Augmented Reality, and the Internet of Things (IoT). This paper discusses upon the first INDEX stage as well as the first step of the second stage, that of the Augment and Virtual reality module. Furthermore, the Ancient City of Philippi serves as a pilot study for the approach. The archaeological site of Philippi, lo- cated in Northern Greece, is one of the heritage sites, listed on the UNESCO World Heritage List. This monument is endangered not by common natural risks but by a particular phenomenon that of the flooding of the Marshlands of Philippi. The article is organized as follows, section 2 pre- sents an overview of the INBO methodology, and sec- tion 3 discusses augment and virtual reality. Section 4 presents an overview of IoT in the context of INBO approach while section 5 discusses the case of Ancient Philippi, Greece. Finally, section 6 discusses related work while section 7 summarizes the added value of the article with some final remarks. 3. INDEX The first phase of the methodology includes the de- velopment of an INDEX for each Monument. This stage will identify, record, classify and prioritize the dangers that threaten a Monument or an Archaeolog- ical site. To this end, an appropriate questionnaire will be shared to site managers and responsible stake- holders. The first page of the questionnaire is pre- sented below indicatively (Fig. 2). This questionnaire will collect data related to natural hazards, such as hurricanes, lightning, flash floods, landslides etc., nat- ural-human induced hazards, such as agro and forest fires, man – made hazards, such as air, water pollu- tion, and technological risks, such as IT Protection Systems failure. Upon the completion of the question- naires, referred to a specific heritage site, INBO meth- odology proceeds with the analysis based on artificial intelligence (AI) techniques. Beyond the assessment and forecast results, INBO will also provide brief guides (Behavior Codes) for visitors and site stake- holders that will contain instructions for protection and/or survival from all the important and most fre- quently occurring risks of Natural and Technological Disasters. In this context, the advice offered through these Guides will be supervisorial enhanced with the help of technologies such as augmented reality (AR) videos and animations. This way, stakeholders and visitors will be better prepared and more familiar with what they should do in case of the Monument, the Archaeological site, and the wider area or even their life is threatened. 2. THE INBO APPROACH Next, IoT and Artificial Intelligence will support the de- signed and developed of a smart real-time control ap- plication that will enable monitoring and manage- ment of the monument using appropriate equipment SCIENTIFIC CULTURE, Vol. 8, No 3, (2022), pp. 169-178 THE CONTRIBUTION OF IT TO THE PROTECTION OF WORLD CULTURAL AND NATURAL HERITAGE MONUMENTS 171 Figure 1. The overview of the INBO methodology. Figure 1. The overview of the INBO methodology. 4. IT BOOKLET and software (Astorga González et al., 2020). This part will include the appropriate IoT equipment, collect- ing and reasoning on data, smart real-time applica- tions, and AI techniques for stakeholders. As a result, INBO provides a custom-made smart real-time sys- tem, which included five (5) modules, namely Haz- ard Analysis, Risk Analysis, Preparedness, Response and Recovery. Yet, it is out of the scope of this article to analyze each of these modules and technologies; hence this article discusses further mainly on the pre- paredness and response modules. and software (Astorga González et al., 2020). This part will include the appropriate IoT equipment, collect- ing and reasoning on data, smart real-time applica- tions, and AI techniques for stakeholders. As a result, INBO provides a custom-made smart real-time sys- tem, which included five (5) modules, namely Haz- ard Analysis, Risk Analysis, Preparedness, Response and Recovery. Yet, it is out of the scope of this article to analyze each of these modules and technologies; hence this article discusses further mainly on the pre- paredness and response modules. The second phase of the methodology includes the development of a two-stage IT Booklet, where ini- tially with the use of augmented and virtual reality the Monument will be reproduced, providing aware- ness to the public and visitors, as well as stakeholders. This part will demonstrate risky locations while evac- uation plans will be provided. Next, the Internet of Things and Artificial Intelligence will support the de- sign and development of a smart real-time control ap- plication that will enable monitoring and manage- ment of the Monument using appropriate equipment Figure 3. INBO Smart real-time system main technologies. Figure 3. INBO Smart real-time system main technologies. Furthermore, access to cultural objects and e-learn- ing gains more attention by providing (a) production of virtual and mixed reality applications, documenta- tion, videos, 3D models, hiking trails, b) production of audiovisual material and 3D movies, and c) visit to virtual museums. Moreover, digitizing the material and developing tools for analyzing and searching for information can support cultural heritage institu- tions, such as libraries and museums, creating large data repositories that will allow access to the preser- vation of cultural heritage. To this end, IT techniques can even support research upon revealing hidden in- formation of the past, bringing to light hidden collec- tions, or uniting antiquities that are spatially remote. Figure 2. Part of the INBO questionnaire. Figure 2. Part of the INBO questionnaire. SCIENTIFIC CULTURE, Vol. 8, No 3, (2022), pp. 169-178 K. KRAVARI et al 172 4. IT BOOKLET However, since technology is constantly changing, the imperative need is to develop local Smart Cultural Heritage strategies and tools to enhance and preserve cultural and environmental resources, which will be integrated with the local Smart City plans (Jelinčić & Glivetić, 2019). In this context, augmented (AR) and virtual (VR) reality technology is able to provide a sig- nificant advantage in the field of monument manage- ment and protection. 5. AUGMENT AND VIRTUAL REALITY Figure 4. AR tour Kavala Helexpo (2014) Figure 4. AR tour Kavala Helexpo (2014) Figure 4. AR tour Kavala Helexpo (2014) Virtual schools make use of high-end technology to achieve the aforementioned goals while, at the same time, it makes technology free for schools. This Vir- tual application led us to think about using it for mu- seums and archaeological sites starting from the area of Philippi. In this context, firstly, was implemented an Augmented Reality (AR) tour for Kavala (Greece) Helexpo 2014 (Fig. 4). Virtual schools make use of high-end technology to achieve the aforementioned goals while, at the same time, it makes technology free for schools. This Vir- tual application led us to think about using it for mu- seums and archaeological sites starting from the area of Philippi. In this context, firstly, was implemented an Augmented Reality (AR) tour for Kavala (Greece) Helexpo 2014 (Fig. 4). A case in that VR was successfully used for educa- tional purposes was when the IHU AETMA Lab al- lowed students to design their own school models, helping them to understand better how they should react to a potential threat, such as an earthquake. This project is called Virtual School and uses augmented and mixed reality experiences in order to raise stu- dents’ awareness of natural disaster management. Figure 5. CARMA AR project in the ancient area of Philippi, Greece by AETMA Lab IHU Figure 5. CARMA AR project in the ancient area of Philippi, Greece by AETMA Lab IHU Following the AR tour, an AR approach for the museum was implemented, too. This approach is called CARMA (Fig. 5) and it is able to inform the vis- itors of the Museum of Philippi or of an open space, for their location and the optimum exploration paths, or evacuation plans in case of a risk. Things. Things able to make decisions and communi- cate. However, the open and distributed network combined with the enormous heterogeneity of things raises important challenges. Challenges that can find an answer to Artificial Intelligence, which can add au- tonomy, context awareness and intelligence, realizing the vision of IoT. On the other hand, every year mil- lions of people visit monuments, museums and art ex- hibitions, hence the need for novel monitoring and protecting heritage solutions is obvious. 5. AUGMENT AND VIRTUAL REALITY In this con- text, the IoT has already shown tremendous potential in monitoring cultural heritage environments (Khan et al., 2020). It has been successfully used to monitor the structural health of buildings, cultural preserva- tion and revitalization as well as to improve the expe- rience of users of the cultural environment. 5. AUGMENT AND VIRTUAL REALITY Over the past years, many initiatives have been fo- cusing on Information Technology (IT) and its poten- tial use for the management and protection of herit- age in a variety of aspects. Such an initiative is the so- called Smart Heritage, a relatively new system and management media that initiated by INTACH Herit- age Academy to answer the challenge that addresses the Cultural Heritage Conservation in the Smart City Era by using the advancement of Information Com- munication Technology (ICT) (Mehta & Piplani, 2017). The aim of the Smart Cultural Heritage is to serve the preservation of identity, tangible and intan- gible, of sites and communities using smart technolo- gies, since technological advancements have already led to a variety of achievements (Siountri et al., 2018). In this context, digital networking of institutes, asso- ciations and organizations, visitors, and cultural ob- jects is already common while crowdsourcing infor- mation, related to monuments, trails, customs, an- thropogeography provides databases and digital paths. SCIENTIFIC CULTURE, Vol. 8, No 3, (2022), pp. 169-178 THE CONTRIBUTION OF IT TO THE PROTECTION OF WORLD CULTURAL AND NATURAL HERITAGE MONUMEN 173 Figure 4. AR tour Kavala Helexpo (2014) A case in that VR was successfully used for educa- nal purposes was when the IHU AETMA Lab al- wed students to design their own school models, lping them to understand better how they should act to a potential threat, such as an earthquake. This oject is called Virtual School and uses augmented d mixed reality experiences in order to raise stu- nts’ awareness of natural disaster management. Virtual schools make use of high-end technology to achieve the aforementioned goals while, at the same time, it makes technology free for schools. This Vir- tual application led us to think about using it for mu- seums and archaeological sites starting from the area of Philippi. In this context, firstly, was implemented an Augmented Reality (AR) tour for Kavala (Greece) Helexpo 2014 (Fig. 4). r Kavala Helexpo (2014) ca- al- ls, ld his ed u- nt. Virtual schools make use of high-end technology to achieve the aforementioned goals while, at the same time, it makes technology free for schools. This Vir- tual application led us to think about using it for mu- seums and archaeological sites starting from the area of Philippi. In this context, firstly, was implemented an Augmented Reality (AR) tour for Kavala (Greece) Helexpo 2014 (Fig. 4). 6. INTERNET OF THINGS & INBO SYSTEM The Internet of Things (IoT) aims to create a world where everyone and everything, called Things, will be connected and the knowledge will be effortlessly diffused in every direction (Mukhopadhyay & Surya- devara, 2014). It has the potential to change our daily lives. It is a world, although still at an early stage, that forms a huge, open and distributed network of SCIENTIFIC CULTURE, Vol. 8, No 3, (2022), pp. 169-178 K. KRAVARI et al 174 Figure 6. UNESCO Relationships of natural hazards and man-made hazards Figure 6. UNESCO Relationships of natural hazards and man-made hazards In this context, INBO uses the IoT, combined with Artificial Intelligence, in order to form the final stage of its contribution (Fig 1). The first step towards this direction was to reveal relationships of natural and man-made hazards to potential risks. For this pur- poses, UNESCO classifications were studied (Fig. 6), revealing that IoT could deal with various challenges based on these categories. INBO proposes each herit- age site, based on a custom study, to be equipped with appropriate IoT devices, enabling a smart net- work in which all entities will communicate and share knowledge. Yet, although IoT technologies cannot stop disasters from happening, they can be very use- ful for disaster preparedness, by prediction and early warning systems, and response by organizing re- sponse and recovery. So far, INBO includes a variety of IoT solutions that can be adapted to specific monu- ment cases based on the risks that they face. The INBO IoT study mitigates many of the emergency chal- lenges, such as a weak communication network and delays due to lack of information and data. Various hazard sensors, such as fire, flood, earthquake, and so on, can be used while local emergency rescue services can be alerted via a cloud service where everything will be connected. Mention that the decision upon which IoT solution is appropriate for a specific case is the result of the first INDEX stage of INBO methodol- ogy. For instance, regarding the monitoring and man- agement of meteorological - hydrological hazards a synergy of GIS and IoT could deal with weather dis- asters. Smart devices and applications from daily life could be used for such cases. Data is usually meas- ured and collected by distributed sensors, placed in different locations. The collected data will be pro- cessed by INBO IoT applications while the system generates alerts. 6. INTERNET OF THINGS & INBO SYSTEM A critical component is to provide dissemination via multiple mechanisms in near real- time to responsible entities and the public. Natural weather, such as hurricanes, forest fires, floods, vol- canoes, tornadoes and earthquakes can be addressed through the aforementioned synergy. Usually, IoT (sensors) monitors natural weather events and notify about critical safety information. Sensor technology offers real-time information during and after a natu- ral weather event occurs. For example, sensors capa- ble of monitoring, are able to detect increased water levels before a hurricane and to track how quickly a forest fire is spreading. However, we have to go beyond that. We use IoT not only to forecast but also to deal with issues related to hazards. For instance, pollution affect harbor sea SCIENTIFIC CULTURE, Vol. 8, No 3, (2022), pp. 169-178 THE CONTRIBUTION OF IT TO THE PROTECTION OF WORLD CULTURAL AND NATURAL HERITAGE MONUMENTS 175 that allows stakeholders and experts to prioritize lo- cal response efforts and manage their resources, mov- ing smart automation a step further. Monitoring is the module that enables hazard identification, up-to-date environmental track changes in order to reflect the se- verity and expected outcome of the natural disaster. Warning communication is based on multi-channel communication protocols while response capability reveals that information alone cannot assure a posi- tive outcome, hence we need technology and collabo- ration among involved parties. water and entire area ecosystem which makes ex- tremely important a constant and reliable monitoring of the (sea) waters. For example, hurricanes can in- crease in speed and intensity as they pass over warm water, which may pose a heightened risk to coastal cities. To this end, monitoring and warning systems including both hardware and software could be the answer. Such a system, developed by EVAE lab of In- ternational Hellenic University, provides a light- weighted ROUV (Remotely Operated Underwater Vehicle) equipped with a complete set of sensors in order to collect data and samples (Fig. 7) and a smart monitoring platform that will enable autonomous de- cision making/suggestion using artificial intelli- gence. 7. PILOT STUDY - THE ANCIENT CITY OF PHILIPPI IN KAVALA, GREECE The Ancient City of Philippi is the 16th and chron- ologically speaking the last Monument of Greece that was included in this list of UNESCO. This site serves as pilot study for our proposed approach. The archae- ological site of Philippi, located in Northern Greece, is one of the heritage sites, listed on the UNESCO World Heritage List, which strongly consolidates its reputation as a unique place of extraordinary value for human civilization. It is an exceptional testimony to different historic periods and civilizations, from prehistoric times to Byzantine periods. What makes it unique is the assembly of the architectural heritage preserved at the site, representing various architec- tural types of monuments expressing the develop- ment of architecture during the Roman, Christianity, and Byzantine periods. The remains of the ancient city of Philippi represent a unique example of Roman architecture, with its specific configuration giving it attributes of a “small Rome”. Undoubtedly, the most impressive building of this period, despite the changes that it has undergone over the centuries, is the ancient theatre of Philippi (Fig. 8) Figure 7. ROUV (Electric Vehicles and Automotive Elec- tronics Lab of IHU) Figure 7. ROUV (Electric Vehicles and Automotive Elec- tronics Lab of IHU) Hence, INBO, based on the aforementioned tech- nologies and AI techniques, proposes among others an early warning systems that includes four compo- nents, namely risk knowledge, monitoring, warning communication and response capability. Risk knowledge is a categorical system of hazard analysis Figure 8. Ancient theatre of Philippi Figure 8. Ancient theatre of Philippi SCIENTIFIC CULTURE, Vol. 8, No 3, (2022), pp. 169-178 SCIENTIFIC CULTURE, Vol. 8, No 3, (2022), pp. 169-178 K. KRAVARI et al 176 Figure 9. Flooding of the Marshlands of Philippi, Greece This monument is significantly endangered neither by common natural disasters, e.g. fire, flood (from Flash Floods) or earthquake, nor by atmospheric pol- lution or other major pollutants. However, it is at risk because of a particular phenomenon of the flooding of the Marshlands of Philippi (Fig. 9) which are lo- cated both all around and just a few hundred meters away. This flood is periodic, every winter, while dur- ing the summer there is a total drought of the marsh- lands. 7. PILOT STUDY - THE ANCIENT CITY OF PHILIPPI IN KAVALA, GREECE The phenomenon of the constant rising and lowering of the surface water body for ongoing years with a particular increasing rate during the last dec- ades is quite possible to lead to the activation of the subsurface soil water table circumferentially the An- cient Town. Thus, this activation could lead to the peril of the overall Geostationary Balance of the area with innumerous repercussions for the Ancient Set- tlement. Figure 9. Flooding of the Marshlands of Philippi, Greece Consequently, all-year-round thorough measure- ments both of several soil and climate parameters but also, and most importantly, of soil and subsoil de- tailed factors are essential. The development of these measurements and their progress also determines ei- ther the existence, or lack, of a direct danger but also the course of the works for protection, even the way visitors may affect the area, especially when there is a load of 5,000-6,000 people with vehicles nearby (An- cient Theater Performances). Philippi Case study leads to the obvious as well as useful inference that all the natural and human-induced dangers do not ap- pear in the same extent of threat for every Natural or Cultural Monument. So, in our case, the Ancient Town does not seem to be threatened by an extended forest fire or air pollution. On the contrary, Ancient Olympia, Greece is clearly threatened by an extended and uncontrollable Forest Fire, while the Acropolis in Athens faces problems with air pollution. Figure 9. Flooding of the Marshlands of Philippi, Greece 8. USING INBO AT THE ANCIENT CITY OF PHILIPPI IN KAVALA, GREECE First, a study is conducted about the ancient city of Philippi in Kavala and the marshlands, including among other the aforementioned questionnaire. The result is an INDEX which will be uploaded on a plat- form. There, it will be real-time updated through the continuous flow of incoming answers from question- naires, as well as the analysis outcomes of these an- swers. Following this stage, proper AR guides for vis- itors and site stakeholders will be also uploaded (such as those discussed in section 3). Fig. 10 depicts a case of emergency in the museum of Kavala where there are important archeological findings of the ancient city. This example will depict better the added-value of the approach. SCIENTIFIC CULTURE, Vol. 8, No 3, (2022), pp. 169-178 SCIENTIFIC CULTURE, Vol. 8, No 3, (2022), pp. 169-178 CONTRIBUTION OF IT TO THE PROTECTION OF WORLD CULTURAL AND NATURAL HERITAGE MONUMENTS 177 Figure 10. Emergency in the museum Figure 10. Emergency in the museum ago by Ministry of Environment (LIFE-IP AdaptInGR Project, 2021), but in fact is different. In Life – IP pro- ject five of the total 18 Greek Heritage sites investi- gated and only in relevance with the factors that affect Climate Change. Moreover, the proposed INDEX is something different from ICOMS – GOOGLE plat- form where five Heritage Sites presented and their Risks and Dangers are measured, monitored and an- alyzed. The proposed by us INDEX is much broader with a Universal character, aiming to include all mon- uments, but of course due to the huge information size, with a brief format. Hence, there is still a lack of a combination of an INDEX with monuments and their degree of threat from hazards and the Artificial Intelligence in order to provide a complete, fairly gen- eral-purpose smart system. Suppose that suddenly a fire breaks out in a closed hall. The security guard is outside checking an incom- ing vehicle, without a clue about the fire. Unfortu- nately, till the guard releases that a fire emergency oc- curs, the fire extends to the adjacent hall where there are visitors and significant historical findings. The se- curity guard panicked, forgets to call the fire depart- ment, and the situation is out of control. The existence of an INBO installation on the other hand could pro- vide better results. INBO provided intelligent soft- ware that can communicate and act upon goals. As a result, a variety of IoT sensors and devices such as cameras or automatic door mechanisms are automat- ically controlled. In this context, as soon as, the AI- based INBO devices detect the first fire, inform the appropriate AI-based INBO entity, e.g. the virtual guard in charge (line 1). On its turn, that entity rea- sons upon the data and extracts the conclusion that the hall must be sealed and the fire station should be informed. 10. CONCLUSION This article discussed upon INBO, a two-phase methodology that consists of an INDEX and an IT Booklet. INBO realizes an intelligent-based approach where both technical and practical guidelines and tools support the protection of Monuments and hu- man lives. It limits the common disadvantages of the existing distributed human-based approaches, by combining distributed sensors with AI technologies, forming a custom-made IoT system able monitor, forecast and take decisions protecting monuments and lives. Yet, although this broad methodology pro- vides valuable edge technologies, it needs the syn- ergy of organization and stakeholders in order to pro- vide accurate policies, prioritizing the needs of all in- volved stakeholders. In this endeavor, assistance from local, national, and international committees and organizations is needed, since we firmly believe that it is absolutely necessary to cooperate with those SCIENTIFIC CULTURE, Vol. 8, No 3, (2022), pp. 169-178 Hence, sends a message request to the ap- propriate device of the group A to close the door, ac- tivate the fire extinguishing system and play a voice message to visitors at the adjacent halls to move calmly outside the building (line 2) while another message is sent to the appropriate gateway (group C) asking it to inform the fire station (line 3), which is done immediately (line 4). Meanwhile, the human se- curity guard. All-in-all, the INBO evaluated the situ- ation real-time, communicated with the appropriate stakeholders coordinating their actions and informed the visitors, eliminating the human factor without time waste. 9. RELATED WORK This proposal seems to have similarities with the LIFE – IP project that has been announced two years SCIENTIFIC CULTURE, Vol. 8, No 3, (2022), pp. 169-178 K. KRAVARI et al 178 system. Hence, the proposed methodology will be further improved, in an attempt to reduce among oth- ers its complexity. To this end, our intention is to fur- ther study each module involved the INBO proposal. that face the everyday practical or policy challenges. As for future directions, our priority is to study the scalability the complexity of the methodology and the involved technologies as well as the scalability of the that face the everyday practical or policy challenges. As for future directions, our priority is to study the scalability the complexity of the methodology and the involved technologies as well as the scalability of the ACKNOWLEDGEMENT Part of this research has received funding from the European Union´s UCPM-2020-KN-AG under grant agree- ment No 101017819 with the acronym RESISTANT. Part of this research has received funding from the European Union´s UCPM-2020-KN-AG under grant agree- ment No 101017819 with the acronym RESISTANT. REFERENCES Astorga González, E. M., Municio, E., Noriega Alemán, M., & Marquez-Barja, J. M. (2020). Cultural Heritage and Internet of Things. In Proceedings of the 6th EAI International Conference on Smart Objects and Technologies for Social Good (GoodTechs '20). Association for Computing Machinery, New York, NY, USA, pp. 248–251. Jelinčić, D. An., & Glivetić, D. (2019), Cultural heritage and sustainability Practical Guide, KEEP ON: Effective policies for durable and self-sustainable projects in the cultural heritage sector, INORDE – Institute for Economic Development of Ourense Province, INTERREG Europe project, financed by the Euro- pean Regional Development Fund, Spain. Kravari, K., & Bassiliades, N. (2019). StoRM: A social agent-based trust model for the internet of things adopt- ing microservice architecture. Simulation Modelling Practice and Theory, 94, 286-302. https://doi.org/10.1016/j.simpat.2019.03.008. Khan, I., Melro, A., Oliveira, L., & Amaro, A.C. (2020). Internet of Things prototyping for cultural heritage dissem- ination. 3. 20-35. 10.34624/jdmi.v3i7.16212. j LIFE-IP AdaptInGR Project. Available at: https://www.adaptivegreece.gr/el-gr/. Last accesse p j p // p g g / g / Mehta, T., & Piplani, N. (2017). INTACH Heritage Academy. Smart Heritage. September 25th 2018. Available at http://heritage.intach.org/smart-heritage-think-tank/ p // g g/ g / Mukhopadhyay, S. C., & Suryadevara, N. K. (2014). Internet of Things: Challenges and Opportunities. Internet of Things Smart Sensors, Measurement and Instrumentation, 1-17. doi:10.1007/978-3-319-04223-7_1 p g g g Mukhopadhyay, S. C., & Suryadevara, N. K. (2014). Internet of Things: Challenges and Opportunities. Internet of Things Smart Sensors, Measurement and Instrumentation, 1-17. doi:10.1007/978-3-319-04223-7_1 Siountri, K., Skondras, E., & Vergados D.D. (2018), Smart Cultural Heritage in Digital Cities, Journal Sustainable Development, Culture, Traditions, Volume 1b/2018, DOI: 10.26341/issn.2241-4002-2018-1b-2. g Siountri, K., Skondras, E., & Vergados D.D. (2018), Smart Cultural Heritage in Digital Cities, Journal Sustainable Development, Culture, Traditions, Volume 1b/2018, DOI: 10.26341/issn.2241-4002-2018-1b-2. SCIENTIFIC CULTURE, Vol. 8, No 3, (2022), pp. 169-178 SCIENTIFIC CULTURE, Vol. 8, No 3, (2022), pp. 169-178 SCIENTIFIC CULTURE, Vol. 8, No 3, (2022), pp. 169-178
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https://www.frontiersin.org/articles/10.3389/fpsyt.2021.789344/pdf
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How Is the History of Early Traumatic Exposure Associated With the Psychopathological Outcomes of COVID-19 Related Lockdown and Subsequent Re-opening in People With Eating Disorders?
Frontiers in psychiatry
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Edited by: Tomasz M. Gondek, Self-employed, Wroclaw, Poland y Tomasz M. Gondek, Self-employed, Wroclaw, Poland Reviewed by: Alfonso Tortorella, University of Perugia, Italy Ekin Sönmez Güngör, Istanbul Erenkoy Training and Research Hospital for Psychiatric and Neurological Diseases, Turkey 1 Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Salerno, Italy, 2 Department of Neuroscience, Eating Disorders Center for Treatment and Research, University of Turin, Turin, Italy, 3 Unit of Psychiatry, DAME, University of Udine, Udine, Italy, 4 Department of Mental Health, ASST Santi Paolo e Carlo, Milan, Italy, 5 Section of Psychiatry, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy, 6 Department of Mental Health, Asl Salerno, Salerno, Italy, 7 Department of Neuroscience, University of Padova, Padua, Italy, 8 Mental Health Department, Center for the Treatment and Research on Eating Disorders, ASL Lecce, Lecce, Italy, 9 Psychiatry Unit, Department of Neurological and Psychiatric Sciences, University of Florence, Florence, Italy, 10 Eating Disorders Centre Portogruaro, AULSS 4 Veneto Orientale, San Donà di Piave, Italy, 11 Department of Medical and Surgical Sciences, University Magna Graecia of Catanzaro, Catanzaro, Italy, 12 Eating Disorders Unit, Casa di Cura “Villa Margherita”, Arcugnano, Italy, 13 Section of Clinical Psychiatry, Department of Clinical Neurosciences/DIMSC, Università Politecnica delle Marche, Ancona, Italy, 14 Department of Translational Medicine, Psychiatry Institute, Università del Piemonte Orientale, Novara, Italy, 15 Department of Psychiatry, University of Campania L. Vanvitelli, Naples, Italy *Correspondence: Giammarco Cascino gcascino14@gmail.com Specialty section: This article was submitted to Public Mental Health, a section of the journal Frontiers in Psychiatry Specialty section: This article was submitted to Public Mental Health, a section of the journal Frontiers in Psychiatry Received: 04 October 2021 Accepted: 15 November 2021 Published: 08 December 2021 The negative impact of COVID-19 pandemic on people with Eating Disorders (EDs) has been documented. The aim of this study was to evaluate whether a history of traumatic experiences during childhood or adolescence was associated with a higher degree of psychopathological worsening during COVID-19 related lockdown and in the following re-opening period in this group of people. People with EDs undergoing a specialist ED treatment in different Italian services before the spreading of COVID-19 pandemic (n = 312) filled in an online survey to retrospectively evaluate ED specific and general psychopathology changes after COVID-19 quarantine. ORIGINAL RESEARCH published: 08 December 2021 doi: 10.3389/fpsyt.2021.789344 How Is the History of Early Traumatic Exposure Associated With the Psychopathological Outcomes of COVID-19 Related Lockdown and Subsequent Re-opening in People With Eating Disorders? Giammarco Cascino 1*, Francesca Marciello 1, Giovanni Abbate-Daga 2, Matteo Balestrieri 3, Sara Bertelli 4, Bernardo Carpiniello 5, Giulio Corrivetti 6, Angela Favaro 7, Caterina Renna 8, Valdo Ricca 9, Pierandrea Salvo 10, Cristina Segura-Garcia 11, Patrizia Todisco 12, Umberto Volpe 13, Patrizia Zeppegno 1 Palmiero Monteleone 1 and Alessio Maria Monteleone 15 Giammarco Cascino 1*, Francesca Marciello 1, Giovanni Abbate-Daga 2, Matteo Balestrieri 3, Sara Bertelli 4, Bernardo Carpiniello 5, Giulio Corrivetti 6, Angela Favaro 7, Caterina Renna 8, Valdo Ricca 9, Pierandrea Salvo 10, Cristina Segura-Garcia 11, Patrizia Todisco 12, Umberto Volpe 13, Patrizia Zeppegno 14, Palmiero Monteleone 1 and Alessio Maria Monteleone 15 Based on the presence of self-reported traumatic experiences, the participants were split into three groups: patients with EDs and no traumatic experiences, patients with EDs and childhood traumatic experiences, patients with EDs and adolescent traumatic experiences. Both people with or without early traumatic experiences reported retrospectively a worsening of general and ED-specific psychopathology during the COVID 19-induced lockdown and in the following re-opening period. Compared to ED participants without early traumatic experiences, those with a self-reported history of early traumatic experiences reported heightened anxious and post-traumatic stress symptoms, ineffectiveness, body Received: 04 October 2021 Accepted: 15 November 2021 Published: 08 December 2021 INTRODUCTION an earlier age at symptom onset, a greater symptom severity and a more frequent concomitance of other psychiatric conditions (60), a poorer treatment response (61), as well as a heightened biological and emotional vulnerability to acute social stress exposure (62) and specific gray and white matter alterations (63), highlighting the need of a multidisciplinary approach to their management (64). The outbreak of coronavirus disease 2019 (COVID-19) pandemic has led to a dramatic loss of human life worldwide and presents an unprecedented challenge to public health, food systems and the world of work. The economic and social disruption caused by the pandemic was devastating and led countries around the world to adopt social and physical distancing to contain virus transmission (1). Closures and restrictions worldwide promoted social isolation and loneliness (2–7). Increased exposition to the Internet and social media messages contributed to the fear of being infected (8–12). As a result of such a stressful situation, a clear-cut increased prevalence of anxiety and depression occurred in the general population (13–25), while people with a pre-existing psychiatric condition showed a heightened vulnerability in terms of physical and mental distress (26–31) as well as a higher frequency of most severe outcomes of the infection (32, 33), emphasizing the need to involve psychiatrists in the management of the emergency (34–41). As the COVID-19 pandemic encompasses different types of stressors, ranging from family and social to health and economic adversities, it may provide the opportunity to explore in vivo the effects of an acute traumatic event in people with a potential vulnerability to acute stressors (65–68). According to the maltreated ecophenotype hypothesis, an increased vulnerability to the pandemic distress may be hypothesized in people with EDs and a history of early maltreatment. Thus, the aim of this study was to evaluate whether a history of traumatic experiences during childhood or adolescence was associated with a higher degree of psychopathological worsening during COVID- 19 related lockdown and in the following re-opening period. Among vulnerable psychiatric patients, people with eating disorders (EDs) have been reported to experience a worsening of their specific psychopathology, although variability in the degree of worsening has been observed across the studies (42–53). Furthermore, a marked impairment in general psychopathological symptoms has been observed in these patients, which tended to persist after the easing of COVID- 19 related restrictions (54, 55). Citation: Citation: Cascino G, Marciello F, Abbate-Daga G, Balestrieri M, Bertelli S, Carpiniello B, Corrivetti G, Favaro A, Renna C, Ricca V, Salvo P, Segura-Garcia C, Todisco P, Volpe U, Zeppegno P, Monteleone P and Monteleone AM (2021) How Is the History of Early Traumatic Exposure Associated With the Psychopathological Outcomes of COVID-19 Related Lockdown and Subsequent Re-opening in People With Eating Disorders? Front. Psychiatry 12:789344. doi: 10.3389/fpsyt.2021.789344 December 2021 | Volume 12 | Article 789344 Frontiers in Psychiatry | www.frontiersin.org 1 Cascino et al. COVID-19 and Eating Disorders dissatisfaction, and purging behaviors. These differences were seen before COVID- 19 related restrictions as well as during the lockdown period and after the easing of COVID-19 related restrictions. In line with the “maltreated ecophenotype” theory, these results may suggest a clinical vulnerability of maltreated people with EDs leading to a greater severity in both general and ED-specific symptomatology experienced during the exposure to the COVID-19 pandemic. INTRODUCTION Several factors, such as social isolation, family conflict, disruption in routine activities, and everyday life, heightened exposure to ED-specific media messages and fear of contagion, may have contributed to the vulnerability of people with EDs to the impact of COVID-19 pandemic (50, 56). We conducted a secondary analysis of data obtained through an online survey filled in by Italian participants with EDs after the easing of lockdown measures (54). We hypothesized that people with EDs and history of early traumatic experiences would exhibit greater worsening of general and ED-related psychopathology during the COVID-19 lockdown and the following re-opening compared to people without early exposure to adverse experiences. Frontiers in Psychiatry | www.frontiersin.org Keywords: COVID-19, eating disorder, childhood maltreatment, stress, psychopathology Participants p Patients previously admitted to specialist ED units located in different regions of Italy and diagnosed with anorexia nervosa (AN), atypical AN, bulimia nervosa (BN), binge-eating disorder (BED), and other specified feeding or eating disorders (OSFED) according to the DSM-5 criteria were asked to fill in an anonymous online survey. The diagnosis was made by expert psychiatrists through face-to-face clinical interviews at admission. Participants had to meet the following inclusion criteria: (a) no comorbid schizophrenia or bipolar disorder; (b) no intellectual disability; (c) absence of physical comorbidity not related to the ED. Participants were invited to participate in the survey during a 20-day period from 1st June 2020 up to and including 21st June 2020. The local ethical committee communicated us that, in line with local legislation and national guidelines, the completion of an anonymous online survey did Traumatic experiences during development have been acknowledged as important risk factors for several psychiatric disorders (57), including EDs (58). Clinical features (for instance, in terms of age at onset of the disorder and psychiatric comorbidity) as well as the identification of specific biological markers in patients with childhood maltreatment led Teicher and Samson (57) to suggest the existence across individuals suffering from a psychiatric condition of a “maltreated ecophenotype” subgroup with possibly different clinical presentation, biological underpinning, and prognosis. This perspective offers a functional understanding of symptoms highlighting their developmental influences (59). In accordance with this hypothesis, people with EDs and a history of childhood maltreatment have been reported to show December 2021 | Volume 12 | Article 789344 Frontiers in Psychiatry | www.frontiersin.org 2 COVID-19 and Eating Disorders Cascino et al. not require their approval. The consent was to be considered implicit when participants accepted to fill in the survey. experience as between-subject factors and post-hoc Tukey’s test were performed. Greenhouse-Geisser sphericity correction was applied where appropriate. Demographic variables that differed among groups were added as covariates in the analyses. A statistical threshold of p < 0.05 was set as significant. General Psychopathology Two way ANOVA with repeated measures showed a significant effect of time for symptoms of anxiety [F(2,614) = 12.27, p = 5.93 × 10−6], depression [F(2,614) = 4.19, p = 0.01], PTSS [F(1.95,599.16) = 6.16, p = 0.002], panic [F(2,614) = 3.41, p = 0.03], insomnia [F(2,614) = 3.72, p = 0.02], suicide ideation [F(1.87,573.74) = 6.08, p = 0.003], but not for OCS [F(1.57,480.1) = 1.13, p = 0.31]. Indeed, compared to the pre-pandemic phase all but OCS scores were significantly higher after the start of COVID-19 related restrictions (Figure 1). Participants were also asked if they had suffered any kind of traumatic experience such as sexual, physical, or emotional abuse or physical or emotional neglect (e.g., my family said hurtful things, I got hit badly enough to be noticed, I was sexually abused, I did not feel loved, I didn’t have enough to eat), and if so if they had suffered it in childhood (up to the age of 10) or adolescence (age between 11 and 18 years). Based on the history of traumatic experiences, the participants were split into three groups: patients with EDs and no traumatic experiences, patients with EDs and childhood traumatic experiences, and patients with EDs and adolescent traumatic experiences. Between-group comparisons and post-hoc Tukey’s test are summarized in Table 2. Post-hoc Tukey’s tests showed that anxiety and PTSS scores were significantly lower in noMal participants compared to both childMal (t = 2.54, p = 0.03 for anxiety and t = 2.44, p = 0.03 for PTSS) and adoMal groups (t = 2.29, p = 0.04 for anxiety and t = 3.91, p < 0.01 for PTSS), while OCS were significantly lower in noMal participants than in adoMal group (t = 2.52, p = 0.03) and panic was significantly lower in noMal participants than in childMal ones (t = 2.73, p = 0.02). Clinical and Demographic Characteristics Based on the self-reported traumatic experience, 91 participants were included in the group without traumatic experience (noMal), 119 participants in the group with a self- reported traumatic experience during childhood (childMal), and 102 participants in the group with a self-reported traumatic experience during adolescence (adoMal). The diagnostic composition of the sample was the following: 179 participants (57.4%) had a current AN or atypical AN, 63 (20.2%) had a current BN, 48 (15.4%) had a current BED, 22 (7.05%) had a current OSFED. No statistically significant difference emerged in the diagnostic composition of the three groups (χ2 = 5.29, p = 0.51). The groups differed in age and self-reported illness duration [F(2,309) = 3.38, p = 0.03 and F(2,309) = 4.12, p = 0.02, respectively], but not in body mass index (BMI) and treatment duration [F(2,309) = 0.09, p = 0.91 and F(2,309) = 2.19, p = 0.11, respectively] (Table 1). Post-hoc Tukey’s test revealed that noMal participants had an older age than adoMal participants (t = 2.58, p = 0.03) while childMal participants had a longer illness duration than adoMal participants (t = 2.85, p = 0.01). Therefore, age and treatment duration were entered as covariates in the ANOVA with repeated measures. The survey included a range of quantitative questions regarding both general and ED-specific psychopathology and it took ∼20 min to be completed. Explored dimensions were anxiety, depression, post-traumatic stress symptoms (PTSS), obsessive-compulsive symptoms (OCS), panic symptoms, insomnia, suicide ideation. Questions related to these dimensions were adapted from the following questionnaires: Generalized Anxiety Disorder 7 (69), Patient Health Questionnaire 9 (70), PTSD Checklist for DSM-5 (71), and Obsessive-Compulsive Inventory (72). Items included were selected as the most consistent with the DSM-5 criteria for each psychiatric disorder. Questions specifically related to EDs psychopathology and behaviors included in the survey were adapted from the Eating Disorders Inventory [EDI-2; (73)]. The selected questions were representative of each EDI-2 subscale. Moreover, participants were asked to account for the use of laxatives and diuretics and the level of physical activity, which were reported as episode/week and hours/day, respectively. Questions referred to three different time periods: 2 weeks before the spread of COVID-19 emergency; the lockdown period or “Phase 1” (that in Italy covered the months of March and April 2020); 2 weeks after the end of lockdown or “Phase 2” (that in Italy started on May 4, 2020). Study Design and Measures The online survey included a broad range of items aimed to assess the impact of the COVID-19 pandemic on the mental health of people with EDs. The online survey included a broad range of items aimed to assess the impact of the COVID-19 pandemic on the mental health of people with EDs. Clinical and Demographic Characteristics Each general psychopathology item was rated on a 10-point scale (0: not at all, 10: maximum), while ED specific items were rated on a 6-point scale, which was consistent with the original version of the EDI-2. RESULTS Participants were asked to report their age, gender identity, geographic location (Italian Region), duration of illness, and undergoing treatments. Four different survey data collectors (one for each main ED diagnosis) were created. Each local investigator sent to the patients of her/his ED unit an email including a hyper- link to the survey from data collectors of the corresponding diagnosis and received completion feedback from patients. Clinical and Demographic Characteristics Clinical and demographic characteristics of the whole sample and changes in general psychopathological dimensions over the three explored time periods are reported in Monteleone et al. (54). Statistical Analysis TABLE 1 | Demographic characteristics of participants according to self-reported traumatic experiences. ted general and specific psychopathology and symptoms in participants with eating disorders according to self-reported history of S, obsessive-compulsive symptoms; PTSS, post-traumatic stress symptoms. *Group effect: p < 0.05; §time effect: p < 0.05. FIGURE 1 | Scores of self-reported general and specific psychopathology and symptoms in participants with eating disorders ac early traumatic experiences. OCS, obsessive-compulsive symptoms; PTSS, post-traumatic stress symptoms. *Group effect: p < significantly these results with the exception for a marginal effect of age on OCS [F(1,307) = 4.51, p = 0.04]. 2.69, p = 0.02) and purge-vomit was lower in noMal group than in adoMal group (t = 2.69, p = 0.04). No significant time X group interaction emerged from the analyses. Participants’ age and illness duration did not affect significantly these results except for the effects of age on binge [F(1,307) = 12.15, p = 0.001], emotional alienation [F(1,307) = 13.69, p = 0.001] and laxative/diuretics abuse [F(1,307) = 5.00, p = 0.02] and the effect of illness duration on emotional alienation [F(1,307) = 10.15, p = 0.002]. ED-Related Psychopathology Two way ANOVA with repeated measures showed a significant effect of time for ineffectiveness [F(2,614) = 7.33, p = 0.001], social security [F(2,614) = 9.57, p = 0.001], weight concern [F(1.8,569.15) = 5.55, p = 0.005], emotional alienation [F(2,614) = 8.35, p = 0.001], and physical activity [F(1.9,588.45) = 5.23, p = 0.006], but not for body satisfaction [F(1.76,541.93) = 1.12, p = 0.32], perfectionism [F(2,614) = 0.25, p = 0.77], impulsivity [F(2,614) = 1.26, p = 0.28], binge [F(2,614) = 2.70, p = 0.07], purge-vomit [F(2,614) = 2.19, p = 0.11], shame of body needs [F(1.89,580.5) = 0.71, p = 0.49], and laxative/diuretics abuse [F(1.7,521.4) = 0.36, p = 0.66], demonstrating that, compared to the pre-pandemic period, these symptoms were significantly more severe after the beginning of COVID-19 related restrictions (Figure 1). Between- group comparisons and post-hoc Tukey’s test are summarized in Table 2. Post-hoc Tukey’s tests showed that ineffectiveness was lower in noMal participants compared to both childMal (t = 3.67, p < 0.01) and adoMal groups (t = 3.37, p < 0.01), while body satisfaction was lower in adoMal group than in noMal group (t = Statistical Analysis Statistical analyses were performed using JASP software (2020). Analysis of variance (ANOVA) was performed to test significant differences among groups in demographic and clinical variables. ANOVA with repeated measures and self-report traumatic No significant time X group interaction emerged from the analyses. Participants’ age and illness duration did not affect December 2021 | Volume 12 | Article 789344 Frontiers in Psychiatry | www.frontiersin.org 3 COVID-19 and Eating Disorders Cascino et al. TABLE 1 | Demographic characteristics of participants according to self-reported traumatic experiences. No trauma (n = 91) Childhood trauma (n = 119) Adolescence trauma (n = 102) F(2,308) p Age 31.71 ± 13.65 28.91 ± 11.97 27.26 ± 10.21 3.38 0.03 Body mass index 20.69 ± 7.48 20.98 ± 9.19 21.22 ± 8.27 0.09 0.91 Illness duration 8.69 ± 9.69 10.73 ± 10.71 7.17 ± 6.73 4.12 0.02 Treatment duration 4.85 ± 7.32 3.94 ± 4.81 3.23 ± 3.65 2.19 0.11 Anorexia nervosa 61 (34%) 64 (36%) 54 (30%) Bulimia nervosa 14 (22%) 27 (43%) 22 (35%) Binge eating disorder 11 (23%) 20 (42%) 17 (35%) OSFED 5 (23%) 8 (36%) 9 (41%) OSFED, Other specified feeding and eating disorders. FIGURE 1 | Scores of self-reported general and specific psychopathology and symptoms in participants with eating disorders according to self-reported history of early traumatic experiences. OCS, obsessive-compulsive symptoms; PTSS, post-traumatic stress symptoms. *Group effect: p < 0.05; §time effect: p < 0.05. TABLE 1 | Demographic characteristics of participants according to self-reported traumatic experiences. No trauma (n = 91) Childhood trauma (n = 119) Adolescence trauma (n = 102) F(2,308) p Age 31.71 ± 13.65 28.91 ± 11.97 27.26 ± 10.21 3.38 0.03 Body mass index 20.69 ± 7.48 20.98 ± 9.19 21.22 ± 8.27 0.09 0.91 Illness duration 8.69 ± 9.69 10.73 ± 10.71 7.17 ± 6.73 4.12 0.02 Treatment duration 4.85 ± 7.32 3.94 ± 4.81 3.23 ± 3.65 2.19 0.11 Anorexia nervosa 61 (34%) 64 (36%) 54 (30%) Bulimia nervosa 14 (22%) 27 (43%) 22 (35%) Binge eating disorder 11 (23%) 20 (42%) 17 (35%) OSFED 5 (23%) 8 (36%) 9 (41%) OSFED, Other specified feeding and eating disorders. FIGURE 1 | Scores of self-reported general and specific psychopathology and symptoms in participants with eating disorders according to self-reported history of early traumatic experiences. OCS, obsessive-compulsive symptoms; PTSS, post-traumatic stress symptoms. *Group effect: p < 0.05; §time effect: p < 0.05. Frontiers in Psychiatry | www.frontiersin.org DISCUSSION These data are in line with research findings demonstrating that a greater symptoms severity characterize people with EDs and history of early traumatic experiences (60) and support the existence of a “maltreated ecophenotype” clinically different from non-maltreated patients (57). and heightened family conflict, disruption in routine activities and everyday life, heightened exposure to social media messages, and fear of contagion, may have contributed to the vulnerability of people with EDs to the impact of COVID-19 pandemic (50, 56). In line with our study hypothesis, participants with EDs and a history of early traumatic experiences showed higher scores in general and ED-related psychopathology in the pre-pandemic period, during the pandemic-induced lockdown and in the following re-opening period compared to participants with EDs without early traumatic experiences. To our knowledge, only one previous study (51) investigated the effect of childhood maltreatment on the psychopathology course during the COVID-19 related lockdown. The authors found that childhood trauma significantly predicted COVID-19- related post-traumatic symptomatology in patients with AN. In line with these data, we observed significantly higher PTS scores in our population of participants with mixed ED diagnoses and history of early traumatic experiences. Furthermore, compared to participants with EDs without trauma history, people with EDs and history of childhood or adolescent traumatic experiences reported higher levels of anxiety, panic, and OCS also in the pre- pandemic period. These data are in line with research findings demonstrating that a greater symptoms severity characterize people with EDs and history of early traumatic experiences (60) and support the existence of a “maltreated ecophenotype” clinically different from non-maltreated patients (57). Other ED specific psychopathological variables (social security, perfectionism, impulsivity, weight concern, binge eating, shame of body needs, physical activity, and laxative/diuretics abuse) did not differ between participants with and without history of early maltreatment. In a previous analysis (54), these psychopathological variables worsened during the COVID-19 lockdown but, differently from general psychopatholgical symptoms, they returned to pre-pandemic levels in the re-opening period. This could be related to the fact that the easing of COVID-19 related restrictions could not mean real changes in the everyday life conditions, even if the survey was taken during June 2020 when the daily number of COVID-19 cases has dropped significantly in Italy. DISCUSSION The present study investigated changes in general and specific psychopathology during the COVID-19 related restrictions and in the following re-opening period in a large population of Italian patients with EDs with or without a history of early traumatic experiences. Compared to the pre-pandemic phase, both people with or without exposure to early traumatic experiences reported a worsening of general and ED-specific psychopathology during the COVID 19-induced lockdown and in the following re- opening period. Perceived social isolation, forced cohabitation Frontiers in Psychiatry | www.frontiersin.org December 2021 | Volume 12 | Article 789344 4 COVID-19 and Eating Disorders Cascino et al. TABLE 2 | Between-group comparison of general and eating disorder related psychopathology scores. F(2,307) p Tukey post-hoc Anxiety 3.81 0.02 noMal < childMal, adoMal Depression 1.25 0.29 PTSS 7.7 5.46 × 10−4 noMal < childMal, adoMal OCS 3.18 0.04 noMal < adoMal Panic (frequency) 4.07 0.02 noMal < childMal Insomnia 2.61 0.08 Suicide ideation 1.01 0.37 Ineffectiveness 8.05 0.001 noMal < childMal, adoMal Social security 1.29 0.28 Body satisfaction 3.83 0.02 adoMal < noMal Perfectionism 1.92 0.14 Impulsivity 0.61 0.54 Weight concern 2.21 0.11 Binge 0.61 0.55 Purge (vomit) 3.21 0.04 noMal < adoMal Emotion alienation 1.47 0.23 Shame for body needs 1.57 0.21 Physical Activity 0.52 0.59 Laxative/diuretics 0.06 0.94 PTSS, Post-traumatic stress symptoms; OCS, obsessive-compulsive symptoms; noMal, patients without history of trauma; childMal, patients with self-reported childhood trauma; adoMal, patients with self-reported adolescence trauma. TABLE 2 | Between-group comparison of general and eating disorder related psychopathology scores. isolation, impairment in the family, and/or individual’s economic condition and fear of being infected. Therefore, the increased severity of anxious symptoms observed in maltreated patients with EDs is also consistent with recent experimental research (62), which hypothesized a biological and emotional vulnerability to stressful events in this subgroup of people with EDs. Previous studies identified an altered emotion regulation and cognitive bias toward social negative stimuli in people with EDs and early adverse experiences (74, 75). Thus, heightened rejection sensitivity and emotion regulation difficulties promoted by early traumatic experiences may contribute to explain the association of these experiences with a more severe psychopathology. This is also in line with the research evidence supporting the central role of affect regulation for mental health (76). Surprisingly, people with EDs and a history of early traumatic experiences did not differ in depression, insomnia, or suicidal ideation from those without childhood adverse experiences. Frontiers in Psychiatry | www.frontiersin.org DISCUSSION This may point to an increased vulnerability of maltreated people with EDs to anxiety symptoms rather than to depressive ones and/or may indicate that the COVID-19 pandemic may exacerbate one type of symptoms more than others, although these hypotheses remain speculative. However, depressive symptoms have been found to be worsened during the lockdown in all people with EDs, suggesting the need for clinicians to address them with ad hoc interventions (77). PTSS, Post-traumatic stress symptoms; OCS, obsessive-compulsive symptoms; noMal, patients without history of trauma; childMal, patients with self-reported childhood trauma; adoMal, patients with self-reported adolescence trauma. As for ED-specific psychopathology, participants with early traumatic experiences reported heightened levels of ineffectiveness, body dissatisfaction, and purging behavior (namely, self-induced vomiting). These results are in line with previous research data. Indeed, low self-esteem and ineffectiveness have been proposed as possible mediators between childhood maltreatment and ED-specific symptoms (78–82). In addition, some studies (83, 84) have reported that a more severe purging behavior may be promoted by the need to regulate trauma-induced negative emotions by engaging in rash actions and risky behaviors. Finally, an association between childhood maltreatment and body dissatisfaction in adulthood has been reported in both community samples (85) and people with EDs (66, 86). and heightened family conflict, disruption in routine activities and everyday life, heightened exposure to social media messages, and fear of contagion, may have contributed to the vulnerability of people with EDs to the impact of COVID-19 pandemic (50, 56). In line with our study hypothesis, participants with EDs and a history of early traumatic experiences showed higher scores in general and ED-related psychopathology in the pre-pandemic period, during the pandemic-induced lockdown and in the following re-opening period compared to participants with EDs without early traumatic experiences. To our knowledge, only one previous study (51) investigated the effect of childhood maltreatment on the psychopathology course during the COVID-19 related lockdown. The authors found that childhood trauma significantly predicted COVID-19- related post-traumatic symptomatology in patients with AN. In line with these data, we observed significantly higher PTS scores in our population of participants with mixed ED diagnoses and history of early traumatic experiences. Furthermore, compared to participants with EDs without trauma history, people with EDs and history of childhood or adolescent traumatic experiences reported higher levels of anxiety, panic, and OCS also in the pre- pandemic period. 1. European Commission. New Report: Loneliness Doubles in Europe During the Pandemic (2021). ETHICS STATEMENT Ethical review and approval was not required for the study on human participants in accordance with the local legislation and institutional requirements. Written informed consent from the participants’ legal guardian/next of kin was not required to participate in this study in accordance with the national legislation and the institutional requirements. AUTHOR CONTRIBUTIONS AM, FM, GCa, and PM designed the study, wrote the protocol, and wrote the manuscript. GA-D, MB, SB, BC, GCo, AF, CR, VR, PS, CS-G, PT, UV, and PZ collected data. GCa did statistical analyses. All authors contributed to the article and approved the submitted version. CONCLUSIONS People with EDs and history of early traumatic experiences reported heightened anxious and PTS symptoms, ineffectiveness, body dissatisfaction, and purging behaviors than those without early adverse experiences, regardless of the age when trauma occurred. These differences were seen before COVID-19 related restrictions as well as during the lockdown period and after the easing of COVID-19 related restrictions. In line with the “maltreated ecophenotype” theory, it is possible to hypothesize a vulnerability of maltreated people with EDs, leading to a greater severity in both general and ED-specific symptomatology experienced during the exposure to the stressful lockdown related to the COVID-19 pandemic. The persistence of this detrimental effect in the following re-opening period may suggest either a slower recover or a heightened sensitivity to the restoring social exposure in this patient subgroup. From a clinical perspective, these findings confirm the need to systematically assess the presence of adverse traumatic experiences in patients with EDs and to therapeutically address the ability to adapt to and face adversities (87, 88), likely impaired in this subgroup of patients with EDs. This may promote more personalized psychotherapeutic approaches (89–93), possibly allowing to overcome treatment resistance (94, 95). The widespread implementation of Internet-delivered psychological treatments (96–99), associated with the relatively positive attitudes toward e-therapies in people with eating problems (100), may be a way to increase access to psychological treatment for people with EDs. Finally, the important role of general psychopathological symptoms in maltreated people with EDs may support the transdiagnostic perspective recently proposed (101, 102) for the treatment of various emotional disorders. DATA AVAILABILITY STATEMENT The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation. Some limitations of the present study need to be acknowledged. First, the retrospective design of our assessment does not allow to exclude recall biases. Indeed, early traumatic experiences were retrospective and self-reported: however, this is the most common methodology of early trauma data collection in EDs (103). Moreover, the survey was proposed and retrieved clinicians who were following the participants with EDs, which might lead to a bias on reporting traumatic experiences. Regarding psychopathology assessment, the short duration of time that elapsed between the beginning of COVID-19 outbreak and data collection partially reduced this bias. Second, in line with the transdiagnostic ED perspective (104, 105) and with experimentally shown lack of differences among different ED diagnoses in the symptom response to stress exposure (62), we did not account for possible differences between the main (AN, BN, BED and OSFED) ED diagnoses. This area needs to be addressed by future studies. Moreover, the methodology of data collection may have affected the study findings, and DISCUSSION In the light of the high pre-pandemic symptom levels in people with EDs, we suggest that the observed lack of differences in those ED-related psychopathological variables between maltreated and non-maltreated people with EDs may be explained by a sort of ceiling effect, which hides a higher vulnerability in maltreated The present data were collected during a traumatic event which included many kinds of stressors such as social December 2021 | Volume 12 | Article 789344 5 COVID-19 and Eating Disorders Cascino et al. the use of a new online survey may also underpin aspects of subjectivity. However, since we built the survey by adopting questions from validated psychometric questionnaires, we are confident that this limitation had a slight impact on our findings, although we cannot completely rule out this bias. The relatively small sample size, in particular the low number of participants with ED diagnosis other than AN, and the self-reported illness duration may affect the generalizability of our results. Finally, the cross-sectional design does not allow to make causal interpretations. people with ED. Since for patients with EDs and history of early adverse experiences social situations could be stressful (62), this hypothesis can also be aligned with the observed lack of difference in the reactivity (e.g., time × group effect) of maltreated people with EDs to the pandemic restrictions as well as to the easing of COVID-19 related restrictions: the higher pre-pandemic levels of psychopathology seen in maltreated people with EDs may persist, hiding a different reactivity. Remarkably, the age at the trauma occurrence (e.g., childhood or adolescence) did not contribute to the psychopathological differences observed in maltreated people with EDs. Previous studies have suggested that the time of the trauma occurrence may promote different biological sequelae (57), although no data have confirmed this hypothesis from a clinical perspective in EDs. However, the retrospective nature of our assessment may affect this finding, suggesting that further research is needed to explore this issue. REFERENCES Prospective impact of COVID-19 on mental health functioning in adolescents with and without ADHD. J Child Psychol Psychiatry. (2021) 62:1132– 9. doi: 10.1111/jcpp.13382 8. Tyrer P. COVID-19 health anxiety. World Psychiatry. (2020) 19:307– 8. doi: 10.1002/wps.20798 27. Hamm ME, Brown PJ, Karp JF, Lenard E, Cameron F, Dawdani A, et al. Experiences of American older adults with pre-existing depression during the beginnings of the COVID-19 pandemic: a multicity, mixed-methods study. Am J Geriatr Psychiatry. (2020) 28:924–32. doi: 10.1016/j.jagp.2020.06.013 9. Mertens G, Gerritsen L, Duijndam S, Salemink E, Engelhard IM. Fear of the coronavirus (COVID-19): predictors in an online study conducted in March 2020. J Anxiety Disord. (2020) 74:102258. doi: 10.1016/j.janxdis.2020.102258 10. Rodríguez-Hidalgo AJ, Pantaleón Y, Dios I, Falla D. Fear of COVID-19, stress, and anxiety in university undergraduate students: a predictive model for depression. Front Psychol. (2020) 11:591797. doi: 10.3389/fpsyg.2020.591797 28. Rutherford BR, Choi CJ, Chrisanthopolous M, Salzman C, Zhu C, Montes- Garcia C, et al. The COVID-19 pandemic as a traumatic stressor: mental health responses of older adults with chronic PTSD. Am J Geriatr Psychiatry. (2021) 29:105–14. doi: 10.1016/j.jagp.2020.10.010 11. Luo F, Ghanei Gheshlagh R, Dalvand S, Saedmoucheshi S, Li Q. Systematic review and meta-analysis of fear of COVID-19. Front Psychol. (2021) 12:661078. doi: 10.3389/fpsyg.2021.661078 j j g 29. Tanir Y, Karayagmurlu A, Kaya I, Kaynar TB, Türkmen G, Dambasan BN, et al. Exacerbation of obsessive compulsive disorder symptoms in children and adolescents during COVID-19 pandemic. Psychiatry Res. (2020) 293:113363. doi: 10.1016/j.psychres.2020.113363 12. Quadros S, Garg S, Ranjan R, Vijayasarathi G, Mamun MA. Fear of COVID 19 infection across different cohorts: a scoping review. Front Psychiatry. (2021) 12:708430. doi: 10.3389/fpsyt.2021.708430 30. Tsamakis K, Triantafyllis AS, Tsiptsios D, Spartalis E, Mueller C, Tsamakis C, et al. COVID-19 related stress exacerbates common physical and mental pathologies and affects treatment. Exp Ther Med. (2020) 20:159– 62. doi: 10.3892/etm.2020.8671 13. Robinson E, Sutin AR, Daly M, Jones A. A systematic review and meta- analysis of longitudinal cohort studies comparing mental health before versus during the COVID-19 pandemic in 2020. J Affect Disord. (2021) 296:567–76. doi: 10.1016/j.jad.2021.09.098 31. Castellini G, Rossi E, Cassioli E, Sanfilippo G, Innocenti M, Gironi V, et al. A longitudinal observation of general psychopathology before the COVID-19 outbreak and during lockdown in Italy. J Psychosom Res. (2021) 141:110328. doi: 10.1016/j.jpsychores.2020.110328 14. Li J, Yang Z, Qiu H, Wang Y, Jian L, Ji J, et al. REFERENCES 2. Galea S, Merchant RM, Lurie N. The mental health consequences of COVID-19 and physical distancing: the need for prevention and early intervention. JAMA Int Med. (2020) 180:817– 8. doi: 10.1001/jamainternmed.2020.1562 December 2021 | Volume 12 | Article 789344 Frontiers in Psychiatry | www.frontiersin.org 6 Cascino et al. COVID-19 and Eating Disorders 3. Saltzman LY, Hansel CH, Bordnick PS. Loneliness, isolation, and social support factors in post-COVID-19 mental health. Psychol Trauma. (2020) 12:S55–7. doi: 10.1037/tra0000703 21. Brown S. Perinatal mental health in the COVID-19 pandemic. World Psychiatry. (2020) 19:333–4. doi: 10.1002/wps.20779 22. Arora T, Grey I, Östlundh L, Lam KBH, Omar OM, Arnone D. The prevalence of psychological consequences of COVID-19: a systematic review and meta-analysis of observational studies. J Health Psychol. (2020) 1359105320966639. doi: 10.1177/1359105320966639. [Epub ahead of print]. 4. Shan Wong SY, Zhang D, Shan Sit RW, Kei Yip BH, Chung RYN, Man Wong CK, et al. Impact of COVID-19 on loneliness, mental health, and health service utilization: a prospective cohort study of older adults with multimorbidity in primary care. Br J Gen Pract. (2020) 70:E817– 24. doi: 10.3399/bjgp20X713021 23. Xiong J, Lipsitz O, Nasri F, Lui LM, Gill H, Phan L, et al. Impact of COVID-19 pandemic on mental health in the general population: a systematic review. J Affect Disord. (2020) 277:55–64. doi: 10.1016/j.jad.2020.08.001 5. Armitage R, Nellums LB. COVID-19 and the consequences of isolating the elderly. Lancet Public Health. (2020) 5:E256. doi: 10.1016/S2468-2667(20)30061-X 24. Aknin L, De Neve J-E, Dunn E, Fancourt D, Goldberg E, Helliwell J, et al. Mental health during the first year of the COVID-19 pandemic: a review and recommendations for moving forward. Perspect Psychol Sci. (2021). doi: 10.31234/osf.io/zw93g 6. Rooksby M, Furuhashi T, McLeod HJ. Hikikomori: a hidden mental health need following the COVID-19 pandemic. World Psychiatry. (2020) 19:399– 400. doi: 10.1002/wps.20804 25. Tsamakis K, Tsiptsios D, Ouranidis A, Mueller C, Schizas D, Terniotis C, et al. COVID-19 and its consequences on mental health. Exp Ther Med. (2021) 21:244. doi: 10.3892/etm.2021.9675 7. Creese B, Khan Z, Henley W, O’Dwyer S, Corbett A, Vasconcelos Da Silva M, et al. Loneliness, physical activity and mental health during Covid-19: a longitudinal analysis of depression and anxiety in adults over 50 between 2015 and 2020. Int Psychogeriatr. (2021) 33:505– 14. doi: 10.1017/S1041610220004135 26. Breaux R, Dvorsky M, Marsh N, Green C, Cash A, ShroffD. REFERENCES Anxiety and depression among general population in China at the peak of the COVID-19 epidemic. World Psychiatry. (2020) 19:249–50. doi: 10.1002/wps. 20758 32. Wang Q, Xu R, Volkow ND. Increased risk of COVID-19 infection and mortality in people with mental disorders: analysis from electronic health records in the United States. World Psychiatry. (2021) 20:124– 30. doi: 10.1002/wps.20806 15. Daly M, Sutin A, Robinson E. Longitudinal changes in mental health and the COVID-19 pandemic: evidence from the UK Household Longitudinal Study. Psychol Med. (2020) 1–10. doi: 10.1017/S0033291720004432. [Epub ahead of print]. 33. De Hert M, Mazereel V, Detraux J, Van Assche K. Prioritizing COVID-19 vaccination for people with severe mental illness. World Psychiatry. (2021) 20:54–5. doi: 10.1002/wps.20826 16. van der Velden PG, Contino C, Das M, van Loon P, Bosmans MW. Anxiety and depression symptoms, and lack of emotional support among the general population before and during the COVID-19 pandemic. A prospective national study on prevalence and risk factors. J Affect Disord. (2020) 277:540– 8. doi: 10.1016/j.jad.2020.08.026 34. Adhanom Ghebreyesus T. Addressing mental health needs: an integral part of COVID-19 response. World Psychiatry. (2020) 19:129–30. doi: 10.1002/wps.20768 17. Kwong ASF, Pearson RM, Adams MJ, Northstone K, Tilling K, Smith D, et al. Mental health before and during the COVID-19 pandemic in two longitudinal UK population cohorts. Br J Psychiatry. (2020) 1– 10. doi: 10.1192/bjp.2020.242. [Epub ahead of print]. 35. Pfefferbaum B, North CS. Mental health and the Covid-19 pandemic. N Engl J Med. (2020) 383:510–2. doi: 10.1056/NEJMp2008017 36. Öngür D, Perlis R, GoffD. Psychiatry and COVID-19. JAMA. (2020) 324:1149–50. doi: 10.1001/jama.2020.14294 37. Fiorillo A, Gorwood P. The consequences of the COVID-19 pandemic on mental health and implications for clinical practice. Eur Psychiatry. (2020) 63:e32. doi: 10.1192/j.eurpsy.2020.35 18. Shanahan L, SteinhoffA, Bechtiger L, Murray AL, Nivette A, Hepp U, et al. Emotional distress in young adults during the COVID-19 pandemic: evidence of risk and resilience from a longitudinal cohort study. Psychol Med. (2020) 1–10. doi: 10.1017/S003329172000241X 38. Marazziti D, Stahl SM. The relevance of COVID-19 pandemic to psychiatry. World Psychiatry. (2020) 19:261. doi: 10.1002/wps.20764 19. Giannopoulou I, Galinaki S, Kollintza E, Adamaki M, Kympouropoulos S, Alevyzakis E, et al. COVID-19 and post-traumatic stress disorder: The perfect ’storm’ for mental health. Exp Ther Med. (2021) 22:1162. doi: 10.3892/etm.2021 39. Unützer J, Kimmel RJ, Snowden M. Psychiatry in the age of COVID-19. World Psychiatry. (2020) 19:130–1. doi: 10.1002/wps.20766 40. Stewart DE, Appelbaum PS. REFERENCES Spitzer RL, Kroenke K, Williams JBW, Lowe B, A. brief measure for assessing generalized anxiety disorder: the GAD-7. Arch Intern Med. (2006) 166:1092– 7. doi: 10.1001/archinte.166.10.1092 51. Shah M, Sachdeva M, Johnston H. Eating disorders in the age of COVID-19. Psychiatry Res. (2020) 290:113122. doi: 10.1016/j.psychres.2020.113122 70. Kroenke K, Spitzer RL, Williams JBW. The PHQ-9: validity of a brief depression severity measure. J Gen Intern Med. (2001) 16:606– 13. doi: 10.1046/j.1525-1497.2001.016009606.x 52. Shevlin M, Butter S, McBride O, Murphy J, Gibson-Miller J, Hartman TK, et al. Refuting the myth of a ’tsunami’ of mental ill-health in populations affected by COVID-19: evidence that response to the pandemic is heterogeneous, not homogeneous. Psychol Med. (2021) 1– 9. doi: 10.1017/S0033291721001665. [Epub ahead of print]. 71. Weathers FW, Litz BT, Keane TM, Palmieri PA, Marx BP, Schnurr PP. The PTSD Checklist for DSM-5 (PCL-5) – Standard. Measurement Instrument. The National Center for PTSD (2013). Available online at: www.ptsd.va.gov (accesed October 1, 2021). 53. Sideli L, Lo Coco G, Bonfanti RC, Borsarini B, Fortunato L, Sechi C, et al. Effects of COVID-19 lockdown on eating disorders and obesity: a systematic review and meta-analysis. Eur Eat Disord Rev. (2021) 29:826–41. doi: 10.1002/erv.2861 72. Foa EB, Kozak MJ, Salkovskis PM, Coles ME, Amir N. The validation of a new obsessive-compulsive disorder scale: the obsessive-compulsive inventory. Psychol Assess. (1998) 10:206–14. doi: 10.1037/1040-3590.10.3.206 54. Monteleone AM, Marciello F, Cascino G, Abbate-Daga G, Anselmetti S, Baiano M, et al. The impact of COVID-19 lockdown and of the following “re-opening” period on specific and general psychopathology in people with Eating Disorders: the emergent role of internalizing symptoms. J Affect Disord. (2021) 285:77–83. doi: 10.1016/j.jad.2021. 02.037 73. Rizzardi M, Trombini E, Trombini G. EDI-2: Manuale. Florence: Giunti Organizzazioni Speciali (1995). 74. Cardi V, Matteo RD, Corfield F, Treasure J. Social reward and rejection sensitivity in eating disorders: an investigation of attentional bias and early experiences. World J Biol Psychiatry. (2013) 14:622–33. doi: 10.3109/15622975.2012.665479 55. Nisticò V, Bertelli S, Tedesco R, Anselmetti S, Priori A, Gambini O, et al. The psychological impact of COVID-19-related lockdown measures among a sample of Italian patients with eating disorders: a preliminary longitudinal study. Eat Weight Disord. (2021) 1:3. doi: 10.1007/s40519-021 -01137-0 75. Moulton SJ, Newman E, Power K, Swanson V, Day K. Childhood trauma and eating psychopathology: a mediating role for dissociation and emotion dysregulation? Child Abuse Negl. (2015) 39:167–74. doi: 10.1016/j.chiabu.2014.07.003 56. REFERENCES COVID-19 and psychiatrists’ responsibilities: a WPA position paper. World Psychiatry. (2020) 19:406–7. doi: 10.1002/wps.20803 20. Wang C, Pan R, Wan X, Tan Y, Xu L, Ho CS, et al. Immediate psychological responses and associated factors during the initial stage of the 2019 coronavirus disease (COVID-19) epidemic among the general population in China. Int J Environ Res Public Health. (2020) 17:1729. doi: 10.3390/ijerph17051729 41. Wasserman D, Iosue M, Wuestefeld A, Carli V. Adaptation of evidence- based suicide prevention strategies during and after the COVID-19 pandemic. World Psychiatry. (2020) 19:294–306. doi: 10.1002/wps.20801 Frontiers in Psychiatry | www.frontiersin.org December 2021 | Volume 12 | Article 789344 7 COVID-19 and Eating Disorders Cascino et al. 58. Caslini M, Bartoli F, Crocamo C, Dakanalis A, Clerici M, Carrà G. Disentangling the association between child abuse and eating disorders. Psychosom Med. (2016) 78:79–90. doi: 10.1097/PSY.0000000000000233 42. Castellini G, Cassioli E, Rossi E, Innocenti M, Gironi V, Sanfilippo G, et al. The impact of COVID-19 epidemic on eating disorders: a longitudinal observation of pre versus post psychopathological features in a sample of patients with eating disorders and a group of healthy controls. Int J Eat Disord. (2020) 53:1855–62. doi: 10.1002/eat.23368 59. Abed R, Brüne M, Wilson DR. The role of the evolutionary approach in psychiatry. World Psychiatry. (2019) 18:370–1. doi: 10.1002/wps.20688 43. Fernández-Aranda F, Munguía L, Mestre-Bach G, Steward T, Etxandi M, Baenas I, et al. COVID Isolation Eating Scale (CIES): analysis of the impact of confinement in eating disorders and obesity—a collaborative international study. Eur Eat Disord Rev. (2020) 28:871–83. doi: 10.1002/erv.2784 60. Molendijk ML, Hoek HW, Brewerton TD, Elzinga BM. Childhood maltreatment and eating disorder pathology: a systematic review and dose-response meta-analysis. Psychol Med. (2017) 47:1402–16. doi: 10.1017/S0033291716003561 g y study. Eur Eat Disord Rev. (2020) 28:871–83. doi: 10.1002/erv.278 61. Castellini G, Lelli L, Cassioli E, Ciampi E, Zamponi F, Campone B, et al. Different outcomes, psy- chopathological features, and comorbidities in patients with eating disorders reporting childhood abuse: a 3-year follow-up study. Eur Eat Disord Rev. (2018) 26:217–29. doi: 10.1002/erv.2586 44. Baenas I, Caravaca-Sanz E, Granero R, Sánchéz I, Riesco N, Testa G, et al. COVID-19 and eating disorders during confinement: analysis of factors associated with resilience and aggravation of symptoms. Eur Eat Disord Rev. (2020) 28:855–63. doi: 10.1002/erv.2771 study. Eur Eat Disord Rev. (2018) 26:217–29. doi: 10.1002/erv.258 45. Branley-Bell D, Talbot C. REFERENCES Exploring the impact of the COVID-19 pandemic and UK lockdown on individuals with experience of eating disorders. J Eat Disord. (2020) 8:44. doi: 10.1186/s40337-020-00319-y 62. Monteleone AM, Cascino G, Ruzzi V, Pellegrino F, Patriciello G, Barone E, et al. Emotional traumatic experiences significantly contribute to identify a maltreated ecophenotype sub-group in eating disorders: experimental evidence. Eur Eat Disorders Rev. (2021) 29:269–80. doi: 10.1002/ erv.2818 46. Giel KE, Schurr M, Zipfel S, Junne F, Schag K. Eating behaviour and symptom trajectories in patients with a history of binge eating disorder during COVID-19 pandemic. Eur Eat Disord Rev. (2021) 29:657– 62. doi: 10.1002/erv.2837 63. Monteleone AM, Monteleone P, Esposito F, Prinster A, Ruzzi V, Canna A, et al. The effects of childhood maltreatment on brain structure in adults with eating disorders. World J Biol Psychiatry. (2019) 20:301– 9. doi: 10.1080/15622975.2017.1395071 47. Graell M, Morón-Nozaleda MG, Camarneiro R, Villaseñor A, Yáñez S, Muñoz R, et al. Children and adolescents with eating disorders during COVID-19 confinement: difficulties and future challenges. Eur Eat Disord Rev. (2020) 28:864–70. doi: 10.1002/erv.2763 64. Monteleone AM, Fernandez-Aranda F, Voderholzer U. Evidence and perspectives in eating disorders: a paradigm for a multidisciplinary approach. World Psychiatry. (2019) 18:369–70. doi: 10.1002/wps.20687 48. Machado PPP, Pinto-Bastos A, Ramos R, Rodrigues TF, Louro E, Goncalves S, et al. Impact of COVID-19 lockdown measures on a cohort of eating disorders patients. J Eat Disord. (2020) 8:57. doi: 10.1186/s40337-020-00340-1 65. Monteleone AM. The impact of the COVID-19 pandemic on eating disorders: a paradigm for an emotional post-traumatic stress model of eating disorders. Eur Neuropsychopharmacol. (2021) 51:84–86. doi: 10.1016/j.euroneuro.2021.05.009 49. Phillipou A, Meyer D, Neill E, Tan E, Lin Toh W, Van Rheenen T, et al. Eating and exercise behaviors in eating disorders and the general population during the COVID-19 pandemic in Australia: initial results from the COLLATE project. Int J Eat Disord. (2020) 53:1158–65. doi: 10.1002/eat.23317 66. Feldman R. What is resilience: an affiliative neuroscience approach. World Psychiatry. (2020) 19:132–50. doi: 10.1002/wps.20729 67. Masten AS. Resilience from a developmental systems perspective. World Psychiatry. (2019) 18:101–2. doi: 10.1002/wps.20591 68. Bryant RA. Post-traumatic stress disorder: a state-of-the-art review of evidence and challenges. World Psychiatry. (2019) 18:259–69. doi: 10.1002/wps.20656 50. Rodgers RF, Lombardo C, Cerolini S, Franko DL, Omori M, Fuller- Tyszkiewicz M, et al. The impact of the COVID-19 pandemic on eating disorder risk and symptoms. Int J Eat Disord. (2020) 53:1166– 70. doi: 10.1002/eat.23318 69. REFERENCES Monteleone AM, Cascino G, Marciello F, Abbate-Daga G, Baiano M, Balestrieri M, et al. Risk and resilience factors for specific and general psychopathology worsening in people with Eating Disorders during COVID- 19 pandemic: a retrospective Italian multicentre study. Eat Weight Disord. (2021) 1:3. doi: 10.1007/s40519-020-01097-x 76. Gross JJ, Uusberg H, Uusberg A. Mental illness and well- being: an affect regulation perspective. World Psychiatry. (2019) 18:130–9. doi: 10.1002/wps.20618 77. McIntyre RS, Lee Y. Preventing suicide in the context of the COVID-19 pandemic. World Psychiatry. (2020) 19:250–1. doi: 10.1002/wps.20767 57. Teicher MH, Samson JA. Childhood maltreatment and psychopathology: a case for ecophenotypic variants as clinically and neurobiologically distinct subtypes. Am J Psychiatry. (2013) 170:1114–33. doi: 10.1176/appi.ajp.2013.12070957 78. Groleau P, Steiger H, Bruce K, Israel M, Sycz L, Ouellette AS, et al. Childhood emotional abuse and eating symptoms in bulimic disorders: An examination of possible mediating variables. Int J Eat Disord. (2012) 45:326–32. doi: 10.1002/eat.20939 December 2021 | Volume 12 | Article 789344 Frontiers in Psychiatry | www.frontiersin.org 8 COVID-19 and Eating Disorders Cascino et al. 79. Wolf NM, Elklit A. Child Maltreatment and Disordered Eating in Adulthood: a Mediating Role of PTSD and Self-Esteem? J Child Adolesc Trauma. (2018) 13:21–32. doi: 10.1007/s40653-018-0224-x 96. Loucas CE, Fairburn CG, Whittington C, Pennant ME, Stockton S, Kendall T. E-therapy in the treatment and prevention of eating disorders: a systematic review and meta-analysis. Behav Res Ther. (2014) 63:122– 31. doi: 10.1016/j.brat.2014.09.011 80. Stanghellini G. Embodiment and the Other’s look in feeding and eating disorders. World Psychiatry. (2019) 18:364–5. doi: 10.1002/wps.20683 97. Brothwood PL, Baudinet J, Stewart CS, Simic M. Moving online: young people and parents’ experiences of adolescent eating disorder day programme treatment during the COVID-19 pandemic. J Eat Disord. (2021) 9:62. doi: 10.1186/s40337-021-00418-4 81. Monteleone AM, Cascino G, Pellegrino F, Ruzzi V, Patriciello G, Marone L, et al. The association between childhood maltreatment and eating disorder psychopathology: A mixed-model investigation. Eur Psychiatry. (2019) 61:111–8. doi: 10.1016/j.eurpsy.2019.08.002 98. Lewis YD, Elran-Barak R, Grundman-Shev Tov R, Zubery E. The abrupt transition from face-to-face to online treatment for eating disorders: a pilot examination of patients’ perspectives during the COVID-19 lockdown. J Eat Disord. (2021) 9:31. doi: 10.1186/s40337-021-00383-y 82. Monteleone AM, Tzischinsky O, Cascino G, Alon S, Pellegrino F, Ruzzi V, et al. The connection between childhood maltreatment and eating disorder psychopathology: a network analysis study in people with bulimia nervosa and with binge eating disorder. Eat Weight Disord. REFERENCES (2021). doi: 10.1007/s40519-021-01169-6 99. Andersson G, Titov N, Dear BF, Rozental A, Carlbring P. Internet- delivered psychological treatments: from innovation to implementation. World Psychiatry. (2019) 18:20–8. doi: 10.1002/wps.20610 83. Racine SE, VanHuysse JL, Keel PK, Burt SA, Neale MC, Boker S, et al. Eating disorder-specific risk factors moderate the relationship between negative urgency and binge eating: a behavioral genetic investigation. J Abnorm Psychol. (2017) 126:481–94. doi: 10.1037/abn00 00204 100. Linardon J, Shatte A, Tepper H, Fuller-Tyszkiewicz M. A survey study of attitudes toward, and preferences for, e-therapy interventions for eating disorder psychopathology. Int J Eat Disord. (2020) 53:907– 16. doi: 10.1002/eat.23268 84. Vanzhula IA, Calebs B, Fewell L, Levinson CA. Illness pathways between eating disorder and post-traumatic stress disorder symptoms: Understanding comorbidity with network analysis. Eur Eat Disord Rev. (2019) 27:147–60. doi: 10.1002/erv.2634 101. Thompson-Brenner H, Boswell JF, Espel-Huynh HM, Brooks GE, Lowe MR. Implementation of transdiagnostic treatment for emotional disorders in residential eating disorder programs: a preliminary pre-post evaluation. Corrected version. Psychother Res. (2018) 29:1045–61. doi: 10.1080/10503307.2018.1446563 85. Brooke L, Mussap AJ. Brief report: maltreatment in childhood and body concerns in adulthood. J Health Psychol. (2013) 18:620–6. doi: 10.1177/1359105312454036 102. Barlow DH, Harris BA, Eustis EH, Farchione TJ. The unified protocol for transdiagnostic treatment of emotional disorders. World Psychiatry. (2020) 19:245–6. doi: 10.1002/wps.20748 86. Dunkley DM, Masheb RM, Grilo CM. Childhood maltreatment, depressive symptoms, and body dissatisfaction in patients with binge eating disorder: the mediating role of self-criticism. Int J Eat Disord. (2010) 43:274– 81. doi: 10.1002/eat.20796 103. Trottier K, MacDonald DE. Update on psychological trauma, other severe adverse experiences and eating disorders: state of the research and future research directions. Curr Psychiatry Rep. (2017) 19:45. doi: 10.1007/s11920-017-0806-6 87. Brewerton TD. Eating disorders, trauma, and comorbidity: focus on PTSD. Eat Disord. (2007) 15:285–304. doi: 10.1080/10640260701454311 88. Reynolds CF. Building resilience through psychotherapy. World Psychiatry. (2019) 18:289–91. doi: 10.1002/wps.20663 104. Fairburn CG, Cooper Z, Shafran R. Cognitive behaviour therapy for eating disorders: a “transdiagnostic” theory and treatment. Behav Res Ther. (2003) 41:509–28. doi: 10.1016/s0005-7967(02)00088-8 89. Lutz W, Saunders SM, Leon SC, Martinovich Z, Kosfelder J, Schulte D, et al. Empirically and clinically useful decision making in psychotherapy: Differential predictions with treatment response models. Psychol Assess. (2006) 18:133–41. doi: 10.1037/1040-3590.18.2.133 105. Fusar-Poli P. TRANSD recommendations: improving transdiagnostic research in psychiatry. World Psychiatry. (2019) 18:361– 2. doi: 10.1002/wps.20681 90. Vall E, Wade TD. Copyright © 2021 Cascino, Marciello, Abbate-Daga, Balestrieri, Bertelli, Carpiniello, Corrivetti, Favaro, Renna, Ricca, Salvo, Segura-Garcia, Todisco, Volpe, Zeppegno, Monteleone and Monteleone. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. REFERENCES Predictors of treatment outcome in individuals with eating disorders: a systematic review and meta-analysis. Int J Eat Disord. (2015) 48:946–71. doi: 10.1002/eat.22411 Conflict of Interest: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. 91. Fairburn CG, Bailey-Straebler S, Basden S, Doll HA, Jones R, Murphy R, et al. A transdiagnostic comparison of enhanced cognitive behaviour therapy (CBT-E) and interpersonal psychotherapy in the treatment of eating disorders. Behav Res Ther. (2015) 70:64–71. https://doi.org/10.1016/j.brat. 2015.04.010 Publisher’s Note: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher. 92. Cuijpers P. Targets and outcomes of psychotherapies for mental disorders: an overview. World Psychiatry. (2019) 18:276–85. doi: 10.1002/wps. 20661 93. Barber JP, Solomonov N. Toward a personalized approach to psychotherapy outcome and the study of therapeutic change. World Psychiatry. (2019) 18:291–2. doi: 10.1002/wps.20666 Copyright © 2021 Cascino, Marciello, Abbate-Daga, Balestrieri, Bertelli, Carpiniello, Corrivetti, Favaro, Renna, Ricca, Salvo, Segura-Garcia, Todisco, Volpe, Zeppegno, Monteleone and Monteleone. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. 94. Abbate-Daga G, Amianto F, Delsedime N, De-Bacco C, Fassino S. Resistance to treatment in eating disorders: a critical challenge. BMC Psychiatry. (2013) 13:294. doi: 10.1186/1471-244X-13-294 95. Demyttenaere K. What is treatment resistance in psychiatry? A “difficult to treat” concept. World Psychiatry. (2019) 18:354–5. doi: 10.1002/wps. 20677 Frontiers in Psychiatry | www.frontiersin.org December 2021 | Volume 12 | Article 789344 9
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Apresentação
Anais do Museu Paulista
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Apresentação Cecilia Helena de Salles Oliveira Diretora do Museu Paulista Cecilia Helena de Salles Oliveira Diretora do Museu Paulista Na obra Combats pour l’histoire, Lucien Fevbre não somente convidou os historiadores a proble- matizar e “complicar” o que parecia simples, como apontou o necessário alargamento dos horizontes em que, até então, a disciplina da história se situava. Essas lições, enunciadas em 1952, ainda se mantêm pertinentes e podem ser encontradas, de modo atualizado, no elenco de artigos que compõem este volume dos Anais do Museu Paulista. duzidos. Este é, sem dúvida, o caso das fontes cartográficas. Os artigos apresentados nesta edição completam e desdobram o Dossiê publicado no número anterior dos Anais (vol. 17, n. 1), igualmente dedicado à divulgação dos resulta- dos obtidos com o projeto de pesqui- sa e a exposição Cartografia de uma história – São Paulo colonial: mapas e relatos. Fruto de uma exitosa parceria multidisciplinar entre pesquisadores da Universidade de São Paulo, liga- dos ao Museu Paulista, ao Departa- mento de História da Faculdade de Filosofia Letras e Ciências Humanas, à Cátedra Jaime Cortesão e à Facul- dade de Arquitetura e Urbanismo, a investigação resultou, como o leitor poderá observar, em contribuições importantes para a discussão dos sentidos políticos, culturais e simbóli- cos dos mapas, particularmente no âmbito da configuração de redes de Alargar horizontes significa incorporar temas e questões possibi- litados pelo distanciamento temporal e pelo acúmulo de conhecimentos. Representa, também, elevar à condi- ção de documentos certos vestígios e sinais que, passaram despercebi- dos quer sob o ponto de vista daqui- lo que registraram, quer em termos das práticas e concepções a partir das quais foram historicamente pro- poder, no período colonial, a entre- laçar Portugal e a América portugue- sa. Mais do que isso, porém, os mapas suscitam interrogações a res- peito das condições políticas e cien- tíficas de sua feitura e difusão, bem como sobre os nexos entre o esqua- drinhamento dos espaços coloniais e a definição empírica e conceitual de um “território”, em especial duran- te o século XVIII. Nesse sentido, o mapa e o território ali fixado emer- gem na condição de artefatos cons- truídos sob circunstâncias históricas precisas, a demarcar conhecimentos e, particularmente, formas de domi- nação e de intervenção na terra e na gente que a habitava. Anais do Museu Paulista. v. 16. n.1. jan.-jun. 2008. Cecilia Helena de Salles Oliveira Diretora do Museu Paulista debate em torno da realização do parque do Ibirapuera, na primeira me- tade da década de 1950, quando a Prefeitura Municipal de São Paulo, com o apoio do Governo do Estado, deci- diu concretizar o projeto, com o obje- tivo de nele sediar as comemorações do 400º aniversário de fundação da cidade. Entretanto, o artigo discute, em outro momento da História e sob pers- pectivas metodológicas específicas, de que modo se criou, no espaço urbano paulistano, um “território” atravessado de intenções políticas e simbólicas que, aos poucos, transformou-se e foi reco- nhecido como referência do solo da metrópole paulista. Mais uma vez, os Anais trazem a público artigos que iluminam os lia- mes entre História e Cultura Material, valorizando o exercício da curadoria e o ofício do historiador nas instituições museológicas. Mas, ao lado do Dossiê, o lei- tor encontrará um artigo que, à pri- meira vista, pouca articulação teria com o restante deste volume da revis- ta. Trata-se de texto voltado para o 8
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Supplemental Table S1 from Tusamitamab ravtansine in patients with advanced solid tumors: Phase 1 study of safety, pharmacokinetics, and antitumor activity using alternative dosing regimens
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Comparative study of root and soil microbiological activity in individual and co-cultivation of cabbage (Brassica oleraceae L. var. capitata L.)
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Растениевъдни науки, 2024, 61 (2) Bulgarian Journal of Crop Science, 2024, 61 (2) https://doi.org/10.61308/EKVR9826 Сравнително проучване на коренова и почвена микробиологична активност при самостоятелно и съвместно отглеждане на зеле (Вrassicа oleraceae L. var. capitata L.) Гергана Младенова, Милена Йорданова, Бойка Малчева* Лесотехнически университет, София, България *E-mail: boika.malcheva@gmail.com Резюме: Проведено е сравнително проучване на коренова и почвена микробиологична активност при самостоятелно и съвместно отглеждане на зеле с други култури: праз, фасул, тагетес, копър и цветен микс. Взаимното отглеждане на зеле и цветен микс повишава количеството на микроорганизмите в непосредствена близост до корените на зелето в най-висока степен. Най-ниска е биогенността на кореновата зона при варианта със зеле и тагетес. При самостоятелното отглеждане на зеле се установява по-висока стойност на общата микрофлора спрямо вариантите с основна култура зеле и допълнителни култури тагетес или праз. Комбинирането на зелето с цветен микс, фасул или копър повишава количеството на микроорганизмите от ризоплана и ризосферата в по-висока степен отколкото самостоятелното отглеждане на зеле. Основен дял в състава на общата микрофлора заемат неспорообразуващите бактерии, следвани от бацилите. Прегрупиране се установява при съвместното отглеждане на зеле и цветен микс, като при този вариант количеството на спорообразуващите бактерии е по-високо от това на неспорообразуващите бактерии. По-слабо представени са актиномицетите и плесенните гъби. Каталазната активност е най-висока при контролата, следвана от варианта със съвместно отглеждане на зеле и праз, а най-ниска при зеле и цветен микс, и зеле и копър, като зависи значително от влажността на вариантите. Целулазната активност е по-висока при вариантите с култури спрямо контролата – най-висока при съвместно отглеждане на зеле и праз, и зеле и тагетес, а най-ниска при зеле и фасул, като зависи значително от общата микрофлора. Ключови думи: коренова микрофлора; почвена биогенност; ензимни активности Comparative study of root and soil microbiological activity in individual and co-cultivation of cabbage (Brassica oleraceae L. var. capitata L.) Gergana Mladenova, Milena Yordanova, Boyka Malcheva* University of Forestry, Sofia, Bulgaria *E-mail: boika.malcheva@gmail.com Citation: Mladenova, G., Yordanova, M., & Malcheva, B. (2024). Comparative study of root and soil microbiological activity in individual and co-cultivation of cabbage (Brassica oleraceae L. var. capitata L.) Bulgarian Journal of Crop Science, 61(2) 37-46 (Bg). Abstract: A comparative study of root and soil microbiological activity was carried out during independent and co-cultivation of cabbage with other crops: leeks, beans, tagetes, fennel and flower mix. The intercropping of cabbage and flower mix increases the amount of microorganisms in the immediate vicinity of the cabbage roots to the highest degree. The biogenicity of the root zone is the lowest in the variant with cabbage and tagetes. In the independent cultivation of cabbage, a higher value of the total microflora is established compared to the variants with the main cabbage crop and additional tagetes or leek crops. Combining cabbage with flower mix, 37 Растениевъдни науки, 2024, 61 (2) Bulgarian Journal of Crop Science, 2024, 61 (2) beans or fennel increased the amount of microorganisms from the rhizoplane and rhizosphere to a higher degree than growing cabbage alone. The main share in the composition of the total microflora is occupied by non-sporeforming bacteria, followed by bacilli. Regrouping was found in the co-cultivation of cabbage and flower mix, and in this variant the amount of spore-forming bacteria was higher than that of non-spore-forming bacteria. Actinomycetes and mold fungi are less represented. Catalase activity was highest in the control, followed by the variant with co-cultivation of cabbage and leek, and lowest in cabbage and flower mix, and cabbage and fennel, depending significantly on the humidity of the variants. Cellulase activity was higher in the variants with crops compared to the control - highest in the co-cultivation of cabbage and leek, and cabbage and tagetes, and lowest in cabbage and beans, depending significantly on the total microflora. Key words: root microflora; soil biogenicity; enzyme activities ВЪВЕДЕНИЕ Проучването на взаимодействията корени-почва-микроорганизми в земеделската поч­ вена екосистема е от съществено значение за повишаване плодородието на почвата, качеството и добива на селскостопанските култури. Корените на растенията са колонизирани от удивителен брой микроорганизми, като броят на микробните гени в ризосферата далеч надвишава броя на растителните гени (Mendes et al., 2013). При проучване на ризосферната бактериална общност на 14 растителни вида са установени повече от 1200 различими бактериални таксони от 35 различни таксономични разреда, като Proteobacteria е най-доминиращият тип (Hawkes et al., 2007). Миксомицетите и свързаните с тях микроорганизми (бактерии, гъбички) са по-изобилни в кореновата зона на зеле (Brassica oleracea) и боб (Vicia faba), отколкото в почва извън кореновата зона (Amewowor & Madelin, 1991). Според друго изследване (Ling et al., 2022) в реалните селскостопански системи има спад в микробното разнообразие в близост до ризосферата. През последните години има доказателства, че няколко полезни за растенията ризосферни бактерии не само се свързват с растенията, но и с насекоми, като по този начин взаимодействията на тези бактерии с тяхната среда са дори по-сложни, отколкото се смяташе досега и могат да се разпрострат далеч извън ризосферата (Pronk et al., 2022). Интересът към използването на полезни ри38 зосферни микроорганизми става глобален, тъй като може да представлява екологична алтернатива на химизацията в ерата на заплахи за отглеждането на културите в съвременния свят (Paliwoda & Mikiciuk, 2020). Ризосферните микроорганизми имат жизненоважна функция за развитието и здравето на растенията (Fan et al., 2017). Главестото зеле Вrassicа oleraceae L. var. capitata L. принадлежи към семейство Brassicaceae. Кореновата му система се състои от централен корен и голям брой странични коренови разклонения, които са разположени на дълбочина 40 – 50 cm. Отделни разклонения могат да проникнат и по-дълбоко до около 75 – 100 cm. Кореновата система има добра възстановителна способност, при загърляне на стъблото се образуват адвентивни корени, които допринасят за увеличаване на нейния обем (Shaban et al., 2014). Ризосферните микробни съобщества са мно­ го разнообразни и силно зависещи от типа растителност, кореновите ексудати и фактори на почвената среда – температура, влажност, рН, тип почва, механичен състав на почвата, наторяване, обработка на почвата и други фактори. В ризосферната почва при отглеждане на китайско зеле Proteobacteria, Acidobacteriota, Actinobacteriota и Bacteroidota са доминиращите бактериални типове, докато Olpidiomycota, Ascomycota, Mortierellomycota и Basidiomycota са преобладаващите гъбични типове (Wei et al., 2023). Изследването на ризосферната почвена микробна общност и нейната връзка с основна- Растениевъдни науки, 2024, 61 (2) та почвена микробна общност е от решаващо значение за поддържане на здравето и плодородието на почвата и подобряване на добивите от селскостопански култури. Общо 20 морфологично различни, култивирани бактериални щама са възстановени от ризосферната почва на зеле, култивирано в биофумигирано поле, като най-голямата част от изолатите принадлежат към род Bacillus, а другите изолирани бактериални родове са Pseudomonas, Serratia, Stenotrophomonas, Microbacterium и Priestia (Al-Daghari et al., 2023). При изследване на ризосферната микрофлора на диво зеле (Brassica oleracea L.) Gols et al. (2023) установяват, че гъбичните общности се различават по-силно отколкото бактериалните общности. По-високото количество на Bacillus subtilis в почвената и ризосферна зони на зеле може да насърчи растежа на растенията чрез отделяне на биоактивни съединения (гиберилини) (Kang et al., 2019). Установени разлики в качеството на отделните растения при отглеждане на зеле според някои автори се дължат на варирането на микробните съобщества в почвата, ризосфера и ризоплана (Gols et al., 2023; Lundberg et al., 2012). Микробната общност притежава потенциал за по-бърз растеж и обмен, поради което е по-реактивен компонент на земната екосистема за външен стрес, отколкото растенията и животните (Panikov, 1999). Почвените микроорганизми са чувствителни към промени в заобикалящата ги среда (Schinner & Sonnletner, 1996). Микробната биомаса и ензимните активности са признати за ранни показатели за настъпващи промени в резултат на различни земеделски практики. Освен това, съществуват значителни доказателства, че те могат да бъдат използвани за оценка на влиянието на управлението и използването на почвите (Caravaca et al., 2002; Saggar et al., 1999). Почвената микробна общност произвежда извънклетъчни ензими, които имат основна роля за разграждането на растителните остатъци и поддържането на кръговратите на хранителните вещества в почвата. Взаимното отглеждане на селскостопански култури значително повишава ензимната активност със средно Bulgarian Journal of Crop Science, 2024, 61 (2) 13% (P <0,001), като ефектът зависи от вида на основната и междинните култури, категорията на ензима, експериментални и екологични фактори (Curtright & Tiemann, 2021). Ризосферните почвени микроорганизми и ензими са най-активните компоненти в почвата, които са тясно свързани с почвения въглероден цикъл и могат да отразяват чувствително динамиката на почвения органичен въглерод (Qu et al., 2022). Ризосферата, в която може да се отдели значително количество нетен фиксиран въглерод, е сферата за микробна активност, където кореновите ексудати и други ризоотлагания играят важна роля при определяне на състава на микробната общност в ризоплана и ризосфера (Jones et al., 2009; Raaijmakers et al., 2009). Повечето проучвания са фокусирани върху бактериални и гъбични съобщества (Zhang et al., 2017) и има ограничени изследвания върху свойствата на микробните съобщества в ризосферата (Fan et al., 2018). Микробите от ризоплана и ризосфера, които директно взаимодействат с корените на растението, влияят положително или отрицателно на растението (Gols et al., 2023). Ризобактериите и арбускуларните микоризни гъби могат да стимулират растежа на растенията, докато патогенните микроби могат да имат вреден ефект върху растенията (Lugtenberg & Kamilova, 2009; Whipps, 2001; Barea et al., 2005; Raaijmakers et al., 2009). Целта на изследването беше проучване и анализ на количеството, състава и активността на микрофлората в ризоплана и ризосфера на зеле при самостоятелно и съвместно отглеждане с други култури. Проучването беше фокусирано върху изследване на микробната общност в зоните най-близо до корените на растенията, а не в почвата като цяло, която микрофлора е определяща за почвеното плодородие и добива от културите. МАТЕРИАЛИ И МЕТОДИ Експерименталната работа е проведена през втората половина на 2022 година в Учеб39 Растениевъдни науки, 2024, 61 (2) но опитно поле “Враждебна” към Лесотехнически университет, София, България, върху алувиално-ливадна, слабо каменлива почва. Опитът е заложен по метода на рандомизираните парцели с по четири повторения, с големина на опитната парцелка от 3,5m на 5m. Основната култура е бяло късно главесто зеле (Вrassicа oleraceae L. var. capitata L.), сорт „Балкан“. Изследването на микрофлората е проведено на корени и полепналите непосредствено върху корените почвени частици (микрофлора от ризоплана и ризосфера) при отглеждане на основна култура зеле – самостоятелно и при съвместно отглеждане с други култури по схемата представена в Таблица 1. Корените на зелето са извадени и съхранени по-малко от 24 часа в стерилни хартиени пликове и в хладилник при температура 4 ℃. Смлени са без отстраняване на почвените частици по тях. Bulgarian Journal of Crop Science, 2024, 61 (2) Микробиологичните изследвания включват определяне на аеробни, мезофилни групи микроорганизми. Използван е метод на пределните разреждания, направени са повърхностни плътни посевки върху твърди хранителни среди (месопептонен агар за неспорообразуващи бактерии и бацили; Actinomycetes isolation agar за актиномицети и бактерии, усвояващи минерален азот; Чапек-Докс агар за плесенни гъби) и последващо култивиране в термостат при 25 ℃ и отчитане на колониеобразуващи единици. Резултатите са преизчислени за 1 гр. абсолютно сух субстрат (Мishustin & Emtsev, 1989). Определена е обща микрофлора и минерализационен коефициент (Мishustin & Runov, 1957; Мalcheva & Naskova, 2018). Каталазната активност е определена по мангано-метричен метод (Khaziev, 1976). Целулазната активност е определена в динамика чрез залагане на филтърни ленти вър- Таблица 1. Варианти на изследване Table 1. Research variants № на вариант/ Variant № В0 Основна култура/ Basic culture Контрола – почва без растителност/ Control – soil without vegetation В1 В2 В3 В4 В5 В6 40 Зеле/ Cabbage Brassica oleraceae L. var. capitate L. Допълнителна култура/ Additional culture Без допълнителна култура/ No additional culture Праз/ Leek Allium porrum L. Фасул/ Beans Phaseolus vulgaris L. Тагетес/ Tagetes Tagetes patula L. Цветен микс: невен (Calendula officinalis L.), копър (Anethum graveolens L.), бораго (Borago officinalis L.), синя метличина (Centaurea cyanus L.), фацелия (Phacelia sp. Jus.), елда (Fagopyrum esculentum Mill.)/ Flower mix: calendula, borage, blue cornflower, phacelia, buckwheat Копър/Dill Anethum graveolens L. Растениевъдни науки, 2024, 61 (2) Bulgarian Journal of Crop Science, 2024, 61 (2) ху смлените корени и полепналата почва по тях в петри, и последващо отчитане на процента разградена площ (Khaziev, 1976). Влажността на пробите е определена на влагомерна везна, марка DBS. Статистическата обработка на резултатите включва осредняване на стойностите за микробиологичните показатели от три повторения и корелационен анализ на MS Excel, показващ зависимости между някои от изследваните показатели. РЕЗУЛТАТИ И ДИСКУСИЯ Биогенността на вариантите показва различия при самостоятелно и съвместно отглеждане на зеле (Tаблица 2). Самостоятелното и съвместно отглеждане на зеле повишава общото количество на микрофлората от ризоплана и ризосфера спрямо контролата (без растителност) - 1,6 пъти при самостоятелно отглеждане на зеле и от 0,8 до 1,6 пъти при съвместно култивиране на зеле с други култури. Съвместното отглеждане на зеле и цветен микс повишава биогенността на този вариант (В5) в най-висока степен. Следват вариантите: В3 (зеле и фасул), В6 (зеле и копър), В1 (зеле). Най-ниска е стойността на общата микрофлора при взаимното отглеждане на зеле и тагетес. Минерализационната активност е най-висока при контролата. Съвместното отглеждане на зеле с други култури повишава скоростта на разграждане на органичните вещества в почвата спрямо самостоятелното отглеждане на зеле с изключение при В5 (зеле и цветен микс). Най-висока е стойността на минерализационния коефициент при В4 (зеле и тагетес), при който вариант общата микрофлора е с най-ниска стойност. Следователно активността на микроорганизмите не зависи еднозначно само от количеството на микроорганизмите. Кореновите разклонения на зелето могат достигнат до 100 Таблица 2. Количество и състав на микрофлора от ризоплана и ризосфера (КОЕ/g) Table 2. Amount and composition of microflora from the rhizoplane and rhizosphere (CFU/g) Вариант/ Variant В0 Контрола - без растителност/ Control - without vegetation В1 Зеле/ Cabbage В2 Зеле+праз/ Cabbage + leek В3 Зеле+фасул/ Cabbage + beans В4 Зеле+тагетес/ Cabbage + tagetes В5 Зеле+цветен микс/ Cabbage+flower mix В6 Зеле+копър/ Cabbage + fennel Микромицети/ Micromycetes Бактерии, усвояващи минерален азот/ Bacteria assimilating mineral nitrogen Минерализационен коефициент/ Mineralization coefficient 694200 53400 4722933 4,063 1287000 54000 9000 1453500 0,499 1679600 884000 81600 54400 5895600 2,300 3273600 2198400 984000 62400 28800 3187200 1,002 2018500 1100000 775500 93500 49500 5214000 2,780 3460200 1576800 1664400 51100 167900 1299400 0,401 3218400 1728000 1339200 113400 37800 2894400 0,944 Обща микрофлора/ Total microflora Неспорообразуващи бактерии/ Бацили/ Non-spore- Bacilli forming bacteria Актиномицети/ Actinomycetes 1909940 1085800 76540 2974500 1624500 2699600 41 Растениевъдни науки, 2024, 61 (2) Bulgarian Journal of Crop Science, 2024, 61 (2) сm дълбочина, което увеличава и разпространението на микроорганизми от ризоплана и ризосферата (Shaban et al., 2014). Amewowor & Madelin (1991) установяват, че бактерии и гъбички са по-изобилни в кореновата зона на зеле (Brassica oleracea), отколкото в почва извън кореновата зона, като гъбичните общности при диво зеле се различават по-силно отколкото бактериалните общности (Gols et al., 2023). Други автори (Ling et al., 2022) установяват, че в реалните селскостопански системи има спад в микробното разнообразие в близост до ризосферата. В ризосферната почва при отглеждане на китайско зеле Proteobacteria, Acidobacteriota, Actinobacteriota и Bacteroidota са доминиращите бактериални типове, докато Olpidiomycota, Ascomycota, Mortierellomycota и Basidiomycota са преобладаващите гъбични типове (Wei et al., 2023). Други автори (Al-Daghari et al., 2023) установяват, че в ризосферната почва на зеле доминира род Bacillus, а другите изолирани бактериални родове са Pseudomonas, Serratia, Stenotrophomonas, Microbacterium и Priestia. Bacillus subtilis в почвената и ризосферна зони на зеле може да насърчи растежа на растенията чрез отделяне на биоактивни съединения (гиберилини) (Kang et al., 2019). Установени разлики в качеството на отделните растения при отглеждане на зеле според някои автори се дължат на варирането на микробните съобщества в почвата, ризосфера и ризоплана (Gols et al., 2023; Lundberg et al., 2012). Основен дял в състава на общата микрофлора заемат неспорообразуващите бактерии (57% при контролата; най-висок процент при В3 зеле и фасул – 67%) при всички варианти, с изключение при съвместното отглеждане на зеле и цветен микс (В5), при който вариант количеството на бацилите е по-високо от това на неспорообразуващите бактерии. При контролата следват актиномицетите (2-ро място), бацилите (3-то място) и най-слабо представени са микромицетите (плесенни гъби). При вариантите с растителност след неспорообразуващите бактерии следват бацилите (2-ро място), актиномицетите (трето място) и най-слабо представени са плесенните гъби. Изключение от тази тенденция се установява при взаимното участие на зеле и цветен микс 1,8 1,6 1,4 1,2 1 0,8 0,6 0,4 0,2 0 В0 Контрола В1 Зеле В2 Зеле+праз В3 Зеле+фасул В4 Зеле+тагетес В5 В6 Зеле+копър Зеле+цветен микс Фигура 1. Каталазна активност (ml O2/30 min) на кореновата и почвена микрофлора Figure 1. Catalase activity (ml O2/30 min) of root and soil microflora 42 Растениевъдни науки, 2024, 61 (2) Bulgarian Journal of Crop Science, 2024, 61 (2) (В5), където количеството на плесенните гъби е по-високо от това на актиномицетите. Каталазната активност на кореновата и почвена микрофлора е представена на Фигура 1. Резултатите показват, че самостоятелното и съвместно отглеждане на зеле не повишава каталазната активност на микрофлората от ризоплана и ризосфера – стойностите на ензима са по-ниски при вариантите с растителност спрямо контролата (без растителност). При вариантите с растителност най-висока е каталазната активност при съвместното отглеждане на зеле и праз (В2), по-висока от тази при самостоятелно отглеждане на зеле (В1). Най-ниски са стойностите на каталазата при съвместно отглеждане на зеле и цветен микс (В5), и зеле и копър (В6). Каталазната активност на почвените микроорганизми не зависи само от тяхното количество. Значение за общата каталазна активност има и каталазата от растителен произход. Активността на каталазата зависи от много фактори, влияещи поотделно и в комплекс – количество на микроорганизмите, подходяща влажност, тем- пература, запасеност с хранителни вещества на почвите, както и от типа растителност. При експеримент с рапица също се установява по-ниска каталазна активност при вариантите с растителност спрямо контролата без растителност (Malcheva et al., 2019). За разлика от калазата целулазната активност се повишава при вариантите с растителност спрямо контролата (без растителност) (Фигура 2). Разграждането на целулозата до 100% протича най-бързо при съвместното отглеждане на зеле и праз (В2), и зеле и тагетес (В4) – 45 дни. Следват вариантите със самостоятелно отглеждане на зеле (В1) и съвместно отглеждане на зеле и цветен микс (В5), и зеле и копър (В6) – 60 дни. При вариантите със съвместно отглеждане най-ниска е целулазната активност при комбинирането на зеле и фасул (В3). Корелационните зависимости за някои от изследваните показатели са представени в следващата Таблица 3. Значителна положителна корелация се установява като влияние на целулазната актив- 100 90 80 70 60 50 40 30 20 10 0 В0 Контрола В1 Зеле В2 Зеле+праз 15-ти ден В3 В4 В5 В6 Зеле+фасул Зеле+тагетес Зеле+цветен Зеле+копър микс 30-ти ден 45-ти ден 60-ти ден Фигура 2. Целулазна активност (% разградена площ) на кореновата и почвена микрофлора Figure 2. Cellulase activity (% degraded area) of root and soil microflora 43 Растениевъдни науки, 2024, 61 (2) Bulgarian Journal of Crop Science, 2024, 61 (2) Таблица 3. Корелационни зависимости Table 3. Correlational dependencies Показател/ Indicator Обща микрофлора/ Total microflora Влажност/ Humidity Каталаза/ Catalase Целулаза/ Cellulase Обща микрофлора/ Total microflora Каталаза/ Catalase Целулаза/ Cellulase 1 -0,424959371 1 -0,535037984 0,5343006 1 0,507441364 -0,6270208 -0,668104 ност от общото количество микроорганизми, а на каталазната активност от влажността на почвата и корените. ИЗВОДИ Самостоятелното и съвместно отглеждане на зеле повишава общото количество на микрофлората от ризоплана и ризосфера на зеле, в най-висока степен при взаимно отглеждане на зеле и цветен микс. Най-ниска е биогенността на кореновата зона при варианта със зеле и тагетес. При самостоятелното отглеждане на зеле се установява по-висока стойност на общата микрофлора спрямо вариантите с основна култура зеле и допълнителни култури тагетес или праз. Докато комбинирането на зелето с цветен микс, фасул и копър повишава биогенността на почвата в непосредствена близост до корените в по-висока степен отколкото самостоятелното отглеждане на зеле. Основен дял в състава на общата микрофлора заемат неспорообразуващите бактерии (с изключение при съвместното отглеждане на зеле и цветен микс, при който вариант спорообразуващите бактерии доминират), а най-слабо представени като цяло са плесенните гъби. Неспорообразуващите бактерии и бацилите участват в началните етапи на разграждане на органичните вещества в почвата, а актиномицетите и плесенните гъби в по-крайните етапи на деструкция на орга44 Влажност/ Humidity 1 ничната материя. Скоростта на разграждане на органичните вещества в почвата не зависи еднозначно от общото количество на микроорганизмите. Каталазната активност на кореновата и почвена микрофлора не се повишава при самостоятелно и съвместно отглеждане на зеле спрямо контролата без растителност. При вариантите с растителност най-висока е каталазната активност при съвместното отглеждане на зеле и праз, по-висока от тази при самостоятелно отглеждане на зеле. Най-ниски са стойностите на каталазата при съвместно отглеждане на зеле и цветен микс, и зеле и копър. Каталазната активност зависи значително от влажността на почвата и корените. Целулазната активност на кореновата и почвена микрофлора е най-висока при съвместното отглеждане на зеле и праз, и зеле и тагетес. Следват вариантите със самостоятелно отглеждане на зеле и съвместно отглеждане на зеле и цветен микс, и зеле и копър. Най-ниска е целулазната активност при съвместното отглеждане на зеле и фасул. Целулазната активност зависи значително от общата микрофлора. БЛАГОДАРНОСТИ Настоящото изследване е подкрепено от МОН по НП „Млади учени и постдокторанти - 2“. Растениевъдни науки, 2024, 61 (2) Конфликт на интереси: Авторите декларират, че липсва конфликт на интереси. ЛИТЕРАТУРА Al-Daghari, D., Al-Sadi, A., Al-Mahmooli, I., Janke, R., & Velazhahan, R. (2023). Biological control efficacy of indigenous antagonistic bacteria isolated from the rhizosphere of cabbage grown in biofumigated soil against Pythium aphanidermatum damping-off of cucumber. Agriculture, 13(3), 626. DOI: https://doi. org/10.3390/agriculture13030626. Amewowor, D., & Madelin, M. (1991). Numbers of myxomycetes and associated microorganisms in the root zones of cabbage (Brassica oleracea) and broad bean (Vicia faba) in field plots. FEMS Microbiology Ecology, 86, 69-82. Barea, J. M., Pozo, M. J., Azcon, R., & Azcon-Aguilar, C. (2005). Microbial co-operation in the rhizosphere. J. Exp. Bot., 56, 1761–1778. Caravaca, F., Masciandaro G., & Ceccanti, B. (2002). Land use in relation to soil chemical and biochemical properties in a semiarid Mediterranean environment. Soil Tillage Res., 68, 23-30. Curtright, A., & Tiemann, L. (2021). Intercropping increases soil extracellular enzyme activity: A metaanalysis. Agriculture, Ecosystems & Environment. DOI: https://doi.org/10.1016/j.agee.2021.107489. Fan, K., Cardona, C., Li, Y., Shi, Y., Xiang, X., Shen, C., Wang, H., Gilbert, J., & Chu, H. (2017). Rhizosphere-associated bacterial network structure and spatial distribution differ significantly from bulk soil in wheat crop fields. Soil Biol. Biochem, 113, 275–284. doi: 10.1016/j.soilbio.06020. Fan, K., Weisenhorn, P., Gilbert, J. A., & Chu, H. (2018). Wheat rhizosphere harbors a less complex and more stable microbial co-occurrence pattern than bulk soil. Soil Biol. Biochem., 125, 251–260. DOI: 10.1016/j. soilbio.07, 022. Gols, R., Geem, M., Bullock, J., Martens, H., Wagenaar, R., Putten, W., & Harvey, J. (2023). Communities of nematodes, bacteria and fungi differ among soils of different wild cabbage population. European Journal of Soil Biology. DOI: https://doi.org/10.1016/j. ejsobi.2023.103512. Hawkes, C. V., DeAngelis, K. M., & Firestone, M. K. (2007). Root interactions with soil microbial communities and processes. In: The rhizosphere (pp. 1-29). Academic press. Elsevier, New York. Jones, D. L., Nguyen, C., & Finlay, R. D. (2009). Carbon flow in the rhizosphere: carbon trading at the soil–root interface. Plant Soil, 321, 5–33. Bulgarian Journal of Crop Science, 2024, 61 (2) Kang, S., Hamayun, M., Khan, M., Iqbal, A., & Lee, I. (2019). Bacillus subtilis JW1 enhances plant growth and nutrient uptake of Chinese cabbage through gibberellins secretion. Journal of Applied Botany and Food Quality, 92, 172 – 178. DOI: 10.5073/JABFQ.2019.092.023. Khaziev, F. (1976). Enzymatic activity of soils. Nauka, Moskva, 180 (Ru). Ling, N., Wang, T. T., & Kuzyakov, Y. (2022). Rhizosphere bacteriome structure and functions. Nat. Commun., 13, 1–13. DOI: 10.1038/s41467-022-28448-9. Lugtenberg, B., & Kamilova, F. (2009). Plant-growthpromoting rhizobacteria. Annu. Rev. Microbiol., 63, 541–556. Lundberg, D. S., Lebeis, S. L., Paredes, S.H., Yourstone, S., Gehring, J., Malfatti, S., Tremblay, J., Engelbrektson, A., Kunin, V., Rio, T.G.d., Edgar, R. S., Eickhorst, T., Ley, R., Hugenholtz, P., Tringe, S. G., & Dangle, J. L. (2012). Defining the core Arabidopsis thaliana root microbiome. Nature, 488, 86–90. Malcheva, B., & Naskova, P. (2018). Guide for laboratory exercises in Microbiology. Universitetsko izdatelstvo pri TU-Varna, Varna, 70 (Bg). Malcheva, B., Naskova, P., Plamenov, D. (2019). Investigation of the influence of mineral nitrogen fertilizers on the microbiological and enzymic activity of soils with rapeseed. Novo znanie, 8-4, 80-90 (Bg). Mendes, R., Garbeva, P. & Raaijmakers, J. (2013). The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev, 37, 634–663. Mishustin, F., & Emtsev, N. (1989). Microbiology. Kolos, Moskva, 367 (Ru). Mishustin, E., & Runov, E. (1957). The success of the development of the principles of microbiological diagnosis of soil condition. Uspekhi sovremennoy biologii, 44, 256-268 (Ru). Paliwoda, D., & Mikiciuk, G. (2020). Use of Rhizosphere Microorganisms in Plant Production – a Review Study. Journal of Ecological Engineering, 21(8), 292-310. DOI: https://doi.org/10.12911/22998993/126597. Panikov, N. S. (1999). Understanding and prediction of soil microbial community dynamics under global change. Applied Soil Ecol., 11, 161-176. Pronk, L., Bakker, P., Keel, C., Maurhofer, M., & Flury, P. (2022). The secret life of plant-beneficial rhizosphere bacteria: insects as alternative hosts. Environmental Microbiology, 24(8), 3273-3289. DOI: 10.1111/1462-2920.15968. Qu, Y., Tang, J., Liu, B., Lyu, H., Duan, Y., Yang, Y., Wang, S., & Li, Z. (2022). Rhizosphere enzyme activities and microorganisms drive the transformation of organic and inorganic carbon in saline–alkali soil 45 Растениевъдни науки, 2024, 61 (2) region. Scientific Reports, 12, 1314. DOI: https://doi. org/10.1038/s41598-022-05218-7. Raaijmakers, J. M., Paulitz, T. C., Steinberg, C., Alabouvette, C., & Moenne-Loccoz, Y. (2009). The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil, 321, pp. 341–361. Saggar, S., McIntosh, M. D., Hedley, C. B., & Knicker, H. (1999). Changes in soil microbial biomass, metabolic quotient and organic matter turnover under Hieracium (H. pilosella L.). Biol. Fert. Soil, 30, pp. 232-238. Schinner, F., & Sonnletner, R. (1996). Soil ecology: Microbiology and soil enzymatics. Springer-Verlag, Berlin (De). Shaban, N., Bistrichanov, S., Moskova, T., Kadum, E., Mitova, I., Tityanov, M., & Bumov, P. (2014). Bulgarian Journal of Crop Science, 2024, 61 (2) Vegetable production (main traditional vegetable species). Izdatelska kashta pri Lesotehnicheski universitet (Bg). Wei, X., Fu, T., He, G., Zhong, Z., Yang, M., Lou, F., & He, T. (2023). Characteristics of rhizosphere and bulk soil microbial community of Chinese cabbage (Brassica campestris) grown in Karst area. Frontiers in Microbiology, 14. DOI: 10.3389/fmicb.2023.1241436. Whipps, J. M. (2001). Microbial interactions and biocontrol in the rhizosphere. Journal of experimental Botany, 52(suppl_1), 487-511. Zhang, K., Adams, J. M., Shi, Y., Yang, T., Sun, R., He, D., ... & Chu, H. (2017). Environment and geographic distance differ in relative importance for determining fungal community of rhizosphere and bulk soil. Environmental Microbiology, 19(9), 3649-3659. Received: November 28 2023; Approved: February 15 2024; Published: April 2024 46
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Panax ginseng and salvia miltiorrhiza supplementation abolishes eccentric exercise-induced vascular stiffening: a double-blind randomized control trial
BMC complementary and alternative medicine
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© 2016 The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Lin et al. BMC Complementary and Alternative Medicine (2016) 16:168 DOI 10.1186/s12906-016-1139-4 Lin et al. BMC Complementary and Alternative Medicine (2016) 16:168 DOI 10.1186/s12906-016-1139-4 Lin et al. BMC Complementary and Alternative Medicine (2016) 16:168 DOI 10.1186/s12906-016-1139-4 Panax ginseng and salvia miltiorrhiza supplementation abolishes eccentric exercise-induced vascular stiffening: a double-blind randomized control trial Hsin-Fu Lin1,6, Kang Tung2, Chun-Chung Chou3, Ching-Che Lin4, Jaung-Geng Lin5 and Hirofumi Tanaka6* * Correspondence: htanaka@austin.utexas.edu 6Department of Kinesiology and Health Education, The University of Texas at Austin, 2109 San Jacinto Blvd, D3700, Austin, TX 78712, USA Full list of author information is available at the end of the article Abstract Background: Muscle damage induced by unaccustomed or eccentric exercise results in delayed onset vascular stiffening. We tested the hypothesis that a 7-day supplementation of panax ginseng and salvia miltiorrhiza prior to an acute eccentric exercise could attenuate arterial stiffening. Methods: By using a double-blind study placebo-controlled randomized design, subjects were randomly assigned to either the Chinese herb (N = 12) or the placebo group (N = 11) and performed a downhill running (eccentric exercise) trial and a control (seated rest) trial. Results: Muscle soreness increased 1–2 days after exercise similarly in both groups, whereas the herb group demonstrated a faster recovery on active range of motion. Plasma creatine kinase concentration increased significantly at 24 h in both groups but the magnitude of increase was attenuated in the herb group. Arterial stiffness as measured by carotid-femoral pulse wave velocity increased significantly at 24 h in the placebo group but such increase was absent in the herb group. Flow-mediated dilation did not change in either group. Plasma concentrations of CRP and IL-6 increased in the placebo group but no such increases were observed in the herb group. Changes in arterial stiffness induced by eccentric exercise were associated with the corresponding changes in IL-6 (r = 0.46, P < 0.05). Conclusions: A short-term Chinese herb supplementation of panax ginseng and salvia miltiorrhiza ameliorated the delayed onset vascular stiffening induced by acute downhill running exercise. Trial registration: ClinicalTrials.gov: NCT02007304. Registered Dec. 5, 2013) Keywords: muscle damage, inflammation, arterial stiffness Participants A total of 24 apparently healthy young male adults sur- rounding by National Taiwan University community were recruited. Exclusions from the study participation were due to: (1) obesity (BMI >30 kg/m2); (2) smoking within past six months; (3) hypertension (high blood pressure >140/90 mmHg); (4) personal history of dia- betes (fasting blood glucose >126 mg/dL), history of heart disease or other cardiovascular problems; (5) orthopedic injury that may prevent him or her from completing the exercise; or (6) the use of over-the- counter supplements or vitamins. Subjects must have been sedentary or recreational active, but not been par- ticipating in any type of resistance or endurance training. All subjects gave their inform written consent prior to study participation and procedures were reviewed and approved by Institutional Review Board of National Taiwan University Hospital. This study is listed in Clini- calTrial.gov (NCT02007304). Both Chinese herb and placebo capsules were identical in appearance and stored in identical bottles with labeled numbers generated by a study-independent researcher. All supplement products were prepared by the Brion Research Institute, Sun Ten Pharmaceutical Co. Analyses of ginseno- sides of panax ginseng as well as Salvianolic acid B and Background onset muscle soreness. An impairment in microcircula- tion [4, 5], an increase in vascular resistance [6], and a reduction in vascular reactivity [7, 8] have been observed after acute eccentric exercise. We [9] and others [10] have demonstrated that acute eccentric exercise induced significant increases in central arterial stiffness and arter- ial stiffening after eccentric exercise was associated with indicators of muscle damage [9]. Muscle damage induced by unaccustomed or eccentric exercise is associated with increases in oxidative stress, inflammatory response, and delayed onset muscle sore- ness [1]. The increases in circulating pro-inflammatory cytokine and C-reactive protein (CRP) are the character- istic responses induced by eccentric exercise [2, 3]. A growing body of evidence indicates that muscle damage may also exert adverse influences on vascular function a day or two days later on a similar time frame to delayed In Chinese Medicine, Ginseng is one of the most com- monly used herbs in over thousands of years [11]. Ginse- nosides, the major compounds of ginseng, and its metabolites are considered to exert protective effects on the vasculature, acting as a free radical scavenger [12] and increasing nitric oxide production and antioxidant Lin et al. BMC Complementary and Alternative Medicine (2016) 16:168 Page 2 of 10 Page 2 of 10 effects [13]. There have been a number of animal studies demonstrating that supplementation with either Asian ginseng (panax ginseng C. A. Meyer) or American ginseng (panax quinquefolium L.) could protect against eccentric or strenuous exercise-induced muscle damage by attenu- ating CK release [14, 15] and inflammatory responses [16]. Danshen (salvia miltiorrhiza) is another widely used Chinese medicinal herb with diverse pharmacological properties to improve circulation and blood stasis [17], in- cluding dilating coronary arteries, increasing blood flow, and scavenging free radicals in ischemic diseases [18]. In- deed danshen has been prescribed to treat angina pectoris, hyperlipidemia, acute ischemic stroke [19], and coronary heart disease [20]. The major compounds of danshen, Tanshinone IIA and salvianolical acid B, have been shown to suppress vasoconstrictor endothelin-1 production [21] and reduce the expression of vascular adhesion molecules in vitro [22, 23]. Panax ginseng and danshen are often mixed in herb formulas in Chinese medicine, which is characterized by adapting several types of herbs or min- erals as a combination of multiple components that could synergistically attack different pathological targets [24]. Body composition Percent body fat was measured noninvasively by using a bioimpedance analyzer Inbody 2.0 (Biospace Co. Ltd., Seoul, South Korea). To avoid the hydration effects, the test was performed in the morning when subjects were fasted. Supplement administration pp Following the pre-testing sessions, subjects were asked to take a total of 7 capsules of either Chinese herb or placebo per day for seven days. Herb supplement was prepared in capsules consisting of 250 mg of panax ginseng and 250 mg salvia miltiorrhiza via the water-extraction method, whereas placebo capsules contained microcrystal- line cellulose. According to the pharmacopoeia of the Peo- ple’s Republic of China [26], the use of 1–3 g danshen extract per day is recommended [27]. A dosage of 1.75 g per day (~60 % of the maximal suggested dosage) was chosen for danshen in order to avoid unexpected adverse event and to take consideration that this was a combin- ation herb therapy. To the best of our knowledge, a combination of panax ginseng and salvia miltiorrhiza together has not been investigated on humans in the literature [24]. Accordingly, we decided to adopt the 1:1 ratio (i.e., the same dosage) of panax ginseng and salvia miltiorrhiza as the supplementation. Similar to danshen, this particular dosage of panax ginseng has been shown to be effective. Hence, the total daily sup- plementation dosage was 3.5 g together. Background Panax ginseng and danshen has been practiced as a for- mula to treat cardiovascular disease in Chinese Medicine [24, 25]; however, scientific evidence to support its use is still lacking. In this study we tested the hypothesis that the supplementation with a combination of panax ginseng and danshen could exert protective effects on the vascula- ture following eccentric exercise. effects [13]. There have been a number of animal studies demonstrating that supplementation with either Asian ginseng (panax ginseng C. A. Meyer) or American ginseng (panax quinquefolium L.) could protect against eccentric or strenuous exercise-induced muscle damage by attenu- ating CK release [14, 15] and inflammatory responses [16]. Danshen (salvia miltiorrhiza) is another widely used Chinese medicinal herb with diverse pharmacological properties to improve circulation and blood stasis [17], in- cluding dilating coronary arteries, increasing blood flow, and scavenging free radicals in ischemic diseases [18]. In- deed danshen has been prescribed to treat angina pectoris, hyperlipidemia, acute ischemic stroke [19], and coronary heart disease [20]. The major compounds of danshen, Tanshinone IIA and salvianolical acid B, have been shown to suppress vasoconstrictor endothelin-1 production [21] and reduce the expression of vascular adhesion molecules in vitro [22, 23]. Panax ginseng and danshen are often mixed in herb formulas in Chinese medicine, which is characterized by adapting several types of herbs or min- erals as a combination of multiple components that could synergistically attack different pathological targets [24]. Panax ginseng and danshen has been practiced as a for- mula to treat cardiovascular disease in Chinese Medicine [24, 25]; however, scientific evidence to support its use is still lacking. In this study we tested the hypothesis that the supplementation with a combination of panax ginseng and danshen could exert protective effects on the vascula- ture following eccentric exercise. and familiarization. In each group, subjects underwent two familiarization sessions followed by a pre-testing ses- sion that consists of the measurements of aerobic power and body composition. Eccentric exercise trials took place following a 7-day supplementation. Subjects were asked to keep their regular diet and sedentary lifestyle throughout the testing sessions. Aerobic power d d l k Individual peak aerobic power (VO2peak) was determined using standard American College of Sports Medicine protocol. After a 5-min warm-up on the treadmill, sub- jects walked or ran while treadmill slope was increased 1 % every minute until the subjects could not continue the test. A mouthpiece and heart rate monitor were worn to collect expired air and assess heart rate throughout the test. VO2peak was used to set the exercise intensity during the eccentric exercise. Exercise protocol Subjects were instructed to fast at least 8 h and refrain from any strenuous exercise for at least 72 h before the test. Experimental trial consisted of baseline measure- ments, downhill running (eccentric exercise) or seated rest (control), and measurements during the recovery period. In order to eliminate diurnal variation of inflammatory re- sponse to eccentric exercise, participants were asked to perform both eccentric exercise and control trials at the same time of day. Subjects warmed up on treadmill on a level grade at the speed that could elicit 75 % of pre- determined individual VO2peak [29] for 5 min. Each sub- ject performed downhill running exercise on treadmill with the same speed at −10° of slope for 30 min. Similar protocols have been successfully used elsewhere to induce delayed onset muscle soreness [10, 30]. Arterial stiffness Arterial stiffness was measured using carotid-femoral pulse wave velocity (cfPWV), which was calculated from the traveling distance and foot-to-foot wave transit time between the two arterial recording sites in the supine position [33], and was the primary outcome measure of this study. Non-invasive pulse tonometer (SPT-301, Millar Inc. Houston TX) connected to a physiological signaling processing system (MP36, Biopac, Goleta CA) was used to detect pulse waves on the carotid and fem- oral arteries. The coefficient of variation for cfPWV in our laboratory were 6.2 %. Measurements The measurements were made 5 times: 30 min pre, 90 min post, 24 h post, 48 h post, and 72 h post. Sub- jects were studied at the same time of day, during the morning hours to minimize the inconvenience of the 8- h fast and to avoid diurnal effects. Blood samples were collected to determine metabolic risk factors, markers of muscle damage, inflammation, and redox state. Serum CK was used as an indicator of muscle membrane permeability or muscle damage [31]. Inflammatory markers (TNF-α, IL-6) as well as blood redox status marker, tiobarbituric acid-reactive substances (TBARS), were analyzed with the use of commercial ELISA kits. Due to the financial constraints, TNF-α, IL-6, and TBARS were measured only in the eccentric exercise condition. The inter- and intra-assay coefficients of vari- ation were less than 10 % in all assays performed. Experimental design Subjects were randomly assigned into either the Chinese herb supplement or the placebo group after pre-screening Lin et al. BMC Complementary and Alternative Medicine (2016) 16:168 Lin et al. BMC Complementary and Alternative Medicine (2016) 16:168 Lin et al. BMC Complementary and Alternative Medicine (2016) 16:168 Page 3 of 10 and blood pressure was measured using an automatic blood pressure monitor (Omron HEM907). Tanshinone IIA in Radix salvia miltiorrhiza were per- formed by using high-performance liquid chromatography- electrospray mass (HPLC-MS) spectrometry method as previously described [26, 28]. These chromatographic quantification results of active compounds in herb supple- ment are shown in Table 1 and Fig. 1. Tanshinone IIA in Radix salvia miltiorrhiza were per- formed by using high-performance liquid chromatography- electrospray mass (HPLC-MS) spectrometry method as previously described [26, 28]. These chromatographic quantification results of active compounds in herb supple- ment are shown in Table 1 and Fig. 1. Muscle soreness Subjects were asked to rate the perception of muscle soreness using a Visual Analog Scale of 0–10 with 0 de- scribing no soreness and 10 describing unbearable sore- ness immediately after a downhill running [32]. In addition, active range of motion was measured while the subjects were placed on bed in prone position with full knee extension and then moved both legs gradually to the flexion point where pain in quadriceps muscle groups was experienced. A manual goniometer was used to measure the knee angle difference from full extension to flexion point with the initiation of pain. This test was repeated three times, and the average was used for stat- istical analysis. Vascular reactivity Flow-mediated dilatation, the secondary outcome meas- ure, was obtained noninvasively at the brachial artery using standardized procedure [34]. Brachial artery diam- eter was measured using an ultrasound machine (Sonosite Ultrasound System; Bothell, WA) equipped with a high- resolution linear array transducer. A blood pressure cuff was placed on the forearm 3–5 cm distal to the antecubi- tal fossa, and longitudinal images of the brachial artery were acquired 5–10 cm proximal to the antecubital fossa. After the acquisition of baseline measurement, the probe position was clearly marked to ensure that the image was acquired from the same location throughout the test. The blood pressure cuff was inflated to 100 mmHg above resting systolic blood pressure for 5 min by using a cus- tomized rapid inflation system. After cuff deflation, ultrasound-derived measurements of artery diameters were taken for 3 min. FMD was calculated by the follow- ing equation: (maximum diameter – baseline diameter)/ baseline diameter × 100. All ultrasound images were re- corded and analyzed by the same investigator who was blinded to the groups and the conditions. Our coefficient Heart rate and blood pressure were measured in the supine position. Heart rate was measured using an ECG, Table 1 Quantitative analyses of major compounds of the herb supplement used in the present study Compound Content (mg/g) Panax ginseng Rb1 2.24 Re 1.13 Rg1 1.47 Salvia miltiorrhiza Salvianolia acid B 28.2 Tanshinone IIA 0.6 Table 1 Quantitative analyses of major compounds of the herb supplement used in the present study Lin et al. BMC Complementary and Alternative Medicine (2016) 16:168 Page 4 of 10 of variation of baseline diameter, maximal diameter, and FMD in our laboratory were 3.7, 4.0, and 14 %. 0.05) and accounting for a 10 % attrition rate, a total of 24 subjects were to be recruited and tested. Fig. 1 High-performance thin-layer chromatography fingerprints of Panax ginseng (a) and Salvia miltiorrhiza (b) f f b l d l d d ) d f l f Fig. 1 High-performance thin-layer chromatography fingerprints of Panax ginseng (a) and Salvia miltiorrhiza (b) 0.05) and accounting for a 10 % attrition rate, a total of 24 subjects were to be recruited and tested. of variation of baseline diameter, maximal diameter, and FMD in our laboratory were 3.7, 4.0, and 14 %. Results Allocation to the herb or placebo supplementation was based on a computer-generated randomization list that was prepared by a study-independent researcher. Block- randomization with a block size of four was used; the group assignment was concealed in an envelope and re- vealed after all data analysis was performed. During study, researchers were blinded and unaware of subjects’ allocation. Subjects were instructed not to reveal any in- formation regarding supplement and exercise treatment during intervention. After screening, twenty-four subjects were eligible and entered into the study (Fig. 2); one subject withdrew from the study during intervention due to time commit- ment unrelated to the study. Selected subject character- istics are presented in Table 2. All the subjects were non-obese, normolipidemic, and normotensive. There were no significant differences in body composition, lipid profile, and baseline hemodynamic parameters be- tween the placebo and the Chinese herb groups. An acute bout of downhill running exercise increased muscle soreness significantly at 90 min, 24 and 48 h post exercise (Fig. 3). Active range of motion decreased sig- nificantly at 24 and 48 h post exercise in both groups, but remained significant at 72 h in the placebo group (Fig. 3). As shown in Fig. 4, the magnitude of the in- crease in plasma CK concentration was significantly greater in the placebo group than in the herb group. Statistical analyses Descriptive statistics were used for the analyses of subject characteristics using SPSS statistical package (version 16.0; Chicago, IL). Dependent variables were analyzed within each treatment to determine the time effect (pre, 90 min, 24 h, 48 h, and 72 h post exercise) using repeated mea- sures ANOVA. A 2-way mixed model ANOVA was used for analyses of time and treatment effects. Bonferroni post-hoc analysis was performed when significance was achieved. Associations were determined by Spearman rank correlations. To detect difference in cfPWV of 5 % at a SD of 4.5 % unit change with 80 % power (α was set at An acute bout of eccentric exercise increased cfPWV at 24 h post exercise in the placebo group (Fig. 5). No such significant increase in cfPWV was observed in the herb group. There were no changes in blood pressure in either group (Table 3). As shown in Fig. 6, there were no significant changes in FMD. Lin et al. BMC Complementary and Alternative Medicine (2016) 16:168 Page 5 of 10 Fig. 2 Study flow chart with changes in cfPWV at 24 to 48 h after exercise (r = 0.57 ~ 0.60, P < 0.05). Plasma CRP concentration increased significantly at 24 h post eccentric exercise in both groups (Table 4). Plasma TBARs and TNF-α concentrations did not change in either group. Plasma IL-6 concentration in- creased significantly at 90 min after eccentric exercise in the placebo group. Discussion The major findings of this study are as follows. Seven days of herb supplementation of panax ginseng and salvia miltiorrhiza prior to downhill running exercise did not affect muscle soreness, but prevented the significant and transient increase in arterial stiffness, and facilitated the recovery of active range of motion induced by muscle damage. This "destiffening" effect was independent of blood The associations between changes in cfPWV and changes in selected biomarkers in combined groups are shown in Table 5. Changes in IL-6 were associated with changes in cfPWV at 48 h post exercise (r = 0.46, P < 0.05). In addition, changes in TNF-α were associated Lin et al. BMC Complementary and Alternative Medicine (2016) 16:168 Page 6 of 10 Page 6 of 10 Table 2 Selected subject characteristics Placebo Herb (n = 11) (n = 12) Age, yr 24 ± 1 26 ± 5 Height, cm 173 ± 1 174 ± 3 Body mass, kg 68 ± 2 68 ± 3 BMI, kg/m2 23 ± 1 22 ± 1 Body fat percentage, % 19 ± 1 18 ± 2 Waist-hip ratio 0.85 ± 0.01 0.85 ± 0.01 Heart rate at rest, bpm 67 ± 3 58 ± 3 Systolic BP, mmHg 118 ± 2 112 ± 3 Diastolic BP, mmHg 66 ± 2 62 ± 2 VO2peak, ml/kg/min 47 ± 2 47 ± 2 HDL cholesterol, mg/dL 53 ± 2 53 ± 3 LDL cholesterol, mg/dL 97 ± 9 86 ± 5 Total cholesterol, mg/dL 180 ± 9 192 ± 8 Triglyceride, mg/dL 78 ± 9 58 ± 8 HbA1C, % 5.4 ± 0.1 5.4 ± 0.1 Values are means ± SEM BMI body mass index, BP blood pressure, VO2peak peak oxygen consumption, HbA1c glycosylated hemoglobin A1c Table 2 Selected subject characteristics the placebo group at 24 h post exercise than in the herb group. Previous studies in animal models reported that North American ginseng, panax ginseng or panax quinque- folus, decreased plasma CK levels after eccentric exercise [15, 37] and preserved mitochondria integrity [14] and de- creased macrophage infiltration [16] in skeletal muscle. One recent human study [38] also found that American ginseng decreased CK concentration at 72 h post exercise when compared with the placebo control. Collectively, these results suggest that Chinese herb supplementa- tion may have reduced the amount of muscle damage induced by eccentric exercise. Discussion Pre in the same condition Lin et al. BMC Complementary and Alternative Medicine (2016) 16:168 Page 7 of 10 Table 3 Hemodynamic responses in control (seated rest) and eccentric exercise sessions Pre 90 min 24 h 48 h 72 h cfPWV, cm/s Placebo Control 530 ± 19 535 ± 17 546 ± 16 547 ± 15 513 ± 13 Exercise 531 ± 12 548 ± 19 577 ± 20* 570 ± 24 552 ± 22 Herb Control 482 ± 14 491 ± 17 490 ± 14 487 ± 13 505 ± 19 Exercise 523 ± 20 497 ± 17 503 ± 16 500 ± 13 505 ± 23 Heart rate, bpm Placebo Control 63 ± 4 58 ± 3 62 ± 3 66 ± 3 65 ± 3 Exercise 62 ± 3 69 ± 4* 66 ± 3 63 ± 3 59 ± 5 Herb Control 57 ± 3 54 ± 1 56 ± 3 59 ± 4 55 ± 3 Exercise 56 ± 2 65 ± 4* 56 ± 3 55 ± 2 53 ± 3 Systolic BP, mmHg Placebo Control 119 ± 2 116 ± 2 118 ± 2 119 ± 2 119 ± 2 Exercise 119 ± 2 114 ± 2 120 ± 2 120 ± 3 117 ± 2 Herb Control 114 ± 2 111 ± 2 114 ± 2 115 ± 3 115 ± 2 Exercise 116 ± 3 114 ± 3 115 ± 2 112 ± 2 111 ± 3 Diastolic BP, mmHg Placebo Control 66 ± 2 67 ± 1 67 ± 2 64 ± 2 67 ± 2 Exercise 66 ± 3 65 ± 2 65 ± 3 66 ± 2 64 ± 2 Herb Control 63 ± 3 63 ± 1 62 ± 2 62 ± 1 62 ± 1 Exercise 63 ± 3 61 ± 2 62 ± 1 63 ± 3 60 ± 1 Pulse pressure, mmHg Placebo Control 52 ± 2 49 ± 1 51 ± 2 55 ± 2 53 ± 2 Exercise 53 ± 2 48 ± 2 55 ± 2 53 ± 2 53 ± 1 Herb Control 51 ± 3 48 ± 3 52 ± 3 54 ± 3 53 ± 3 Exercise 53 ± 3 52 ± 3 53 ± 2 49 ± 3 51 ± 3 Values are means ± SEM cfPWV carotid-femoral pulse wave velocity, BP blood pressure *P<0.05 vs. Discussion In the present study, arterial stiffening effects were at- tenuated when the subjects were supplemented with Chinese herbs for 7 days before the unaccustomed exer- cise was performed. These effects were not related to changes in blood pressure in either group. To our know- ledge, this is the first study to demonstrate that Chinese herb supplementation effectively prevented the adverse effects on vascular stiffening induced by eccentric exer- cise. Specifically, downhill running increased arterial stiffness significantly as early as 24 h after the eccentric exercise in the placebo group. In the previous study [10] including ours [9], the increase in arterial stiffness was somewhat delayed showing up at 48 h after exercise. The exact reasons for the slight differences in the time course are not known. But compared with our previous study [9] that used localized resistance exercise as an eccentric stimulus, in the present study, we used more systemic downhill running exercise that elicit greater and more robust responses [39]. Moreover, compared with the previous study that utilized moderately-trained young adults [10], the subjects in the current study were mainly sedentary adults. Current literature indicates that people who repeatedly perform eccentric muscle contrac- tions demonstrate so-called “repeated bout effect” or adap- tation in skeletal muscle that inflammatory and muscle biomarker responses were substantially lowered in the pressure changes as arterial pressure did not change in either group. A lack of changes in arterial stiffness with the herb supplementation was in part associated with the attenuated increases in inflammatory markers. These results suggest that the Chinese herb supplementation may be an effective strategy to minimize the delayed onset vascular stiffening induced by eccentric exercise. The presence of elevated plasma CK has been recognized a marker of increased sarcolemma permeability or muscle damage resulted from unaccustomed exercise or eccentric muscle contractions [31, 35, 36]. In the present study, an acute bout of downhill running exercise increased plasma CK concentration significantly following eccentric exercise. The increase in plasma CK concentration was greater in on (AROM) (b) following downhill running exercise. *P < 0.05 vs. Pre in the Fig. 3 Delayed onset muscle soreness (a) and active range of motion (AROM) (b) following downhill running exercise. *P < 0.05 vs. Pre in the same condition Fig. 3 Delayed onset muscle soreness (a) and active range of motion (AROM) (b) following downhill running exercise. *P < 0.05 vs. Discussion BMC Complementary and Alternative Medicine (2016) 16:168 Page 8 of 10 Page 8 of 10 d h h d h l Table 4 Changes in muscle damage markers, inflammatory and oxidative stress markers in response to downhill running exercise in the placebo and herb group Pre 90 min 24 h 48 h 72 h Placebo CRP, mg/dL Control 0.07 ± 0.04 0.07 ± 0.04 0.07 ± 0.03 0.06 ± 0.02 0.05 ± 0.02 Exercise 0.08 ± 0.02 0.11 ± 0.05 0.15 ± 0.05* 0.11 ± 0.05 0.10 ± 0.03 CK, U/L Control 94 ± 10 98 ± 8 89 ± 8 87 ± 9 90 ± 11 Exercise 93 ± 8 126 ± 13 396 ± 72*, ** 257 ± 48*, ** 192 ± 32* Herb CRP, mg/dL Control 0.13 ± 0.05 0.14 ± 0.05 0.11 ± 0.04 0.11 ± 0.04 0.11 ± 0.03 Exercise 0.10 ± 0.03 0.09 ± 0.03 0.15 ± 0.03* 0.10 ± 0.02 0.10 ± 0.02 CK, U/L Control 110 ± 12 108 ± 9 119 ± 17 109 ± 11 113 ± 16 Exercise 106 ± 9 195 ± 51* 291 ± 35*, ** 204 ± 26*, ** 151 ± 20 TBARs, μM Placebo 7.1 ± 1.1 8.1 ± 1.5 7.9 ± 1.0 6.5 ± 1.0 - Herb 7.0 ± 1.0 6.6 ± 0.8 8.1 ± 0.9 5.7 ± 0.6 - IL-6, pg/ml Placebo 0.44 ± 0.1 0.69 ± 0.1* 0.32 ± 0.1 0.46 ± 0.1 - Herb 0.50 ± 0.2 0.45 ± 0.1 0.23 ± 0.1* 0.29 ± 0.1 - TNF-α, pg/ml Placebo 0.45 ± 0.14 0.28 ± 0.06 0.30 ± 0.06 0.30 ± 0.06 - Herb 0.44 ± 0.06 0.34 ± 0.06 0.38 ± 0.08 0.34 ± 0.06 - Values are means ± SEM. TBARs, IL-6, and TNF-α were measured only during the eccentric exercise session CRP C-reactive protein, CK creatine kinase, TBARs thiobarbituric acid reactive substances, IL-6 interleukin-6, TNF-α tumor necrosis factor-α *P<0.05 vs. Pre in the same condition. **P<0.05 vs. Control or Placebo at the same time point minimized the arterial stiffening effects. Our present results using Chinese herbs as “cocktail” anti-oxidants are in ac- cordance with a previous study [43] that supplementation with the mixture of vitamins C and E attenuated the IL-6 mRNA expression and CRP response to long-duration muscle contractions in humans. In addition to central arterial stiffness, endothelium- dependent vascular reactivity was also measured in this study. Discussion Eccentric resistance exercise has been shown to im- pair FMD and linked with the increase in reactive oxygen species and a subsequent reduction in NO [7, 8]. In the present study, however, there were no significant reduc- tions in FMD in either the placebo or the herb group. The increases in oxidative stress and inflammation have been documented in association with endothelial dysfunction [44, 45], and anti-oxidant status could play a role in modulating vascular function after eccentric exercise [46]. There were significant increases in inflammatory markers after eccentric exercise in the present study. However, FMD did not change. The discrepancy between our find- ings and others could be attributed to the difference in ex- ercise mode and measured time points. Acute resistance exercise [47, 48] has been shown to reduce FMD, whereas FMD increases after an acute bout of aerobic exercise [49, 50]. The present study utilized acute downhill run- ning exercise as a mode of eccentric exercise. FMD is also known to display biphasic response after acute exercise in that FMD decreases immediately but increases 1 to 24 h following exercise and reversed to the baseline in 48 h [46]. In the study [7] that found reductions in FMD after eccentric resistance exercise, measurements were made 45 min after exercise. We performed the measurement of FMD at 90 min post exercise. Additionally, the differ- ence in subject characteristics may be another factor since FMD may respond differently following exercise in people of different physical fitness levels [46, 50]. associated with the corresponding changes in plasma IL- 6 concentrations after 48 h post exercise. It is possible to speculate that the supplementation using panax ginseng and salvia miltiorrhiza reduced systemic inflammation induced by eccentric exercise and through such effect, There are a number of limitations in the present study that should be mentioned. First, the number of subjects studied is relatively small. Second, even though pharmaco- logical compounds of panax ginseng and salvia miltior- rhiza were identified, it is unknown which compound of the herb supplementation was effective. Additionally, pharmacological interactions between the compounds are also unknown. Lastly, correlations between inflammatory markers and arterial stiffness were found only at selected time points. Additionally, some inflammatory markers (e.g., TNF- α) did not change with eccentric exercise. Thus, the associations should be interpreted with caution. Discussion Pre in the same condition Fig. 4 Relative changes in serum creatine kinase (CK) concentration in response to eccentric exercise sessions. *P < 0.05 vs. Pre in the same condition. †P < 0.05 vs. Placebo at the same time point Table 3 Hemodynamic responses in control (seated rest) and eccentric exercise sessions Fig. 4 Relative changes in serum creatine kinase (CK) concentration in response to eccentric exercise sessions. *P < 0.05 vs. Pre in the same condition. †P < 0.05 vs. Placebo at the same time point following challenge [1], suggesting that exercise training status plays a role in determining the response to this exer- cise challenge. The underlying mechanisms by which muscle damage induced by eccentric exercise results in increased arterial stiffness remain unclear. However, arterial stiffening follow- ing eccentric exercise has been associated with increases in subjective muscle soreness [10], a marker of muscle dam- age (i.e., plasma CK) [9]. In the present study, plasma IL-6 levels increased significantly after eccentric exercise in the placebo group. Previous studies have demonstrated that the acute inflammation induced by a vaccination increased not only IL-6 and CRP concentrations [40, 41] but also ar- terial stiffness [42]. Collectively, these results suggest that arterial stiffening induced by muscle damage is associated with markers of muscle damage and/or systemic inflammation. Consistent with this concept, we found that Chinese herb supplementation minimized the increases in IL-6 levels. Additionally, changes in arterial stiffness were Fig. 5 Effects of Chinese herb supplementation on carotid-femoral pulse wave velocity (cfPWV). *P < 0.05 vs. Pre. †P < 0.05 vs. Herb supplementation Fig. 6 Changes in flow-mediated vasodilatation in response to the eccentric exercise Fig. 5 Effects of Chinese herb supplementation on carotid-femoral pulse wave velocity (cfPWV). *P < 0.05 vs. Pre. †P < 0.05 vs. Herb supplementation Fig. 5 Effects of Chinese herb supplementation on carotid-femoral pulse wave velocity (cfPWV). *P < 0.05 vs. Pre. †P < 0.05 vs. Herb supplementation Fig. 6 Changes in flow-mediated vasodilatation in response to the eccentric exercise Fig. 5 Effects of Chinese herb supplementation on carotid-femoral pulse wave velocity (cfPWV). *P < 0.05 vs. Pre. †P < 0.05 vs. Herb supplementation Fig. 6 Changes in flow-mediated vasodilatation in response to the eccentric exercise Lin et al. Discussion Table 5 Associations between relative changes (%) in arterial stiffness and selected biomarkers ΔcfPWV 24 h ΔcfPWV 48 h ΔCK 0.05 0.08 CRP 0.17 0.21 ΔIL-6 0.11 0.46* ΔTNF-α 0.60* 0.57* ΔTBARs 0.09 0.36 cfPWV carotid-femoral pulse wave velocity, CK creatine kinase, CRP C-reactive protein, IL-6 interlukin-6, TNF-α tumor necrosis factor-α, TBARs thiobarbituric acid reactive substances *P<0.05 Table 5 Associations between relative changes (%) in arterial Funding h d 11. Yue PY, Mak NK, Cheng YK, Leung KW, Ng TB, Fan DT, Yeung HW, Wong RN. Pharmacogenomics and the yin/yang actions of ginseng: anti-tumor, angiomodulating and steroid-like activities of ginsenosides. Chin Med. 2007;2:6 g This study was supported by a research grant from the Ministry of Science and Technology in Taiwan (MOST-101-2410-H-002-201-MY2 and MOST 103-2410-H-002 -196 -MY2). 12. Kang KS, Yokozawa T, Kim HY, Park JH. Study on the nitric oxide scavenging effects of ginseng and its compounds. J Agric Food Chem. 2006;54(7):2558–62. Authors’ contributions 15. Estaki M, Noble EG. North American ginseng protects against muscle damage and reduces neutrophil infiltration after an acute bout of downhill running in rats. Appl Physiol Nutr Metab. 2015;40(2):116–21. Study concept and design: HL, HT, CL, JL; data collection: HL, TK, CC; data analysis: HL, TK, CC, CL; data interpretation: HL, TK, JL, HT; manuscript drafting: HL, HT; revising manuscript critically for important intellectual content: HL, TK, CC, CL, JL. HT. All authors have read, edited, approved the final manuscript, and have agreed to be held accountable for all aspects of manuscript in ensuring that questions related to the accuracy or integrity of any part of manuscript are appropriately investigated and resolved. 16. Yu SH, Huang CY, Lee SD, Hsu MF, Wang RY, Kao CL, Kuo CH. Decreased eccentric exercise-induced macrophage infiltration in skeletal muscle after supplementation with a class of ginseng-derived steroids. PLoS One. 2014; 9(12):e114649. 17. Han JY, Fan JY, Horie Y, Miura S, Cui DH, Ishii H, Hibi T, Tsuneki H, Kimura I. Ameliorating effects of compounds derived from salvia miltiorrhiza root extract on microcirculatory disturbance and target organ injury by ischemia and reperfusion. Pharmacol Ther. 2008;117(2):280–95. 17. Han JY, Fan JY, Horie Y, Miura S, Cui DH, Ishii H, Hibi T, Tsuneki H, Kimura I. Ameliorating effects of compounds derived from salvia miltiorrhiza root extract on microcirculatory disturbance and target organ injury by ischemia and reperfusion. Pharmacol Ther. 2008;117(2):280–95. Availability of data and materials 13. Lu JM, Yao Q, Chen C. Ginseng compounds: an update on their molecular mechanisms and medical applications. Curr Vasc Pharmacol. 2009;7(3):293–302. The datasets supporting the conclusions of this article are presented in this paper. 14. de Oliveira AC C, Perez AC, Prieto JG, Duarte ID, Alvarez AI. Protection of Panax ginseng in injured muscles after eccentric exercise. J Ethnopharmacol. 2005;97(2):211–4. Ethics approval and consent to participate 20. Cheng TO. Danshen: a versatile Chinese herbal drug for the treatment of coronary heart disease. Int J Cardiol. 2006;113(3):437–8. All subjects gave their written informed consent prior to study participation and procedures were reviewed and approved by the Institutional Review Board of National Taiwan University Hospital. 21. Tang C, Wu AH, Xue HL, Wang YJ. Tanshinone IIA inhibits endothelin-1 production in TNF-alpha-induced brain microvascular endothelial cells through suppression of endothelin-converting enzyme-1 synthesis. Acta Pharmacol Sin. 2007;28(8):1116–22. Consent for publication Consent for publication Not applicable. 19. Zhou L, Zuo Z, Chow MS. Danshen: an overview of its chemistry, pharmacology, pharmacokinetics, and clinical use. J Clin Pharmacol. 2005;45(12):1345–59. Received: 17 September 2015 Accepted: 25 May 2016 25. Liang X, Chen X, Wang Y, Liang Q, Wu J, Luo G. Effect of compatibilities and proportions of Shuanglong formula on acute myocardial infarction in rats. Zhongguo Zhong Yao Za Zhi. 2011;36(22):3176–9. Conclusions A short-term Chinese herb supplementation incorporat- ing panax ginseng and salvia miltiorrhiza was effective in ameliorating the delayed onset vascular stiffening Lin et al. BMC Complementary and Alternative Medicine (2016) 16:168 Page 9 of 10 Page 9 of 10 induced by acute eccentric exercise, possibly via the re- ductions in oxidative stress and systemic inflammation. induced by acute eccentric exercise, possibly via the re- ductions in oxidative stress and systemic inflammation. 5. Kano Y, Sampei K, Matsudo H. Time course of capillary structure changes in rat skeletal muscle following strenuous eccentric exercise. Acta Physiol Scand. 2004;180(3):291–9. 6. Ray CA, Mahoney ET, Hume KM. Exercise-induced muscle injury augments forearm vascular resistance during leg exercise. Am J Physiol. 1998;275(2 Pt 2):H443–7. Abbreviations BMI, body mass index; BP, blood pressure; cfPWV, carotid-femoral pulse wave velocity; CK, creatine kinase; CRP, C-reactive protein; HbA1c, glycosylated hemoglobin A1c; IL-6, interleukin-6; TBARs, thiobarbituric acid reactive substances; TNF-α, tumor necrosis factor-α; VO2peak, peak oxygen consumption 7. Choi Y, Akazawa N, Miyaki A, Ra SG, Shiraki H, Ajisaka R, Maeda S. Acute effect of high-intensity eccentric exercise on vascular endothelial function in young men. J Strength Cond Res. In press. 7. Choi Y, Akazawa N, Miyaki A, Ra SG, Shiraki H, Ajisaka R, Maeda S. Acute effect of high-intensity eccentric exercise on vascular endothelial function in young men. J Strength Cond Res. In press. y 8. Franklin NC, Ali MM, Robinson AT, Norkeviciute E, Phillips SA. Massage therapy restores peripheral vascular function after exertion. Arch Phys Med Rehabil. 2014;95(6):1127–34. 8. Franklin NC, Ali MM, Robinson AT, Norkeviciute E, Phillips SA. Massage therapy restores peripheral vascular function after exertion. Arch Phys Med Rehabil. 2014;95(6):1127–34. Competing interests The authors declare that they have no competing interests. 18. Ji XY, Tan BK, Zhu YZ. Salvia miltiorrhiza and ischemic diseases. Acta Pharmacol Sin. 2000;21(12):1089–94. Acknowledgements We would like to thank Han-Jen Lin from Molecular Biology Laboratory in De- partment of Animal Science of National Taiwan University, Dr. Hao-Min Cheng and Dr. Chen-Huan Chen from Taipei Veterans General Hospital for their technical assistance on biomarker and hemodynamic analysis. 9. Barnes JN, Trombold JR, Dhindsa M, Lin HF, Tanaka H. Arterial stiffening following eccentric exercise-induced muscle damage. J Appl Physiol. 2010;109(4):1102–8. 10. Burr JF, Boulter M, Beck K. Arterial stiffness results from eccentrically biased downhill running exercise. J Sci Med Sport. 2015;18(2):230–5. 10. Burr JF, Boulter M, Beck K. Arterial stiffness results from eccentrically biased downhill running exercise. J Sci Med Sport. 2015;18(2):230–5. Author details 1 f 1Department of Athletics, National Taiwan University, Taipei, Taiwan. 2Department of Physical Education, National Taiwan Normal University, Taipei, Taiwan. 3Physical Education Office, National Taipei University of Technology, Taipei, Taiwan. 4Brion Research Institute, Taipei, Taiwan. 5School of Chinese Medicine, China Medical University, Taichung City, Taiwan. 6Department of Kinesiology and Health Education, The University of Texas at Austin, 2109 San Jacinto Blvd, D3700, Austin, TX 78712, USA. 22. Tang C, Xue HL, Bai CL, Fu R. Regulation of adhesion molecules expression in TNF-α-stimulated brain microvascular endothelial cells by Tanshinone Iia: Involvement of NF-κb and ROS generation. Phytother Res. 2011;25(3):376–80. 23. Chen YH, Lin SJ, Ku HH, Shiao MS, Lin FY, Chen JW, Chen YL. Salvianolic acid B attenuates VCAM-1 and ICAM-1 expression in TNF-alpha-treated human aortic endothelial cells. J Cell Biochem. 2001;82(3):512–21. 24. Liang X, Chen X, Liang Q, Zhang H, Hu P, Wang Y, Luo G. Metabonomic study of Chinese medicine Shuanglong formula as an effective treatment for myocardial infarction in rats. J Proteome Res. 2011;10(2):790–9. References 1. Peake J, Nosaka K, Suzuki K. Characterization of inflammatory responses to eccentric exercise in humans. Exerc Immunol Rev. 2005;11:64–85. 2. Toft AD, Jensen LB, Bruunsgaard H, Ibfelt T, Halkjaer-Kristensen J, Febbraio M, Pedersen BK. Cytokine response to eccentric exercise in young and elderly humans. Am J Physiol Cell Physiol. 2002;283(1):C289–95. 3. Bruunsgaard H, Galbo H, Halkjaer-Kristensen J, Johansen TL, MacLean DA, Pedersen BK. Exercise-induced increase in serum interleukin-6 in humans is related to muscle damage. J Physiol. 1997;499(Pt 3):833–41. 4. Kano Y, Padilla DJ, Behnke BJ, Hageman KS, Musch TI, Poole DC. Effects of eccentric exercise on microcirculation and microvascular oxygen pressures in rat spinotrapezius muscle. J Appl Physiol. 2005;99(4):1516–22. References Age-related loss of associations between acute exercise-induced Il-6 and oxidative stress. Am J Physiol Endocrinol Metab. 2006;291(2):E340–9. 32. Clarkson PM, Tremblay I. Exercise-induced muscle damage, repair, a adaptation in humans. J Appl Physiol. 1988;65(1):1–6. 33. Tanaka H, DeSouza CA, Seals DR. Absence of age-related increase in central arterial stiffness in physically active women. Arterioscler Thromb Vasc Biol. 1998;18(1):127–32. 34. Corretti MC, Anderson TJ, Benjamin EJ, Celermajer D, Charbonneau F, Creager MA, Deanfield J, Drexler H, Gerhard-Herman M, Herrington D. Guidelines for the ultrasound assessment of endothelial-dependent flow- mediated vasodilation of the brachial artery: a report of the international brachial artery reactivity task force. J Am Coll Cardiol. 2002;39(2):257–65. 35. Baird MF, Graham SM, Baker JS, Bickerstaff GF. Creatine-kinase- and exercise- related muscle damage implications for muscle performance and recovery. J Nutr Metab. 2012;2012:960363. 36. Armstrong RB, Ogilvie RW, Schwane JA. Eccentric exercise-induced injury to rat skeletal muscle. J Appl Physiol. 1983;54(1):80–93. 37. de Oliveira AC C, Perez AC, Merino G, Prieto JG, Alvarez AI. Protective effects of Panax ginseng on muscle injury and inflammation after eccentric exercise. Comp Biochem Physiol C Toxicol Pharmacol. 2001;130(3):369–77. 38. Jung HL, Kwak HE, Kim SS, Kim YC, Lee CD, Byurn HK, Kang HY. Effects of Panax ginseng supplementation on muscle damage and inflammation after uphill treadmill running in humans. Am J Chin Med. 2011;39(3):441–50. 39. Lin HF, Chou CC, Cheng HM, Tanaka H. Delayed onset vascular stiffening induced by eccentric resistance exercise and downhill running. Clin J Sport Med. In press. 40. Vlachopoulos C, Dima I, Aznaouridis K, Vasiliadou C, Ioakeimidis N, Aggeli C, Toutouza M, Stefanadis C. Acute systemic inflammation increases arterial stiffness and decreases wave reflections in healthy individuals. Circulation. 2005;112(14):2193–200. 41. Jae SY, Yoon ES, Jung SJ, Jung SG, Park SH, Kim BS, Heffernan KS, Fernhall B. Effect of cardiorespiratory fitness on acute inflammation induced increases in arterial stiffness in older adults. Eur J Appl Physiol. 2013;113(8):2159–66. 41. Jae SY, Yoon ES, Jung SJ, Jung SG, Park SH, Kim BS, Heffernan KS, Fernhall B. Effect of cardiorespiratory fitness on acute inflammation induced increases in arterial stiffness in older adults. Eur J Appl Physiol. 2013;113(8):2159–66. 42. Yasmin, McEniery CM, Wallace S, Mackenzie IS, Cockcroft JR, Wilkinson IB. C-reactive protein is associated with arterial stiffness in apparently healthy individuals. Arterioscler Thromb Vasc Biol. 2004;24(5):969–74. 42. Yasmin, McEniery CM, Wallace S, Mackenzie IS, Cockcroft JR, Wilkinson IB. References 26. China Pharmacopoeia Commission. Pharmacopoeia of the People’s Republic of China (Part I). Beijing: Chemical lndustry Press; 2010. 1. Peake J, Nosaka K, Suzuki K. Characterization of inflammatory responses to eccentric exercise in humans. Exerc Immunol Rev. 2005;11:64–85. 2. Toft AD, Jensen LB, Bruunsgaard H, Ibfelt T, Halkjaer-Kristensen J, Febbraio M, Pedersen BK. Cytokine response to eccentric exercise in young and elderly humans. Am J Physiol Cell Physiol. 2002;283(1):C289–95. 3. Bruunsgaard H, Galbo H, Halkjaer-Kristensen J, Johansen TL, MacLean DA, Pedersen BK. Exercise-induced increase in serum interleukin-6 in humans is related to muscle damage. J Physiol. 1997;499(Pt 3):833–41. 4. Kano Y, Padilla DJ, Behnke BJ, Hageman KS, Musch TI, Poole DC. Effects of eccentric exercise on microcirculation and microvascular oxygen pressures in rat spinotrapezius muscle. J Appl Physiol. 2005;99(4):1516–22. 1. Peake J, Nosaka K, Suzuki K. Characterization of inflammatory responses to eccentric exercise in humans. Exerc Immunol Rev. 2005;11:64–85. 27. van Poppel PC, Breedveld P, Abbink EJ, Roelofs H, van Heerde W, Smits P, Lin W, Tan AH, Russel FG, Donders R, et al. Salvia miltiorrhiza root water-extract (danshen) has no beneficial effect on cardiovascular risk factors. A randomized double-blind cross-over trial. PLoS One. 2015; 10(7):e0128695. 2. Toft AD, Jensen LB, Bruunsgaard H, Ibfelt T, Halkjaer-Kristensen J, Febbraio M, Pedersen BK. Cytokine response to eccentric exercise in young and elderly humans. Am J Physiol Cell Physiol. 2002;283(1):C289–95. 3. Bruunsgaard H, Galbo H, Halkjaer-Kristensen J, Johansen TL, MacLean DA, Pedersen BK. Exercise-induced increase in serum interleukin-6 in humans is related to muscle damage. J Physiol. 1997;499(Pt 3):833–41. 28. Hu P, Luo GA, Zhao Z, Jiang ZH. Quality assessment of radix Salviae miltiorrhizae. Chem Pharm Bull (Tokyo). 2005;53(5):481–6. 4. Kano Y, Padilla DJ, Behnke BJ, Hageman KS, Musch TI, Poole DC. Effects of eccentric exercise on microcirculation and microvascular oxygen pressures in rat spinotrapezius muscle. J Appl Physiol. 2005;99(4):1516–22. 29. American College of Sports Medicine. ACSM’s guidelines for exercise testing and prescription. Baltimore: Lippincott Williams & Wilkins; 2006. Page 10 of 10 Lin et al. BMC Complementary and Alternative Medicine (2016) 16:168 Lin et al. BMC Complementary and Alternative Medicine (2016) 16:168 30. Peake JM, Suzuki K, Wilson G, Hordern M, Nosaka K, Mackinnon L, Coombes JS. Exercise-induced muscle damage, plasma cytokines, and markers of neutrophil activation. Med Sci Sports Exerc. 2005;37(5):737–45. 31. Sacheck JM, Cannon JG, Hamada K, Vannier E, Blumberg JB, Roubenoff R. Lin et al. BMC Complementary and Alternative Medicine (2016) 16:168 References C-reactive protein is associated with arterial stiffness in apparently healthy individuals. Arterioscler Thromb Vasc Biol. 2004;24(5):969–74. 43. Fischer CP, Hiscock NJ, Penkowa M, Basu S, Vessby B, Kallner A, Sjoberg LB, Pedersen BK. Supplementation with vitamins C and E inhibits the release of interleukin-6 from contracting human skeletal muscle. J Physiol. 2004;558(Pt 2):633–45. 44. Donato AJ, Eskurza I, Silver AE, Levy AS, Pierce GL, Gates PE, Seals DR. Direct evidence of endothelial oxidative stress with aging in humans: relation to impaired endothelium-dependent dilation and upregulation of nuclear factor-kappaB. Circ Res. 2007;100(11):1659–66. 45. Ferroni P, Basili S, Paoletti V, Davi G. Endothelial dysfunction and oxidative stress in arterial hypertension. Nutr Metab Cardiovasc Dis. 2006;16(3):222–33. 46. Dawson EA, Green DJ, Cable NT, Thijssen DH. Effects of acute exercise on flow- mediated dilatation in healthy humans. J Appl Physiol. 2013;115(11):1589–98. 47. Varady KA, Bhutani S, Church EC, Phillips SA. Adipokine responses to acute resistance exercise in trained and untrained men. Med Sci Sports Exerc. 2010;42(3):456–62. 48. Phillips SA, Das E, Wang J, Pritchard K, Gutterman DD. Resistance and aerobic exercise protects against acute endothelial impairment induced by a single exposure to hypertension during exertion. J Appl Physiol. 2011;110(4):1013–20. 46. Dawson EA, Green DJ, Cable NT, Thijssen DH. Effects of acute exercise on flow- mediated dilatation in healthy humans. J Appl Physiol. 2013;115(11):1589–98. Submit your next manuscript to BioMed Central and we will help you at every step: Submit your next manuscript to BioMed Central and we will help you at every step: 49. Tinken TM, Thijssen DH, Hopkins N, Black MA, Dawson EA, Minson CT, Newcomer SC, Laughlin MH, Cable NT, Green DJ. Impact of shear rate modulation on vascular function in humans. Hypertension. 2009;54(2):278–85. • We accept pre-submission inquiries • Our selector tool helps you to find the most relevant journal • We provide round the clock customer support • Convenient online submission • Thorough peer review • Inclusion in PubMed and all major indexing services • Maximum visibility for your research Submit your manuscript at www.biomedcentral.com/submit and we will help you at every step: 50. Harris RA, Padilla J, Hanlon KP, Rink LD, Wallace JP. The flow-mediated dilation response to acute exercise in overweight active and inactive men. Obesity (Silver Spring). 2008;16(3):578–84.
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Overriding TKI resistance of renal cell carcinoma by combination therapy with IL-6 receptor blockade
Oncotarget
2,017
cc-by
10,351
Correspondence to: Walburgis Brenner, email: brenner@uni-mainz.de Kei Ishibashi, email: keikun@fmu.ac.jp Keywords: renal cell carcinoma, tyrosine kinase inhibitor, resistance, IL-6, tocilizumab Received: March 01, 2017        Accepted: July 12, 2017        Published: July 21, 2017 Copyright: Ishibashi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Copyright: Ishibashi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. www.impactjournals.com/oncotarget Overriding TKI resistance of renal cell carcinoma by combination therapy with IL-6 receptor blockade p Kei Ishibashi1,2, Tobias Haber2, Ines Breuksch3, Susanne Gebhard3, Takashi Sugino4, Hitoshi Kubo5, Junya Hata1, Tomoyuki Koguchi1, Michihiro Yabe1, Masao Kataoka1, Soichiro Ogawa1, Hiroyuki Hiraki1, Tomohiko Yanagida1, Nobuhiro Haga1, Joachim W. Thüroff2, Dirk Prawitt6,*, Walburgis Brenner2,3,* and Yoshiyuki Kojima1,* 1Department of Urology, Fukushima Medical University, Fukushima, Japan 2Department of Urology, Johannes Gutenberg University Medical Center, Mainz, Germany 3Department of Gynecology and Obstetrics, Johannes Gutenberg University Medical Center, Mainz, Germany 4Department of Pathology, Shizuoka Cancer Center, Shizuoka, Japan 5Advanced Clinical Research Center, Fukushima Medical University, Fukushima, Japan 6Center for Pediatrics and Adolescent Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany *These authors contributed equally to this work Correspondence to: Walburgis Brenner, email: brenner@uni-mainz.de Kei Ishibashi, email: keikun@fmu.ac.jp www.impactjournals.com/oncotarget/ www.impactjournals.com/oncotarget/ ABSTRACT Metastatic renal cell carcinoma (RCC) is a tumor entity with poor prognosis due to limited therapy options. Tyrosine kinase inhibitors (TKI) represent the standard of care for RCCs, however a significant proportion of RCC patients develop resistance to this therapy. Interleukin-6 (IL-6) is considered to be associated with poor prognosis in RCCs. We therefore hypothesized that TKI resistance and IL-6 secretion are causally connected. We first analyzed IL-6 expression after TKI treatment in RCC cells and RCC tumor specimens. Cell proliferation and signal transduction activity were then quantified after co-treatment with tocilizumab, an IL-6R inhibitor, in vitro and in vivo. 786-O RCC cells secrete high IL-6 levels after low dose stimulation with the TKIs sorafenib, sunitinib and pazopanib, inducing activation of AKT-mTOR pathway, NFκB, HIF-2α and VEGF expression. Tocilizumab neutralizes the AKT-mTOR pathway activation and results in reduced proliferation. Using a mouse xenograft model we can show that a combination therapy with tocilizumab and low dosage of sorafenib suppresses 786-O tumor growth, reduces AKT-mTOR pathway and inhibits angiogenesis in vivo more efficient than sorafenib alone. Furthermore FDG-PET imaging detected early decrease of maximum standardized uptake values prior to extended central necrosis. i Our findings suggest that a combination therapy of IL-6R inhibitors and TKIs may represent a novel therapeutic approach for RCC treatment. INTRODUCTION the mammalian target of rapamycin (mTOR) pathways represents the standard of care in metastatic RCC. Multitargeted tyrosine kinase inhibitors (TKIs) lead to clearly prolonged overall and progression-free survival [2]. The TKI sorafenib inhibits VEGFR-2, VEGFR-3, the platelet-derived growth factor receptor family (PDGFR-β and Kit) as well as both C-RAF and B-RAF [3]. Sunitinib Renal cell carcinomas (RCC) account for about 85 percent of renal cancers and a quarter of the patients present with advanced disease, including locally invasive or metastatic renal cell carcinoma [1]. Currently, therapy targets the vascular endothelial growth factor (VEGF) and www.impactjournals.com/oncotarget Oncotarget 55230 is a highly potent, selective inhibitor of VEGF-R types 1  to 3, PDGF-Rα, and PDGFR-β [4]. Pazopanib also inhibits all the VEGFR subtypes and the PDGFR subtypes. In addition, it inhibits the fibroblast growth factor receptor, as well as transmembrane glycoprotein receptor tyrosine kinases [5]. However, despite the development of many types of TKIs, their effects are still limited and have been shown to be not curative [6]. A number of approved molecular targeted agents allow the sequential use of these drugs as empirical standard of care, although the optimum order of application has not been defined [7, 8]. Moreover, treatment has been associated with the development of resistance after a median of 6–15 months [9]. Alternative signaling pathway activation has been shown to be responsible for this resistance for most of the listed targeted RCC therapies. According to these studies, one of the central effects involved in TKI resistance [10] is probably due to sphingosine kinase-1 (SK1) activation, that stabilizes HIF-1α via enhanced AKT and ERK signaling [11]. To date it is not clear which mechanisms lead to these enhanced signaling activities. The finding that IL-6 seems to be involved in the development of TKI resistance [12, 13] suggests that cytokines are important in this process. IL-6-induced AKT phosphorylation activates mTOR that consequently activates its downstream targets p70S6 kinase (p70S6K), 40S ribosomal protein S6 (S6RP) and the eukaryotic initiation factor 4E binding protein-1 (4EBP1), that control mRNA translation and protein synthesis [14]. Consequently, IL-6-induced activation of AKT is involved in protection against apoptosis, as well as in enhanced proliferation in some cancer cells [15–17]. a strong (10-fold) enhanced secretion of IL-6 in 786-O cells, even at a low concentration (Figure 1A). VEGF secretion was also strongly increased in 786-O cells after stimulation with each of the three TKIs (Figure 1B). Gene expression of IL-6 and VEGF in 786-O cells To find out if the enhanced secretion of IL-6 and VEGF proteins in 786-O cells corresponds to an enhanced mRNA level of the respective genes, we investigated the influence of TKIs on IL-6 and VEGF expression. All TKIs used (sorafenib, sunitinib and pazopanib), induced increased IL-6 and VEGF mRNA expression one hour after stimulation, with exception of pazopanib treatment, that did not result in a significant VEGF induction. Increased mRNA expression levels after TKI treatment sustained until 24 hours after TKI stimulation (Figure 1C) with the exception of IL-6 expression after pazopanib treatment. INTRODUCTION In all other RCC cell lines tested, TKI treatment caused no significant changes in cytokine secretion (data not shown). IL-6 expression in RCC surgical specimens We retrospectively analyzed the expression of IL-6 in RCC specimens from 15 patients who underwent radical nephrectomy. Among the 15 patients, 3 were neoadjuvantly treated with TKIs (two with sorafenib, one with sunitinib) before they were referred to our institution for surgery. The surgical specimens from these 3 patients showed strong IL-6 expression. In contrast, weak or no IL-6 expression was observed in specimens from non- TKIs treated patients (Figure 2). Tocilizumab, a humanized antihuman IL-6 receptor (IL-6R) antibody, is currently available as one of the therapeutically effective reagents against inflammatory diseases such as rheumatoid arthritis [18]. We have previously reported the effect of a combination therapy using the antihuman IL-6R antibody together with IFN-α, that suggests a novel therapeutic approach for the treatment of RCC [19]. Impact of TKI stimulation on the IL-6 signaling Since we observe a high expression of IL-6R in 786-O cells (Figure 3), we studied the impact of TKI stimulation on the associated IL-6 signaling pathway. We examined the pathway activation by Western blot, monitoring phospho-AKT, phospho-mTOR, phospho- 4EBP1, phospho-S6RP, phospho-p70S6, phospho-NFκB, phospho-STAT3 and HIF-2α in 786-O cells treated with TKIs in combination with or without the blocking antihuman IL-6R antibody tocilizumab. In 786-O cells we found a concentration depend enhanced phosphorylation of AKT, mTOR, 4EBP1, S6RP, p70S6, NFκB and STAT3 after treatment with all of the TKIs tested, with exception of 4EBP1 and S6RP after pazopanib treatment. Sorafenib in a concentration of 0.5 µM significantly activated all investigated signaling molecules. STAT3 was additionally activated by sorafenib in a concentration of 1 µM, whereas the activity of p70S6K, mTOR and HIF2α was enhanced after sorafenib treatment in all concentrations investigated. Sunitinib treatment in a concentration of 0.5 µM resulted in an enhanced, but slightly non-significant, activity of AKT and a significant enhanced activity of all other signaling molecules investigated. Additionally, In the presented study, we analyzed the impact of cytokines during TKI treatment of RCC cells. We show that the autocrine secretion of IL-6 induced by TKIs- stimulation causes the activation of AKT, mTOR and STAT3, which consequently lead to VEGF expression in 786-O RCC cells. We also show that a combination therapy with tocilizumab, a humanized anti-IL-6 receptor antibody, and TKI can effectively suppress 786-O RCC tumor growth. www.impactjournals.com/oncotarget TKIs induce IL-6 secretion by 768-O cells Comprising all cytokines analyzed, IL-6 and VEGF secretion by 786-O cells were remarkably enhanced after TKI treatment. Sorafenib, sunitinib and pazopanib induced www.impactjournals.com/oncotarget Oncotarget 55231 sunitinib induced activation of p70S6, STAT3, mTOR, S6RP and HIF-2α in a concentration of 1 µM. In a concentration of 5 µM p70S6 and in a concentration of 10 µM mTOR was activated. Although all signaling mediators with exception of S6RP were activated by pazopanib treatment, the enhancement was only significant in case of AKT by treatment with 0.5 µM and of mTOR and HIF-2α in concentrations between 0.5 and 5 µM. The enhanced phosphorylation of the named proteins after TKI treatment at all concentrations used was also associated with enhanced HIF-2α protein amounts, one of the transcription factors of VEGF (Figure 4). Treatment with the IL6-R blocking tocilizumab abolished the effect of the TKIs on the activation of AKT, mTOR, 4EBP1, S6RP, p70S6, NFκB, STAT3 and HIF-2α (Figure  4), arguing that the observed TKI effects depend on the enhanced IL-6 signaling in 786-O cells. In addition, treatment with tocilizumab alone did not influence the activation of any of the signaling molecules investigated (Figure 4). gure 1: TKI-induced IL-6 and VEGF expression in RCC cells. RCC cell line 786-O was cultured with sorafenib, sunitinib ib f h d l d b V MAP D l t S t i th ti f t ki D t t d tj l / t t e 1: TKI-induced IL-6 and VEGF expression in RCC cells. RCC cell line 786-O was cultured with sorafenib, suni opanib for one hour, and analyzed by VersaMAP Development System concerning the secretion of cytokines. Demonstrated nes with clear changes in secretion compared to untreated cells: IL-6 (A), and VEGF (B). Untreated cells served as control. Rel expressions (C) of TKI treated (two concentrations, three time points) compared with those of non-treated cells are indicated p-regulate IL-6 and VEGF mRNA expression up to 400 fold (for IL-6) and 25 fold (for VEGF), irrespective of their concentrat Figure 1: TKI-induced IL-6 and VEGF expression in RCC cells. RCC cell line 786-O was cultured with sorafenib, sunitinib or pazopanib for one hour, and analyzed by VersaMAP Development System concerning the secretion of cytokines. Demonstrated are cytokines with clear changes in secretion compared to untreated cells: IL-6 (A), and VEGF (B). Untreated cells served as control. Alteration on susceptibility to TKIs by IL-6 pathway blockade To confirm that tocilizumab improves the effect of low dose TKIs in the MTT assay, we employed a nude mice xenograft model, applying low dose sorafenib with or without tocilizumab. The growth of tumors in athymic mice receiving a combination therapy with tocilizumab and sorafenib was retarded in comparison to those in the sorafenib-alone and non-treated (PBS) groups (Figure 6A). In the earlier stage of the challenge (up to 30 days), growth of tumors in the group treated with tocilizumab alone seemed to be retarded, yet there was no significant difference to the control / sorafenib treated groups at the time of sacrifice (41 days). However, the tumor volume in the group with combination therapy (sorafenib and tocilizumab) was significantly lower compared with other groups at the end of the study (p = 0.044). Our data suggested that 786-O cells are resistant to a sole TKI treatment and most likely proliferate due to the increased IL-6 secretion. To study the impact of IL-6 on cell proliferation, we determined the effect of TKIs on 786-O cells under the blockade of IL-6 signaling by tocilizumab in a MTT assay. TKIs in low doses and tocilizumab alone (value of 0.93±0.09, relative to control) did not influence the cell count. The addition of tocilizumab to TKIs results in a significant reduction of the 786-O cell count (Figure 5A). i We quantified the protein secretion levels of VEGF by ELISA in 786-O cells treated with tocilizumab. As suggested by the STAT3 and HIF-2α Western blot analyses described above, sorafenib treatment resulted in a strongly enhanced VEGF secretion. Treatment with the other TKIs sunitinib or pazopanib also induced an enhanced VEGF secretion in this cell line (Figure 5B). However blocking of the IL-6R by tocilizumab attenuated the effect of sorafenib and sunitinib significantly (p = 0.035 for sorafenib 1 µM, p = 0.019 for sunitinib 1 µM and p = 0.044 for sunitinib 5 µM). Subsequently, tumors were processed for microscopic morphological description. The tumors from the control mice displayed a clear cell-type, specific for renal cell carcinoma. Immunohistochemical examination confirmed the absence of IL-6 and negligible activation of Figure 2: Immunohistochemical staining of IL-6 in specimens of RCC patients treated with TKIs or without therapy before nephrectomy. HE and immunohistochemical staining of IL-6 of surgical RCC specimens diagnosed with over pT3 clear cell renal cell carcinoma. TKIs induce IL-6 secretion by 768-O cells Relative mRNA expressions (C) of TKI treated (two concentrations, three time points) compared with those of non-treated cells are indicated. All TKIs up-regulate IL-6 and VEGF mRNA expression up to 400 fold (for IL-6) and 25 fold (for VEGF), irrespective of their concentration. www.impactjournals.com/oncotarget Oncotarget 55232 Alteration on susceptibility to TKIs by IL-6 pathway blockade Three patients were treated with TKIs for two months prior to surgery. The surgical specimens from the three patients showed strong IL-6 expression (Figure 2 framed blue). In contrast, all of 12 patients without TKIs treatment before surgery did not show IL-6 expression in the tumor parenchyma. Figure 2: Immunohistochemical staining of IL-6 in specimens of RCC patients treated with TKIs or without therapy before nephrectomy. HE and immunohistochemical staining of IL-6 of surgical RCC specimens diagnosed with over pT3 clear cell renal cell carcinoma. Three patients were treated with TKIs for two months prior to surgery. The surgical specimens from the three patients showed strong IL-6 expression (Figure 2 framed blue). In contrast, all of 12 patients without TKIs treatment before surgery did not show IL-6 expression in the tumor parenchyma. www.impactjournals.com/oncotarget Oncotarget 55233 mTOR signaling in the tumor cells of non-treated mice. No remarkable differences were observed in the tumors treated with tocilizumab alone. Tumor sections obtained from the mice after sorafenib-only treatment showed enhanced expression of p-S6RP, p-p70S6K and p-4EBP1 as a result of an activation of the mTOR pathway. In contrast, the combination therapy with sorafenib and tocilizumab blocked the enhanced activation of the mTOR signaling cascade and showed lower amounts of p-S6RP, p-p70S6K and p-4EBP1 compared to tumors treated with sorafenib- only (Figure 7B). The vascularization of the xenograft tumors was also dependent on the treatment. Tumors of mice treated with sorafenib or tocilizumab alone showed a slightly reduced vascularization of the tumor, determined by CD31 staining (Figure 6C). However, a remarkable reduction of angiogenesis (compared with PBS-control, sorafenib- or tocilizumab-only) was observed when mice were treated with tocilizumab in combination with low dose sorafenib (Figure 6C). differences were found on day 3 between the two groups, despite decreased CD31 positive cells and significantly lower signal intensity on the FDG-PET in the mice treated with combination therapy (Figure 7C). After 21 days, hematoxylin-eosin staining showed extensive necrosis, both in mice treated with sorafenib monotherapy and sorafenib / tocilizumab combination therapy (Figure 7C). However, there still remain viable tumor cells within the necrotic area of tumors in the mice treated with sorafenib monotherapy. Also, the CD31 positive cells increased again in the tumor region treated with sorafenib along on the day 21. In contrast, when tocilizumab was given in combination with sorafenib, the tumors showed extensive central necrosis with absence of CD31 positive cells (Figure 7C). Alteration on susceptibility to TKIs by IL-6 pathway blockade Immunohistochemical examination confirmed suppressed activation of S6RP, p70S6K and 4EBP1 in the tumors after combination therapy, although IL-6 was detected (Figure 8). FDG-PET imaging The present study demonstrates that low concentration TKI treatment induces IL-6 and VEGF expression and secretion only in 786-O cells, whereas other RCC cell lines were not affected by TKI concerning cytokine secretion. The finding that in all cases of neoadjuvant TKI treated patient’s RCC specimens IL-6 was highly expressed, whereas in patients without TKI treatment no or only very low IL-6 expression was detectable, suggests that the cell line 786-O reflects the situation in vivo and we therefore used it for all further investigations. 786-O cells differ from the other cell lines by simultaneous mutations of VHL and HIF-1α [20]. HIF- 1α and HIF-2α are known to reciprocally influence each other concerning VEGF expression and in renal cancer, To investigate TKI resistance in RCC and the possibility of its prevention by combination therapy with sorafenib and tocilizumab in vivo, we employed FDG-PET imaging. Tumor viability, determined by maximum standardized uptake value (SUVmax), of mice treated with sorafenib alone remained unchanged with a tendency to enhanced viability at day 21 (Figure 7A). In the mice treated by combination therapy, tumor viability was significantly decreased after 3 days compared to the mice treated with sorafenib alone (p = 0.04). Also on day 21, the tumor viability of mice treated with sorafenib in combination with tocilizumab was clearly lower than that of sorafenib treated mice, although this difference was not significant (Figure 7B). No histopathological Figure 3: Immunohistochemical staining of IL-6R in 768-O cells. Cells show a clear positive IL-6R staining, whereas the negative control remains unstained. Figure 3: Immunohistochemical staining of IL-6R in 768-O cells. Cells show a clear positive IL-6R staining, whereas the negative control remains unstained. www.impactjournals.com/oncotarget Oncotarget 55234 ffects of IL-6 signaling blockade on activity of the AKT-mTOR pathway after (A) sorafenib, (B) sunitinib or (C) pazopanib fluence of tocilizumab (50 µg/ml) on activation of AKT-mTOR pathway in 786-O cells after treatment with TKI was determined ot. The concentrations of TKIs are indicated on the X axis of each graph. In combinational treatment (right part of each graph) was used in a concentration of 50 µg/ml. The column labeled by 0 µg/ml in the right part of each graph represents treatment with lone. Phosphorylation of AKT, mTOR, 4EBP1, S6RP, NFκB, and STAT3 was enhanced after TKI treatment at concentration IF-2α was enhanced by treatment with TKIs in all concentrations used. Tocilizumab neutralized these effects. FDG-PET imaging The results are he relative mean value ± standard deviation of three independent analyses, each in triplicate, related to untreated control cells. mpared with the control cells. Figure 4:  Effects of IL-6 signaling blockade on activity of the AKT-mTOR pathway after (A) sorafenib, (B) sunitinib or (C) pazopanib treatment. Influence of tocilizumab (50 µg/ml) on activation of AKT-mTOR pathway in 786-O cells after treatment with TKI was determined by Western blot. The concentrations of TKIs are indicated on the X axis of each graph. In combinational treatment (right part of each graph) tocilizumab was used in a concentration of 50 µg/ml. The column labeled by 0 µg/ml in the right part of each graph represents treatment with tocilizumab alone. Phosphorylation of AKT, mTOR, 4EBP1, S6RP, NFκB, and STAT3 was enhanced after TKI treatment at concentration of 0.5 µM. HIF-2α was enhanced by treatment with TKIs in all concentrations used. Tocilizumab neutralized these effects. The results are presented as the relative mean value ± standard deviation of three independent analyses, each in triplicate, related to untreated control cells. *p < 0.05 compared with the control cells. www.impactjournals.com/oncotarget Oncotarget 55235 VEGF secretion particularly is regulated by HIF-2α [21]. Due to the VHL mutation in 786-O cells, HIF-2α is persistently highly expressed [22] and due to the loss of HIF-1α, the reciprocal interaction between HIF-1α and HIF-2α probably is abolished, suggestively leading to a higher secretion of VEGF. This coincidence may cause the here described strong IL-6-VEGF vicious circle especially in 786-O cells. from RCC patients who were treated with TKIs prior to surgery showed strong IL-6 expression in the tumor parenchyma, although the number of the patients was quite small. One can assume that tumor necrosis due to TKI treatment causes inflammatory changes and leads to cytokine secretion. Inflammatory cytokines such as IL-6 might then affect the viability of the cells which survive after TKI treatment. IL-6 is a pleiotropic cytokine with widespread effects on hematopoietic lineages [23, 24] and is considered to be a key mediator of inflammation [25]. Dysregulation of IL-6 signaling contributes to the onset and maintenance of several diseases including some types of cancer, i.e. multiple myeloma, gastric cancer and prostate cancer [26, 27]. IL-6 induces activation of the PI3K/AKT pathway, and is involved in protection against apoptosis and in enhanced proliferation of multiple myeloma cells [15, 16]. FDG-PET imaging In this context it is not surprising that inflammation dependent secretion of IL-6 induces TKI resistance in lung cancer [28]. It has been described, that in RCC circulating cytokine levels, including IL-6, are increased in advanced RCC patients treated with sunitinib from baseline values before tumor progression [29]. Interestingly, all three clinical specimens we obtained We found that the elevated IL-6 secretion is correlated with an increased VEGF secretion, suggesting a functional coupling of the two events. A mandatory requirement for such a loop is the expression of the IL-6 receptor, which we observed in 786-O cells in our study. It is known, that in response to IL-6R stimulation, cytoplasmic STAT3, an independent prognostic marker in RCC [30], gets activated. STAT3 is known to play an important role in tumor progression of several high-malignant cancer entities. In intrahepatic cholangiocarcinoma STAT3 overexpression negatively correlates with the outcome of the patients [31], and in breast and lung cancer STAT3 has a key role in metastatic processes [32, 33]. Phosphorylation of STAT3 triggers a transcriptional response favoring survival, proliferation and angiogenesis. Phosphorylated STAT3 rapidly accumulates in the nucleus [34] and igure 5: Cell viability as well as VEGF secretion after IL-6 signaling inhibition. (A) Antihuman IL-6R antibody, tocilizumab 50 µg/ml), was used for the inhibition of IL-6 signaling. Cell count was determined by an MTT assay. Tocilizumab significantly increased usceptibility to TKIs, especially at low dosage of 5 µM for sorafenib, 1 µM for sunitinib and 1 and 5 µM for pazopanib. *p < 0.05 for wo-tailed paired t-test compared with combination with tocilizumab and TKIs. (B) Tocilizumab inhibits low dosage TKI-induced VEGF xpression, determined by ELISA. *p < 0.05 for two-tailed paired t-test compared with the TKI treated cells. Figure 5: Cell viability as well as VEGF secretion after IL-6 signaling inhibition. (A) Antihuman IL-6R antibody, tocilizumab (50 µg/ml), was used for the inhibition of IL-6 signaling. Cell count was determined by an MTT assay. Tocilizumab significantly increased susceptibility to TKIs, especially at low dosage of 5 µM for sorafenib, 1 µM for sunitinib and 1 and 5 µM for pazopanib. *p < 0.05 for two-tailed paired t-test compared with combination with tocilizumab and TKIs. (B) Tocilizumab inhibits low dosage TKI-induced VEGF expression, determined by ELISA. *p < 0.05 for two-tailed paired t-test compared with the TKI treated cells. FDG-PET imaging www.impactjournals.com/oncotarget Oncotarget 55236 Figure 6: Effect of combination therapy with sorafenib and tocilizumab on a nude mice xenografts model of 786-O cells Mice were treated three times a week with tocilizumab (100 µg i.p.) or control PBS (n = 5 each) followed by daily sorafenib administratio at 10 mg/kg/day as described elsewhere [54]. Phosphate-buffered saline (PBS) was used in the control (non-treated) mouse group (n = 5) Tocilizumab alone was used in another group of mice (n = 5). Mice were sacrificed after 40 days and tumors were analyzed. (A) Time cours of tumor volume was analyzed by ellipsoid volume formulas (pi/6 x L x W x H). The tumor volumes by low-dose sorafenib + tocilizuma herapy were significantly decreased compared to sorafenib therapy alone (p < 0.05). A repeated experiment yielded similar results. (B Endothelial cells of xenografts were visualized by an immunohistochemical staining of CD31 Sorafenib or tocilizumab administratio Figure 6: Effect of combination therapy with sorafenib and tocilizumab on a nude mice xenografts model of 786-O cells. Mice were treated three times a week with tocilizumab (100 µg i.p.) or control PBS (n = 5 each) followed by daily sorafenib administration at 10 mg/kg/day as described elsewhere [54]. Phosphate-buffered saline (PBS) was used in the control (non-treated) mouse group (n = 5). Tocilizumab alone was used in another group of mice (n = 5). Mice were sacrificed after 40 days and tumors were analyzed. (A) Time course of tumor volume was analyzed by ellipsoid volume formulas (pi/6 x L x W x H). The tumor volumes by low-dose sorafenib + tocilizumab therapy were significantly decreased compared to sorafenib therapy alone (p < 0.05). A repeated experiment yielded similar results. (B) Endothelial cells of xenografts were visualized by an immunohistochemical staining of CD31. Sorafenib or tocilizumab administration alone partially inhibited angiogenesis in the tumor as demonstrated by reduced CD31 levels. The combination therapy with sorafenib and tocilizumab strongly inhibited the angiogenesis. (C) Signaling pathways of xenografts were analyzed immunohistochemically. Sorafenib at a low dose of 10 mg/kg/day induced activation of S6RP, p70S6K and 4EBP1 of mTOR pathway. Tocilizumab administration resulted in no remarkable morphological changes. The combination therapy diminished the effect induced by sorafenib alone on the activation of mTOR pathway. ation therapy with sorafenib and tocilizumab on a nude mice xenografts model of 786-O cells. FDG-PET imaging k i h ili b (100 i ) l S ( h) f ll d b d il f ib d i i i Figure 6: Effect of combination therapy with sorafenib and tocilizumab on a nude mice xenog i d h i k i h ili b ( i ) l ( h) f ll d b Figure 6: Effect of combination therapy with sorafenib and tocilizumab on a nude mice xenografts model of 786-O cells. Mice were treated three times a week with tocilizumab (100 µg i.p.) or control PBS (n = 5 each) followed by daily sorafenib administration at 10 mg/kg/day as described elsewhere [54]. Phosphate-buffered saline (PBS) was used in the control (non-treated) mouse group (n = 5). Tocilizumab alone was used in another group of mice (n = 5). Mice were sacrificed after 40 days and tumors were analyzed. (A) Time course of tumor volume was analyzed by ellipsoid volume formulas (pi/6 x L x W x H). The tumor volumes by low-dose sorafenib + tocilizumab therapy were significantly decreased compared to sorafenib therapy alone (p < 0.05). A repeated experiment yielded similar results. (B) Endothelial cells of xenografts were visualized by an immunohistochemical staining of CD31. Sorafenib or tocilizumab administration alone partially inhibited angiogenesis in the tumor as demonstrated by reduced CD31 levels. The combination therapy with sorafenib and tocilizumab strongly inhibited the angiogenesis. (C) Signaling pathways of xenografts were analyzed immunohistochemically. Sorafenib at a low dose of 10 mg/kg/day induced activation of S6RP, p70S6K and 4EBP1 of mTOR pathway. Tocilizumab administration resulted in no remarkable morphological changes. The combination therapy diminished the effect induced by sorafenib alone on the activation of mTOR pathway. www.impactjournals.com/oncotarget www.impactjournals.com/oncotarget www.impactjournals.com/oncotarget Oncotarget 55237 Figure 7: A nude mice xenograft model of 786-O cells was evaluated by FDG-PET imaging during a time course of 3 and 21 days. Mice were treated with sorafenib alone (30 mg/kg/day) or in combination with tocilizumab (100 mg three times a week). (A) Sorafenib as well as combination therapy with sorafenib and tocilizumab lead to a decrease of the viable region in the central area of the tumor. (B) SUVmax was significantly decreased in the tumor in the combination therapy compared with sorafenib alone at day 3 (SUVmax 9.6 vs. 11.9, p = 0.04). At day 21, FDG-PET imaging showed that the SUV value remained low in the tumor with the combination therapy, although value difference was not significant compared with sorafenib treatment alone (p = 0.10). (C) RCC in nude mice were analyzed by HE and endothelial cell staining (CD31) on day 3 and day 21. Tumors from mice treated with sorafenib, as well as with the combination therapy, showed no remarkable change on day 3 of challenge. CD31 positive cells were only marginal in both groups. On day 21 tumors from mice treated with sorafenib, as well as with combination therapy, showed central necrosis in the tumor. However, tumors from mice treated with sorafenib alone retain a viable tumor area at the central tumor region and show CD31 positive cells among the viable tumor cells. A nude mice xenograft model of 786-O cells was evaluated by FDG-PET imaging during a t nograft model of 786-O cells was evaluated by FDG-PET imaging during a time course of Figure 7: A nude mice xenograft model of 786-O cells was evaluated by FDG-PET imaging during a time course of 3 and 21 days. Mice were treated with sorafenib alone (30 mg/kg/day) or in combination with tocilizumab (100 mg three times a week). (A) Sorafenib as well as combination therapy with sorafenib and tocilizumab lead to a decrease of the viable region in the central area of the tumor. (B) SUVmax was significantly decreased in the tumor in the combination therapy compared with sorafenib alone at day 3 (SUVmax 9.6 vs. 11.9, p = 0.04). At day 21, FDG-PET imaging showed that the SUV value remained low in the tumor with the combination therapy, although value difference was not significant compared with sorafenib treatment alone (p = 0.10). www.impactjournals.com/oncotarget (C) RCC in nude mice were analyzed by HE and endothelial cell staining (CD31) on day 3 and day 21. Tumors from mice treated with sorafenib, as well as with the combination therapy, showed no remarkable change on day 3 of challenge. CD31 positive cells were only marginal in both groups. On day 21 tumors from mice treated with sorafenib, as well as with combination therapy, showed central necrosis in the tumor. However, tumors from mice treated with sorafenib alone retain a viable tumor area at the central tumor region and show CD31 positive cells among the viable tumor cells. Figure 7: A nude mice xenograft model of 786-O cells was evaluated by FDG-PET imaging during a time course of 3 and 21 days. Mice were treated with sorafenib alone (30 mg/kg/day) or in combination with tocilizumab (100 mg three times a week). (A) Sorafenib as well as combination therapy with sorafenib and tocilizumab lead to a decrease of the viable region in the central area of the tumor. (B) SUVmax was significantly decreased in the tumor in the combination therapy compared with sorafenib alone at day 3 (SUVmax 9.6 vs. 11.9, p = 0.04). At day 21, FDG-PET imaging showed that the SUV value remained low in the tumor with the combination therapy, although value difference was not significant compared with sorafenib treatment alone (p = 0.10). (C) RCC in nude mice were analyzed by HE and endothelial cell staining (CD31) on day 3 and day 21. Tumors from mice treated with sorafenib, as well as with the combination therapy, showed no remarkable change on day 3 of challenge. CD31 positive cells were only marginal in both groups. On day 21 tumors from mice treated with sorafenib, as well as with combination therapy, showed central necrosis in the tumor. However, tumors from mice treated with sorafenib alone retain a viable tumor area at the central tumor region and show CD31 positive cells among the viable tumor cells. www.impactjournals.com/oncotarget Oncotarget 55238 downstream molecules like mTOR, a key factor in this pathway. STAT3 is directly phosphorylated by activated mTOR. STAT3, 4EBP1 and S6K1 act in concert to drive the angiogenic response through mTOR complex 1 (mTORC1) [43]. The mTORC1 activation causes protein synthesis, which induces cell proliferation, survival, motility and invasion leading to cancer initiation and progression [44]. www.impactjournals.com/oncotarget On the other hand, mTOR complex 2 (mTORC2) again activates AKT and can induce the expression of HIF-2α [45], an anti-apoptotic transcription factor, highly important in tumorigenesis [46]. HIF-2α has been demonstrated to be more important in RCC tumorigenesis than HIF-1α, since blocking HIF-2α results in a strong reduction of RCC tumor formation and angiogenesis [47]. In our study activation of mTOR after low-concentration TKI treatment correlates clearly with an enhanced HIF-2α expression, probably inducing resistance to TKI treatment. However, the enhanced VEGF secretion observed after treatment with TKI in low concentration seems not only to be caused by HIF-2α, since HIF-2α was highly expressed after treatment in all TKI concentrations tested. In contrast, STAT3 was primarily enhanced after treatment with low TKI concentrations, corresponding to the high VEGF secretion, which is in good accordance with the fact that STAT3 is known to be able to induce VEGF secretion [48].i leads to the production of VEGF [35, 36]. The activated STAT3 can increase NFκB activity and NFκB itself is an important mediator for activation of the IL-6 gene [37]. This activation cascade is effective within short time, since inhibition of NFκB results in a reduced IL-6 secretion after a period of one hour [38], a time period also selected in our study. Within the cell IL-6 is stored in vesicles and secreted after stimulation [39]. Apparently, IL-6 transcription seems to be simultaneously enhanced or degradation diminished. NFκB-triggered positive feedback for IL-6 signaling, also known as inflammation amplifier, induces various molecules to create a microenvironment which promotes cancer development [40]. In our study we show, that TKI treatment enhances IL-6 secretion, associated with activation of the AKT pathway including AKT, mTOR and p70S6K as well as STAT3 and NFκB activation and consequently VEGF secretion. This suggests a similar amplifier loop in renal cancer, whereby IL-6 is induced by TKIs in RCC cells, consequently up-regulating VEGF expression via AKT and STAT3 (Figure 9). The observation that the AKT-mTOR pathway is activated only when low concentrations of TKIs are used, although enhanced secretion of IL-6 and VEGF also occur when higher TKI concentrations are added, may be caused by the circumstance that not the AKT-mTOR pathway alone is responsible for the enhanced cytokine secretion, but also other mechanisms not detected in this study. www.impactjournals.com/oncotarget This is in good accordance with the finding, that a higher VEGF baseline level is associated with less progression-free survival in sunitinib treated RCC patients [41, 42]. TKI treatment alone had no significant effect on proliferation of 786-O cells in vitro, probably due to the low concentrations used. Tocilizumab, an inhibitory IL- 6R antibody, that is approved for rheumatoid arthritis, juvenile idiopathic arthritis, Castleman’s disease, and Crohn’s disease [49–52], inhibits IL-6 signaling. An additive treatment of RCC cells with TKI together with tocilizumab in the present study resulted in a reduced It has been reported, that IL-6-induced activation of the PI3K/AKT pathway is involved in protection against apoptosis, as well as in enhanced proliferation in some cancer cells [15–17]. Phosphorylated AKT activates Figure 8: mTOR pathway activity in mouse tumor specimens after sorafenib treatment in combination with tocilizumab. The mTOR pathway in the tumors was immunohistochemically analyzed on day 21. Tumors from mice treated with sorafenib showed phosphorylation of mTOR pathway components 4EBP1, p70S6K and S6RP, correlating with IL-6 expression. In contrast, tumors from mice of the combination therapy group showed suppressed activation of the mTOR pathway. Figure 8: mTOR pathway activity in mouse tumor specimens after sorafenib treatment in combination with tocilizumab. The mTOR pathway in the tumors was immunohistochemically analyzed on day 21. Tumors from mice treated with sorafenib showed phosphorylation of mTOR pathway components 4EBP1, p70S6K and S6RP, correlating with IL-6 expression. In contrast, tumors from mice of the combination therapy group showed suppressed activation of the mTOR pathway. www.impactjournals.com/oncotarget Oncotarget 55239 vascularity in the tumor was reduced only temporarily by sorafenib and returned to control levels on day 14–21 after treatment. The combination with IL-6R antibody prolonged the time of reduced vascularity, and we observed decreased vessels at the periphery of the lesion even on day 21 after combinational therapy with sorafenib and tocilizumab. This supports the idea, that the tumor angiogenesis is inhibited by an IL-6R blockade. We have previously reported that the inhibition of IL-6 signaling alone is insufficient to inhibit 786-O tumor growth in vivo [19]. Only the combination with sorafenib and tocilizumab inhibited tumor growth and angiogenesis. TKI resistance of renal cancer includes insensitivity against anti-proliferative effects of TKIs as well as resistance to anti-angiogenic TKI effects. The observed effect occurs after TKI treatment in low concentration. www.impactjournals.com/oncotarget This can appear during dosage reductions in patients or after discontinuation of the TKI therapy, which may finally lead to TKI-resistance in anti-proliferative and anti-angiogenesis effects of further TKI treatment. In our cellular model, a combination of TKI with tocilizumab effectively circumvents TKI resistance. In vivo we confirmed this observation concerning angiogenesis. IL-6 secretion can activate VEGF expression and thus contribute to angiogenesis, cell proliferation and survival of tumor cells. We suggest that the IL-6 secretion of RCC cells might lead to renal cancer resistance towards TKI therapy, due to the discussed feedback loops. In this scenario, the combination of TKI with tocilizumab would have at least additive effects, since we observed tumor cell proliferation. Additionally, VEGF secretion was reduced after combination treatment, compared to treatment with TKI alone. These results were significant only when the TKIs sorafenib and sunitinib were used, whereas in case of pazopanib we only could observe a tendency in the according direction. These combination effects were confirmed by our in vivo study using sorafenib together with tocilizumab, where the combination therapy enhanced anti-tumor effects of sorafenib in 786-O RCC cells in nude mice. We have previously reported that IFN-α induces IL-6 in human RCC cell lines and that IL-6 plays a crucial role for resistance also against IFN-α treatment through suppressed STAT1 phosphorylation and induced phosphorylation of STAT3 and ERK [19]. Tocilizumab restored the inhibitory effect of IFN-α, in vitro and in vivo, in an IFN-α-resistant RCC cell line in which IL-6 was highly induced by IFN-α [19]. This further supports the possibility to block multiple treatment resistance mechanisms, induced by an enhanced IL-6 secretion, by inhibiting IL-6R, as we show here in RCC. The 786-O tumors of mice treated with low doses of sorafenib monotherapy activated p70S6K, S6RP and 4EBP1, apparently leading to tumor cell proliferation under the insufficient effect of sorafenib. The combination with IL-6R antibody decreased this activation and significantly reduced the tumor volume compared to the sorafenib monotherapy. In addition, as shown in the in vivo study using arterial spin-labeling magnetic resonance [53], the Figure 9: Feedback loop in TKI therapy. IL-6 and VEGF activate AKT-mTOR and the STAT3 signaling cascade, consequently leading to enhanced secretion of IL-6 and VEGF. Secreted IL-6 and VEGF can again re-activate tumor cells and thus trigger tumor progression. A combination therapy of TKI together with an anti-IL-6R antibody could inhibit this amplifier circle. Cell lines/TKIs/tocilizumab The human RCC cell lines 786-O, A489, Caki1 and Caki2, obtained from the American Tissue Culture Collection (ATCC), were cultured at 37°C in 5% CO2 using RPMI 1640 with 10% fetal bovine serum. Three kinds of TKIs, sorafenib, sunitinib and pazopanib, were purchased from LC Laboratories (Woburn, MA, USA), sorafenib additionally kindly provided from BAYER. The optimum concentration of tocilizumab was determined to be 50 mg/ml, as described previously [19]. Patient surgical specimens Surgical specimens were obtained from 15 patients with renal cell carcinoma who underwent radical nephrectomy for cT3N0M0 disease at the department of Urology, Fukushima Medical University, between 2010 and 2012. Mean patient age was 66 years. Patients who were diagnosed with clear cell renal cell carcinoma were included in this study. The research protocol was approved by the Ethics review committee of Fukushima Medical University (approval #2663). Among the 15 patients, two were neoadjuvantly treated with sorafenib, one with sunitinib for two months before surgery to reduce the tumor volume. RNA isolation and real-time quantitative PCR RNA isolation and cDNA construction were performed using a Cells-to-CTTM Kit (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions. TaqMan PCR reagents for IL-6 (Hs00985639) and VEGFA (Hs00900055_m1) were purchased from ABI (Applied Biosystems, Foster, CA, USA). Quantitative Real-time PCR was carried out using TaqMan Master Mix reagents kit protocol with a StepOne Real-time PCR System (Life Technologies). The data were standardized against beta-actin gene expression using Pre-Developed TaqMan Assay Reagents (Applied Biosystems). www.impactjournals.com/oncotarget Figure 9: Feedback loop in TKI therapy. IL-6 and VEGF activate AKT-mTOR and the STAT3 signaling cascade, consequently leading to enhanced secretion of IL-6 and VEGF. Secreted IL-6 and VEGF can again re-activate tumor cells and thus trigger tumor progression. A combination therapy of TKI together with an anti-IL-6R antibody could inhibit this amplifier circle. Figure 9: Feedback loop in TKI therapy. IL-6 and VEGF activate AKT-mTOR and the STAT3 signaling cascade, consequently leading to enhanced secretion of IL-6 and VEGF. Secreted IL-6 and VEGF can again re-activate tumor cells and thus trigger tumor progression. A combination therapy of TKI together with an anti-IL-6R antibody could inhibit this amplifier circle. www.impactjournals.com/oncotarget Oncotarget 55240 by VersaMAP Development System (R&D systems, Minneapolis, MN, USA) according to the manufacturer's instructions. Briefly, 50 ml of Microparticle Cocktail was added to each well of the filter-bottomed microplate and 50 µl cell culture supernatant was added to each well. After a 2-hour incubation at room temperature on a microplate shaker, the liquid was removed and the plate was washed with wash buffer. Then 50 ml of Biotin Antibody Cocktail was added to the well and incubated for 1 hour at room temperature. After three wash cycles Streptavidin-PE was added to the wells and the plate was incubated 30 minutes at room temperature. The cytokine concentration was measured using a Bio-Rad analyzer (Bio-Rad, Germany). early decline of SUVmax as well as earlier appearance and increase of the necrotic areas by FDG-PET after combination therapy. In conclusion, the presented study demonstrates that sunitinib and sorafenib treatment in low concentrations leads to activation of AKT- and STAT3-signaling, consequently resulting in a secretion of IL-6 and VEGF. The latter then seems to result in an amplifier circle, which consecutive reduces sensitivity to TKIs. Inhibition of the IL-6 signaling by tocilizumab may block the amplifier circle and re-activate the anti-tumor activity of TKIs, both in vitro and in vivo. Our findings suggest that a combination therapy using an antihuman IL-6R antibody with TKIs may represent a novel therapeutic approach for the antiangiogenic treatment of RCC, also in the light of previously reported IFN-α effects. Immunohistochemical staining of IL-6 in tumor specimens Formalin-fixed, paraffin-embedded human tissues including renal cell carcinoma were processed for immunohistochemical staining with an anti-IL-6 antibody (ROCKLANDTM Gilbertsville, PA). Sections (2 μm thick) were deparaffinized in three changes of xylene, hydrated through a descending series of ethanol. The endogenous peroxidase activity was blocked with methanol containing 0.5% hydrogen peroxide for 20 minutes. Then sections were treated at 4 °C overnight with primary antibodies for IL-6 (1:600 dilution). Subsequent reactions were carried out with the DAKO EnVision Detection System (Dako, Hamburg, Germany) according to the manufacturer’s instructions. MTT assay mice were separated into four groups of five animals. One group received an i.p. injection of 100 mg antihuman IL-6 receptor (IL-6R) antibody, tocilizumab, three times a week, together with sorafenib in a daily of 10 mg/kg by oral administration as described previously [54]. The other groups received sorafenib alone, tocilizumab alone or phosphate-buffered saline (PBS; non-treated control group), respectively. Tumor size was measured and tumor volume was calculated by ellipsoid volume formulas (pi/6 x L x W x H) [55]. After treatment for 40 days, mice were sacrificed and the tumors were removed and used for histo-morphological analyses. For determination of cellular proliferation and viability, MTT (3-[4,5-dimethylthiazol-2-yl]-2,5- diphenyltetrazolium bromide) assays were performed using a Cell Proliferation Kit I (Roche Applied Science, Basel, Switzerland) according to the manufacturer’s protocol. Briefly, 72 hours after incubation of the cells with TKIs and tocilizumab, the MTT labeling reagent was added to each well, which were then incubated for 4 hours at 37°C before the addition of the solubilization solution to each well. Spectrophotometrical absorbances of the samples were measured using a microplate reader. The absorbances were compared with those of non-treated cells. Measurement of cytokines using VersaMAP development System For IL-6R staining on 786-O cells a Dako-REAL- EnVision HRP system was used (Dako, Hamburg, Germany). Cells were acetone fixed, peroxidase blocked and stained using an antihuman IL-6R antibody (1:25, R&D systems, Minneapolis, MN, USA) for one hour at room temperature. Second antibody (ready to use) and DAB staining was performed according to the manufacturer’s instructions. Cells were HE counterstained. The primary antibody was omitted as negative control. 786-O cells were treated by TKIs at a final concentration of 0.5, 1.0, 5.0, 10.0 µM for sorafenib and sunitinib and 1.0, 5.0, 10.0, 50.0 µM for pazopanib. The supernatant was collected 1, 2, and 24 hours after TKIs stimulation. The amount of cytokine production (IL-6, VEGF, IL-1ra, IL-17, IL-19, IL-23, IL-18BPa, Leptin, HGF, Cript-1, HB-EGF, EGF) was measured www.impactjournals.com/oncotarget Oncotarget 55241 Tumor xenografts All animal studies were conducted in compliance with Japanese animal use regulations and approval for these studies was obtained from the Committee on Animal Research of Fukushima Medical University. Six-week-old female BALB/C nu/nu nude mice (CLEA Japan, Inc.) were inoculated subcutaneously (s.c.) in the flank with 4 × 106 786-O cells (n = 20). The tumor-bearing Measurement of VEGF using an enzyme-linked immunosorbent assay (ELISA) Paraffin-embedded sections of tumors from the mouse xenograft models were prepared and stained with hematoxylin and eosin (HE). To detect activation of AKT- mTOR pathway, sections were stained with anti-CD31, anti-p-S6RP, anti-p-p70S5K and anti-p-4EBP1 antibodies (Cell Signaling Technology, Danvers, MA, USA). Staining was detected using a streptavidin-biotin kit (Nichirei, Trappes, France) according to the manufacturer’s protocol. 786-O cells were treated by TKIs at various concentrations for two hours. The VEGF concentration in the supernatant of TKI treated 786-O cells with or without tocilizumab treatment were measured using a Human VEGF Quantikine ELISA kit (R&D systems, MN) according to the manufacturer’s instructions. FDG-PET imaging 786-O cells were treated with sorafenib with or without tocilizumab for 2 hours. Whole-cell protein was extracted from the cells treated with TKIs and/or tocilizumab and sodium dodecyl sulfate–polyacrylamide gel electrophoresis was carried out. Antibodies specific for phospho-AKT (p-AKT, Ser473), AKT, phospho-mTOR (p-mTOR, Ser2448), mTOR, phospho-STAT3 (p-STAT3, Tyr705), STAT3, phospho-4EBP1 (p-4EBP1,Thr37/46), phospho-p70S6K (p-p70S6K Ser411), phospho-S6 Ribosomal Protein (p-S6RP Ser235/236), phospho- NFκB (p-NFκB, Ser536), NFκB and HIF-2α were used as primary antibodies (Cell Signaling, Beverly, MA, USA). Anti-beta-actin antibody (SIGMA, St. Louis, MO, USA) was used as an internal control. Protein bands were visualized using ECL Advanced Western detection reagents (GE Healthcare, Buchinghamshire, UK), and imaged with a ChemiDoc XRS plus system (BIO-RAD, Hercules, CA, USA). Individual bands were quantified with Image Lab 2.0 software (BIO-RAD), and normalized against the control value (untreated cells). To evaluate a potential impact of tocilizumab on a TKI therapy of RCC, FDG-PET imaging in xenograft models of mice treated with sorafenib alone and the combination sorafenib with tocilizumab was performed. Xenograft tumors in nude mice were achieved as described above. To reinforce the effect observed in the xenograft experiments, the experimental group received 30 mg/kg of sorafenib 6 days a week (n = 8), for the duration of the study starting from time when the tumors reached 10 mm in diameter. For combination therapy (n = 7) tocilizumab (i.p. injection of 100 mg three times a week) was additionally administered. Mice were fasted for 6 hours prior to start of imaging session. FDG (obtained as an aliquot from daily clinical productions at Fukushima Medical University Hospital, 7–8 MBq per mouse, maximum volume of 200 μl) was administered to mice by a bolus injection via the tail vein. PET data were acquired in fully 3-dimensional (3- D) mode. Standard Uptake Values (SUV) were calculated for 3D regions of interest (ROI), using Inveon Research Workplace software (Siemens Medical Solutions). FDG- PET imaging was performed at baseline and at scheduled intervals on days 3 and 21 (each n = 3 or 4). Animals were sacrificed for radiologic-pathologic correlation according to the schedule. FUNDING This work was supported by a Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (No.22591773). 13. Xu Z, Yang F, Wei D, Liu B, Chen C, Bao Y, Wu Z, Wu D, Tan H, Li J. Long noncoding RNA-SRLR elicits intrinsic sorafenib resistance via evoking IL-6/STAT3 axis in renal cell carcinoma. Oncogene. 2017; 36:1965–77. Statistical analysis Determination of TKI treated cell proliferation, mRNA expression level and Western blot analysis were repeated in triplicate, and the results were expressed as the www.impactjournals.com/oncotarget Oncotarget 55242 Bjarnason GA, Garcia-del-Muro X, Sosman JA, Solska E, et al. Overall survival and updated results for sunitinib compared with interferon alfa in patients with metastatic renal cell carcinoma. J Clin Oncol. 2009; 27:3584–90. mean ± SD. The mRNA and protein expression levels as well as tumor volume from the mouse xenograft models were analyzed using a Wilcoxon rank sum test. Abbreviations 3. Adnane L, Trail PA, Taylor I, Wilhelm SM. Sorafenib (BAY 43-9006, Nexavar), a dual-action inhibitor that targets RAF/ MEK/ERK pathway in tumor cells and tyrosine kinases VEGFR/PDGFR in tumor vasculature. Methods Enzymol. 2006; 407:597–612. 4EBP1: eukaryotic initiation factor 4E binding protein-1, AKT: AKT8 virus oncogene cellular homolog, ERK: extracellular Signal-regulated Kinase, FDG: fluorine-18 fluorodeoxyglucose, HIF: hypoxia-inducible factor, IL-6: interleukin 6, IL-6R: interleukin 6 receptor, JAK/STAT: janus kinase/signal transducer and activator of transcription, MAPK: mitogen-activated protein kinase, NFκB: nuclear factor κ B, mTOR: mammalian target of rapamycin, mTORC: mTOR complex, p706SK: p70S6 kinase, PDGFR: platelet-derived growth factor receptor, PET: positron emission tomography, RCC: renal cell carcinoma, S6RP: 40S ribosomal protein S6, SK1: sphingosine kinase-1, SUV: standardized uptake value, TKI: tyrosine kinase inhibitor, VEGF: vascular endothelial growth factor, VEGFR: vascular endothelial growth factor receptor. 4. Motzer RJ, Michaelson MD, Redman BG, Hudes GR, Wilding G, Figlin RA, Ginsberg MS, Kim ST, Baum CM, DePrimo SE, Li JZ, Bello CL, Theuer CP, et al. Activity of SU11248, a multitargeted inhibitor of vascular endothelial growth factor receptor and platelet-derived growth factor receptor, in patients with metastatic renal cell carcinoma. J Clin Oncol. 2006; 24:16–24. 5. Gupta S, Spiess PE. The prospects of pazopanib in advanced renal cell carcinoma. Ther Adv Urol. 2013; 5:223–32. 6. Coppin C, Kollmannsberger C, Le L, Porzsolt F, Wilt TJ. Targeted therapy for advanced renal cell cancer (RCC): a Cochrane systematic review of published randomised trials. BJU Int. 2011; 108:1556–63. Authorsʼ contributions 7. Calvo E, Grunwald V, Bellmunt J. Controversies in renal cell carcinoma: treatment choice after progression on vascular endothelial growth factor-targeted therapy. Eur J Cancer. 2014; 50:1321–9. Conception and design: K. Ishibashi, W. Brenner, D. Prawitt; Development of methodology: K. Ishibashi, T. Haber, W. Brenner Development of methodology: K. Ishibashi, T. Haber, W. Brenner 8. Iacovelli R, Carteni G, Sternberg CN, Milella M, Santoni M, Di Lorenzo G, Ortega C, Sabbatini R, Ricotta R, Messina C, Lorusso V, Atzori F, De Vincenzo F, et al. Clinical outcomes in patients receiving three lines of targeted therapy for metastatic renal cell carcinoma: results from a large patient cohort. Eur J Cancer. 2013; 49:2134–42. Acquisition of data: K. Ishibashi, I. Breuksch, S Gebhard T Sugino H Kubo J Hata M Yabe T Acquisition of data: K. Ishibashi, I. Breuksch, S. Gebhard, T. Sugino, H. Kubo, J. Hata, M. Yabe, T. Koguchi, M. Kataoka, S. Ogawa, H. Hiraki, T. Yanagida, N Haga Acquisition of data: K. Ishibashi, I. Breuksch, S. Gebhard, T. Sugino, H. Kubo, J. Hata, M. Yabe, T. Koguchi, M. Kataoka, S. Ogawa, H. Hiraki, T. Yanagida, N. Haga, Analysis and interpretation of data: K. Ishibashi, T. Analysis and interpretation of data: K. Ishibashi, T. Haber, W. Brenner W iti i d/ i i f th i t Analysis and interpretation of data: K. Ishibashi, T. Haber, W. Brenner Writing, review and/or revision of the manuscript: 9. Rini BI, Atkins MB. Resistance to targeted therapy in renal- cell carcinoma. Lancet Oncol. 2009; 10:992–1000. Haber, W. Brenner Writing, review and/or revision of the manuscript: 10. Sakai I, Miyake H, Fujisawa M. Acquired resistance to sunitinib in human renal cell carcinoma cells is mediated by constitutive activation of signal transduction pathways associated with tumour cell proliferation. BJU Int. 2013; 112:E211–20. K. Ishibashi, D. Prawitt, W. Brenner Administrative, technical, or material support: K. K. Ishibashi, D. Prawitt, W. Brenner Administrative, technical, or material support: K. Ishibashi, T. Haber, Y. Kojima, J.W. Thüroff, W. Brenner Study supervision: W. Brenner. Ishibashi, T. Haber, Y. Kojima, J.W. Thüroff, W. Brenner Study supervision: W. Brenner. 11. Gao H, Deng L. Sphingosine kinase-1 activation causes acquired resistance against Sunitinib in renal cell carcinoma cells. Cell Biochem Biophys. 2014; 68:419–25. CONFLICTS OF INTEREST The authors declare no potential conflicts of interest. 12. Huang WC, Hung CM, Wei CT, Chen TM, Chien PH, Pan  HL, Lin YM, Chen YJ. Interleukin-6 expression contributes to lapatinib resistance through maintenance of stemness property in HER2-positive breast cancer cells. Oncotarget. 2016; 7:62352–63. https://doi.org/10.18632/ oncotarget.11471. REFERENCES 1. Cohen HT, McGovern FJ. Renal-cell carcinoma. N Engl J Med. 2005; 353:2477–90. 1. Cohen HT, McGovern FJ. Renal-cell carcinoma. N Engl J Med. 2005; 353:2477–90. 14. Dancey J. mTOR signaling and drug development in cancer. Nat Rev Clin Oncol. 2010; 7:209–19. 15. Shi Y, Hsu JH, Hu L, Gera J, Lichtenstein A. Signal pathways involved in activation of p70S6K and 2. Motzer RJ, Hutson TE, Tomczak P, Michaelson MD, Bukowski RM, Oudard S, Negrier S, Szczylik C, Pili R, 2. Motzer RJ, Hutson TE, Tomczak P, Michaelson MD, Bukowski RM, Oudard S, Negrier S, Szczylik C, Pili R, www.impactjournals.com/oncotarget Oncotarget 55243 on some human myeloma cell lines. Cytokine. 2001; 14: 352–6. phosphorylation of 4E-BP1 following exposure of multiple myeloma tumor cells to interleukin-6. J Biol Chem. 2002; 277:15712–20. 28. Yao Z, Fenoglio S, Gao DC, Camiolo M, Stiles B, Lindsted T, Schlederer M, Johns C, Altorki N, Mittal V, Kenner L, Sordella R. TGF-beta IL-6 axis mediates selective and adaptive mechanisms of resistance to molecular targeted therapy in lung cancer. Proc Natl Acad Sci U S A. 2010; 107:15535–40. 16. Hsu JH, Shi Y, Hu L, Fisher M, Franke TF, Lichtenstein A. Role of the AKT kinase in expansion of multiple myeloma clones: effects on cytokine-dependent proliferative and survival responses. Oncogene. 2002; 21:1391–400. 17. Hideshima T, Nakamura N, Chauhan D, Anderson KC. Biologic sequelae of interleukin-6 induced PI3-K/Akt signaling in multiple myeloma. Oncogene. 2001; 20:5991–6000. 29. Porta C, Paglino C, Imarisio I, Ganini C, Sacchi L, Quaglini S, Giunta V, De Amici M. Changes in circulating pro-angiogenic cytokines, other than VEGF, before progression to sunitinib therapy in advanced renal cell carcinoma patients. Oncology. 2013; 84:115–22. 18. Kihara M, Davies R, Kearsley-Fleet L, Watson KD, Lunt M, Symmons DP, Hyrich KL, British Society for Rheumatology Biologics Register. Use and effectiveness of tocilizumab among patients with rheumatoid arthritis: an observational study from the British Society for Rheumatology Biologics Register for rheumatoid arthritis. Clin Rheumatol. 2017; 36:241–50. 30. Cuadros T, Trilla E, Sarró E, Vilà MR, Vilardell J, de Torres I, Salcedo M, López-Hellin J, Sánchez A, Ramón y Cajal S, Itarte E, Morote J, Meseguer A. HAVCR/KIM-1 activates the IL-6/STAT-3 pathway in clear cell renal cell carcinoma and determines tumor progression and patient outcome. Cancer Res. 2014; 74:1416–28. 19. REFERENCES Oguro T, Ishibashi K, Sugino T, Hashimoto K, Tomita S, Takahashi N, Yanagida T, Haga N, Aikawa K, Suzutani T, Yamaguchi O, Kojima Y. Humanised antihuman IL-6R antibody with interferon inhibits renal cell carcinoma cell growth in vitro and in vivo through suppressed SOCS3 expression. Eur J Cancer. 2013; 49:1715–24. 31. Yang XW, Li L, Hou GJ, Yan XZ, Xu QG, Chen L, Zhang BH, Shen F. STAT3 overexpression promotes metastasis in intrahepatic cholangiocarcinoma and correlates negatively with surgical outcome. Oncotarget. 2017; 8:7710–21. https://doi.org/10.18632/oncotarget.13846. 20. Brodaczewska KK, Szczylik C, Fiedorowicz M, Porta C, Czarnecka AM. Choosing the right cell line for renal cell cancer research. Mol Cancer. 2016; 15:83. 32. McDaniel JM, Varley KE, Gertz J, Savic DS, Roberts BS, Bailey SK, Shevde LA, Ramaker RC, Lasseigne BN, Kirby MK, Newberry KM, Partridge EC, Jones AL, et al. Genomic regulation of invasion by STAT3 in triple negative breast cancer. Oncotarget. 2017; 8:8226–38. https://doi. org/10.18632/oncotarget.14153. 21. Carroll VA, Ashcroft M. Role of hypoxia-inducible factor (HIF)-1alpha versus HIF-2alpha in the regulation of HIF target genes in response to hypoxia, insulin-like growth factor-I, or loss of von Hippel-Lindau function: implications for targeting the HIF pathway. Cancer Res. 2006; 66:6264–70. 33. Müller S, Chen Y, Ginter T, Schäfer C, Buchwald M, Schmitz LM, Klitzsch J, Schütz A, Haitel A, Schmid K, Moriggl R, Kenner L, Friedrich K, et al. SIAH2 antagonizes TYK2-STAT3 signaling in lung carcinoma cells. Oncotarget. 2014; 5:3184–96. https://doi.org/10.18632/oncotarget.1899. 22. Maxwell PH, Wiesener MS, Chang GW, Clifford SC, Vaux EC, Cockman ME, Wykoff CC, Pugh CW, Maher ER, Ratcliffe PJ. The tumour suppressor protein VHL targets hypoxia-inducible factors for oxygen-dependent proteolysis. Nature. 1999; 399:271–5. 34. Schaper F, Rose-John S. Interleukin-6: Biology, signaling and strategies of blockade. Cytokine Growth Factor Rev. 2015; 26:475–87. 23. O’Hagan-Wong K, Nadeau S, Carrier-Leclerc A, Apablaza F, Hamdy R, Shum-Tim D, Rodier F, Colmegna I. Increased IL-6 secretion by aged human mesenchymal stromal cells disrupts hematopoietic stem and progenitor cells’ homeostasis. Oncotarget. 2016; 7:13285–96. https:// doi.org/10.18632/oncotarget.7690. 35. Niu G, Wright KL, Huang M, Song L, Haura E, Turkson J, Zhang S, Wang T, Sinibaldi D, Coppola D, Heller R, Ellis LM, Karras J, et al. Constitutive Stat3 activity up- regulates VEGF expression and tumor angiogenesis. Oncogene. 2002; 21:2000–8. 24. Kishimoto T, Akira S, Narazaki M, Taga T. Interleukin-6 family of cytokines and gp130. Blood. 1995; 86:1243–54. 36. REFERENCES Gray MJ, Zhang J, Ellis LM, Semenza GL, Evans DB, Watowich SS, Gallick GE. HIF-1alpha, STAT3, CBP/p300 and Ref-1/APE are components of a transcriptional complex that regulates Src-dependent hypoxia-induced expression of VEGF in pancreatic and prostate carcinomas. Oncogene. 2005; 24:3110–20. 25. Nemeth E, Valore EV, Territo M, Schiller G, Lichtenstein A, Ganz T. Hepcidin, a putative mediator of anemia of inflammation, is a type II acute-phase protein. Blood. 2003; 101:2461–3. 26. Zhao G, Zhu G, Huang Y, Zheng W, Hua J, Yang S, Zhuang J, Ye J. IL-6 mediates the signal pathway of JAK-STAT3-VEGF-C promoting growth, invasion and lymphangiogenesis in gastric cancer. Oncol Rep. 2016; 35:1787–95. 37. Yu H, Pardoll D, Jove R. STATs in cancer inflammation and immunity: a leading role for STAT3. Nat Rev Cancer. 2009; 9:798–809. 27. Thabard W, Collette M, Mellerin MP, Puthier D, Barille S, Bataille R, Amiot M. IL-6 upregulates its own receptor 38. Novotny NM, Markel TA, Crisostomo PR, Meldrum DR. Differential IL-6 and VEGF secretion in adult and neonatal www.impactjournals.com/oncotarget Oncotarget 55244 mesenchymal stem cells: role of NFkB. Cytokine. 2008; 43:215–9. 48. Pages G, Pouyssegur J. Transcriptional regulation of the Vascular Endothelial Growth Factor gene--a concert of activating factors. Cardiovasc Res. 2005; 65:564–73. 39. Lauritzen HP, Brandauer J, Schjerling P, Koh HJ, Treebak JT, Hirshman MF, Galbo H, Goodyear LJ. Contraction and AICAR stimulate IL-6 vesicle depletion from skeletal muscle fibers in vivo. Diabetes. 2013; 62:3081–92. 49. Nishimoto N, Yoshizaki K, Miyasaka N, Yamamoto K, Kawai S, Takeuchi T, Hashimoto J, Azuma J, Kishimoto T. Treatment of rheumatoid arthritis with humanized anti- interleukin-6 receptor antibody: a multicenter, double-blind, placebo-controlled trial. Arthritis Rheum. 2004; 50:1761–9. 40. Atsumi T, Singh R, Sabharwal L, Bando H, Meng J, Arima Y, Yamada M, Harada M, Jiang JJ, Kamimura D, Ogura H, Hirano T, Murakami M. Inflammation amplifier, a new paradigm in cancer biology. Cancer Res. 2014; 74:8–14. 50. Imagawa T, Yokota S, Mori M, Miyamae T, Takei S, Imanaka H, Nerome Y, Iwata N, Murata T, Miyoshi M, Nishimoto N, Kishimoto T. Safety and efficacy of tocilizumab, an anti-IL-6-receptor monoclonal antibody, in patients with polyarticular-course juvenile idiopathic arthritis. Mod Rheumatol. 2012; 22:109–15. 41. Porta C, Paglino C, De Amici M, Quaglini S, Sacchi L, Imarisio I, Canipari C. Predictive value of baseline serum vascular endothelial growth factor and neutrophil gelatinase-associated lipocalin in advanced kidney cancer patients receiving sunitinib. Kidney Int. 2010; 77:809–15. 51. REFERENCES Fujiwara S, Mochinaga H, Nakata H, Ohshima K, Matsumoto M, Uchiba M, Mikami Y, Hata H, Okuno Y, Mitsuya H, Nosaka K. Successful treatment of TAFRO syndrome, a variant type of multicentric Castleman disease with thrombotic microangiopathy, with anti-IL-6 receptor antibody and steroids. Int J Hematol. 2016; 103:718–23. 42. Harmon CS, DePrimo SE, Figlin RA, Hudes GR, Hutson TE, Michaelson MD, Negrier S, Kim ST, Huang X, Williams JA, Eisen T, Motzer RJ. Circulating proteins as potential biomarkers of sunitinib and interferon-alpha efficacy in treatment-naive patients with metastatic renal cell carcinoma. Cancer Chemother Pharmacol. 2014; 73:151–61. 52. Ito H, Takazoe M, Fukuda Y, Hibi T, Kusugami K, Andoh A, Matsumoto T, Yamamura T, Azuma J, Nishimoto  N. A pilot randomized trial of a human anti-interleukin-6 receptor monoclonal antibody in active Crohn’s disease. Gastroenterology. 2004; 126:989–96. 43. Dodd KM, Yang J, Shen MH, Sampson JR, Tee AR. mTORC1 drives HIF-1alpha and VEGF-A signalling via multiple mechanisms involving 4E-BP1, S6K1 and STAT3. Oncogene. 2015; 34:2239–50. 53. Schor-Bardach R, Alsop DC, Pedrosa I, Solazzo SA, Wang X, Marquis RP, Atkins MB, Regan M, Signoretti S, Lenkinski RE, Goldberg SN. Does arterial spin-labeling MR imaging-measured tumor perfusion correlate with renal cell cancer response to antiangiogenic therapy in a mouse model? Radiology. 2009; 251:731–42. 44. Hsieh AC, Liu Y, Edlind MP, Ingolia NT, Janes MR, Sher A, Shi EY, Stumpf CR, Christensen C, Bonham MJ, Wang S, Ren P, Martin M, et al. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature. 2012; 485:55–61. 45. Toschi A, Lee E, Gadir N, Ohh M, Foster DA. Differential dependence of hypoxia-inducible factors 1 alpha and 2 alpha on mTORC1 and mTORC2. J Biol Chem. 2008; 283:34495–9. 54. Takeuchi A, Eto M, Tatsugami K, Yamada H, Oki T, Kiyoshima K, Yoshikai Y, Naito S. Mechanism of synergistic antitumor effect of sorafenib and interferon- alpha on treatment of renal cell carcinoma. J Urol. 2010; 184:2549–56. 46. Gordan JD, Simon MC. Hypoxia-inducible factors: central regulators of the tumor phenotype. Curr Opin Genet Dev. 2007; 17:71–7. 55. Tomayko MM, Reynolds CP. Determination of subcutaneous tumor size in athymic (nude) mice. Cancer Chemother Pharmacol. 1989; 24:148–54. 47. Kondo K, Kim WY, Lechpammer M, Kaelin WG Jr. Inhibition of HIF2alpha is sufficient to suppress pVHL- defective tumor growth. PLoS Biol. 2003; 1:E83. www.impactjournals.com/oncotarget Oncotarget 55245
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Maintaining phagosome integrity during fungal infection: do or die?
Microbial cell
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Maintaining phagosome integrity during fungal infection: do or die? Mabel Yang1, Glenn F.W. Walpole1,2 and Johannes Westman1,* 1 Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada. 2 Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada. * Corresponding Author: Mabel Yang1, Glenn F.W. Walpole1,2 and Johannes Westman1,* 1 Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada. 2 Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada. * Corresponding Author: Johannes Westman, Program in Cell Biology, The Hospital for Sick Children, 686 Bay St, Toronto, ON, Canada M5G 0 E-mail: johannes.westman@sickkids.ca Professional phagocytes represent a critical node in innate immunity and tissue homeostasis through their specialized ability to eat, drink, and digest material from the extracellular milieu. The degradative and mi- crobicidal functions of phagocytes rely on the fusion of lysosomes with endosomal compartments such as phagosomes, resulting in the digestion and recycling of internalized prey and debris. Despite these efforts, several particularly dangerous infections result from a class of tenacious pathogens that resist digestion, of- ten surviving and even proliferating within the con- fines of the phagosomal membrane. One such example, Candida albicans, is a commensal polymorphic fungus that colonizes ~50% of the population and can cause life-threatening infections in immunocompromised patients. Not only can C. albicans survive within phag- osomes, but its ingestion by macrophages triggers a yeast-to-hyphal transition promoting rapid intra- phagosomal growth (several microns per hour) while imposing a substantial mechanical burden on the phagosomal membrane surrounding the fungus. Preservation of membrane integrity is essential to maintain the hostile internal environment of the phagosome, a functionality of degradative enzymes and oxidative stress. Yet, biological membranes such as phagosomes have a limited capacity to stretch. Us- ing C. albicans as a model intracellular pathogen, our recent work reveals a mechanism by which phago- somes respond to intraphagosomal growth of patho- gens by expanding their surface area, and as a result, maintain the integrity of the phagosomal membrane. We hypothesized that this expansion would be facili- tated by the delivery and fusion of membrane from extraneous sources with the phagosome. Consistently, macrophages respond to the yeast-to-hyphal transition through a stretch-induced release of phagosomal cal- cium, leading to recruitment and insertion of lyso- somes that accommodate the expansion of the phago- lysosome and preserve its integrity. Below, we discuss this calcium-dependent mechanism of lysosome inser- tion as a means of avoiding phagosomal rupture. Microreview www.microbialcell.com MICROREVIEW on: Westman J, Walpole GFW, Kasper L, Xue BY, Elshafee O, Hube B, Grinstein S (2020). Lysosome Fusion Maintains Phago- some Integrity during Fungal Infection. Cell Host Microbe S1931-3128(20): 30505-9. doi: 10.1016/j.chom.2020.09.004 doi: 10.15698/mic2020.12.738 Received 17.11.2020, Accepted 24.11.2020, Published 03.12.2020. Keywords: Candida albicans, phagosome, lysosome, macrophage, fungi, calcium. Maintaining phagosome integrity during fungal infection: do or die? (A) Phagosomes expand their surface area by insertion of lysosomes. As C. albicans initiates filamentation inside the mature phagosome, luminal Ca2+ is released, leading to recruitment and inser- tion of lysosomes. This preserves phagosome integrity while restricting fungal growth. (B) The second wave of lysosome insertion can be inhibited by applying the Ca2+ chelator BAPTA. Preventing cytosolic Ca2+ transients during intraphagosomal growth leads to early phagosome rupture, NLRP3 inflammasome activation, and subsequent macrophage cell death. Actin polymerizes at the site where the hypha protrudes through the plasma membrane, possibly re-sealing the macrophage membrane and preventing leakage of cytosolic content. FIGURE 1: Lysosome fusion maintains phagosome integrity during fungal infection. (A) Phagosomes expand their surface area by insertion of lysosomes. As C. albicans initiates filamentation inside the mature phagosome, luminal Ca2+ is released, leading to recruitment and inser- tion of lysosomes. This preserves phagosome integrity while restricting fungal growth. (B) The second wave of lysosome insertion can be inhibited by applying the Ca2+ chelator BAPTA. Preventing cytosolic Ca2+ transients during intraphagosomal growth leads to early phagosome rupture, NLRP3 inflammasome activation, and subsequent macrophage cell death. Actin polymerizes at the site where the hypha protrudes through the plasma membrane, possibly re-sealing the macrophage membrane and preventing leakage of cytosolic content. Compromising the host macrophages' ability to main- tain phagosome membrane integrity can lead to dire con- sequences for the host cell. During the intraphagosomal growth of C. albicans, inhibition of lysosome insertion by calcium buffering triggered early phagosome rupture, de- tected by phagosomal leakage of a small fluorescent dye Sulforhodamine B. The resulting phagosomal rupture cor- related tightly with host cell death, increased fungal growth, and escape of the hyphal tip from the host macro- phage (Figure 1B). Accordingly, maintaining phagosome integrity is essential, not only for macrophage viability, but also to restrict the engulfed prey's growth. However, in the case of candidiasis, it remains to be explored if phagosome expansion ultimately improves fungal survival and persis- tence by 'cloaking' the organism from nearby immune cells. On the other hand, enhanced fungal growth could promote rupture and leakage of phagosome contents alerting nearby sentinel cells and engaging additional arms of the immune system to limit the infection. Consistent with the latter, our work identified that a major conse- quence of phagosome rupture is the activation of the NLRP3 inflammasome (Figure 1B). Maintaining phagosome integrity during fungal infection: do or die? Fur- ther, we examine the implications of membrane integ- rity on the delicate balance between the host and pathogen by focusing on fungal stress responses, nu- trient acquisition, inflammasome activation, and cell death. Insertion of lysosomes is required for canonical phagosome maturation. However, this maturation process is self- limiting; macrophages detect when adequate lysosomes have fused with the maturing phagosome and terminate further insertion. After engulfment, the yeast form of C. albicans can survive inside phagosomes, undergoing continuous growth, and more importantly, triggering a secondary wave of lysosome fusion (Figure 1A). This sec- ond wave of lysosome recruitment and insertion requires intact microtubules as well as the centripetal motor pro- tein dynein. But what mediates the second wave of lyso- some fusion? At a first glance, transient increases in calci- um which mediate the activation of calcium-dependent SNARE proteins, were of obvious interest. Cytosolic calcium transients can be buffered with a membrane-permeable acetoxymethyl precursor of BAPTA (BAPTA-AM): a 'fast' cytosolic calcium chelator. In our study, BAPTA-AM was added 30 minutes post-infection − a time when canonical phagosome maturation had already been completed. Buff- ering cytosolic calcium transients impaired lysosome inser- Insertion of lysosomes is required for canonical phagosome maturation. However, this maturation process is self- limiting; macrophages detect when adequate lysosomes have fused with the maturing phagosome and terminate further insertion. After engulfment, the yeast form of C. albicans can survive inside phagosomes, undergoing continuous growth, and more importantly, triggering a secondary wave of lysosome fusion (Figure 1A). This sec- ond wave of lysosome recruitment and insertion requires intact microtubules as well as the centripetal motor pro- tein dynein. But what mediates the second wave of lyso- some fusion? At a first glance, transient increases in calci- um which mediate the activation of calcium-dependent SNARE proteins, were of obvious interest. Cytosolic calcium transients can be buffered with a membrane-permeable acetoxymethyl precursor of BAPTA (BAPTA-AM): a 'fast' cytosolic calcium chelator. In our study, BAPTA-AM was added 30 minutes post-infection − a time when canonical phagosome maturation had already been completed. Buff- ering cytosolic calcium transients impaired lysosome inser- doi: 10.15698/mic2020.12.738 Received 17.11.2020, Accepted 24.11.2020, Published 03.12.2020. Keywords: Candida albicans, phagosome, lysosome, macrophage, fungi, calcium. Microbial Cell | DECEMBER 2020 | Vol. 7 No. 12 OPEN ACCESS | www.microbialcell.com 323 M. Yang et al. (2020) FIGURE 1: Lysosome fusion maintains phagosome integrity during fungal infection. Maintaining phagosome integrity during fungal infection: do or die? This multi-component protein complex can sense minute perturbations to the host cytosol and trigger the processing and secretion of the pro-inflammatory cytokines IL-1β and IL-18. Although in- flammasome activation results in death of the infected macrophage, the process is altruistic in that these pro- inflammatory cytokines stimulate the recruitment of circu- lating neutrophils that may better limit fungal spread. To- gether, these observations raise the question of whether the fungus or the macrophage benefits from maintaining phagosome integrity as NLRP3 inflammasome activation could lead to different outcomes depending on the clinical setting. In the context of our study, it is clear that the fun- gus benefits from phagosome rupture despite NLRP3 in- flammasome activation within infected macrophages. tion, but unexpectedly, neither calcium from the endo- plasmic reticulum nor extracellular calcium was required for this process. To understand the source of the calcium, changes in cytosolic calcium were monitored by expressing the genetically-encoded fluorescent calcium indicator GCaMP6s. Micro-fissures induced in the phagosomal membrane using LLOMe —a lysomotropic compound that accumulates in acidic compartments where it is converted into a lytic form— revealed that the lumen of the phago- some itself is a significant source of calcium. In turn, phag- osome expansion requires the release of this phagosomal calcium pool triggering a secondary wave of lysosome fu- sion (Figure 1A). Previous work studying canonical phago- some maturation identified an essential role for the lyso- somal transient receptor potential family channel-1 (TRPML-1) in local calcium release and phagosome matura- tion. Although local calcium release mediates the ongoing recruitment of lysosomes, phagosome expansion persisted in macrophages lacking TRPML-1. Additionally, the endoly- sosomal lipid PtdIns(3,5)P2, which activates TRPML-1, was also not required for phagosome expansion. As such, the second wave of lysosome fusion appears to bypass several hallmarks of canonical phagosome maturation. These find- ings may point towards an interesting case of convergent molecular evolution, whereby the second wave of lyso- some fusion occurs by re-harnessing pre-existing calcium- dependent fusion machinery. Impaired lysosome fusion in macrophages treated with calmidazolium, a calmodulin inhibitor, implicates the involvement of SNARE proteins and tethering factors in the phagosome-lysosome insertion pathway. Thus, the cooperative action of previously impli- cated endolysosomal SNAREs, Rab GTPases, and tethering factors may help facilitate phagosome expansion and shed light upon the interplay of various membrane fusion ma- chineries. Microbial Cell | DECEMBER 2020 | Vol. 7 No. 12 Maintaining phagosome integrity during fungal infection: do or die? tion, but unexpectedly, neither calcium from the endo- plasmic reticulum nor extracellular calcium was required for this process. To understand the source of the calcium, changes in cytosolic calcium were monitored by expressing the genetically-encoded fluorescent calcium indicator GCaMP6s. Micro-fissures induced in the phagosomal membrane using LLOMe —a lysomotropic compound that accumulates in acidic compartments where it is converted into a lytic form— revealed that the lumen of the phago- some itself is a significant source of calcium. In turn, phag- osome expansion requires the release of this phagosomal calcium pool triggering a secondary wave of lysosome fu- sion (Figure 1A). Previous work studying canonical phago- some maturation identified an essential role for the lyso- somal transient receptor potential family channel-1 (TRPML-1) in local calcium release and phagosome matura- tion. Although local calcium release mediates the ongoing recruitment of lysosomes, phagosome expansion persisted in macrophages lacking TRPML-1. Additionally, the endoly- sosomal lipid PtdIns(3,5)P2, which activates TRPML-1, was also not required for phagosome expansion. As such, the second wave of lysosome fusion appears to bypass several hallmarks of canonical phagosome maturation. These find- ings may point towards an interesting case of convergent molecular evolution, whereby the second wave of lyso- some fusion occurs by re-harnessing pre-existing calcium- dependent fusion machinery. Impaired lysosome fusion in macrophages treated with calmidazolium, a calmodulin inhibitor, implicates the involvement of SNARE proteins and tethering factors in the phagosome-lysosome insertion pathway. Thus, the cooperative action of previously impli- cated endolysosomal SNAREs, Rab GTPases, and tethering factors may help facilitate phagosome expansion and shed light upon the interplay of various membrane fusion ma- chineries. Microbial Cell | DECEMBER 2020 | Vol. 7 No. 12 OPEN ACCESS | www.microbialcell.com 324 M. Yang et al. (2020) Phagosome expansion during fungal infection somal growth. In contrast, a significant withdrawal in tran- scriptional stress responses were observed when phago- some expansion was inhibited. The downregulation of C. albicans genes associated with oxidative and nitrosative stress and metabolism compared to intact phagosomes demonstrates reduced microbiostatic capacity in ruptured phagosomes. In addition to benefiting from elevated pH and disseminating antimicrobial effectors, these findings support the notion that the escaping fungi gain access to the nutrient-rich cytosol. Collectively, these factors lead to increased fungal growth and escape. This final aspect of our study could have important implications for the fungus' ability to spread throughout tissues and cause systemic dissemination in vivo. The authors declare no conflict of interests. A final intriguing finding was that disruption of phago- some integrity led to enhanced pathogen growth and es- cape (Figure 1B). Within the hostile environment of the phagosome, C. albicans exhibits transcriptional responses associated with starvation and oxidative/nitrosative stress. C. albicans is metabolically flexible and is known to adapt to the nutrient-deprived phagosome. For example, gluco- neogenesis via the glyoxylate cycle has previously been reported as a metabolic adaptation inside the macrophage phagosome. Whole-genome microarrays were performed on RNA isolated from C. albicans grown in intact phago- somes. We confirmed that the fungal stress responses were maintained even after several hours of intraphago- Please cite this article as: Mabel Yang, Glenn F.W. Walpole and Johannes Westman (2020). Maintaining phagosome integrity during fungal infection: do or die? Microbial Cell 7(12): 323-325. doi: 10.15698/mic2020.12.738 Maintaining phagosome integrity during fungal infection: do or die? However, even when phagosomes expand without interruption, the fungus ultimately escapes from the macrophage. Intriguingly, we observed that mac- rophages were able to survive this fungal escape without loss of plasma membrane integrity. As the hypha protrudes out of the cell membrane, actin polymerization mediated the formation of a tight seal, preventing cytosol leakage and consequent host cell death. How macrophages cope with the protruding hypha through the plasma membrane remains to be elucidated. Further investigation into the benefits and drawbacks of phagosome rupture in the con- text of pathogen growth, inflammasome activation, and host cell death are important and exciting aspects awaiting host-pathogen biologists. Our work revealed that macrophages can accommo- date the unrelenting intracellular growth of C. albicans infection by incorporating additional membrane derived from lysosomes. Beyond fungal infection, the data impli- cates lysosome insertion as a general response to intra- phagosomal growth of pathogens and appears to have biological importance for other intracellular pathogens. For example, intraphagosomal growth of various fungi, bacte- ria, and protozoa have been described in macrophages. Indeed, phagosomes containing Candida glabrata and Staphylococcus aureus expand by lysosome insertion, albe- it at a reduced rate, correlating with the reduced intra- phagosomal growth of these prey. However, the factors that mediate the pre-initiation of lysosome-phagosome traffic and fusion in mature phagolysosomes are not ap- parent and could differ based on the identity of the intra- cellular pathogen. Macrophages containing filamentous fungi or bacteria may trigger a fissure-mediated fusion mechanism similar to C. albicans, but it is unclear if this is always the case. For example, Salmonella enterica remod- els the host cell endolysosomal system by recruiting modi- fied late endosomal compartments to expand the Salmo- nella-containing vacuole. In contrast, some pathogens may purposefully lyse the phagosome to access the nutrient- rich cytosol. Pathogens that manipulate phagosome matu- ration to prevent lysosome insertion clearly obtain a dras- tically different intracellular niche than that of C. albicans. Further investigation is required to uncover how the identi- fied mechanism of phagosome expansion is modified by different intracellular prey. Please cite this article as: Mabel Yang, Glenn F.W. Walpole and Johannes Westman (2020). Maintaining phagosome integrity during fungal infection: do or die? Microbial Cell 7(12): 323-325. doi: 10.15698/mic2020.12.738 COPYRIGHT © 2020 Yang et al. This is an open-access article released under the terms of the Creative Commons Attribution (CC BY) license, which allows the unrestricted use, distribution, and reproduction in any medium, provided the original author and source are acknowledged. Please cite this article as: Mabel Yang, Glenn F.W. Walpole and Johannes Westman (2020). Maintaining phagosome integrity during fungal infection: do or die? Microbial Cell 7(12): 323-325. doi: 10.15698/mic2020.12.738 Microbial Cell | DECEMBER 2020 | Vol. 7 No. 12 325 OPEN ACCESS | www.microbialcell.com
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German
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Th. Kölliker, Die Gipsdrahtschiene
Deutsche medizinische Wochenschrift/Deutsche Medizinische Wochenschrift
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DEUTSCHE IDTCIIHSOHE WOCIIENSCURIFT. DEUTSCHE IDTCIIHSOHE WOCIIENSCURIFT. 8. August 543 Th. K1Iîker, Die Gipsdrahtsehiene. Leipzig, F. C. W. Vogel, 1900. 12 S,, 0,60 M. - Th. K1Iîker, Die Gipsdrahtsehiene. Leipzig, F. C. W. Vogel, 1900. 12 S,, 0,60 M. - Die in erster Linie für den Feldsanitätsdienst bestimmte -ips- drahtschieno wird hergestellt aus engmaschigem, sehr dtinncm Draht- geflecht und aus Gipsbinden. Aus dem Drahtgeflecht wird zunächst die Schiene in der gewünschten Grösse und Form zurechtgeschnitten, dann wird die Schiene mit Gipshindentoiu'en umwickelt, so zwar, dass der Verband drei Lagen der Gipabinde stsrk wird. Die auf diese Weise fertiggestellte Gipsdrahtschiene hat nun den grossen Vorzug, vollkommen plastisch zu sein; sie kann beliebig gebogen und auch mit einer Hohlkehle versehen werden, sie schmiegt sich der Extremität vollkommen an. de zum persönlichen Gebrauch heruntergeladen. Vervielfältigung nur mit Zustimmung des Verlages. Die Vorzüge der Gi1sdraht.schiene fasst Kölliker in folgenden Sätzen zusammen: 1. Sie vereinfacht don Gipsverband, indem sie durch den geringen Consum an Gipsbinden und au Polsterung am Material spart. 2. Sie ist leicht abzunehmen und leicht wieder anzulegen, ge- stattet somit ohne Schwierigkeiten und Zeitaufwand ein e Besichtigung und Revision der verletzten Stelle. 3. Sie ersetzt eine i\nzahl Schienen, die die Kriegssanitätsordnung vorsieht, die demnach nicht im Fc1d mitzuführen wären. 4. Se vereinfacht aber auch in der Civiiprauis (lie Behandlung von Frakturen und entzündlichen Prozessen am Rmipfe und an den Extremitäten. Die verschiedenen Drahtmodelle werden durch eine Reihe von Ab- bildungen veranschaulicht. P. Wagner (Leipzig).
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Kirigami-inspired, three-dimensional piezoelectric pressure sensors assembled by compressive buckling
npj flexible electronics
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Check for updates Check for updates Yi Zhang1,2, Changbo Liu 2,3 , Ben Jia2,3, Dongqin Ma2,3, Xuecheng Tian1,2, Yuanyuan Cui1,2 & Yuan Deng1,2 Piezoelectric sensors whose sensing performances can be flexibly regulated hold significant promise for efficient signal-acquisition applications in the healthcare field. The existing methods for regulating the properties of polyvinylidene fluoride (PVDF) films mainly include material modification and structural design. Compared to material modification, which has a long test period and an unstable preparation process, structural design is a more efficient method. The irigami structure combined with compressive buckling can endow the flexible film with rich macrostructural features. Here, a method is fabricated to modulate the sensing performance by employing distinct 3D structures and encapsulation materials with varying Young’s moduli. The relationship among the aspect ratio (α), pattern factor (η), elastic modulus of encapsulation materials, and equivalent stiffness is obtained by finite element simulation, which provides theoretical guidance for the design of the 2D precursor and the selection of encapsulation materials. In the demonstration applications, the sensor accurately captures pulse waveforms in multiple parts of the human body and is employed for the pressure monitoring of different parts of the sole under various posture states. This method of structure design is efficient, and the preparation process is convenient, providing a strategy for the performance control of piezoelectric pressure sensors. Advanced piezoelectric pressure sensors play a pivotal role in the field of healthcare monitoring, encompassing critical applications such as blood pressure measurement1, plantar- pressure analysis2, respiratory monitoring3, human-motion detection4, and human-speech recognition5. This is attributed to their fast response6, wide measuring range7, compact size8 and easy fabrication9. Due to their elevated piezoelectric coefficient, which can reach up to 1500 pC N−1 10 and far exceeds those of other piezoelectric materials11–13, piezoelectric ceramics have been extensively utilized in the manufacture of pressure sensors. However, they cannot bend and stretch because of their high stiffness and density values, limiting their application in healthcare monitoring. They also exhibit a high acoustic impedance,which hinders the effective conversion between mechanical and electrical energy. In contrast, piezoelectric polymers exhibit exceptional flexibility and an acoustic impedance closely matching that of the human body. Among them, polyvinylidene fluoride (PVDF) exhibits a high sen- sitivity, and its impedance is compatible with the human skin. npj | flexible electronics Article Published in partnership with Nanjing Tech University Published in partnership with Nanjing Tech University https://doi.org/10.1038/s41528-024-00310-6 npj | flexible electronics npj | flexible electronics 1Research Institute for Frontier Science, Beihang University, Beijing 100191, China. 2Key Laboratory of Intelligent Sensing Materials and Chip Integration Tech- nology of Zhejiang Province, Hangzhou Innovation Institute of Beihang University, Hangzhou 310051, China. 3School of Materials Science and Engineering, Beihang University, Beijing 100191, China. e-mail: liuchb@buaa.edu.cn; dengyuan@buaa.edu.cn Check for updates Structural design is another effective way to alter PVDF sensor performance. For instance, the microstructural design of materials can enhance sensor performance46,47. However, its impact remains constrained, and the struc- tural formation remains intricate. The basic shape of the 2D precursor determines the shape of the 3D structure. In this work, the 2D basic shapes, square, circle, and triangle, are designed with the same area as the basis (the corresponding samples are named BS1, BS2, and BS3). The structural images of the above three 3D kirigami structures are depicted in Fig. 1b. Finite Element Analysis (FEA) indicates that different basic shapes correspond to different maximum principal strain limits, with BS2 having the maximum value and BS3 having the minimum. When external pressure within the range of approximately 300–1,400 kPa is vertically applied to the sensors, their open-circuit voltage changes approximately linearly, as shown in Fig. 1c. The sensitivity of the three sensors (shown in Fig. 1d) are significantly higher than those of the control group. In comparison with the control group, the BS2 sample, featuring 2D circular precursors, offers more than a double increase in sensitivity and output voltage at the same pressure. The 3D structural dia- gram in the finite element analysis shows that the sensor with a 3D structure hasalargerstrainthantheplanarstructure(controlgroup,withzero strain). Consequently, it has better sensitivity and output voltage than the control group. The maximum principal strain of BS2 is greater than those of BS1 and BS3. The 3D-formed film has higher strains at the bending points, and due to the curved boundaries, BS2 has more significant strain areas. The larger strain generated during 3D forming improves the deformation cap- ability of BS2, resulting in the highest output among all samples. Addi- tionally, when conducting measurements exceeding 100 instances, we observe a verysmall marginof error. In thiscontext,the output of the sensor can be significantly improved through 3D kirigami structural design, and further optimization of the 2D pattern can adjust the sensor’s performance. As a traditional artistic processing technique, kirigami introduces macroscopic changes to materials beyond their inherent elasticity by guiding deformation from two to three dimensions. When combined with compressive buckling, kirigami can generate various intriguing structures. The 3D kirigami structure is primarily influenced by the shape of the 2D planar precursor, and the cutting pattern is pivotal to the structural design. Check for updates Thus, it has become one of the most employed materials for flexible, wearable pressure- sensing equipment14–19 and has shown significant application potential in human–machine interfaces20, pulse signal acquisition21–24, flexible electronic skin25–27, energy collection28–31 and other fields. However, the low piezoelectric coefficient of PVDF restricts its per- formance in pressure sensors. In particular, for faint physiological signals, PVDF-basedpressuresensorsfrequentlystruggleto achieveprecisecapture, and they present significant measurement errors in the presence of envir- onmental interference32,33. In human signal monitoring, sensors are expected to be portable, exhibit excellent linearity, and possess high flexibility34. In this regard, straightforward signal-processing circuits have been demonstrated to meet these requirements, and the resulting sensors can withstand varying degrees of deformation. Nevertheless, the acquisition of different signals imposes distinct performance-attribute requirements on pressure sensors.Forinstance,the typicalplantarpressureis 1900kPa34,and the reported upper limit is 3 MPa35. In contrast, sensors employed for 1Research Institute for Frontier Science, Beihang University, Beijing 100191, China. 2Key Laboratory of Intelligent Sensing Materials and Chip Integration Tech- nology of Zhejiang Province, Hangzhou Innovation Institute of Beihang University, Hangzhou 310051, China. 3School of Materials Science and Engineering, Beihang University, Beijing 100191, China. e-mail: liuchb@buaa.edu.cn; dengyuan@buaa.edu.cn npj Flexible Electronics | (2024) 8:23 1 https://doi.org/10.1038/s41528-024-00310-6 Article pulse-signal measurement have a maximum detection limit of 500 Pa36. Given the substantial force exerted by the plantar pressure, it becomes imperative for pulse sensors to maintain a significant output voltage even under minimal pressure. Moreover, the presence of high cyclic loads may lead to deformation or fatigue37, emphasizing the importance of sensor stability during prolonged foot-pressure measurements. Therefore, flexible performance adjustments are vital to cater to diverse application scenarios. increasing as the degree of released prestrain increases. The phenomenon of charge cancelation is inevitable in the process of film compression and tension. This is mainly due to the negative deformation tendency of 3D structures caused by improper graphic design. We minimize intuitive canceling deformations through graphic design, which significantly reduces charge cancelation and ensures efficient sensor output. The device fabri- cation is finalized by pouring a silicone elastic encapsulation material (EcoflexTM 00-10), which is employed to protect the PVDF film from moisture and harmful contaminants and provide deformation recovery capability. Currently, the performance modulation of PVDF piezoelectric films primarily relies on material modification methods38–41, such as adding nanofillers (NaNbO3 and RGO)42, doping MXene and BaTiO3 7, or pre- paring PVDF/ZnO nanofibers43. These methods involve extended devel- opment cycles and involve complex fabrication processes44,45. Check for updates For 3D, kirigami-structured piezoelectric sensors, most reported applica- tions involve cutting a planar PVDF film to construct a tensile structure48–50, with highly controllable tensile properties. However, the deformation is mostly confined within the plane, and the variety of pattern designs is not extensive, lacking development potential. In reality, strategically designed geometries and cutting patterns enable the assembly of 2D films into 3D kirigami structures, offering far greater applicability and topological com- plexity compared with other methods51. For example, piezoelectric micro- systems with intricate 3D frameworks exhibit excellent mechanical properties and functional capabilities52. Electronic devices with multilayer cage-like structures demonstrate excellent collapse resistance and can dynamically transmit compression force and temperature53. Here, we develop a piezoelectric pressure sensor featuring 3D kirigami structures.Sensorswithdistinctstructures,designed usingsimplegeometric shapes, exhibit varying sensitivities and different output voltages. Differing from prior investigations on 3D flexible electronic devices, our study combines experimental testing with finite element analysis to explore the impact of 3D structural design and encapsulation materials on the sensi- tivity and output voltage of PVDF-based piezoelectric pressure devices. Additionally, the finite element model that successfully predicts the 3D shape and output performance. Sensors equipped with 3D kirigami struc- tures find application in human-pulse-signal and plantar-pressure mea- surements, showcasing exceptional operational stability under prolonged pressure conditions. This study introduces efficient 3Ddesign concepts for PVDF-based pressure sensors and presents strategies for tackling the challenges associated with flexible, wearable pressure sensors. To verifythe repeatabilityof the fabricationprocessof the 3Dkirigami- structured sensor, we prepare three sensors with the same structure (Shape 1 shown in Fig. 2a). The performancetest results are shown in Fig. 1e,where the three sensors exhibit comparable output voltages with sensitivity dif- ferences within 5%. This indicates the high repeatability of the fabrication process. As depicted in Fig. 1f, the output voltage remains stable after 6,000 pressurization release cycles of the 3D kirigami-structured sensor (Shape 1) with a pressure of 1,356 kPa. The proposed piezoelectric pressure sensor, which has a 3D structure, exhibits excellent operational stability. Sensor designs with various shapes and patterns g p p To investigate the influence of kirigami patterns on the device output per- formance, variouskirigami patterns basedona circular shape are fabricated, whose performances are superior to those of the patterns based on square and triangular shapes,asillustrated inFig. 2a. Here,fourdifferentshapes are designed and named as Shape 1, Shape 2, Shape 3, and Shape 2s. Different shapes result in distinct 3D kirigami structures, with Shape 1 forming a pyramid-like structure. Among the four different shapes, the cutting- damage percentages for Shape 1, Shape 3, and Shape 2s are approximately 12%. Under the same pattern as Shape 2, the cutting-damage percentage for Shape 2 is approximately 50%. Figure 2a shows that the different 3D structures exhibit varying levels of deformation at the same compression- buckling degree. Despite the pressure being applied vertically above the device,theencapsulationmaterialenvelopsthefilmwitha3Dstructure,and the film structures have gradually increasing radii from top to bottom. Therefore, the vertically applied pressure extrudes the encapsulation material below, causing outward compression. The sensor deformation gradually reduces the out-of-plane dimensions and increases the in-plane dimensions until the structure becomes planar. Results and discussions F b i ti f th 3D t t a Fabrication process of the 3D- structured piezoelectric pressure sensors on the prestrain forming. b Two-dimensional precursors, optical images, and FEA predictions for three basic shapes: square, circular, and triangular (scale bars: 5 mm). c Variation in the open-circuit voltage with different forces for the three stereoscopic and con- trol groups (planar structures). d Sensitivity of the three stereoscopic and control groups (planar structures). e Variation in the open-circuit voltage with different forces for the three samples with the same structure (Shape 1). f Variation in the voltage of the pressure sensor with Shape1 after 6000 pres- surization/release cycles at 1356 kPa. a b e c d f Number 2D precursor 3D structure (FEA) 3D structure (Experiment) BS1 BS2 BS3 p g a b e c d f Number 2D precursor 3D structure (FEA) 3D structure (Experiment) BS1 BS2 BS3 Fig. 1 | Piezoelectric pressure sensor with 3D structures. a Fabrication process of the 3D- structured piezoelectric pressure sensors on the prestrain forming. b Two-dimensional precursors, optical images, and FEA predictions for three basic shapes: square, circular, and triangular (scale bars: 5 mm). c Variation in the open-circuit voltage with different forces for the three stereoscopic and con- trol groups (planar structures). d Sensitivity of the three stereoscopic and control groups (planar structures). e Variation in the open-circuit voltage with different forces for the three samples with the same structure (Shape 1). f Variation in the voltage of the pressure sensor with Shape1 after 6000 pres- surization/release cycles at 1356 kPa. a b c c b c Number 2D precursor 3D structure (FEA) 3D structure (Experiment) BS1 BS2 BS3 c d f d e e f f f As shown in Fig. 2b, with the same pattern elements, Shape 2s provides an output voltage of over 4 V at the maximum pressure, whereas Shape 2 only provides about 1 V. This indicates that the effective area of the film directly influences the signal output and sensitivity. The smaller the area of the film involved in the deformation, the lower the output voltage under the same pressure. The sensitivities of the four structures are 4.1 × 103V kPa−1 (Shape 1), 0.94 × 103V kPa−1 (Shape 2), 2.19 × 103V kPa−1 (Shape 3), and 2.63 × 103V kPa−1 (Shape 2s), respectively. Among Shape 1, Shape 3, and Shape 2s with similar cutting-damage percentages, Shape 1 exhibits the highest sensitivity. Results and discussions F b i ti f th 3D t t Fabrication of the 3D-structured piezoelectric pressure sensor The fabrication process of the piezoelectric pressure sensor with a 3D kir- igami structure is illustrated in Fig. 1a, and photos of the 3D kirigami- structured PVDF and the tensile platform are provided in Supplementary Fig. 1a. Femtosecond laser milling is utilized for the high-precision pat- terning of the PVDF film coated with a silver electrode layer. The optical image of the patterned piezoelectric film is shown in Supplementary Fig. 1b, with the edges of the 2D precursor retaining four symmetric anchor points to facilitate the 3D shaping process. The reserved four anchor points are mechanically affixed to a prestretched elastic substrate, which is subse- quently uniformly relaxed to achieve the 3D structure. Releasing the pre- strain generates compressive forces, causing all regions, except the anchored areas, to bend out of the plane. Intermediate shapes corresponding to dif- ferent levels of released prestrains are shown in Supplementary Fig. 2. The strainwithinthethin-filmconcentratesinthe out-of-planebendingregions, npj Flexible Electronics | (2024) 8:23 2 2 https://doi.org/10.1038/s41528-024-00310-6 Article As shown in Fig. 2b, with the same pattern elements, Shape 2s provides an output voltage of over 4 V at the maximum pressure, whereas Shape 2 only provides about 1 V. This indicates that the effective area of the film directly influences the signal output and sensitivity. The smaller the area of the film involved in the deformation, the lower the output voltage under the same pressure. The sensitivities of the four structures are 4.1 × 103V kPa−1 (Shape 1), 0.94 × 103V kPa−1 (Shape 2), 2.19 × 103V kPa−1 (Shape 3), and 2.63 × 103V kPa−1 (Shape 2s), respectively. Among Shape 1, Shape 3, and Shape 2s with similar cutting damage percentages Shape 1 exhibits the Considering that besides the shape, the design details of the 2D pre- cursor influence the sensor’s performance, six different kirigami patterns based on Shape 2s are designed, and the corresponding 3D kirigami- structured sensors are fabricated. The 2D precursor designs, as well as the 3D structure in FEA and in the experiment, are shown in Fig. 2a. In the six patternsofthe2Dprecursordesigns,asshowninFig.2a,theinternalcutting patterns of Patterns 1–3 are similar, whereas the external cutting lines of Pattern 1 and Pattern 2 are rotated 45° relative to each other. The number of outer cutting lines of Pattern 3 increases from two to four compared with Fig. 1 | Piezoelectric pressure sensor with 3D structures. Results and discussions F b i ti f th 3D t t Initially,onlythesmalltop areaof thefilmdeformswhen pressureisapplied.Thus,theoutputvoltageofShape1issmallerthanthatof Shape 2s. As a larger area of the film participates in deformation, the structural advantage of a larger α value gives Shape 1 the highest sensitivity. The 3Dstructure of Shape 3is similar to that of Shape 2s, resulting in similar sensitivity values. However, Shape 2s has longer cutting lines, which allows for a larger number of narrower, free-bending strip elements given the same cutting area. Shape 2s has a larger α value, leading to a higher output voltage compared with Shape 3. Shape 3 and Shape 2s exhibit similar sensitivities; however, their output voltages are 1.5 times different, confirming that the sensitivityandoutputvoltageofthesensorcanbeadjustedbyoptimizingthe pattern design. Considering that besides the shape, the design details of the 2D pre- cursor influence the sensor’s performance, six different kirigami patterns based on Shape 2s are designed, and the corresponding 3D kirigami- structured sensors are fabricated. The 2D precursor designs, as well as the 3D structure in FEA and in the experiment, are shown in Fig. 2a. In the six patternsofthe2Dprecursordesigns,asshowninFig.2a,theinternalcutting patterns of Patterns 1–3 are similar, whereas the external cutting lines of Pattern 1 and Pattern 2 are rotated 45° relative to each other. The number of outer cutting lines of Pattern 3 increases from two to four, compared with that for Pattern 2. The cutting patterns of Pattern 4 and Pattern 5 are basically similar, except that the pattern is rotated 45° relative to the anchor point. The difference between pattern 6 and pattern 4 is that the former has four cut lines inside. As shown in Fig. 2c, Pattern 1, Pattern 2, and Pattern 3 exhibit sensitivities of 3.17 × 103, 2.56 × 103, and 2.78 × 103V kPa−1, respectively. Pattern1alsoexhibitsthe highestoutputvoltage in the fulltest- pressure range as well as the highest sensitivity, whereas Pattern 2 exhibits the lowest values in the above two properties. The sensitivities of Pattern 4, Pattern 5, and Pattern 6 are 3.07 × 103, 2.95 × 103, and 3.41 × 103V kPa−1, respectively, as presented in Fig. 2d. Although the output voltages of Pattern 5 and Pattern 6 are similar, the sensitivity of Pattern 6 is higher than that of Pattern 5. Results and discussions F b i ti f th 3D t t The sensitivity of Pattern 4 is similar to that of Pattern 5, and Considering that besides the shape, the design details of the 2D pre- cursor influence the sensor’s performance, six different kirigami patterns based on Shape 2s are designed, and the corresponding 3D kirigami- structured sensors are fabricated. The 2D precursor designs, as well as the 3D structure in FEA and in the experiment, are shown in Fig. 2a. In the six patternsofthe2Dprecursordesigns,asshowninFig.2a,theinternalcutting patterns of Patterns 1–3 are similar, whereas the external cutting lines of Pattern 1 and Pattern 2 are rotated 45° relative to each other. The number of outer cutting lines of Pattern 3 increases from two to four, compared with that for Pattern 2. The cutting patterns of Pattern 4 and Pattern 5 are basically similar, except that the pattern is rotated 45° relative to the anchor point. The difference between pattern 6 and pattern 4 is that the former has four cut lines inside. As shown in Fig. 2c, Pattern 1, Pattern 2, and Pattern 3 exhibit sensitivities of 3.17 × 103, 2.56 × 103, and 2.78 × 103V kPa−1, respectively. Pattern1alsoexhibitsthe highestoutputvoltage in the fulltest- pressure range as well as the highest sensitivity, whereas Pattern 2 exhibits the lowest values in the above two properties. The sensitivities of Pattern 4, Pattern 5, and Pattern 6 are 3.07 × 103, 2.95 × 103, and 3.41 × 103V kPa−1, respectively, as presented in Fig. 2d. Although the output voltages of Pattern 5 and Pattern 6 are similar, the sensitivity of Pattern 6 is higher than that of Pattern 5. The sensitivity of Pattern 4 is similar to that of Pattern 5, and npj Flexible Electronics | (2024) 8:23 3 https://doi.org/10.1038/s41528-024-00310-6 Article Article Fig. 2 | Designs with various shapes and patterns of the piezoelectric pressure sensor. a Two- dimensional precursors, photographs, and FEA predictions for four different shapes and six similar patterns (scale bars: 5 mm). Variation in the open- circuit voltage with different forces for (b) Shape 1, Shape 2, Shape 3, and Shape 2s; (c) Pattern 1, Pattern 2, and Pattern 3; and (d) Pattern 4, Pattern 5, and Pattern 6 in the experiment. Variation in the force with different displacements for (e) Shape 1, Shape 2, Shape 3, and Shape 2s; (f) Pattern 1, Pattern 2, and Pattern 3; and (g) Pattern 4, Pattern 5, and Pattern 6 in FEA. Results and discussions F b i ti f th 3D t t h Sensitivity of the 3D structure formed by four shapes and six patterns structures. i Variation in the equivalent stiffness with different α values based on three sensors with various shapes. j Variation in the equivalent stiffness with different η based on six sensors with various patterns. Number Shape1 Shape2 Shape3 Shape2s Pattern1 2D precursor 3D structure (FEA) 3D structure (Experiment) Number Pattern2 Pattern3 Pattern4 Pattern5 Pattern6 2D precursor 3D structure (FEA) 3D structure (Experiment) a a e sensors fabricatedbased on in performance, suggesting uence sensor performance. derlying reasons. itivity and output voltage of established accordingto the d f ti f th displacement in the direction perpendicular to the bottom surface is adopted to describe the deformation degree of the sensor. The equivalent stiffness is employed to evaluate the deformation capability of the sensor, which is defined as the ratio of the external load on the sensor to the compression length of the sensor in the vertical direction. FEA reveals that with the increase in pressure, the vertical compression displacement linearly i Th l ti b t d i di l t Number Shape1 Shape2 Shape3 Shape2s Pattern1 2D precursor 3D structure (FEA) 3D structure (Experiment) Number Pattern2 Pattern3 Pattern4 Pattern5 Pattern6 2D precursor 3D structure (FEA) 3D structure (Experiment) i a c j e b d f g h Pattern 4 exhibits the lowest output voltage. The sensors fabricatedbased on different patterns exhibit significant variations in performance, suggesting that even subtle changes in patterns can influence sensor performance. Further research is required to explore the underlying reasons. To explore the factors that affect the sensitivity and output voltage of the sensors,afiniteelement simulationmodelisestablished accordingto the test environment in the experiment. Since the deformation of the sensor during the compression process is relatively complex, the compression displacement in the direction perpendicular to the bottom surface is adopted to describe the deformation degree of the sensor. The equivalent stiffness is employed to evaluate the deformation capability of the sensor, which is defined as the ratio of the external load on the sensor to the compression length of the sensor in the vertical direction. FEA reveals that with the increase in pressure, the vertical compression displacement linearly increases. The correlation between pressure and compression displacement of the four shapes and Patterns 1–6 is shown in Fig. Sensor designs with various encapsulation materials The η value increases linearly with the equivalent stiffness, indicating that when the number of beams reaches the maximum and the angle between the beam and the anchor point on the line is 0°, the equivalent stiffness is the lowest. In other words, the smaller the η value, the stronger the deformation ability of the corresponding 3D struc- ture.Thiscanplayaguidingroleinthegraphicdesignofthe2Dprecursorof the piezoelectric pressure sensor with such a 3D structure: the basic shape is circular, and the number of supporting beams, as well as the angle between them and the anchor point, is supposed to be prioritized while maximizing theaspectratio.Furthermore,tovalidatetheeffectivenessofFEA,theoutput performances of the 10 sensors shown in Fig. 2a are computed using a finite element model, and the results are presented in Supplementary Figs. 4a and 4b. Evidently, the finite element model can accurately predict the sensor’s output performance, although there is a slight deviation between where n1 and n2 are the numbers of the outerand inner beams, respectively, and “2/3” indicates that the ratio of the outer to the inner area is 3:2. Due to symmetry, the angle is set to 0° and 45°, so the components in the formula related to the angle should be cosine values. Since there are two types of beams, their quantity should be a product of cosine values. Additionally, considering the difference in the area of the inner and outer sides of the beam,thepatternfactor’scomponents’weightsaredetermined basedonthe ratio of the areas. Due to symmetry, the angle is set to 0° and 45°, so the components in the formula related to the angle should be cosine values. Since there are two types of beams, their quantity should be a product of cosine values. Additionally, considering the difference in the area of the inner and outer sides of the beam, the pattern factor’s components’ weights are determined based on the ratio of the areas. The variation in the η value with different equivalent stiffness values based on the six sensors with various patterns is depicted in Fig. 2j. The η value increases linearly with the equivalent stiffness, indicating that when the number of beams reaches the maximum and the angle between the beam and the anchor point on the line is 0°, the equivalent stiffness is the lowest. https://doi.org/10.1038/s41528-024-00310-6 Although Patterns 1–6 have the same shape and similar α values, their performances differ, indicating that factors other than the α value influence their sensitivity and output voltage. Since laser cutting generates a hinged circular structure with a radius from the connecting point to the centralpoint,theouterandinnerbeamsaredefinedastheconnectingpoints between the rings in the pattern, which provides support for the 3D structure, as shown in Supplementary Fig. 3c. Angle1 is the angle between the anchor point (red region) and the outer beam, and Angle2 is the angle between the outer beam and the inner beam; the relationship between them and the equivalent stiffness under different patterns are shown in Supplementary Fig. 3d. To ensure symmetry in the 3D structures, all the included angles are only set to 0° or 45°. In the three patterns with the smallest equivalent stiffness values, the two angles are 0°. In addition to the values of the included angles, the number of angles also affects the deformation characteristics of the structure. Here, η is defined as a pattern factorthatrepresentstheeffectofthemagnitudeandthenumbersofthetwo types of angles in the 2D design pattern: wheredout and din aredefinedasthemaximumout-of-planedimensionand in-plane extent, respectively (see Supplementary Fig. 3a and b). The α value of Shape 1 is 0.4583, whereas that of Shape 2s is 0.3443, which is larger than that of Shape 3 (0.2977). This indicates that the performance of the sensor increase with the increase in the 3D extension. For Shape 1, Shape 3, and Shape 2s, when the packaging material is the same, the relationship between the α value and the equivalent stiffness is shown in Fig. 2i. With the increase in the effective stiffness, the α value decreases, which indicates that the extension size of the 3D structure affects the deformation ability to a certain extent. Although Patterns 1–6 have the same shape and similar α values, their performances differ, indicating that factors other than the α value influence their sensitivity and output voltage. Since laser cutting generates a hinged circular structure with a radius from the connecting point to the centralpoint,theouterandinnerbeamsaredefinedastheconnectingpoints between the rings in the pattern, which provides support for the 3D structure, as shown in Supplementary Fig. 3c. Angle1 is the angle between the anchor point (red region) and the outer beam, and Angle2 is the angle between the outer beam and the inner beam; the relationship between them and the equivalent stiffness under different patterns are shown in Supplementary Fig. 3d. Results and discussions F b i ti f th 3D t t 2e–g, where the 2D precursor 3D structure (FEA) 3D structure (Experiment) i c j e b d f g h d d g b e b c f c f f e g j g e h i f h j i j i h Pattern 4 exhibits the lowest output voltage. The sensors fabricatedbased on different patterns exhibit significant variations in performance, suggesting that even subtle changes in patterns can influence sensor performance. Further research is required to explore the underlying reasons. displacement in the direction perpendicular to the bottom surface is adopted to describe the deformation degree of the sensor. The equivalent stiffness is employed to evaluate the deformation capability of the sensor, which is defined as the ratio of the external load on the sensor to the compression length of the sensor in the vertical direction. FEA reveals that with the increase in pressure, the vertical compression displacement linearly increases. The correlation between pressure and compression displacement of the four shapes and Patterns 1–6 is shown in Fig. 2e–g, where the To explore the factors that affect the sensitivity and output voltage of the sensors,afiniteelement simulationmodelisestablished accordingto the test environment in the experiment. Since the deformation of the sensor during the compression process is relatively complex, the compression npj Flexible Electronics | (2024) 8:23 4 https://doi.org/10.1038/s41528-024-00310-6 Sensor designs with various encapsulation materials Notably, the deformation ability of the 3D-structured piezoelectric pressure sensors can be adjusted by changing the packaging material. Four types of silicone resin materials are used as encapsulation materials, with Young’s moduli of 50, 170, 418, and 1,000 kPa, respectively. The results of the tensile tests are shown in Supplementary Fig. 5. The test data are shown in Fig. 3a, b, and c. For Shape 1, the sensitivities of M1–M4 are 4.1 × 103, 3.15 × 103, 1.73 × 103, and 1.35 × 103V kPa−1, respectively. For sensors with three different 3D kirigami structures, as the Young modulus of the encapsulation material decreases, the output voltage increases under the same applied pressure, resulting in improved sensitivity. For instance, for Shape 1, when the pressure is approximately 1,300 kPa, the sensor encapsulated with M1 provides an output voltage of over 5 V, which is approximately 1.3, 2.2, and 2.7 times those of M2, M3, and M4, respec- tively. This indicates that the modulus of the encapsulation material sig- nificantly affects the performance of the sensor. ð2Þ 1=η ¼ 2=3 × n1 × cos Angle1   þ 1=3 × n2 × cos Angle2   ð2Þ where n1 and n2 are the numbers of the outerand inner beams, respectively, and “2/3” indicates that the ratio of the outer to the inner area is 3:2. Due to symmetry, the angle is set to 0° and 45°, so the components in the formula related to the angle should be cosine values. Since there are two types of beams, their quantity should be a product of cosine values. Additionally, considering the difference in the area of the inner and outer sides of the beam,thepatternfactor’scomponents’weightsaredetermined basedonthe ratio of the areas. Due to symmetry, the angle is set to 0° and 45°, so the components in the formula related to the angle should be cosine values. Since there are two types of beams, their quantity should be a product of cosine values. Additionally, considering the difference in the area of the inner and outer sides of the beam, the pattern factor’s components’ weights are determined based on the ratio of the areas. The variation in the η value with different equivalent stiffness values based on the six sensors with various patterns is depicted in Fig. 2j. https://doi.org/10.1038/s41528-024-00310-6 Article Article the simulated output voltage and the test data, as shown in Supplementary Fig.4c.Thisdiscrepancycanbeattributedtodifferencesbetweenthedefined elastic material model and the actual material properties. The established FEA model holds significance in the design of 3D-structured sensors. As shown in Supplementary Fig. 4d, the sensor’s performance is optimal when the two angles tend to 0°, as shown by the higher sensitivity values of Patterns 1 and 6. When the angles are consistent, the number of inner and outer beams also affects the sensor’s output, with Pattern 6 having slightly highersensitivitythanPattern1duetohavingmoreouterbeams.Therefore, the angles and numbers of inner and outer beams jointly determine structural performance. For instance, the difference between Patterns 2 and 1 is reflected in the angle, and the difference between Patterns 2 and 3 is reflected in the number of outer beams. Besides, because the basic shape of the 2D precursor was circular, the cutting elements consist of arcs with the same radii, thus somewhat limiting the freedom of graphic design. In the future, various structural designs can be expanded by altering the radii and angles of the cutting elements, including the spacing between different cutting lines, based on symmetry. This approach will enable the exploration of factors withsignificantimpactsondesign,allowingforfurthertypicaland diverse design explorations. compression displacement varies from 1 to 7 mm, and the height of the sensor is 10 mm. The sensitivity of the 3D structure formed by four shapes and six patterns structures is shown in Fig. 2h. To illustrate the impact of different shapes on the sensor’s performance, the 3D extension among various shapes is defined using the aspect ratio (α) expressed as follows: α ¼ dout=din ð1Þ ð1Þ wheredout and din aredefinedasthemaximumout-of-planedimensionand in-plane extent, respectively (see Supplementary Fig. 3a and b). The α value of Shape 1 is 0.4583, whereas that of Shape 2s is 0.3443, which is larger than that of Shape 3 (0.2977). This indicates that the performance of the sensor increase with the increase in the 3D extension. For Shape 1, Shape 3, and Shape 2s, when the packaging material is the same, the relationship between the α value and the equivalent stiffness is shown in Fig. 2i. With the increase in the effective stiffness, the α value decreases, which indicates that the extension size of the 3D structure affects the deformation ability to a certain extent. https://doi.org/10.1038/s41528-024-00310-6 To ensure symmetry in the 3D structures, all the included angles are only set to 0° or 45°. In the three patterns with the smallest equivalent stiffness values, the two angles are 0°. In addition to the values of the included angles, the number of angles also affects the deformation characteristics of the structure. Here, η is defined as a pattern factorthatrepresentstheeffectofthemagnitudeandthenumbersofthetwo types of angles in the 2D design pattern: Sensor designs with various encapsulation materials 3 | Stress-test performance of the piezoelectric pressure sensors with dif- erent encapsulation materials. Variation in the open-circuit voltage with different orces for (a) S1, (b) S3, and (c) P1 encapsulated with M1, M2, M3, and M4. Variation in the force with different displacements for (d) S1, (e) S3, and (f) P1 encapsulated with M1, M2, M3, and M4 in the FEA. g Strain distribution of the sensors encapsulated with four materials under a pressure of 1000 kPa in the The colors in the FEA results correspond to the magnitudes of the maximum principal strain. https://doi.org/10.1038/s41528 024 00310 6 Art Fig. 3 | Stress-test performance of the piezoelectric pressure sensors with dif- ferent encapsulation materials. Variation in the open-circuit voltage with different forces for (a) S1, (b) S3, and (c) P1 encapsulated with M1, M2, M3, and M4. Variation in the force with different displacements for (d) S1, (e) S3, and (f) P1 encapsulated with M1, M2, M3, and M4 in the FEA. g Strain distribution of the t sensors encapsulated with four materials under a pressure of 1000 kPa in the F The colors in the FEA results correspond to the magnitudes of the maximum principal strain. ig. 3 | Stress-test performance of the piezoelectric pressure sensors with dif- rent encapsulation materials. Variation in the open-circuit voltage with different rces for (a) S1, (b) S3, and (c) P1 encapsulated with M1, M2, M3, and M4. ariation in the force with different displacements for (d) S1, (e) S3, and (f) P1 encapsulated with M1, M2, M3, and M4 in the FEA. g Strain distribution of th sensors encapsulated with four materials under a pressure of 1000 kPa in th The colors in the FEA results correspond to the magnitudes of the maximum principal strain. encapsulated with M1, M2, M3, and M4 in the FEA. g Strain distribution of the three sensors encapsulated with four materials under a pressure of 1000 kPa in the FEA. The colors in the FEA results correspond to the magnitudes of the maximum principal strain. Fig. 3 | Stress-test performance of the piezoelectric pressure sensors with dif- ferent encapsulation materials. Variation in the open-circuit voltage with different forces for (a) S1, (b) S3, and (c) P1 encapsulated with M1, M2, M3, and M4. Variation in the force with different displacements for (d) S1, (e) S3, and (f) P1 (2000 kPa and 5000 kPa). Sensor designs with various encapsulation materials In other words, the smaller the η value, the stronger the deformation ability of the corresponding 3D struc- ture.Thiscanplayaguidingroleinthegraphicdesignofthe2Dprecursorof the piezoelectric pressure sensor with such a 3D structure: the basic shape is circular, and the number of supporting beams, as well as the angle between them and the anchor point, is supposed to be prioritized while maximizing theaspectratio.Furthermore,tovalidatetheeffectivenessofFEA,theoutput performances of the 10 sensors shown in Fig. 2a are computed using a finite element model, and the results are presented in Supplementary Figs. 4a and 4b. Evidently, the finite element model can accurately predict the sensor’s output performance, although there is a slight deviation between The relationship between the compression displacement and the applied pressure is shown in Fig. 3d–f. Similar to the previous case, a similar trend is observed for sensors prepared using different encapsulation materials. The vertical compression displacement shows a linear increase with the pressure, as confirmed by finite element simulation calculations. The relationship between Young’s modulus and the equivalent stiffness of the encapsulation materials for the three structures is shown in Supple- mentary Fig. 6. FEA reveals that the equivalent stiffness exhibits a nonlinear variation with the changes in the Young modulus of the encapsulation material. Notably, when the Young’s modulus falls within the range of 200–400 kPa, the equivalent stiffness experiences a significant increase. However, the variation in the equivalent stiffness is less pronounced beyond this range. This indicates that the performance of the sensor is sensitive to the Young modulus of the encapsulation material in the range of 200 – 400 kPa. When the pressure is 1000 kPa, the distribution of the maximum principal strain for various sensors in the FEA is illustrated in Fig. 3g. For Shape 1, as the Young modulus of the encapsulation material increases, the deformation of the sensor under the same pressure gradually reduces. The reductionin the sensor deformationleadstoa decrease inthe sensitivity and output voltage, which is evident in Fig. 3a–c. The FEA results closely resemble the experimental findings, offering valuableinsightsforguidingsensordesignandperformanceprediction.Asa result of the limitations imposed by the pressure-generation system, the true detection limit of the sensor cannot be obtained. To address this, FEA is implemented to predict the measurement limits of the various sensors. In theFEA,astheloadsincrease,thepressurereachesasaturationstate,andthe output voltage follows suit. We use finite element simulation analysis to predict the force limit of packaging materials with larger Young’s modulus npj Flexible Electronics | (2024) 8:23 5 https://doi.org/10.1038/s41528-024-00310-6 Article Fig. Pulse-signal measurement and motion-posture sensing Pressure sensors play a very important role in health monitoring, and dif- ferent application scenarios have different performance requirements for pressuresensors,suchaspulseandfoot-pressuremonitoring.Fortheelderly population, pulse signals can serve as indicators of cardiovascular health54, and plantar pressure can be utilized to diagnose conditions, such as Par- kinson’s disease, diabetes, and stroke2. The prepared sensors exhibit a high output voltage and sensitivity. They can be flexibly designed according to different needs and working conditions. To verify the application potential of the sensors in the field of health monitoring, pulse and plantar-pressure detection systems are developed based on the self-designed 3D kirigami structures. A series of sensors based on Shape 1 are fabricated, encapsulated with M1–M4, and integrated with a wristband to create a pulse detection system, as shown in Fig. 4a. Due to the large 3D structure, the sensor cannot be perfectly con- formal with the skin, which brings discomfort to wear. However, comfort can be improved by designing smaller patterns, controlling pre-stretched base tension, and reducing sensor package thickness. In practical applica- tions, the sensor can be installed in an upright or inverted orientation because the orientation does not affect its signal output, ensuring con- sistency in test results. The sensor is secured to the wrist using a wrist strap. SupplementaryFig.8ashowsthedetailsofthesensor–skincontactinterface. The pulse-signal detection performances of the sensors encapsulated with different materials are tested, as depicted in Fig. 4b. M1 exhibits the lowest Young’s modulus, and its corresponding pulse-signal output voltage is the highest,exceeding0.2 V,whereasM4exhibitsthelowestpulse-signaloutput voltage. The sensors fabricated with different encapsulation materials cap- ture identical pulse details, including the length of the cardiac cycle and the temporal position of the tidal wave. This indicates that the signal output can be enhanced by selecting appropriate encapsulation materials, thereby improving the signal-to-noise ratio. To validate the reliability of the 3D sensor in wearable-device applications, we subject the sensors to simulated sweat-inducedcorrosioninterferencetests.Saltwaterwithamassfractionof 1% is employed to simulate the sweat, and the sensor is soaked for 96 h at 37°C. The pulse-test results before and after soaking are shown in Fig. 4c. Aftersoaking,theperformanceofthesensorremainsstable,and itretainsits ability to accurately capture intricate pulse details. This is primarily attrib- uted to the excellent hydrophobic properties of the encapsulation material employed. The difference in the waveform may be due to the changes in the physical state of the volunteer, which is also reflected in Fig. 4d. Sensor designs with various encapsulation materials Our study demonstrates that under the same material conditions, performance can be further enhanced through the design of kirigami structures. In our study, the sensitivity of the control group (planar PVDF film) is 0.014 V·N−1, and the sensitivity range that can be achieved via graphic regulation is 0.025–0.056 V·N−1. The variation in human plantar pressure is intricate, influenced by different motion states and various walking postures, leading to distinct pressures across different regions of the sole. Consequently, sensors with broad measurement ranges and high sensitivity are required. As depicted in Fig. 4f, the common plantar-pressure areas can be categorized into four types: the first, third, and fifth metatarsal heads, as well as the heel. As mentioned earlier, the sensing range and sensitivity of 3D kirigami- structuredsensorscanbedynamicallytailored usingdifferentencapsulation materials and patterns, rendering them an ideal choice for plantar-pressure measurement. Therefore, based on this concept, a plantar-pressure- detection system is developed. In the plantar pressure monitoring, the subject’s gravity was about 740 N, higher than the maximum pressure of about 130 N in the previous cycle test. However, the sensor does not undergo plastic deformation due to excessive pressure from the body weight. The robust mechanical performance of the sensor is due to the excellent elasticity of the encapsulation material, which allows the device to maintain stable compression and recovery under the weight of the human body, as shown in Supplementary Fig. 8b. We examine pressure variations in four different plantar regions for various posture states, as illustrated in Fig. 4g. In the tiptoeing state, the main force is the root of the first metatarsal bone. Owing to the slight contact between the heel and the ground, the sensor picks up a weak signal. In the walking and running states, the fifth metatarsal root is the most stressed, probably due to the certain degree of foot valgus. A good gait can help maintain normal posture while preventing muscle and joint strains. In particular, for patients who require rehabilita- tion exercise, the accurate detection of plantar pressure can help accelerate their recovery. The difference among waveforms can be exploited to dis- tinguish different stress positions and motionstates, which can be applied to the long-term monitoring of plantar pressure. To validate the sensor’s performance under prolonged high-pressure conditions, a continuous running/jumpingalternatingtestisconducted,withthesensorpositioned at the base of the fifth metatarsal, as depicted in Fig. 4h. Sensor designs with various encapsulation materials The sensor accurately captures walking signals even after multiple jumps, highlighting its high stability. This signifies the significant potential of the sensor in dynamically monitoring plantar pressure. The pulse signal and plantar pressure mea- surements showed that Shape 1, which performed best in the sensor per- formance characterization, was the best fit for the application. Through adjusting design patterns and altering encapsulation materials, flexible control of sensor performance can be achieved. These findings will enable the design of sensors for detecting signals of varying intensities, presenting significant prospects for applications in wearable devices and health monitoring. Sensor designs with various encapsulation materials The maximum detection limits of each sensor predicted by FEA are shown in Supplementary Fig. 7. Additionally, when conducting measurements exceeding one hundred instances, we observe a very small margin of error. When the same encapsulation material is used, the maximum detection limits of most structures are similar. With the increase in the Young’s modulus, the maximum detection limit also increases, up to 4500 kPa, indicating that the measurement range of the sensor can be regulated by selecting appropriate encapsulation materials, npj Flexible Electronics | (2024) 8:23 6 https://doi.org/10.1038/s41528-024-00310-6 Article Article vary significantly at different locations, with the highest pulse intensity observed at the carotid artery and the lowest at the ankle,which is consistent with the results obtained by normal finger touch. Although the measure- ment positions are different, the signal change cycle is the same, indicating that the signals measured in different parts are indeed human pulse signals. The shape and detailed parameters of the pulse signals from different locations correspond well to those reported in the literature, validating the measurement results55,56. This indicates that the sensor can detect physio- logical signals in multiple parts of the human body. Pulse signals at different positions are simultaneously monitored, and blood pressure information can be measured using the time difference. By simultaneously monitoring pulse signals at different positions, blood pressure information can be measured using the time difference. In the future, through integration with various external devices, sensors can be employed to monitor a broader range of physiological signals in the human body, such as blood pressure57, and respiratory rate58. enabling flexible sensor-performance design. In practical applications, the choice of encapsulation material should be specific to the measurement range and environmental conditions. Simply reducing the stiffness of the encapsulation material can degrade the overall load-bearing capacity of the device, potentially resulting in delayed compression recovery or irreversible deformation. Small variations in pressure signals require devices with high sensitivity for accurate measurements. Although low stiffness of encapsu- lation materials may enhance measurement performance, it imposes high demands on the fabrication process, such as curing time and other condi- tions, thereby increasing production costs. Therefore, the selection of encapsulationmaterialsshouldbetailoredtodifferentapplicationscenarios. In previous studies, the sensitivity of kirigami-inspired pressure sensors varies greatly due to different materials and sensor structures, such as 0.0051 V·N−1 49, 0.067 V·N−1 39, 0.060 V·N−1 52. Pulse-signal measurement and motion-posture sensing The pulse waveform exhibits noticeable changes in shape before and after exercises, the cardiac cycle is shortened, and the pulse-signal intensity is increased. In additiontothewrist,pulse-signalmeasurementsareperformedatfourother locations using the prepared system, and the results are illustrated in Fig. 4e. The Shape 1 sensor encapsulated with M1 is employed to measure the pulse at the above positions simultaneously. The pulse waveform and intensity In summary, we fabricate 3D, kirigami-structured pressure sensors based on PVDF piezoelectric thin films. By modifying the design of a 2D precursor and employing different encapsulation materials, the sensitivity and output voltage of the sensor could be flexibly adjusted. This method exhibits excellent reproducibility, resulting in flexible sensors with high mechanical durability. We also establish effective finite element models to guide the sensor design and predict the sensor’s performance. Furthermore, npj Flexible Electronics | (2024) 8:23 7 a b c M1 M2 M3 M4 Before saline soak After 96 hours of saline soak Before exercise After exercise d e f h g Jumping Walking Walking Running Tiptoeing Walking Running Tiptoeing Walking Running Tiptoeing Walking Running Tiptoeing | Pulse-signal measurement and motion-posture sensing using the piezo- ic pressure sensor. a Photograph of the P1 sensor conformally attached to the n wrist using an adjustable watchband. b Radial artery pulse signals detected by sensor encapsulated with four different materials. Pulse measurement before ter (c) sensor soak in saline and (d) exercise. e Pulse-signal measurement in different parts of the human body. f Schematics of different plantar po the sensor is attached. g The open-circuit voltage of the P1 sensor att different positions in tiptoeing, walking, and running states. h The op voltage of the P1 sensor placed at position ③in alternating jumping/w ://doi.org/10.1038/s41528-024-00310-6 Article https://doi.org/10.1038/s41528-024-00310-6 b a b M1 M2 M3 M4 d a Before exercise After exercise d d c Before saline soak After 96 hours of saline soak c e e f g f h Jumping Walking h Fig. 4 | Pulse-signal measurement and motion-posture sensing using the piezo- electric pressure sensor. a Photograph of the P1 sensor conformally attached to the human wrist using an adjustable watchband. b Radial artery pulse signals detected by the P1 sensor encapsulated with four different materials. Pulse measurement before and after (c) sensor soak in saline and (d) exercise. e Pulse-signal measurement in different parts of the human body. f Schematics of different plantar positions where the sensor is attached. Packaging of piezoelectric pressure sensors The elastic substrate is removed from the tensile platform after the 3D structureis formed.Themold iscovered onthe filmwiththe3Dstructure in order to control the shape of the sensor. The packaging material solution is then cast into the mold. The overall dimensions of the encapsulated sensor are 15 mm × 15 mm × 10 mm. A photo and cross-sectional image of the encapsulated device are shown in the Supplementary Fig. 1d and e. Here, four packaging materials, which include platinum-catalyzed silicones Finite element analysis The finite element analysis is performed using the StructuralMechanics and AC/DC modules of COMSOL Multiphysics. PVDF material parameters are subsequently configured. The PVDF material from the COMSOL material library is primarily utilized, with a Poisson’s ratio set to 0.35 and a Young’s modulusof2600 MPa.Subsequently,thefouranchorpointsaresubjectedto inward displacements of 2.8 mm along the x and y axes, respectively, simulating the film’s contraction inward according to the length of con- traction of the elastic substrate, ultimately forming a three-dimensional structure. Then a cuboid packaging material model with dimensions of 15 × 15 × 10 mm is created around the film to construct the sensor model. Simultaneously, a cuboid steel plate model is positioned above the sensor to mimic the pressure application device. For simulating the packaging material, the third-order superelastic material model Yeoh is chosen, and the parameters (c1, c2, and c3) correspond to the packaging Materials and are derived from the Soft Robotics Materials Database59. The material is considered incompressible. In the Electrical module, the upper surface voltageofthefilmiszeroandthelowersurfaceisgrounded.IntheStructural Mechanic module, the lower surface of the sensor model is kept moving freely in the lateral direction and constrained in the longitudinal direction. Meanwhile, the steel plate gradually moves downward, and its motion parameters are the same as those of the linear guide rail in the experiment, and are set as the acceleration, uniform speed and deceleration process, in which the acceleration and deceleration process are the same. Changes in strain distribution, pressure, and output voltage can be obtained by simu- lating the sensor compression process. https://doi.org/10.1038/s41528-024-00310-6 https://doi.org/10.1038/s41528-024-00310-6 Article (EcoflexTM 00-10, Smooth-On) and three kinds of silicone materials (San- jingxinde Technology) with different Young’s moduli, are used to provide the sensor with deformation recovery capabilities. The Young’s moduli of the packaging materials are 50 kPa, 170 kPa, 410 kPa and 1000 kPa respectively, which are tested by the intelligent electronic tensile testing machine (XLW-EC-A, Labthink). The stress-strain curves are shown in Supplementary Fig. 5. The curing condition is normal temperature curing. Mold and substrate removal are performed after the encapsulation material is cured. The encapsulation material wrapping ensures the stable com- pressionandrecoveryofthe3Dstructureduringoperationaftertheremoval of the substrate. (EcoflexTM 00-10, Smooth-On) and three kinds of silicone materials (San- jingxinde Technology) with different Young’s moduli, are used to provide the sensor with deformation recovery capabilities. The Young’s moduli of the packaging materials are 50 kPa, 170 kPa, 410 kPa and 1000 kPa respectively, which are tested by the intelligent electronic tensile testing machine (XLW-EC-A, Labthink). The stress-strain curves are shown in Supplementary Fig. 5. The curing condition is normal temperature curing. Mold and substrate removal are performed after the encapsulation material is cured. The encapsulation material wrapping ensures the stable com- pressionandrecoveryofthe3Dstructureduringoperationaftertheremoval of the substrate. our sensors successfully monitor both pulse signals and plantar pressure. In the future, more intriguing structural designs and superior encapsulation materials will be explored while further reducing the sensor size. In sum- mary,thisworkprovidesasimpleandeffectiveapproachformodulatingthe performance of piezoelectric pressure sensors. We anticipate that the macroscopic structural design of piezoelectric thin films would find broad application in various pressure-sensing devices. Design of 2D precursors Highly symmetric graphic designs are made for the 2D precursors to ensure the symmetry of the 3D structures and the stability of device operation. Squares and circles, representing classic shapes with straight and curved boundaries, respectively, exhibit different structural characteristics and dis- tinct compression effects after formation. Both squares and circles have four anchorpointsand90°angles.Additionally,triangleswiththreeanchorpoints, each with angles of 120°, are considered basic shapes in the design. Drawing inspiration from common 3D structural elements in daily life, we devised a pyramid-like top-protruding (conical) structure (Shape 1), a concave-topped structure resembling an ancient Chinese coin (Shape 3), and three-layer disc- like structures (Shapes 2 and 2s). We kept the film area constant to investigate theimpact ofthe structureas the sole variable on performance.Thedifference incuttingareabetweenShapes2and2swasusedtodemonstratetheinfluence oftheeffectivefilmareaontheperformance.Furthermore,forthesamethree- layer disc-like shape, given identical design elements for the 2D precursor, various interestingstructureswith the same planarshape but different pattern details can be created by changing the length and quantity of the cutting lines. We make further adjustments and create a second three-layer disc-like structure, Shape 2s, to obtain six different pattern designs. Experimental setup for pressure and electrical characterization The packaged sensor is placed on a fixed platform. The mechanical force perpendicular to the sensor’s surface is provided using a strain system consisting of linear guides (H01, Linmot) and load cell (DYMH-103, DAYSENSOR) and is recorded by a high precision dynamometer (DY920, DAYSENSOR). The digit multimeter (Keithley 6500) is employed to cap- ture and record the open-circuit voltage of the sensors. The pressure applied to the sensor surface varies with the moving distanceof the linear guide. The absolute value of the open circuit voltage generates when the sensor is squeezed is recorded as the output voltage at that pressure. The force measuringdeviceindicatesthatthesensorcandetectforcesassmallas0.1 N. Pulse signal detection Radial pulse is measured by placing a sensor on the surface of the radial artery of the wrist and securing it with a watch strap. The pulse of the neck, fingertip, elbow and ankle is measured by placing the sensor in the designated position and fixing it in place with a band-aid. The pulse after exercise is measured after running lasts for 1 minute. The saline soak meant that the sensor is immersed in salt water with 1% at 37 °C. Pulse signals are collected using a shielded junction box (SCB-68A, National Instruments). Fabrication of 3D structures A PVDF film coated with electrodes (52 μm metallized piezo film, TE Connectivity) is patterned by Femtosecond laser (Pharos 20, Light Conver- sion) with a single-pulse energy of 2 mJ, a repetition frequency of 0.4 kHz, a processing speed of 150 mm s-1, and 200 processing cycles. The pre-designed 2D precursor design drawing (CAD data) and cutting parameters are input into the machining control system, and the machining process is auto- matically completed by the controller. Appropriate laser and cutting para- meters can ensure effective cutting while the upper and lower electrode layers of the film are not conducting. The wires are connected in the rectangular region (Supplementary Fig. 1b) of the patterned film using conductive silver glue. At the same time, an elastic substrate with dimensions of 5×5 cm and thickness of 2 mm is fabricated by platinum-catalyzed silicones (EcoflexTM 00-10, Smooth-On) in a 1:1 ratio under the condition of curing at 80°C for 30 minutes. The elastic substrate is then fixed on the manual tensile platform (PT-ST50,PDV,SupplementaryFig.1a).Thepre-strainof130%isapplied to the elastic substrate using tensile platforms. After the four anchor points are threadedthroughsmallholesatthetargetpositionsintheelasticsubstrate,the mechanicalfixationoftheanchorpointsisachievedbyreleasingtheprestrain in the elastic substrate, thereby completing the formation of the 3D structure. As for lead wires, we cure the silver paste within the working temperature range of PVDF and then reinforce the connection points with the encapsu- lation material, ensuring electrode and conductor stability during testing and application. The image of the thin film section after laser cutting, which is shown in Supplementary Fig. 1c can show that the thin film does not short- circuit, which ensures the effectiveness of the voltage output. Pulse-signal measurement and motion-posture sensing g The open-circuit voltage of the P1 sensor attached to four different positions in tiptoeing, walking, and running states. h The open-circuit voltage of the P1 sensor placed at position ③in alternating jumping/walking states. npj Flexible Electronics | (2024) 8:23 8 8 npj Flexible Electronics | (2024) 8:23 References Stretchable piezoelectric energy harvesters and self- powered sensors for wearable and implantable devices. Biosens. Bioelectron. 168, 112569 (2020). 8. Jiang, X., Kim, K., Zhang, S., Johnson, J. & Salazar, G. High- temperature piezoelectric sensing. Sensors 14, 144–169 (2014). 32. Su, Y. et al. Muscle fibers inspired high-performance piezoelectric textiles for wearable physiological monitoring. Adv. Funct. Mater. 31, 2010962 (2021). 9. Zu, H., Wu, H. & Wang, Q.-M. High-temperature piezoelectric crystals for acoustic wave sensor applications. IEEE Trans. Ultrason., Ferroelectr., Frequency Control 63, 486–505 (2016). 10. Li, F. et al. Ultrahigh piezoelectricity in ferroelectric ceramics by design. Nat. Mater. 17, 349–354 (2018). 33. Lin, W. et al. Skin-inspired piezoelectric tactile sensor array with crosstalk-free Row+Column electrodes for spatiotemporally distinguishing diverse stimuli. Adv. Sci. 8, 2002817 (2021). 11. Lee, Y. et al. Flexible ferroelectric sensors with ultrahigh pressure sensitivity and linear response over exceptionally broad pressure range. ACS Nano 12, 4045–4054 (2018). 34. Abdul Razak, A. H., Zayegh, A., Begg, R. K. & Wahab, Y. Foot plantar pressure measurement system: A review. Sensors 12, 9884–9912 (2012). 12. Huang, Y. et al. Enhanced piezoelectricity from highly polarizable oriented amorphous fractions in biaxially oriented poly(vinylidene fluoride) with pure β crystals. Nat. Commun. 12, 675 (2021). 35. Urry, S. Plantar pressure-measurement sensors. Meas. Sci. Technol. 10, R16 (1999). 36. Meng, K. et al. Wearable pressure sensors for pulse wave monitoring. Adv. Mater. 34, 2109357 (2022). 13. Liao, W.-Q. et al. A molecular perovskite solid solution with piezoelectricity stronger than lead zirconate titanate. Science 363, 1206–1210 (2019). 37. Gad-el-Hak, M. The MEMS Handbook. (CRC Press, 2001). 38. Kong, H., Jin, Y., Li, G., Zhang, M. & Du, J. Design and Fabrication of a Hierarchical Structured Pressure Sensor Based on BaTiO 3 /PVDF Nanofibers via Near‐Field Electrospinning. Adv. Eng. Mater. 2201660 https://doi.org/10.1002/adem.202201660 (2023) 14. He, J. et al. A Universal high accuracy wearable pulse monitoring system via high sensitivity and large linearity graphene pressure sensor. Nano Energy 59, 422–433 (2019). 15. Lin, M.-F., Cheng, C., Yang, C.-C., Hsiao, W.-T. & Yang, C.-R. A wearable and highly sensitive capacitive pressure sensor integrated a dual-layer dielectric layer of PDMS microcylinder array and PVDF electrospun fiber. Org. Electron. 98, 106290 (2021). 39. Yang, Y. et al. Flexible piezoelectric pressure sensor based on polydopamine-modified BaTiO3/PVDF composite film for human motion monitoring. Sens. Actuat. A-Phys. 301, 111789 (2020). 40. Chen, X. et al. References 23. Park, D. Y. et al. Self-powered real-time arterial pulse monitoring using ultrathin epidermal piezoelectric sensors. Adv. Mater. 29, 1702308 (2017). 1. Yi, Z., Zhang, W. & Yang, B. Piezoelectric approaches for wearable continuous blood pressure monitoring: a review. J. Micromech. Microeng. 32, 103003 (2022). 1. Yi, Z., Zhang, W. & Yang, B. Piezoelectric approaches for wearable continuous blood pressure monitoring: a review. J. Micromech. Microeng. 32, 103003 (2022). 24. Boutry, C. M. et al. Biodegradable and flexible arterial-pulse sensor for the wireless monitoring of blood flow. Nat. Biomed. Eng. 3, 47–57 (2019). 2. Chen, J.-L. et al. Plantar pressure-based insole gait monitoring techniques for diseases monitoring and analysis: A review. Adv. Mater. Technol. 7, 2100566 (2022). 2. Chen, J.-L. et al. Plantar pressure-based insole gait monitoring techniques for diseases monitoring and analysis: A review. Adv. Mater. Technol. 7, 2100566 (2022). 25. Yang, Y. et al. Breathable electronic skins for daily physiological signal monitoring. Nano-Micro Lett. 14, 161 (2022). 3. Chen, X. et al. Flexible fiber-based hybrid nanogenerator for biomechanical energy harvesting and physiological monitoring. Nano Energy 38, 43–50 (2017). 26. Liu, D. et al. Intrinsically stretchable polymer semiconductor based electronic skin for multiple perceptions of force, temperature, and visible light. Nano Res 16, 1196–1204 (2023). 4. Ghosh, S. K. & Mandal, D. Synergistically enhanced piezoelectric output in highly aligned 1D polymer nanofibers integrated all-fiber nanogenerator for wearable nano-tactile sensor. Nano Energy 53, 245–257 (2018). 27. Duan, S. et al. Water-modulated biomimetic hyper-attribute-gel electronic skin for robotics and skin-attachable wearables. ACS Nano 17, 1355–1371 (2023). 5. Guo, W. et al. Wireless piezoelectric devices based on electrospun PVDF/BaTiO3 NW nanocomposite fibers for human motion monitoring. Nanoscale 10, 17751–17760 (2018). 28. Wang, Y., Hong, M., Venezuela, J., Liu, T. & Dargusch, M. Expedient secondary functions of flexible piezoelectrics for biomedical energy harvesting. Bioact. Mater. 22, 291–311 (2023). 29. Kim, M. & Yun, K.-S. Helical piezoelectric energy harvester and its applicationtoenergyharvestinggarments.Micromachines8,115(2017). 6. Dagdeviren, C. et al. Conformable amplified lead zirconate titanate sensors with enhanced piezoelectric response for cutaneous pressure monitoring. Nat. Commun. 5, 4496 (2014). 30. Hu, N. et al. Stretchable kirigami polyvinylidene difluoride thin films for energy harvesting: design, analysis, and performance. Phys. Rev. Appl. 9, 021002 (2018). 7. Liu, X. et al. BaTiO 3 /MXene/PVDF-TrFE composite films via an electrospinning method for flexible piezoelectric pressure sensors. J. Mater. Chem. C. 11, 4614–4622 (2023). 31. Zhou, H. et al. Data availability All data needed to evaluate the conclusions in the paper are present in the paper and the Supplementary Information. 21. Self-powered, high sensitivity printed e-tattoo sensor for unobtrusive arterial pulse wave monitoring. Nano Energy 102, 107625 (2022). Received: 31 October 2023; Accepted: 29 March 2024; Received: 31 October 2023; Accepted: 29 March 2024; Received: 31 October 2023; Accepted: 29 March 2024; 22. Hao, Z. & Wang, D. Arterial pulse signal amplification by adding a uniform PDMS layer to a pyrex-based microfluidic tactile sensor. IEEE Sens. J. 20, 2164–2172 (2020). Plantar pressure detection The sensor secures using tape are placed at the heel and at the base of the first, third and fifth metatarsal bones on the sole of foot respectively. Tip- toeingmeantthatbodyweightismovingfromtheheelto theballofthefoot. npj Flexible Electronics | (2024) 8:23 9 https://doi.org/10.1038/s41528-024-00310-6 Article 18. Wang, X., Liu, Z. & Zhang, T. Flexible sensing electronics for wearable/ attachable health monitoring. Small 13, 1602790 (2017). The difference between walking and running is the step frequency of the volunteers wearing the sensors, where the frequency is 1 Hz for walking and 3 Hz for running. Alternating jumping and running mean that the switch between jumping and running is quick. The wire of sensors is connected to the junction box of the shielding chamber and the open circuit voltage is recorded by the upper computer software. 19. Pang, Y. et al. Flexible, highly sensitive, and wearable pressure and strain sensors with graphene porous network structure. ACS Appl. Mater. Interfaces 5, 26458–26462 (2016). 20. Gao, C., Long, Z., Zhong, T., Liang, S. & Xing, L. A self-powered intelligent glove for real-time human-machine gesture interaction based on piezoelectric effect of T-ZnO/PVDF film. J. Phys. D: Appl. Phys. 55, 194004 (2022). https://doi.org/10.1038/s41528-024-00310-6 https://doi.org/10.1038/s41528-024-00310-6 Article 59. Marechal, L. et al. Toward a common framework and database of materials for soft robotics. Soft Robot. 8, 284–297 (2020). 59. Marechal, L. et al. Toward a common framework and database of materials for soft robotics. Soft Robot. 8, 284–297 (2020). 42. Singh, H. H., Singh, S. & Khare, N. Design of flexible PVDF/NaNbO3/ RGO nanogenerator and understanding the role of nanofillers in the output voltage signal. Compos. Sci. Technol. 149, 127–133 (2017). References High-performance piezoelectric nanogenerators with imprinted P(VDF-TrFE)/BaTiO3 nanocomposite micropillars for self- powered flexible sensors. Small 13, 1604245 (2017). 16. Jin, C. et al. A wearable combined wrist pulse measurement system using airbags for pressurization. Sensors 19, 386 (2019). 41. Yang, C.-R. et al. Highly sensitive and wearable capacitive pressure sensors based on PVDF/BaTiO3 composite fibers on PDMS microcylindrical structures. Measurement 202, 111817 (2022). 17. Bijender & Kumar, S. Flexible and wearable capacitive pressure sensor for blood pressure monitoring. Sens. Bio-Sens. Res. 33, 100434 (2021). npj Flexible Electronics | (2024) 8:23 10 Acknowledgements 43. Deng, W. et al. Cowpea-structured PVDF/ZnO nanofibers based flexible self-powered piezoelectric bending motion sensor towards remote control of gestures. Nano Energy 55, 516–525 (2019). This work is supported by the National Natural Science Foundation of China (NSFC) (62004009 for C. L.), the National Key Research and Development Program ofChina(Grant No.2018YFA0702100), the ZhejiangProvincial Key Research and Development Program of China (Grant Nos. 2021C01026and 2021C05002), the Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang (2020R01007) and Beijing Nova Program (20230484412). 44. Bhatt, A. et al. Enhanced piezoelectric response using TiO2/MoS2 heterostructure nanofillers in PVDF based nanogenerators. J. Alloy. Compd. 960, 170664 (2023). 45. Li, S., Zhang, M., Sun, J., Sun, J. & Wang, Y. Preparation and characterization of superior hydrophilic PVDF/DA membranes by the self-polymerization approach of dopamine. Front. Chem. 11, 1162348 (2023). Competing interests 48. Song, J. et al. Stretchable Strain and Strain Rate Sensor Using Kirigami ‐Cut PVDF Film. Adv. Mater. Technol. 2201112 https://doi. org/10.1002/admt.202201112 (2023). 49. Meng, K. et al. Kirigami‐inspired pressure sensors for wearable dynamic cardiovascular monitoring. Adv. Mater. 34, 2202478 (2022). 49. Meng, K. et al. Kirigami‐inspired pressure sensors for wearable dynamic cardiovascular monitoring. Adv. Mater. 34, 2202478 (2022). 50. Kim, Y.-G., Song, J.-H., Hong, S. & Ahn, S.-H. Piezoelectric strain sensor with high sensitivity and high stretchability based on kirigami 50. Kim, Y.-G., Song, J.-H., Hong, S. & Ahn, S.-H. Piezoelectric strain sensor with high sensitivity and high stretchability based on kirigami design cutting. npj Flex. Electron. 6, 52 (2022). 51. Zhang, Y. et al. A mechanically driven form of Kirigami as a route to 3D mesostructures in micro/nanomembranes. Proc. Natl Acad. Sci. USA 112, 11757–11764 (2015). Correspondence and requests for materials should be addressed to Changbo Liu or Yuan Deng. Correspondence and requests for materials should be addressed to Changbo Liu or Yuan Deng. 52. Han, M. et al. Three-dimensional piezoelectric polymer microsystems for vibrational energy harvesting, robotic interfaces and biomedical implants. Nat. Electron. 2, 26–35 (2019). Author contributions 46. Pang, C. et al. Highly skin-conformal microhairy sensor for pulse signal amplification. Adv. Mater. 27, 634–640 (2015). C.L. developed the concepts. Y.Z. performed device fabrication. Y.Z., D.M., B.J., X.T. and Y.C. performed device characterization. Y.Z. analyzed the experimental data. Y.Z. performed simulations. C.L. and Y.D. provided funding support. C.L. and Y.Z. wrote the manuscript. 47. Kim, Y., Lee, J., Hong, H., Park, S. & Ryu, W. Self‐Powered Wearable Micropyramid Piezoelectric Film Sensor for Real‐Time Monitoring of Blood Pressure. Adv. Eng. Mater. 2200873 https://doi.org/10.1002/ adem.202200873 (2022). Reprints and permissions information is available at 53. Cheng, X. et al. Bioinspired design and assembly of a multilayer cage- shaped sensor capable of multistage load bearing and collapse prevention. Nanotechnology 32, 155506 (2021). Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 54. Wang, J. et al. Diaphragm-based optical fiber sensor for pulse wave monitoring and cardiovascular diseases diagnosis. J. Biophotonics 12, e201900084 (2019). Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. 55. Janjua, G. M. W., Finlay, D., Guldenring, D., Haq, A. U. & McLaughlin, J. Evaluation of pulse transit time for different sensing methodologies of arterial waveforms. IEEE Access 11, 33928–33933 (2023). 56. Kil, H.-J. & Park, J.-W. Carotid artery monitoring patch using a supercapacitive pressure sensor with piezoelectricity. Nano Energy 114, 108636 (2023). 57. Luo, N. et al. Flexible piezoresistive sensor patch enabling ultralow power cuffless blood pressure measurement. Adv. Funct. Mater. 26, 1178–1187 (2016). 58. Chiu, Y.-Y., Lin, W.-Y., Wang, H.-Y., Huang, S.-B. & Wu, M.-H. Development of a piezoelectric polyvinylidene fluoride (PVDF) polymer-based sensor patch for simultaneous heartbeat and respiration monitoring. Sens. Actuat. A-Phys. 189, 328–334 (2013). npj Flexible Electronics | (2024) 8:23 11
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A late Paleoproterozoic (1.74 Ga) deep‐sea, low‐temperature, iron‐oxidizing microbial hydrothermal vent community from Arizona, USA
Geobiology
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Received: 27 March 2020  |  Revised: 18 January 2021  |  Accepted: 1 February 2021 Received: 27 March 2020  |  Revised: 18 January 2021  |  Accepted: 1 February 2021 DOI: 10.1111/gbi.12434 O R I G I N A L A R T I C L E O R I G I N A L A R T I C L E Crispin T. S. Little1  | Karen C. Johannessen2  | Stefan Bengtson3  | Clara S. Chan4  | Magnus Ivarsson3,5 | John F. Slack6  | Curt Broman7 | Ingunn H. Thorseth2  | Tor Grenne8  | Olivier J. Rouxel9  | Andrey Bekker10,11 Crispin T. S. Little1  | Karen C. Johannessen2  | Stefan Bengtson3  | Clara S. Chan4  | Magnus Ivarsson3,5 | John F. Slack6  | Curt Broman7 | Ingunn H. Thorseth2  | Tor Grenne8  | Olivier J. Rouxel9  | Andrey Bekker10,11 Crispin T. S. Little1  | Karen C. Johannessen2  | Stefan Bengtson3  | Clara S. Chan4  | Magnus Ivarsson3,5 | John F. Slack6  | Curt Broman7 | Ingunn H. Thorseth2  | Tor Grenne8  | Olivier J. Rouxel9  | Andrey Bekker10,11 1School of Earth and Environment, University of Leeds, Leeds, UK 2Department of Earth Science, University of Bergen, Bergen, Norway 3Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden 4Department of Earth Sciences, University of Delaware, Newark, USA 5Department of Biology, University of Southern Denmark, Odense M, Denmark 6U.S. Geological Survey (Emeritus), National Center, Reston, USA 7Department of Geological Sciences, Stockholm University, Stockholm, Sweden 8Geological Survey of Norway, Trondheim, Norway 9Marine Geosciences Research Unit, IFREMER, Plouzané, France 10Department of Earth and Planetary Sciences, University of California, Riverside, USA 11Department of Geology, University of Johannesburg, Johannesburg, South Africa Correspondence Crispin T. S. Little, School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK. Email: earctsl@leeds.ac.uk Funding information Research Council of Norway Grant (197411/ V30). Swedish Research Council Contracts No. 2012-­4364 and 2017-­04129. Villum Investigator Grant (No. 16518). 1School of Earth and Environment, University of Leeds, Leeds, UK 2Department of Earth Science, University of Bergen, Bergen, Norway 3Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden 4Department of Earth Sciences, University of Delaware, Newark, USA 5Department of Biology, University of Southern Denmark, Odense M, Denmark 6U.S. Geological Survey (Emeritus), National Center, Reston, USA 7Department of Geological Sciences, Stockholm University, Stockholm, Sweden 8Geological Survey of Norway, Trondheim, Norway 9Marine Geosciences Research Unit, IFREMER, Plouzané, France 10Department of Earth and Planetary Sciences, University of California, Riverside, USA 11Department of Geology, University of Johannesburg, Johannesburg, South Africa Correspondence Crispin T. S. Little, School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK. Email: earctsl@leeds.ac.uk Funding information Research Council of Norway Grant (197411/ V30). Swedish Research Council Contracts No. 2012-­4364 and 2017-­04129. Villum Investigator Grant (No. 16518). A late Paleoproterozoic (1.74 Ga) deep-­sea, low-­temperature, iron-­oxidizing microbial hydrothermal vent community from Arizona, USA Crispin T. S. Little1  | Karen C. Johannessen2  | Stefan Bengtson3  | Clara S. Chan4  | Magnus Ivarsson3,5 | John F. Slack6  | Curt Broman7 | Ingunn H. Thorseth2  | Tor Grenne8  | Olivier J. Rouxel9  | Andrey Bekker10,11 Abstract Modern marine hydrothermal vents occur in a wide variety of tectonic settings and are characterized by seafloor emission of fluids rich in dissolved chemicals and rapid mineral precipitation. Some hydrothermal systems vent only low-­temperature Fe-­ rich fluids, which precipitate deposits dominated by iron oxyhydroxides, in places together with Mn-­oxyhydroxides and amorphous silica. While a proportion of this mineralization is abiogenic, most is the result of the metabolic activities of benthic, Fe-­oxidizing bacteria (FeOB), principally belonging to the Zetaproteobacteria. These micro-­organisms secrete micrometer-­scale stalks, sheaths, and tubes with a variety of morphologies, composed largely of ferrihydrite that act as sacrificial structures, preventing encrustation of the cells that produce them. Cultivated marine FeOB generally require neutral pH and microaerobic conditions to grow. Here, we de- scribe the morphology and mineralogy of filamentous microstructures from a late Paleoproterozoic (1.74 Ga) jasper (Fe-­oxide-­silica) deposit from the Jerome area of the Verde mining district in central Arizona, USA, that resemble the branching tubes formed by some modern marine FeOB. On the basis of this comparison, we interpret the Jerome area filaments as having formed by FeOB on the deep seafloor, at the interface of weakly oxygenated seawater and low-­temperature Fe-­rich hydrother- mal fluids. We compare the Jerome area filaments with other purported examples of Precambrian FeOB and discuss the implications of their presence for existing redox models of Paleoproterozoic oceans during the “Boring Billion.” 2Department of Earth Science, University of Bergen, Bergen, Norway 3Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden 4Department of Earth Sciences, University of Delaware, Newark, USA 5Department of Biology, University of Southern Denmark, Odense M, Denmark 6U.S. Geological Survey (Emeritus), National Center, Reston, USA Stockholm University, Stockholm, Sweden 8Geological Survey of Norway, Trondheim, Norway 1 | INTRODUCTION anoxic, Fe-­rich, S-­poor, low-­temperature (10 s of °C) hydrothermal fluids mix with oxygenated seawater at ambient temperatures (e.g., Edwards et al., 2011; Emerson et al., 2007; Forget et al., 2010; Glazer & Rouxel, 2009; Langley et al., 2009; Sun et al., 2013). The mineral- ogy of these hydrothermal Fe-­rich deposits is dominated by iron oxy- hydroxides (e.g., ferrihydrite and goethite), commonly accompanied by Mn-­oxyhydroxides and locally with significant amounts of amor- phous silica (e.g., Dekov et al., 2015; Jones et al., 2008; Li et al., 2012; Peng et al., 2015; Rouxel et al. 2018; Toner et al., 2012); hematite (Fe2O3) has been reported from only one, higher-­temperature site (estimated to be ≥115°C; Hein et al., 2008). 1 In the decades since their first discovery in 1977, marine hydrother- mal vents have been reported from all of the world's oceans in a wide variety of tectonic settings where a heat source is present, in- cluding at more than 400 sites on mid-­ocean ridges, fore-­ and back-­ arc spreading centers, arc volcanoes, and intra-­plate volcanoes and seamounts (e.g., Beaulieu et al., 2013; Corliss et al., 1979; Fouquet et  al.,  2010; Karl et  al.,  1988; Pedersen et  al.,  2010; Petersen et  al.,  2019). Many of these hydrothermal systems are character- ized by seafloor emission of high-­temperature (up to 400°C) fluids rich in dissolved chemicals, which rapidly precipitate chimney and mound structures formed largely of metal sulfides (e.g., pyrite, chal- copyrite, sphalerite), sulfates (e.g., anhydrite, barite), and silica (e.g., Hannington, 2014; Hannington et al., 1995; Tivey, 2007). However, most hydrothermal fluid exits the seafloor at lower temperatures (in the 10 s of °C) and typically is much lower in dissolved chemicals, because of mixing with ambient seawater in the subsurface. The resulting hydrothermal seafloor precipitates commonly have a dif- ferent mineralogy (e.g., Fe-­oxides and iron oxyhydroxides) to those that form from high-­temperature fluids. Some marine hydrothermal systems only vent low-­temperature fluids, and these are charac- terized by the precipitation of Fe-­oxide-­rich deposits that display a wide variety of morphologies from layered sediments to small-­scale chimney structures (e.g., Hein et al., 2008; Sun et al., 2013, 2015 and references therein). Funding information Arizona, Fe-­oxidizing bacteria, hydrothermal vents, jasper, late Paleoproterozoic, Verde mining district 228  |   Geobiology. 2021;19:228–249. wileyonlinelibrary.com/journal/gbi This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2021 The Authors. Geobiology published by John Wiley & Sons Ltd. | This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2021 The Authors. Geobiology published by John Wiley & Sons Ltd. Geobiology. 2021;19:228–249. LITTLE et al. 229 precipitation, increasing the overall Fe/C ratio of the aging stalks, and also causing them to thicken, obscuring some of the fine details, like twisting (Chan et al., 2011; Chan, McAllister, et al., 2016, figure 5C, 7F). At regular intervals, M. ferrooxydans cells detach from the stalks and swim actively away to form new stalks elsewhere. M. fer- rooxydans lives at the narrow interface between the anoxic Fe-­rich vent fluid and ambient, oxygenated seawater (Edwards et al., 2011; Glazer & Rouxel, 2009). In culture, the PV-­1 strain requires neutral pH and microaerobic conditions, producing stalks at 2.7 to 28 μM O2 (Krepski et al., 2013), with Fe(II) used as an electron donor (Emerson et al., 2007). The stalks of M. ferrooxydans are 0.6 to 2.2 µm wide and can bifurcate, as a result of cell division (Figure 1). The stalks typi- cally occur in parallel, a result of coordinated growth of cells follow- ing a chemical gradient (Chan, McAllister, et al., 2016). In addition to M. ferrooxydans, in natural samples from low-­temperature Fe-­oxide deposits other Zetaproteobacteria are present, forming different structures. These include unbranching cylindrical sheaths ca. 1 µm in diameter and hundreds of microns long (Fleming et al., 2013), and Y-­ shaped tubes ca. 2 to 4 µm in diameter and ca. 5 to 50 μm long (Chan, McAllister, et al., 2016; Emerson et al. 2017; Peng et al., 2015). The latter are stalk structures formed by apical cells, similar to the way M. ferrooxydans forms its stalks, but these are shorter than M. fer- rooxydans stalks and are hollow (Chan, McAllister, et  al.,  2016; Emerson et  al. 2017; Peng et  al.,  2015). Although the organisms that form sheaths and Y-­shaped tubes have not been isolated, ge- nomic analyses of major Zetaproteobacteria taxa (cultured and un- cultured) show that all Zetaproteobacteria are aerobic iron oxidizers (McAllister et  al.,  2020). Zetaproteobacteria co-­occur with other micro-­organisms at low-­temperature vents to collectively form mat-­ like structures on the seafloor (e.g., Chan, McAllister, et al., 2016; Johannessen et al., 2017; Vander Roost et al., 2017, 2018) that are partially organic and partially mineralogical, and are often associ- ated with amorphous silica (e.g., Rouxel et al., 2018). However, the main framework of these mats is formed by the Zetaproteobacteria (Figure 1). Importantly, the extracellular stalks and sheaths produced by modern FeOB contain only minor amounts of organic carbon (e.g., 0.3 wt% TOC; Laufer et al., 2017), being Fe-­oxide waste products rather than cells (Bennett et al., 2014; Chan et al., 2011; Emerson & Revsbech, 1994). The Phanerozoic contains many examples of marine hydrothermal vent deposits, termed Volcanogenic Massive Sulfides (VMS), from a wide variety of tectonic settings (e.g., Hannington, 2014; Huston et al., 2010). Some of these VMS deposits are closely associated with layers or lenses of jasper (hematite-­silica rocks), which in many cases can be traced along strike laterally for hundreds of meters to locally several kilometers (e.g., Duhig et al., 1992; Grenne & Slack, 2003, 2005; Juniper & Fouquet, 1988; Little et al., 2004). Jasper occur- rences without lateral continuity may be analogues for the isolated, Si-­Fe-­oxyhydroxides forming at modern, low-­temperature, Fe-­rich, and sulfide-­poor vents. Many of these Phanerozoic jaspers contain filamentous structures, hundreds of micrometers in length and 5 to 30 μm in diameter, composed of hematite within a microcrystal- line quartz matrix (Little et al., 2004 and references therein). The filaments display a variety of morphologies including branching and coiled structures, and dendrites. It has been suggested that these filaments are fossils of FeOB (e.g., Emerson & Moyer, 2002; Little et  al.,  2004 and references therein; Chan, Emerson, et  al.,  2016); however, none has yet convincingly been shown to display the char- acteristic twisted stalks formed by Mariprofundus ferrooxydans. Further back in geological time, VMS deposits as old as 3.5 Ga are known (Huston et al., 2010). Some of these Precambrian VMS are as- sociated with small-­scale jaspers and iron formations (Fe-­oxides that FI G U R E 2 (a) Location of Verde mining district in central Arizona. (b) Simplified stratigraphic section of the VMS-­hosting Paleoproterozoic volcanic sequence in northern part of the mining district (modified from Slack et al., 2007), showing stratigraphic positions of VMS deposits, jaspers, and iron formations. Not shown is a stratigraphically lower horizon of jasper and iron formation, in the southern part of the district, between the Shea Basalt and overlying Deception Rhyolite. Total thickness of section varies from 1 to 2.5 km. Note that thicknesses of VMS deposits, jasper units, and iron formations are exaggerated. 1 | INTRODUCTION Such deposits occur at the interface where While some of the iron oxyhydroxide precipitation in these systems is abiogenic (occurring as micrometer-­scale Fe-­oxide parti- cles), it is now well established that a proportion, and generally the majority, of the volume of iron oxyhydroxide precipitate is formed by benthic, Fe-­oxidizing bacteria (FeOB), principally belonging to the Zetaproteobacteria (Chan, Emerson & Luther,  2016; Chan et  al.,  2011; Chan, McAllister, et  al.,  2016; Davis & Moyer,  2008; Davis et al., 2009; Edwards et al., 2011; Emerson & Moyer, 2002; Emerson et al., 2007, 2017; McAllister et al., 2019). The best known of this group is Mariprofundus ferrooxydans, which has a bean-­shaped cell that secretes stalks of organic-­encased ferrihydrite, which pre- cipitates as a waste product from its metabolic activity (Figure 1). The stalks are usually twisted, but sometimes this trait is not present in the stalks of the PV-­1 type strain (Chan et al., 2011, figure S1). These stalks can then serve as a substrate for further iron oxyhydroxide FI G U R E 1 FeOB structures from modern low-­temperature hydrothermal vent sites. (a-­d) Scanning electron microscope (SEM) images of siliceous ferrihydrite-­coated filaments from Troll Wall vent field, Mohns Ridge. (a) Mat of tubular filaments and variably twisted filaments, with straight to curved morphologies; some parallel aligned. (b) Variably twisted filaments; white arrow points to highly twisted example. (c) Highly branched hollow filaments. (d) Twisted filaments enclosed in silica matrix. (e) TEM image of filaments from Loihi Seamount microbial mats showing a variety of morphologies, including cylindrical tubes, twisted stalks, and highly branching filaments. (f) TEM image of cell (black arrow) and twisted stalk of cultured Mariprofundus ferrooxydans PV-­1 strain, together with Fe-­oxide particles FI G U R E 1 FeOB structures from modern low-­temperature hydrothermal vent sites. (a-­d) Scanning electron microscope (SEM) images of siliceous ferrihydrite-­coated filaments from Troll Wall vent field, Mohns Ridge. (a) Mat of tubular filaments and variably twisted filaments, with straight to curved morphologies; some parallel aligned. (b) Variably twisted filaments; white arrow points to highly twisted example. (c) Highly branched hollow filaments. (d) Twisted filaments enclosed in silica matrix. (e) TEM image of filaments from Loihi Seamount microbial mats showing a variety of morphologies, including cylindrical tubes, twisted stalks, and highly branching filaments. (f) TEM image of cell (black arrow) and twisted stalk of cultured Mariprofundus ferrooxydans PV-­1 strain, together with Fe-­oxide particles 230 LITTLE et al. One example of Precambrian VMS deposits with associated Fe-­rich exhalites is in the Jerome area of the Verde mining district in central Arizona, USA (Figure  2a; Lindberg,  2008). Here occur several Cu-­rich VMS deposits with associated bedded jaspers and tuffaceous rocks with local rip-­up clasts of jasper at the same strati- graphic levels (Slack et al., 2007; Figures 2b and 3a,c,d). Jaspers also occur interlayered with hematite iron formation at a higher strati- graphic level in the Grapevine Gulch Formation, but without asso- ciated VMS deposits (Figures 2b and 3b). The VMS deposits in the district are hosted by a thick succession of late Paleoproterozoic (1.74 Ga) rhyolites. This succession lacks evidence of a terrigenous siliciclastic component, suggesting formation within an intraoce- anic island arc distal from any continental margin (Anderson, 1989). Occurrence in the district of geographically widespread rhyolite tuffs and cauldron ring fractures implies that the VMS mineralization From mineralogical and geochemical studies of the jaspers in the Jerome area, Slack et al. (2007) inferred that late Paleoproterozoic deep seawater was in a transitional, suboxic state that allowed the oxidation of hydrothermal Fe2+ to Fe3+, which in their model was preserved in hematite within the jaspers. This inference is at odds with many (but not all, e.g., Ohmoto et al., 2006; Planavsky et  al.,  2018; Slack et  al.,  2009; Sperling et  al.,  2014) reconstruc- tions of Proterozoic seawater redox states, derived largely from geochemical studies of shales in marine sedimentary sequences FI G U R E 3 (a) Field photograph of orange and red jasper layers and intervening rhyolite tuff (dark-­gray) containing angular jasper clasts, from lowermost part of lower Cleopatra Rhyolite (Figure 2b). Upper red jasper layer is near base of outcrop that contains sample JS-­05-­1. Sample JS-­05-­03 was collected ca. 20 m along strike from this outcrop. Hammer is 40 cm long. (b) Field photograph of folded layers of jasper and hematite iron formation (dark), from lower part of Grapevine Gulch Formation (Figure 2b). Coin is 2.1 cm in diameter. (c) Field photograph of angular jasper and chert rip-­up clasts in crystal-­rich rhyolite tuff. Note dark-­gray rim on elongated jasper clast and completely bleached jasper clast to the left, caused by variable diagenetic reduction in ferric to ferrous iron during sediment burial. Knife is 8.9 cm long. (d) Field photograph of angular jasper rip-­up clasts in rhyolite lapilli tuff, enclosed by massive rhyolite tuff. Stratigraphic levels of samples JS-­05-­1, JS-­05-­3, and that used for U-­Pb zircon age of 1.74 Ga (Slack et al., 2007) are indicated FI G U R E 2 (a) Location of Verde mining district in central Arizona. (b) Simplified stratigraphic section of the VMS-­hosting Paleoproterozoic volcanic sequence in northern part of the mining district (modified from Slack et al., 2007), showing stratigraphic positions of VMS deposits, jaspers, and iron formations. Not shown is a stratigraphically lower horizon of jasper and iron formation, in the southern part of the district, between the Shea Basalt and overlying Deception Rhyolite. Total thickness of section varies from 1 to 2.5 km. Note that thicknesses of VMS deposits, jasper units, and iron formations are exaggerated. Stratigraphic levels of samples JS-­05-­1, JS-­05-­3, and that used for U-­Pb zircon age of 1.74 Ga (Slack et al., 2007) are indicated LITTLE et al. 231 lack abundant silica). Such Fe-­rich and Si-­poor seafloor-­hydrothermal deposits, together with jaspers and other VMS-­related hydrother- mal chemical precipitates, are termed exhalites (e.g., Slack,  2012; Spry et al., 2000). Iron-­rich exhalites are similar in some respects to volcanic-­hosted, deep-­water, Algoma-­type Banded Iron Formation (BIF), but differ in being proximal to VMS deposits. In contrast, the generally larger Superior-­type BIFs formed in sedimentary basins at shallow-­water depths, as shown by the presence of local stro- matolites and other sedimentary features (e.g., Bekker et al., 2010; Konhauser et al., 2017). took place in a submarine volcanic caldera (Lindberg, 2008). These and other geologic features led Briggs (2018) to propose the Izu–­ Bonin–­Mariana Arc in the South Pacific as a modern analogue. The host volcanic rocks and the VMS deposits were subjected to polyphase deformation and lower greenschist-­facies metamorphism during the Paleoproterozoic (Gustin, 1990; Lindberg, 2008). Water depth during formation of the Verde mining district VMS deposits was inferred by Slack et al. (2007) to be ≥850 m, based on the Cu-­ rich nature of the ores and a related fluid temperature of >300°C required to transport appreciable Cu in solution (e.g., Hannington et al., 1995), together with the hydrostatic pressure needed for sta- bilization of aqueous Cu in seafloor-­hydrothermal fluids having near-­ seawater salinities. Using more recent data in Hannington (2014), however, a minimum water depth of 500 m is adopted here with a revised formational temperature of ≥265°C for depositing the Cu-­ rich mineralization in the district. 2.1 | Optical and scanning electron microscopy Details of collection of the Jerome area jaspers, together with background geology and related whole-­rock geochemical data, are given in Slack et al. (2007). The studied materials come from a 1-­m-­thick jasper layer that occurs at the same stratigraphic level as the small Verde Central VMS deposit ca. 160 m to the south (Slack et al., 2007; Figures 2 and 3a). Hereafter, we refer to this layer as the Verde Central jasper (VCJ). VCJ samples JS-­05-­1 and JS-­05-­3 were used in this study for detailed investigation. Filamentous struc- tures within these samples were identified initially in polished thin sections (100 or 200 µm thick) using a Leica DM750P petrographic microscope under plane and crossed polarized light, fitted with a Leica DFC290HD digital camera. One thin section from VCJ JS-­05-­3 was used to obtain digital measurements of the filaments via Leica Application Suite v.3.7.0. Two thin sections from VCJ JS-­05-­1 were prepared with 14-­nm-­thick carbon coats and examined by scanning electron microscopy (SEM) and backscattered electron (BSE) imag- ing at 10 keV, using a FEI Quanta 650 FEG-­ESEM with an Oxford X-­max 80 SDD Energy Dispersive Spectrometer (EDS) at the Leeds Electron Microscopy and Spectroscopy Centre, University of Leeds, UK. Herein, we present a detailed investigation of these filaments using a variety of techniques, in order to fully eluci- date their morphology and formation. Based on the new information and by comparison with Phanerozoic jasper filaments and modern FeOB, we interpret the Jerome area filaments as having a biological origin and suggest these are fossil products of benthic, microaer- obic, FeOB that lived at low-­temperature hydrothermal vents. We further discuss the implications of this interpretation for the redox state of late Paleoproterozoic deep seawater, and the deposition of Precambrian iron formations. 2.4 | Focused ion beam-­transmission electron microscopy (FIB-­TEM) Another thin section (200 µm thick) from VCJ sample JS-­05-­3 was analyzed using FIB-­TEM. Potential target filaments for FIB were iden- tified optically using a Nikon Eclipse LV100 polarizing microscope at the University of Bergen, Norway. The slide was then coated with a 30-­nm-­thick layer of Au, and locations of individual microfossils were confirmed by SEM using a Zeiss Supra 55VP SEM, also at the University of Bergen. For easy recognition of the FIB-­TEM target filaments, only horizontally oriented specimens that intersected the surface of the section were selected. 2.3 | Synchrotron-­based X-­ray tomographic microscopy (SRXTM) SRXTM was carried out at the X02DA (TOMCAT) beamline (Stampanoni et al., 2006) at the Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland. The figured sample was broken out from a ~200-­µm-­thick, double-­polished section from VCJ sample JS-­ 05-­3 and glued to a brass pin. It was then scanned at a beam energy of 20 keV. Transmitted radiation was converted to visible light using a 20-­µm-­thick LAG:Ce scintillator or a 5.9-­µm-­thick LSO:Tb scintil- lator. The image was magnified with 10x, 20x, or 40x microscope objectives and digitized by a sCMOS camera (PCO.edge). The re- sulting voxel size was 0.65 µm for the 10×, 0.325 µm for the 20×, and 0.1625 µm for the 40× objective. For each scan, 1,501 to 2,001 projections equiangularly spaced over 180° were acquired, with ex- posure times of 220 to 800 ms per single projection. Tomographic reconstruction was done using a highly optimized algorithm based on the Fourier method (Marone & Stampanoni, 2012), and the ob- tained tomographic volumes were visualized and rendered using Avizo software (Thermo Fisher Scientific). Note lack of hematite in matrix of lapilli tuff. Coin is 2.1 cm in diameter FI G U R E 3 (a) Field photograph of orange and red jasper layers and intervening rhyolite tuff (dark-­gray) containing angular jasper clasts, from lowermost part of lower Cleopatra Rhyolite (Figure 2b). Upper red jasper layer is near base of outcrop that contains sample JS-­05-­1. Sample JS-­05-­03 was collected ca. 20 m along strike from this outcrop. Hammer is 40 cm long. (b) Field photograph of folded layers of jasper and hematite iron formation (dark), from lower part of Grapevine Gulch Formation (Figure 2b). Coin is 2.1 cm in diameter. (c) Field photograph of angular jasper and chert rip-­up clasts in crystal-­rich rhyolite tuff. Note dark-­gray rim on elongated jasper clast and completely bleached jasper clast to the left, caused by variable diagenetic reduction in ferric to ferrous iron during sediment burial. Knife is 8.9 cm long. (d) Field photograph of angular jasper rip-­up clasts in rhyolite lapilli tuff, enclosed by massive rhyolite tuff. Note lack of hematite in matrix of lapilli tuff. Coin is 2.1 cm in diameter 232 LITTLE et al. | (−70°C), 1,024  ×  256 pixel CCD (charge-­coupled device) detec- tor. Acquisitions were obtained with an 1,800  lines/mm grating. Excitation was provided by an Ar-­ion laser (λ  =  514  nm) source. Spectra were recorded using a low laser power of 0.1–­1 mW at the sample surface to avoid laser-­induced degradation. Sampling was carried out using an Olympus BX41 microscope coupled to the in- strument; the laser beam was focused through a 100× objective to obtain a spot size of ca. 1 mm. The spectral resolution was ~0.3 cm−1 pixel−1. Typical exposure time was 10 s with 10 accumulations. The accuracy of the instrument was controlled by repeated use of a sili- con wafer calibration standard with a characteristic Raman line at 520.7 cm−1. (e.g., Canfield,  1998; Bekker et  al.,  2004; Poulton et  al.,  2004; Canfield, 2005; Canfield et al., 2008; Meyer & Kump, 2008; Kendall et al., 2009; Poulton et al., 2010; Poulton & Canfield, 2011; Planavsky et al., 2011; Reinhard et al., 2013), which suggest that either ferrugi- nous or euxinic conditions prevailed in the deep sea during this long time period between 1.8 and 0.8 Ga (the so-­called “Boring Billion”). Light microscope investigations of the Jerome area jaspers revealed in some samples distinctive hematitic filaments, described briefly by Slack et al. (2007). Herein, we present a detailed investigation of these filaments using a variety of techniques, in order to fully eluci- date their morphology and formation. Based on the new information and by comparison with Phanerozoic jasper filaments and modern FeOB, we interpret the Jerome area filaments as having a biological origin and suggest these are fossil products of benthic, microaer- obic, FeOB that lived at low-­temperature hydrothermal vents. We further discuss the implications of this interpretation for the redox state of late Paleoproterozoic deep seawater, and the deposition of Precambrian iron formations. (e.g., Canfield,  1998; Bekker et  al.,  2004; Poulton et  al.,  2004; Canfield, 2005; Canfield et al., 2008; Meyer & Kump, 2008; Kendall et al., 2009; Poulton et al., 2010; Poulton & Canfield, 2011; Planavsky et al., 2011; Reinhard et al., 2013), which suggest that either ferrugi- nous or euxinic conditions prevailed in the deep sea during this long time period between 1.8 and 0.8 Ga (the so-­called “Boring Billion”). Light microscope investigations of the Jerome area jaspers revealed in some samples distinctive hematitic filaments, described briefly by Slack et al. (2007). 2.2 | Raman spectroscopy One thin section (200  µm thick) from VCJ sample JS-­05-­3 was analyzed at the Department of Geological Sciences, Stockholm University, Sweden, using a confocal laser Raman microspectrom- eter (Horiba instrument LabRAM HR 800; Horiba Jobin Yvon, Villeneuve d’Ascq, France), equipped with a multichannel, air-­cooled Three ultrathin filament cross sections were prepared from the slide using a FEI Helios NanoLab 600 DualBeam FIB-­SEM at the NTNU NanoLab in Trondheim, Norway. The target areas were identified and monitored with a FEG-­SEM, while milling was performed with a focused Ga+ ion beam. A Pt protection layer LITTLE et al. 233 | TA B LE 1 Whole-­rock analyses of jaspers from the Verde Central horizon Sample No. JS-­05-­1 JS-­05-­2 JS-­05-­3 JS-­05-­3 BEK JS-­05-­4 SiO2 (wt %) 94.47 96.15 94.24 89.51 95.34 Al2O3 0.30 0.74 0.17 0.20 0.38 Fe2O3 3.08 1.44 3.41 7.78 0.65 FeO 1.13 1.07 0.96 1.21 2.14 MnO 0.004 0.011 0.018 0.005 0.010 MgO 0.02 0.02 0.03 0.04 0.17 CaO 0.02 0.03 0.03 0.06 0.02 Na2O 0.08 0.08 0.07 0.09 0.06 K2O 0.07 0.04 0.07 0.06 0.06 TiO2 0.010 0.016 0.007 0.016 0.007 P2O5 <0.01 <0.01 <0.01 <0.01 0.05 LOI 0.51 0.46 0.66 0.55 0.62 Total 99.68 100.05 99.63 99.50 99.53 Be (ppm) <1 <1 <1 <1 <1 Br <0.5 0.5 <0.5 <0.5 0.5 Ga <1 1 <1 <1 1 Ge 1.0 1.1 0.7 0.7 0.9 Sc 0.6 0.7 0.3 0.3 1.9 V <5 <5 <5 <5 <5 Cr 9 29 13 459 94 Nb 0.7 0.9 0.9 0.5 1.3 Ta <0.01 <0.01 <0.01 0.10 <0.01 Zr 7 7 7 5 22 Hf 0.1 0.2 <0.1 <0.1 0.2 Th 0.11 0.18 0.05 0.08 0.06 U 0.36 0.32 0.25 0.19 0.53 Ni 4 12 4 13 10 Cu 7 27 4 9 13 Pb 4 <3 <3 <3 <3 Zn 21 24 5 4 19 Cd 0.3 <0.3 <0.3 0.5 0.4 Ag <0.3 <0.3 <0.3 <0.3 <0.3 Au (ppb) 69 55 32 <2 14 As 5.5 6.3 3.5 3.8 10.8 Sb 0.72 0.96 0.48 0.48 1.04 Se <3 <3 <3 <3 <3 Mo <2 3 <2 10 <2 Sn <1 <1 <1 <1 <1 W 1.2 0.7 1.0 1.4 0.9 Tl <0.05 <0.05 <0.05 <0.05 <0.05 Bi 0.6 0.2 0.3 <0.1 0.4 In <0.1 <0.1 <0.1 <0.1 <0.1 Ir <5 <5 <5 <5 <5 Cs <0.1 <0.1 <0.1 <0.1 <0.1 Rb <1 <1 <1 <1 <1 TA B LE 1 Whole-­rock analyses of jaspers from the Verde Central horizon TA B LE 1 Whole-­rock analyses of jaspers from the Verde Central horizon LITTLE et al. LITTLE et al. 234 234  |     LITTLE et al. Sample No. TA B LE 1 (Continued) Figure 7 and Figure S2, the pixel size and dwell time in the EDS element maps were 10 nm/0.03 s and 5 nm/0.05 s, respectively, but acquired with 16  ×  16 sub-­pixel scanning to avoid severe beam damage. The beam dose during STEM-­EDS was 7,000 e/Å2 in Figure 7 and ca. 45,000 e/Å2 in Figure S2. The EDS maps were processed in MATLAB using the jet color scale with matrix values from 0 (dark blue) to 255 (dark red). EELS was performed with a GIF Quantum ER, operated in dual-­EELS mode. A 110  pA beam current and 27 mrad semi-­convergence angle were combined with a 33 mrad collection semi-­angle into the GIF. An energy dispersion of 0.025 eV/channel gave an energy resolution of 0.50 eV as de- termined from the full width at half maximum of the zero-­loss peak (ZLP). The energy scale of the core-­loss spectra was calibrated from the position of the ZLP in the low-­loss spectra. The EEL spec- tra in Figure S1 were acquired while the beam was quickly scanned (512 × 512 pixels with 2 µs pixel time and 0.5 s frame time) over a ca. 100 nm × 100 nm region, giving a fluence rate of 690 e/(Å2s). The acquisition time for the Fe L2,3 spectra was 5 s, exposing the sample to a total beam dose of 3,430 e/Å2. The chemical shift method (e.g., Tan et al., 2012) was used in combination with the ratio and distance between the L3 and L2 peaks to determine the oxidation state of Fe in poorly crystalline material. Hematite grains identified by diffraction were used as a reference for Fe3+. Figure 7 and Figure S2, the pixel size and dwell time in the EDS element maps were 10 nm/0.03 s and 5 nm/0.05 s, respectively, but acquired with 16  ×  16 sub-­pixel scanning to avoid severe beam damage. The beam dose during STEM-­EDS was 7,000 e/Å2 in Figure 7 and ca. 45,000 e/Å2 in Figure S2. The EDS maps were processed in MATLAB using the jet color scale with matrix values from 0 (dark blue) to 255 (dark red). EELS was performed with a GIF Quantum ER, operated in dual-­EELS mode. A 110  pA beam current and 27 mrad semi-­convergence angle were combined with a 33 mrad collection semi-­angle into the GIF. JS-­05-­1 JS-­05-­2 JS-­05-­3 JS-­05-­3 BEK JS-­05-­4 Sr 12 18 <2 3 2 Ba 10 9 9 6 6 Y 34.2 79.4 31.0 3.76 251 La 1.24 2.53 0.73 0.36 1.79 Ce 2.52 5.09 1.56 0.76 4.36 Pr 0.36 0.68 0.22 0.10 0.59 Nd 1.86 3.63 1.24 0.49 3.88 Sm 0.58 1.23 0.44 0.14 2.16 Eu 0.149 0.330 0.119 0.036 0.861 Gd 1.20 3.19 1.04 0.22 7.29 Tb 0.31 0.82 0.30 0.05 2.12 Dy 2.65 6.70 2.50 0.39 18.7 Ho 0.70 1.74 0.67 0.10 5.34 Er 2.48 6.29 2.50 0.36 20.4 Tm 0.431 1.095 0.442 0.062 3.670 Yb 3.13 8.02 3.23 0.46 26.4 Lu 0.514 1.367 0.524 0.076 4.325 La/Yb 0.396 0.315 0.226 0.787 0.068 LaSN/YbSN 0.029 0.023 0.017 0.058 0.005 Ce/Ce* 0.87 0.90 0.90 0.92 0.98 Eu/Eu* 0.84 0.78 0.83 0.97 1.02 Note: REE anomalies are calculated by shale normalization (SN) using data for average Post-­Archean Australian Shale (PAAS; Taylor & McLennan, 1985): Ce∕Ce ∗ SN = CeSN∕√(LaSN × PrSN ); Eu∕Eu ∗ SN = EuSN∕√(SmSN × GdSN ). TA B LE 1 (Continued) McLennan, 1985): Ce∕Ce ∗ SN = CeSN∕√(LaSN × PrSN ); Eu∕Eu ∗ SN = EuSN∕√(SmSN × GdSN ). 3.1 | Filament occurrence, morphologies, and mineralogical composition Filaments in the VCJ samples occur in millimeter-­scale domains bounded by multiple cross-­cutting quartz veins and areas of vari- ably sized quartz grains with greater or lesser quantities of dissemi- nated hematite crystals (Figure 4a-­c, Figure 5a). Within the studied samples, the area of filament-­rich domains is small (<5%) relative to the overall rock volume. The filaments within the domains are en- closed by equigranular quartz grains 5 to 40 μm in diameter hav- ing triple-­junction and slightly curved to straight grain boundaries (Figure 4c-­f, Figure 6c); many filaments continue across grain bound- aries (Figure 4c,f), thus demonstrating they are not grain-­boundary artifacts. In addition to the filaments, the quartz grains enclose scattered, micrometer-­scale hematite crystals with variable shapes (Figures 4a,d and 6b). 2.6 | Comparative modern material Material from modern, low-­temperature hydrothermal vent areas at Troll Wall on Mohns Ridge, Norwegian-­Greenland Sea, and on Lōʻihi Seamount, off-­shore Hawaii, was used for comparison with the VCJ filaments (Figure 1). For collection and imaging details of the modern material, see Pedersen et al. (2010) and Glazer and Rouxel (2009), respectively. An energy dispersion of 0.025 eV/channel gave an energy resolution of 0.50 eV as de- termined from the full width at half maximum of the zero-­loss peak (ZLP). The energy scale of the core-­loss spectra was calibrated from the position of the ZLP in the low-­loss spectra. The EEL spec- tra in Figure S1 were acquired while the beam was quickly scanned (512 × 512 pixels with 2 µs pixel time and 0.5 s frame time) over a ca. 100 nm × 100 nm region, giving a fluence rate of 690 e/(Å2s). The acquisition time for the Fe L2,3 spectra was 5 s, exposing the sample to a total beam dose of 3,430 e/Å2. The chemical shift method (e.g., Tan et al., 2012) was used in combination with the ratio and distance between the L3 and L2 peaks to determine the oxidation state of Fe in poorly crystalline material. Hematite grains identified by diffraction were used as a reference for Fe3+. was deposited on the surface of the target cross section prior to FIB milling. The first part of the protection layer was deposited by electron beam-­assisted deposition to avoid ion beam damage into the subsurface of the sample. Each lamella was transferred to dedicated Cu half-­grids for TEM by standard lift-­out-­technique. All coarse thinning was performed at 30 kV acceleration voltage for the Ga+ ions. Final thinning was first performed at 5 kV and then 2 kV acceleration voltage on either side of the lamella to minimize surface damage. The final thickness of the FIB lamellae was ca. 100 nm. The three FIB foils were analyzed at the TEM Gemini Centre at NTNU in Trondheim using a double Cs-­corrected, cold-­FEG JEOL ARM 200F, operated at 200  kV. Prior to insertion, the samples were gently plasma cleaned in a gas mixture of 75% Ar and 25% O2 for 30 s to remove adventitious hydrocarbon contamination. EDS and EELS were done in scanning transmission electron mi- croscopy (STEM) mode. EDS was performed with a 27 mrad beam semi-­convergence angle and a beam current of 380  pA. These conditions gave a 1.4  Å spatial resolution, but on amorphous material or on crystals away from high symmetry orientations, the beam diameter quickly increases through the sample due to the large convergence angle of the beam. A 100-­mm2 Centurio detector, covering a solid angle of 0.98 sr, was used for EDS. In LITTLE et al. 235 2.5 | Whole-­rock geochemistry and many display irregular branching patterns and bifurcations (Figures 4a,e,f, and 5d). The filaments are quartz-­filled cylinders with walls formed of hematite crystals as documented by TEM diffraction and Raman spectroscopy (Figures 4d-­f, 6b, and 7a; Figure S1). Thicknesses of the walls vary but are typically less than 1 µm. In many filaments, the hematite crystals forming the walls are so sparse that they do not touch each other (Figure 7a). TEM of two filaments shows the hematite crystals that form walls have a blocky shape and are 0.2 to 0.5  µm along the long axes (Figure  7b). An additional Si-­ Fe phase is present in one of the cross sections (Figure 7b). This phase displays a locally ordered microstructure but lacks long-­ range crystallographic order and therefore gives a diffuse, circu- lar diffraction pattern characteristic of poorly crystalline material (Figure  S1). Silicon content is significantly higher in the poorly crystalline phase than in the hematite crystals, and the content of iron is lower (Figure  7c-­e). The poorly crystalline phase and the hematite reference grains show identical chemical shifts, Fe L3/L2 ratios, and distances between L3 and L2 peaks in the EELS spectra, thus indicating that the oxidation state of Fe in the poorly crys- talline material is +3. There is no carbon present in the two fila- ments investigated using TEM (Figure 7f), and we did not find the characteristic D and G bands of the ordering of organic carbon in our Raman investigation. However, very small amounts of carbon occur in the third TEM section, which did not transect an obvious filament (Figure S2). Here, the carbon is present in the interface between larger hematite crystals and quartz and has a distinct fi- brous habit (not shown). Five jasper samples from the Verde Central horizon (Figure 2b) were analyzed for major, trace, and rare earth elements (REE) in a com- mercial laboratory by fusion-­based ICP-­MS methods as described in Slack et al. (2007). Details of the analytical methods, including ac- curacy and precision, are available at www.actla​bs.com. Analyses of these five samples, which have not been reported previously, are listed in Table 1. 3.2 | Rare earth element geochemistry Major and trace element data for the VCJ samples are similar to those for the other jaspers analyzed from the Verde mining dis- trict (Slack et al., 2007). However, results for REE differ signifi- cantly in terms of abundances and especially shale-­normalized patterns (Figure 8a). Relative to jaspers from the United Verde and Copper Chief horizons (Figure  2b), the VCJ samples dis- play mostly higher REE abundances, with strong enrichments particularly in the heavy rare earth elements (HREE) and con- sequently very low ratios of light rare earth elements (LREE) to HREE (LaSN/YbSN = 0.005–­0.058; Table 1). All five analyzed VCJ samples have very small negative or no Eu anomalies (Eu/ Eu* 0.78–­1.02) using the geometric mean calculation method of Taylor and McLennan (1985). This same method yields uniformly small negative Ce anomalies (Ce/Ce* 0.87–­0.98). However, the scheme of Lawrence and Kamber (2006), which does not rely on La data because of the common presence of positive La anom- alies in marine sediments, yields uniformly small to moderate positive Ce anomalies (1.14–­1.48) but these values are likely overestimated by as much as 20% (cf. Kamber et al., 2014). The largest Ce anomaly of 1.48, determined using this latter scheme, exceeds the value of 1.3 proposed by Tostevin et al. (2016) as Filament diameters vary between 0.9 and 4.7  μm (mean 2.5 μm; n = 43) in VCJ sample JS-­05-­1 (measured using binocu- lar microscope) and between 2.3 and 12.4 µm in VCJ sample JS-­ 05-­3 (based on tomographic volume renderings in Figure 5a–­c). In general, the filaments have constant diameters along their length, apart from places where branches exist. The longest traceable filaments are 120 μm in length (Figure 5a), although this can be regarded as a minimum value because the longest examples cross the plane of the petrographic thin sections. The filaments form densely to loosely packed meshworks (Figures 4a-­c and 5). In some places, the filaments are roughly parallel to each other, forming bundles of >10 individuals (Figure 5a,b). Individual filaments have sinuous to curved shapes; a few are tightly coiled (Figure  5a,c). Several filaments show possible twisted shapes (Figure  4b,d), 236  | LITTLE et al. 236 236  | FI G U R E 4 Hematite filaments from Verde Central jasper sample JS-­05-­1. | | FI G U R E 5 Synchrotron-­based X-­ray tomographic microscopy volume (a–­c) and surface (d) renderings of hematite filaments from Verde Central jasper sample JS-­05-­3. (a) shows sharply delimited area with dense filaments. Insets show filaments with parallel bundles (b), with looped morphology (c), and those with branches highlighted in yellow in (d). White arrow E indicates the filament from which Raman spectra were obtained (Figure 6). For stereo anaglyph of 5c, see Figure S3. For 3-­D animations of 5a,b, and d, see Video S1-­S3 4 | INTERPRETATION AND DISCUSSION metamorphism. However, we emphasize that the lack of carbon in the studied VCJ filaments does not preclude a biological origin, because the stalks and sheaths produced by modern Zetaproteobacteria con- tain little organic carbon (<1 wt% TOC; Bennett et al., 2014; Laufer et al., 2017). Further, the cells that create the stalks and sheaths are only loosely attached to these structures and can become easily detached from them, with consequent carbon loss. In addition, any carbon originally present in the VCJ protolith could have been mobi- lized later, by dissimilatory Fe reduction (Emerson, 2009), or during diagenesis/low-­grade metamorphism (Johannessen et al., 2020). 3.2 | Rare earth element geochemistry (a-­c) Photomicrographs in plane-­polarized light of branching (white arrow in A) and putative twisted filaments (white arrow in b); insets in (c) show detailed areas (e,f). (d-­f) Scanning electron microscope-­ backscattered electron (SEM-­BSE) images of filaments, showing branching (black arrows in e,f) and putative twisted (black arrow in d) forms. White arrows in (d) and (e) show filaments in transverse section. (c) and (f) show a filament that transgresses quartz grain boundaries (c,f) FI G U R E 4 Hematite filaments from Verde Central jasper sample JS-­05-­1. abundances, low LREE/HREE ratios, and small to moderate negative Eu anomalies (Figure 8b). a minimum to define true positive Ce anomalies, but the use of this scheme is questionable because it relies on a linear projec- tion of Sm-­Nd-­Pr to Ce, which is not applicable to the VCJ sam- ples that display highly curved trends for PAAS-­normalized LREE (Figure 8a). We therefore take a conservative approach and sug- gest that the five VCJ samples lack significant Ce anomalies, ei- ther negative or positive. REE data for representative examples of modern Fe-­Si oxyhy- droxide deposits show a large range in abundances and LREE/HREE ratios, with small negative Ce anomalies and small to moderate pos- itive Eu anomalies (Figure 8c). However, none of these modern Fe-­Si samples has the extremely low LREE/HREE ratios that characterize the VCJ samples. In terms of modern fluids, only waters from Mono Lake in California display a similar LREE/HREE ratio with relatively flat HREE abundances; typical seawater and some modern, low-­Fe marine pore fluids have slightly higher ratios (Figure 8d). Importantly, fluids from modern submarine-­hydrothermal vents also differ greatly in having large positive Eu anomalies that reflect reduced, high-­ temperature (>300°C) conditions (e.g., Mills & Elderfield, 1995). In contrast, jaspers from the United Verde and Copper Chief horizons (e.g., JS-­05-­37, JS-­05-­39) have either no, or small positive or negative, Ce anomalies and small to moderate positive Eu anomalies. Low-­silica iron formation samples in the district (lower Grapevine Gulch Formation; Figure  2b) show higher REE abundances, higher LREE/HREE ratios, and small positive Ce and Eu anomalies (Figure 8a). For comparison, the rhyolitic host rocks display high REE 237 LITTLE et al. 4.1 | Biogenicity of VCJ filaments The VCJ filaments conform to the majority of established biogenic- ity criteria for documenting Precambrian microfossils (Buick, 1990; Cady et  al.,  2003). These criteria include the following: (a) being intrinsic to the rock and pre-­dating quartz crystallization (probably from an original silica gel; see Grenne & Slack, 2003) and subsequent quartz veining; (b) having a narrow range of diameters that generally do not vary longitudinally, and that are within the size range of mod- ern micro-­organisms; (c) co-­existing with other filaments of similar morphology; and (d) occurring in a paleoenvironment analogous to those where bacteria grow today (see below). The only biogenicity criterion of Buick (1990) not satisfied by the VCJ filaments is their apparent lack of organic matter (e.g., kerogen). The weak EDS carbon signal we found in one of the FIB-­TEM sections (Figure S2) is not spatially associated with a well-­defined filament, and its origin could have several explanations, including being contemporaneous to fila- ment formation, or a later contamination related to diagenesis or An alternative explanation for the formation of the VCJ fila- ments is that they are “biomorphs,” that is, abiogenic features that resemble biological structures (e.g., Garcia-­Ruiz et al., 2009). In laboratory experiments, McMahon (2019) was able to grow filamentous tubular structures formed of Fe-­(oxyhydr)oxides and amorphous hydrated Fe-­Si phases, from polycrystalline fer- rous sulfate granules placed into aqueous solutions of sodium silicate or sodium carbonate at ambient temperature and pres- sure. The tubes were of the same scale as the VCJ filaments in terms of diameters, and had some of the same morphologies, LITTLE et al. LITTLE et al. 238 FI G U R E 6 Raman spectra and light microscope images of filament area indicated in Figure 5a. Yellow spots indicate where laser beam was focused for analysis. (a) Hematite spectrum of filament mixed with a peak at 464 cm−1 from surrounding quartz. (b) Hematite spectrum of filament. (c) Quartz spectrum of surrounding mineralogy. Photomicrographs are in transmitted light (a and b), and reflected light (b) Johannessen et al. (2020, figure 9) listed five criteria for the identi- fication of biosignatures for Fe-­oxidizing bacteria in modern, silici- fied, low-­temperature hydrothermal deposits. 4.1 | Biogenicity of VCJ filaments The VCJ filaments pass biosignature criteria 3, 4, and 5, because they show sequential bifurcation rather than nodes with multiple branches (criterion 3), have semi-­parallel filamentous textures rather than highly direc- tional radial textures (criterion 4), and show dendritic and radial fil- amentous textures rather than banded dendrites (criterion 5). The VCJ filaments also pass one of the two biosignature criteria for fil- ament construction (criterion 2), in that they are not hollow silica tubes, although the VCJ filaments do have greater diameters than the biogenic filaments of criterion 2. Criterion 1 of Johannessen et al. (2020) is that Fe-­oxidizing bacterial filaments have solid cores, whereas abiotic filaments have cores formed of separate spherules. The VCJ filaments lack solid cores, but instead have walls formed of isolated hematite crystals (Figure  7). This discrepancy can be explained by the biogenic filaments in criterion 1 of Johannessen et al. (2020) representing zetaproteobacterial stalks, rather than ze- taproteobacterial tubes, which have hollow cores and walls formed of iron oxyhydroxides (see Johannessen et al., 2020, figure S3E,F, and Li et  al.,  2012, figure 3). For these reasons and those given above, we interpret the VCJ filaments as having a biological rather than an abiogenic origin. 4.2 | VCJ filaments as FeOB Using the Uniformitarian principle, the obvious organisms with which to compare the VCJ filaments are Zetaproteobacteria FeOB from modern, deep-­marine, low-­temperature hydrother- mal vents (Figure  1). Many similarities exist in terms of size and morphology, with filaments forming mesh-­like networks (compare Figure 1a,b with Figures 4a,b and 5a), occurring in parallel (compare Figure 1a with Figure 5a,b), and having regular branches (compare Figure 1c,e and Figures 4a,e,f, and 5d). The diameters of the thin- nest VCJ filaments in sample JS-­05-­1 are within the range of modern Zetaproteobacteria (Figure 1), but the thickest filaments in sample JS-­05-­3 are around three times as wide. It is possible that a few of the VCJ filaments are twisted (Figure 4b,d), like Mariprofundus stalks (Figure 1f), although this is unclear in our samples. Because most of the VCJ filaments are cylindrical, they were probably originally not Mariprofundus-­like stalks, but rather branching tubular struc- tures, similar to those shown in Figure 1c,e. The comparison with modern FeOB allows us to infer a preservational (i.e., taphonomic) pathway to explain the morphology and mineralogy of the VCJ fila- ments, and also the metabolism of the micro-­organisms that formed them, which has paleoenvironmental implications. We suggest that the VCJ filaments were formed by cells that oxidized reduced iron from vent fluids as an energy source, with iron oxyhydroxides being a product from this reaction. The cells precipitated the resultant iron oxyhydroxides as tubular structures, rather than having minerals forming on the cell surfaces. The VCJ cells would have undergone division at regular intervals to form branched tubes (see Emerson FI G U R E 6 Raman spectra and light microscope images of filament area indicated in Figure 5a. Yellow spots indicate where laser beam was focused for analysis. (a) Hematite spectrum of filament mixed with a peak at 464 cm−1 from surrounding quartz. (b) Hematite spectrum of filament. (c) Quartz spectrum of surrounding mineralogy. Photomicrographs are in transmitted light (a and b), and reflected light (b) FI G U R E 6 Raman spectra and light microscope images of filament area indicated in Figure 5a. Yellow spots indicate where laser beam was focused for analysis. (a) Hematite spectrum of filament mixed with a peak at 464 cm−1 from surrounding quartz. (b) Hematite spectrum of filament. (c) Quartz spectrum of surrounding mineralogy. |  239 LE et al. U R E 7 Focused ion beam-­ smission electron microscopy images ematite filament from Verde Central er sample JS-­05-­3. (a) SEM-­BSE image nalyzed filament; inset shows area m which FIB foil was recovered. (b) htfield STEM image of FIB foil from X marks poorly crystalline grain. (c-­f) maps of B: (c) Fe Kɑ, (d) O Kɑ, (e) Si (f) C Kɑ |  239 FI G U R E 7 Focused ion beam-­ transmission electron microscopy images of hematite filament from Verde Central jasper sample JS-­05-­3. (a) SEM-­BSE image of analyzed filament; inset shows area from which FIB foil was recovered. (b) Brightfield STEM image of FIB foil from (a); X marks poorly crystalline grain. (c-­f) EDS maps of B: (c) Fe Kɑ, (d) O Kɑ, (e) Si Kɑ, (f) C Kɑ Figure 1d), helping to preserve delicate structures from mechanical degradation (Grenne & Slack, 2003; Hein et al., 2008; Johannessen et  al.,  2020; Toner et  al.,  2012). Later, during diagenesis, the iron oxyhydroxides on the tubes and surrounding matrix would have matured to hematite and the amorphous silica to quartz, forming the studied jasper rock. This model is supported by experimental diagenesis of modern FeOB stalks at 170°C and 120  MPa, which transforms ferrihydrite to hematite and magnetite, and maintains morphologies at even higher temperatures (250°C) and pressures (140 MPa) (Picard et al., 2015), and also by the presence of hematitic filaments in modern Fe-­oxide-­Si mounds that precipitated from flu- ids at ≥115°C (Hein et al., 2008). Subsequent tectonic and regional metamorphic events would have caused multiple episode of quartz recrystallization and quartz veining in the jasper, leaving only small domains with preserved filaments, consistent with our observations. et al., 2017), eventually producing bush-­like structures, together ap- pearing as complex meshes. In our model, the cells were growing on the seafloor in mat-­like structures, rather than as flocs within buoy- ant hydrothermal plumes (Slack et  al.,  2007). Modern marine mi- croaerobic, Fe-­oxidizing Zetaproteobacteria can occur in the water column, but the described planktonic strains Mariprofundus aestu- arium and M. ferrinatatus excrete dreadlock-­like bundles of poorly crystalline iron oxyhydroxide rods that are significantly shorter and weigh less than the extracellular stalks and sheaths produced by M. ferrooxydans and other benthic relatives, and in modern seawater do not accumulate in filamentous microbial mats (Chiu et al., 2017). FI G U R E 7 Focused ion beam-­ transmission electron microscopy images of hematite filament from Verde Central jasper sample JS-­05-­3. (a) SEM-­BSE image of analyzed filament; inset shows area from which FIB foil was recovered. (b) Brightfield STEM image of FIB foil from (a); X marks poorly crystalline grain. (c-­f) EDS maps of B: (c) Fe Kɑ, (d) O Kɑ, (e) Si Kɑ, (f) C Kɑ 4.2 | VCJ filaments as FeOB Photomicrographs are in transmitted light (a and b), and reflected light (b) FI G U R E 6 Raman spectra and light microscope images of filament area indicated in Figure 5a. Yellow spots indicate where laser beam was focused for analysis. (a) Hematite spectrum of filament mixed with a peak at 464 cm−1 from surrounding quartz. (b) Hematite spectrum of filament. (c) Quartz spectrum of surrounding mineralogy. Photomicrographs are in transmitted light (a and b), and reflected light (b) including both straight and strongly curved shapes, and true (non-­ crystallographic) branching structures. However, there are quite a few differences between the McMahon biomorphs and the VCJ filaments; in particular, the latter commonly form parallel bundles and lack tapering terminations, and do not originate at seed crys- tal “knobs”. The most obvious difference is that many of the VCJ filaments have walls formed of isolated hematite crystals, and thus cannot be “crystal garden” structures formed of minerals growing on pre-­existing minerals. In contrast, all of the biomorphs grown by McMahon (2019) have contiguous mineral walls. In modern low-­temperature marine FeOB mats and Fe-­oxide deposits, a wide variety of filamentous and dendritic structures are present (e.g., Hopkinson et al., 1998; Johannessen et al., 2020), which are also seen in Phanerozoic jaspers (e.g., Little et al., 2004). LITTLE et al. 239 Further, genomic studies of microbial communities from modern hydrothermal vent plumes have not found Zetaproteobacteria or genes for iron oxidation, but rather show sulfur oxidation is the most important biogeochemical process occurring (Anantharaman et al., 2016). At the VCJ site, iron-­rich hydrothermal activity may then have waned and the VCJ cells actively swam away from or dropped off the mineralized tubes, with consequent loss of organic carbon from the VCJ microbial mats. Silica would then have precipitated as an amorphous phase within and around the mineralized tubes (as in Some (if not all) of the hematitic microfossils in the older, ca. 1.88 Ga Gunflint Iron Formation had ferrous iron-­rich mineral inter- mediates such as greenalite, siderite, and pyrite (Lepot et al., 2017; Shapiro & Konhauser, 2015; Wacey et al., 2013). In this case, the fer- rous intermediates could have formed from the diagenetic reduction 240  |     LITTLE et al. FI G U R E 8 Shale-­normalized REE plots. (a) Paleoproterozoic jasper and iron formation from Verde mining district; note positive Eu anomalies for jasper samples JS-­05-­37 and JS-­05-­039. Data from Slack et al. (2007, Table S1; and Table 1). (b) Paleoproterozoic volcanic rocks from Verde district (see Figure 2b for stratigraphic positions); data from Slack et al. (2007, Table S1). (c) Modern Si-­Fe seafloor-­ hydrothermal sediments; Endeavor data from Bao et al. (2008); Blanco Fracture Zone data from Hein et al. (2008); Loihi data from Edwards et al. (2011, Table S1); Jan Mayen data from Johannessen et al. (2017). (d) Modern waters; seawater data from Byrne and Sholkovitz (1996); Low-­Fe marine pore fluid data from Haley et al. (2004); TAG data from Mills and Elderfield (1995); Manus Basin data from Douville et al. (1999); Mono Lake data from Johannesson and Lyons (1994). Shale normalization based on average Post-­Archean Australian Shale (PAAS; Taylor & McLennan, 1985) LITTLE et al. LITTLE et al. 240 240  | FI G U R E 8 Shale-­normalized REE plots. (a) Paleoproterozoic jasper and iron formation from Verde mining district; note positive Eu anomalies for jasper samples JS-­05-­37 and JS-­05-­039. Data from Slack et al. (2007, Table S1; and Table 1). (b) Paleoproterozoic volcanic rocks from Verde district (see Figure 2b for stratigraphic positions); data from Slack et al. (2007, Table S1). (c) Modern Si-­Fe seafloor-­ hydrothermal sediments; Endeavor data from Bao et al. (2008); Blanco Fracture Zone data from Hein et al. Based on these morphological comparisons and paleoenviron- mental arguments, we suggest that the VCJ filaments represent fossilized FeOB and that these FeOB could well have been microaer- obic, living on the deep seafloor of an intraoceanic island arc in the mixing zone of Fe-­rich, sulfide-­poor, low-­temperature, slightly acidic (see section 4.4) vent fluid and weakly oxygenated seawater. By their metabolic activity, these FeOB formed a percentage of the Fe pre- cipitation that created the VCJ jasper units, together with abiogenic Fe precipitation from the vent fluid and distal fallout from a non- buoyant hydrothermal plume (see Slack et al., 2007). Filamentous microstructures within intertidal to shallow subtidal ooidal and stromatolitic ironstones from the terminal Paleoproterozoic (ca. 1.65 to 1.64  Ga) Chuanlinggou Formation of North China have been interpreted as fossil FeOB by Lin et al. (2019). The filaments are spatially associated with silicified he- matitic ooids and display a range of sizes (0.3–­6.8 μm in diameter and up to 100 μm in length) and morphologies, including hematite-­ lined sheaths, some of which are twisted along their lengths. Unlike the VCJ filaments, the Chuanlinggou Formation microfossils do not branch and do form mat-­like structures. Another shallow-­water po- tential FeOB occurrence is in phosphatic stromatolites from the ca. 1.7 Ga Jhamarkotra Formation, India (Crosby et al. 2014). Here, mi- crofossils are hosted by an apatite matrix and comprise bundles of subparallel filaments and filaments with radial growth patterns. The filaments are 100s of micrometers in length, and ca. 5 to 6 μm in diameter with a central space (lumen) ca. 1 to 1.5 μm in diameter, which locally show a twisted pattern. Some of the filaments display branching patterns and knobs. The filament walls are formed of a solid layer of goethite, and traces of kerogen occur in the lumens of some specimens. These Jhamarkotra Formation microfossils are quite convincing as being fossil FeOB. Fadel et al. (2017) interpreted three morphologies of carbonaceous microfossils associated with siderite and Fe-­silicates as being potential iron-­oxidizing bacteria from the ca. 2.45–­2.43 Ga Turee Creek Group, Western Australia (Bekker et al., 2020). wide that link to others via filaments 0.3 μm in diameter. The cells reproduce by budding along the filaments, which typically branch, leading to the formation of mesh-­like colonies. Chi Fru et al. (2013) found fossilized examples of what could be this organism in early Quaternary banded jaspers that formed from hydrothermal vents in a restricted, shallow marine basin in Milos, Greece. The VCJ filaments share some of the features with the Milos structures, having elon- gated hematitic forms of roughly the same size, which have branches and form complex meshes. However, the VCJ filaments lack evidence of former cells occurring between linking filaments, hence are not the same as the Milos structures or colonies of Rhodomicrobium vanielii. Another more fundamental issue for comparing anoxygenic or oxy- genic photoferrotrophic micro-­organisms with the VCJ filaments is that the latter formed in deep water, far below the photic zone. This constraint also precludes other explanations for the origin of the VCJ filaments, such as passive Fe-­oxide precipitation in or on phototro- phic organisms like cyanobacteria, as has been suggested for some of the microfossils (e.g., Gunflintia) in the Gunflint Iron Formation (Lepot et al., 2017; Shapiro & Konhauser, 2015). potential FeOB microfossils, all but one of which are from demon- strably shallow-­water settings. These include the well-­known he- matitic microfossils belonging to the Paleoproterozoic Gunflint biota (see review in Javaux & Lepot,  2018). When these were first de- scribed from stromatolites in the Gunflint Iron Formation in Canada (Barghoorn & Tyler, 1965; Cloud, 1965), some of the microfossil mor- phologies were noted to be similar in size and shape to freshwater FeOB, such as the sheath-­forming Leptothrix and the twisted, stalk-­ forming Gallionella (Barghoorn & Tyler, 1965; Cloud, 1965). In sub- sequent reports, authors tended to discount these earlier potential FeOB identifications and assign all Gunflint microfossils to various groups of cyanobacteria (e.g., Awramik & Barghoorn, 1977), an in- terpretation supported more recently by detailed studies of the typi- cal Gunflint microfossils Gunflintia and Huroniospora by Shapiro and Konhauser (2015) and Lepot et al. (2017). However, based on iron isotope composition and REE patterns in the Gunflint and Biwabik Iron formations, Planavsky et al. (2009) resurrected the potential link between Gunflint Iron Formation microfossils and FeOB, although recent studies have shown that cyanobacteria can produce similar iron isotope fractionations (Mulholland et al., 2015). These microfossils come from a black chert nod- ule within the lower siliciclastic-­dolostone member of the Kungarra Formation that contains four upward-­shallowing depositional se- quences with basal mudrocks overlain by fine-­grained sandstones and dolostones deposited in a lower part of prodelta and off-­shore to slope settings at the base and inner shelf to supratidal environ- ments at the top (Barlow et al., 2016; Bekker et al., 2020). The micro- fossils display a filamentous morphology and are formed of variably preserved sheaths of kerogen, with lengths of 100s of micrometers Because of the morphological similarities between the VCJ fila- ments and FeOB from modern marine hydrothermal vent settings, it is tempting to suggest that the VCJ filaments were formed by Zetaproteobacteria and that they could thus act as a calibration point for molecular phylogenetic studies of micro-­organisms (e.g., Betts et al., 2018). However, there are several reasons to be cautious in mak- ing this link. First, members of both marine Zetaproteobacteria and freshwater Betaproteobacteria produce very similar structures in iron-­ rich reducing habitats (compare twisted stalks of marine Mariprofundus and freshwater Gallionella, and non-­branching sheaths of marine “veil-­like mat” Zetaproteobacteria and freshwater Leptothrix; Fleming et al., 2013; Chan, Emerson, et al., 2016) and both Zetaproteobacteria and Betaproteobacteria occur in marine “iron mats” (Vander Roost et al., 2018). Second, there is likely to have been significant evolution- ary changes in FeOB over the past 1.74 billion years, so the compar- isons presented here between the VCJ filaments and modern FeOB point to analogues rather than phylogenetic proximity. (2008); Loihi data from Edwards et al. (2011, Table S1); Jan Mayen data from Johannessen et al. (2017). (d) Modern waters; seawater data from Byrne and Sholkovitz (1996); Low-­Fe marine pore fluid data from Haley et al. (2004); TAG data from Mills and Elderfield (1995); Manus Basin data from Douville et al. (1999); Mono Lake data from Johannesson and Lyons (1994). Shale normalization based on average Post-­Archean Australian Shale (PAAS; Taylor & McLennan, 1985) in ferric biominerals (Fadel et al., 2017; Lepot et al., 2017) before a late oxidation event returned them to their ferric state (Lepot et al., 2017; Shapiro & Konhauser, 2015). This mineralogical pathway is very un- likely for the VCJ filaments. Firstly, in contrast to the Gunflint Iron Formation studies, our detailed investigation of the VCJ filaments shows no clear indication of a ferrous mineral phase precursor. The Fe-­Si-­O mineral seen in one FIB section (Figure 7) may have formed by the weathering of such a ferrous mineral, or possibly the reduction in ferric biominerals, or even analytical beam damage. Moreover, the presence of rip-­up clasts of jasper in tuffaceous sedimentary rocks in the sequence, where hematitic jasper clasts occur in a hematite-­free tuff matrix (Figure 3c,d), demonstrates that formation of hematite (or a ferric oxyhydroxide precursor) occurred prior to diagenesis and greenschist-­facies metamorphism, thus providing strong evidence against the oxidation within the enclosing tuffs by late oxidizing flu- ids. In addition, the likely transformation in the jasper precursor of amorphous silica to chalcedony during early diagenesis (see Grenne & Slack, 2003) would make this highly siliceous rock more resistant to later oxidation than the more permeable lapilli tuff. As well as the microaerobic FeOB, other modern micro-­organisms use iron oxidation in their metabolic pathways, including freshwater microaerobic Betaproteobacteria, such as the stalk-­forming Gallionella spp. and sheath-­forming Leptothrix spp., acidophilic Actinobacteria and Archaea, phototrophic Alphabacteria, and bacteria belonging to a wide range of phylogenetic groups that are nitrate-­dependent (e.g., Chan, Emerson, et al., 2016). However, in the marine realm, only a few of these produce filamentous structures that can be compared to the VCJ filaments and thus considered as potential alternative candidates for their origin. One of these microbes is the BS-­1 strain of the purple, non-­sulfur, alphaproteobacterium Rhodomicrobium vanielii, which is an anoxygenic photoferrotroph (e.g., Heising & Schink, 1998). This bacterium has oval cells ca. 2 μm long and 1.5 μm 241 LITTLE et al. volcanic-­dominated settings are characterized by low-­pH values in the range of 2.0 to 5.8 (e.g., Hannington, 2014). and diameters of 5 to 7.5 µm (Type 2) and >3 µm (Type 3). The fila- ments have relatively constant diameters along their lengths and do not show any branching patterns. It is this character, together with the presence of kerogen, that distinguishes the Turee Creek Group microfossils from the VCJ filaments. The REE patterns of some low-­Fe marine pore fluids, excluding the large negative Ce anomaly, are broadly similar to those of the VC jaspers (Haley et al., 2004; Figure 8d). However, possible depo- sition of the VC jaspers from low-­Fe fluids is rejected because these jaspers are relatively Fe-­rich (Table 1), and assuming that the REEs precipitated with precursor iron oxyhydroxides as in modern ana- logues, the parent fluids would have had high, not low, iron contents. Development of the high HREE contents and very low LREE/HREE ratios by post-­depositional alteration is also considered unlikely, be- cause of the lack of supporting textural or mineralogical evidence for such alteration in either wall rocks or the jaspers and because of the typical low mobility of REEs during alteration of this type (Bau, 1991, 1993). Hallberg and Broman (2018) reported microstructures from lami- nated carbonaceous shales in the Neoarchean (ca. 2.63 Ga) Jeerinah Formation, Australia, as representing fossil FeOB. The microstruc- tures are lath-­shaped with some twists, ca. 2 to 4 μm across and up 20 μm long. They are formed of carbonaceous material and have low-­Fe contents (max 8.1 wt%), so differ substantially in terms of mineralogy (and morphology) from the hematite-­rich VCJ filaments, and indeed from other putative fossil FeOB. The oldest potential FeOB reported from the geological record are the microstructures in jaspers from the Eoarchean (minimum age 3.77 Ga, possibly 4.28 Ga) Nuvvuagittuq supracrustal belt (NSB), Canada (Dodd et al., 2017). These jaspers occur between sequences of variably altered tholeiitic and calc-­alkaline metabasalt, locally with pillow lavas, and so formed at the same stage of volcanic evolution, most likely in a seafloor hydrothermal setting. The microstructures in the jaspers comprise filaments formed of hematite that are between 2 and 14 μm in di- ameter and up to 500 μm in length. Some of the filaments exhibit loose coils, some are branched, and some form twisted plates of hematite around a core that radiate from terminal knobs. Some of the hematite filaments occur within straight, quartz-­filled cylindrical tubes 16 to 30 μm in diameter and 80 to 400 μm in length, with walls composed of dense, nanoscale hematite grains. Whereas some similarities exist between the VCJ and NSB filaments, there are also differences, including the lack of quartz-­filled tubes in the VCJ sam- ples and the fact that the NSB filaments do not form meshworks. Our preferred model involves the deposition of primary silica iron oxyhydroxides from low-­temperature and slightly acidic fluids. This model is linked to the experimental study of Liu et al. (2017) on differential sorption of REE to iron oxyhydroxides, which demon- strated that LREE versus HREE adsorption depends strongly on pH; a near-­neutral to slightly alkaline fluid like normal seawater leads to little or no LREE/HREE fractionation, whereas a moderately acidic fluid with a pH of 5 to 6 will yield far lower LREE/HREE ratios in the precipitates. These data show that fluids spanning pH values of 0 to 3 units below that of normal modern seawater (pH = 7.8) can effectively produce a range of LREE/HREE ratios in iron oxyhydrox- ide similar to those observed for the VCJ samples, and also like the LREE/HREE range from VC jaspers to other Verde district jaspers as well as to modern Fe-­Si precipitates (Figure  8a,c). Importantly, given the lack of definitive Ce anomalies in the VCJ samples, our REE data show very limited impact of redox processes on Ce and are thus inconsistent with precipitation of iron oxyhydroxides above the redoxcline via Fe oxidation. However, iron cannot be oxidized non-­ biologically below the redoxcline (e.g., Lewis & Landing, 1991), and our estimate of >500 m for a minimum water depth puts this deposi- tional site well below the photic zone. The only process known to ox- idize iron below the photic zone and redoxcline is by microaerophilic bacteria, in agreement with our interpretations of a biological origin for the hematitic filaments in the VC jaspers. 4.3 | Other potential Precambrian FeOB occurrences In addition to the VCJ filaments, a number of other Precambrian oc- currences of filamentous microstructures have been identified as 242 LITTLE et al. 4.4 | REE constraints on local fluid chemistry At some distance from the continental margin with associated ferruginous and euxinic conditions, we show the Jerome arc and associated hydrothermal activity being influenced by weakly oxygenated seawater, either downwelling from surface waters or upwelling from deeper waters driven by thermohaline circulation. The presence of the continental margin and back-­arc basin is speculative. VC VMS, Verde Central volcanogenic massive sulfide LITTLE et al. |  243 LITTLE et al. FI G U R E 9 Paleoceanographic redox model for the Jerome area volcanic arc. At some distance from the continental margin with associated ferruginous and euxinic conditions, we show the Jerome arc and associated hydrothermal activity being influenced by weakly oxygenated seawater, either downwelling from surface waters or upwelling from deeper waters driven by thermohaline circulation. The presence of the continental margin and back-­arc basin is speculative. VC VMS, Verde Central volcanogenic massive sulfide 243 FI G U R E 9 Paleoceanographic redox model for the Jerome area volcanic arc. At some distance from the continental margin with associated ferruginous and euxinic conditions, we show the Jerome arc and associated hydrothermal activity being influenced by weakly oxygenated seawater, either downwelling from surface waters or upwelling from deeper waters driven by thermohaline circulation. The presence of the continental margin and back-­arc basin is speculative. VC VMS, Verde Central volcanogenic massive sulfide from 292 m depth in the Cariaco Basin that contains ca. 1 μM O2 and lacks a Ce anomaly (Ce/Ce*PAAS = 0.98; calculated from data in De Baar et al., 1988). Formation of this redox state in deep 1.74 Ga seawater around the Jerome volcanic arc may have involved diffu- sion downwards of oxygenated surface waters, perhaps facilitated by the oceanographic situation analogous to modern seamounts, where both upwelling and downwelling can develop (e.g., Read & Pollard, 2017), and/or upwelling of variably oxygenated deep water driven by thermohaline circulation (Figure 9). The latter scenario is preferred here, based on patterns in the modern ocean where such oxygenated deep water transits the bases of major volcanic arcs in the South Pacific including the Kermadec Arc (e.g., Broecker, 2010). low-­temperature hydrothermal vents that maintained relatively low, but variable, pH values during precipitation of iron oxyhydroxide phases. 4.4 | REE constraints on local fluid chemistry The distinctive shale-­normalized REE patterns of the VC jasper sam- ples have extremely low LREE/HREE ratios in most cases (Figure 8a) and are very different from those typical of modern Fe-­Si deposits (Figure 8c). In natural fluids, such very low LREE/HREE ratios are rare and are apparently limited to highly alkaline waters in restricted lakes such as Mono Lake in California (Johannesson & Lyons, 1994; Figure 8d) and Lake Van in Turkey (Möller & Bau, 1993). However, we consider it unlikely that the VC jaspers formed from such high-­pH (>9) fluids. Firstly, a model whereby the REE content of the jasper protoliths was controlled by alkaline ambient seawater can be ruled out based on the large variation in LREE/HREE ratios shown by the jaspers at this particular stratigraphic level. Second, a model involv- ing precipitation from alkaline seafloor-­hydrothermal fluids would require serpentinization of underlying ultramafic rocks within the hydrothermal convection system as occur in modern systems (e.g., Kelley et al., 2005; Palandri & Reed, 2004), but ultramafic rocks are absent in the Paleoproterozoic rhyolite to basalt sequence of the Verde district (Lindberg, 2008). Importantly, excluding such uncom- mon ultramafic settings, modern seafloor-­hydrothermal fluids in The other jasper units in the Verde district, occurring at differ- ent stratigraphic levels, have very different REE patterns and greater lateral continuity (Figure 2b) and likely formed by plume fallout as suggested by Slack et al. (2007). This model is problematic for the VC jaspers, however, owing to the major dilution of hydrothermal fluids in plumes that occurs during venting and mixing with seawater. Such rapid mixing results instantly in a rise in pH to ambient sea- water values within the plume (see Grenne & Slack, 2005), which conflicts with the variably low pH need to produce the distinctive REE patterns of the VC jaspers. The lack of positive Eu anomalies in these jasper samples (Figure  8a) also argues against formation from high-­temperature fluids. Consequently, we propose that the jasper samples from the Verde Central horizon, and their contained microbial remains, formed not by plume fallout but from isolated, |  24 LITTLE et al. FI G U R E 9 Paleoceanographic redox model for the Jerome area volcanic arc. 4.4 | REE constraints on local fluid chemistry The hydrothermal fluids with low pH (5–­6), indicated by very low LREE/HREE ratios in deposited iron oxyhydroxide phases (Liu et  al.,  2017), may have been involved in deposition of these phases within microbial mats having amorphous silica caps (see Sun et al., 2015; Zeng et al., 2012) that reduced dilution by ambient sea- water. This interpretation is supported by low-­pH values of 1.4 to 5.8 measured in some modern low-­temperature hydrothermal systems, including within pore waters of actively forming iron oxyhydroxide deposits (Rouxel et al., 2018; Seewald et al., 2015). Such low-­pH flu- ids likely formed in concert with a major component of magmatic fluid (Douville et al., 1999; Seewald et al., 2015). We suggest that the Fe-­Si protoliths of the VC jaspers formed at a minimum water depth of 500 m based on the Cu-­rich nature of the ores, and a maximum depth of ~2,000 m based on the typically deep- est examples of VMS-­style hydrothermal activity known in modern volcanic arcs (Baker, 2017; de Ronde et al., 2003). This modern ac- tivity includes sites in the Kermadec Arc at Brothers and Giggenbach volcanoes, which contain Fe-­Si deposits compositionally like the VC jaspers and in the latter area filamentous microbial remains (Jones et al., 2008; de Ronde et al., 2005). 4.5 | Implications for Paleoproterozoic ocean redox and iron oxyhydroxide deposition Our interpretation of the VCJ filaments as microaerobic FeOB (if correct) implies that some deep waters in the late Paleoproterozoic oceans were not anoxic, but rather weakly oxygenated, thus sup- porting the suboxic model of Slack et al. (2007). We speculate that the concentration of dissolved oxygen in the VCJ FeOB mats could have been between 3 and 30 μM, with the lower limit from condi- tions for experimental growth of Mariprofundus ferrooxydans (Krepski et al., 2013) and the upper limit from maximum O2 values measured within FeOB mats on Loihi Seamount (Glazer & Rouxel, 2009; Scott et al., 2017). This would imply equivalent, or perhaps even higher, O2 concentrations in the seawater overlying the mats. A minimum O2 concentration of 3 μM for growth of FeOB mats is consistent with REE data for the modern Cariaco Basin, where a concentration spike in particulate iron (reflecting one or more Fe3+ phases) at the redox- cline, at 280 m water depth, coincides with water samples having ca. 2 μM O2 and 0 μM H2S (De Baar et al., 1988). The lack of negative Ce anomalies and Mn-­enrichment in the VMS-­related Verde Central as well as other Verde district jaspers (Slack et al., 2007) is consistent with these suggested oxygen levels, including for the water sample Our proposal that weakly oxygenated deep waters existed around the Jerome volcanic arc is also consistent with anoxia (both euxinic and ferruginous conditions) occurring on contem- poraneous continental margins, because such margins are where the greatest flux of nutrients via riverine run-­off and upwelling would have existed, leading to increased primary productiv- ity and thus oxygen depletion (Figure  9). It is important to em- phasize that it is not known whether the mid-­Proterozoic deep ocean was persistently and pervasively anoxic. Importantly, all existing geochemical proxies for extensive anoxia and euxinia in the mid-­Proterozoic deep oceans do not require that redox state (e.g., Asael et al., 2018; Partin et al., 2013; Reinhard et al., 2013; Scott et  al.,  2008; Sheen et  al.,  2018). The deep ocean is not highly productive now and hence is not expected to have been highly productive in the mid-­Proterozoic, and thus, it played an insignificant role in the burial of organic matter and consequently 244 LITTLE et al. Switzerland, for provision of synchrotron radiation beamtime at the TOMCAT beamline X02DA of the SLS and thank Federica Marone for assistance. ORCID Crispin T. S. Little  https://orcid.org/0000-0002-1917-4460 Karen C. Johannessen  https://orcid.org/0000-0001-8790-8123 Stefan Bengtson  https://orcid.org/0000-0003-0206-5791 Clara S. Chan  https://orcid.org/0000-0003-1810-4994 John F. Slack  https://orcid.org/0000-0001-6600-3130 Ingunn H. Thorseth  https://orcid.org/0000-0003-3432-6968 Tor Grenne  https://orcid.org/0000-0003-1193-4127 Olivier J. Rouxel  https://orcid.org/0000-0002-1431-222X Andrey Bekker  https://orcid.org/0000-0002-1154-0585 Our finding of weakly oxygenated deep seawater in the late Paleoproterozoic may have implications for eukaryotic evolution, because at least during some time periods in the Proterozoic, oxy- gen was not confined to surface waters, and thus, a larger potentially habitable realm existed for these organisms, relative to that proposed in previous models (e.g., Martin et al., 2003). We further note that deep-­water (≥500 m) jasper and oxide-­facies iron formation occur in other Proterozoic and Archean volcano-­sedimentary sequences (Bekker et al., 2010; Slack et al., 2007, appendix 2), thus raising the possibility that some of these ancient seafloor-­hydrothermal depos- its also contain filamentous microfossils that, if identified and doc- umented, could be used as proxies for the oxidation state of coeval deep seawater. 4.5 | Implications for Paleoproterozoic ocean redox and iron oxyhydroxide deposition AB acknowledges support from NSERC Discovery and Accelerator programs and the University of Johannesburg in the form of a Distinguished Visiting Professorship. We thank three anonymous reviewers for comments and suggestions on an earlier version of the paper. redox-­sensitive elements. Further, the paradigm of a persistently anoxic, ferruginous mid-­Proterozoic deep ocean has shifted over the last decade to a consensus view that its redox state was vari- able over this long time interval (e.g., Diamond et al., 2018; Doyle et  al.,  2018; Planavsky et  al.,  2018; Shang et  al.,  2019; Sperling et al., 2014; Yang et al., 2017; Zhang et al., ,2016, 2018). In our case, we cannot resolve whether our observations indicate episodic or pervasive weak oxygenation of the deep ocean, and hence, further studies of different windows of the mid-­Proterozoic in separate basins are required. These deep ocean, weakly oxygenated waters once upwelled on the highly productive continental margins would rapidly lose their oxidation potential on mixing. We thus expect highly variable oxygen contents to have existed along shallow-­to-­ deep transects across the mid-­Proterozoic oceans (e.g., Planavsky et al., 2018). REFERENCES Anantharaman, K., Breier, J. A., & Dick, G. J. (2016). Metagenomic res- olution of microbial functions in deep-­sea hydrothermal plumes across the Eastern Lau Spreading Center. ISME Journal, 10, 225–­239. https://doi.org/10.1038/ismej.2015.81 Anderson, P. (1989). Proterozoic plate tectonic evolution of Arizona. Arizona Geological Society Digest, 17, 17–­55. Our finding of FeOB within a Proterozoic iron-­rich sediment is another piece of data supporting suggestions that biologically as- sisted Fe(II) oxidation was responsible for the deposition of BIF, at least to some extent (e.g., Chan, Emerson, et al., 2016; Holm, 1989; Konhauser et al., 2017; Posth et al., 2013). We emphasize that in the Verde Central case, deposition of the Fe-­rich exhalites was closely associated with deep seafloor-­hydrothermal activity, and hence, our results might not be applicable to shallow-­water, Superior-­type gran- ular iron formation. Asael, D., Rouxel, O., Poulton, S. W., Lyons, T. W., & Bekker, A. (2018). Molybdenum record from black shales indicates oscillating atmo- spheric oxygen levels in the early Paleoproterozoic. American Journal of Science, 318, 275–­299. https://doi.org/10.2475/03.2018.01 Awramik, S. M., & Barghoorn, E. S. (1977). The Gunflint mi- crobiota. Precambrian Research, 5, 121–­142. https://doi. org/10.1016/0301-­9268(77)90025​-­0 Baker, E. T. (2017). Exploring the ocean for hydrothermal venting: New techniques, new discoveries, new insights. Ore Geology Reviews, 86, 55–­69. https://doi.org/10.1016/j.orege​orev.2017.02.006 Bao, S.-­X., Zhou, H.-­Y., Peng, X.-­T., Ji, F.-­W., & Yao, H.-­Q. (2008). Geochemistry of REE and yttrium in hydrothermal fluids from the Endeavor segment, Juan de Fuca Ridge. Geochemical Journal, 42, 359–­370. DATA AVAILABILITY STATEMENT The data that support the findings of this study are available in the Supplementary Material of this article. Integrated genomic and fossil evidence illu- minates life’s early evolution and eukaryote origin. Nature Ecology and Evolution, 2, 1556–­1562. https://doi.org/10.1038/s4155​ 9-­018-­0644-­x Davis, R. E., Stakes, D. S., Wheat, C. G., & Moyer, C. L. (2009). Bacterial variability within an iron-­silica-­manganese-­rich hydro- thermal mound located off-­axis at the Cleft segment, Juan de Fuca Ridge. Geomicrobiology Journal, 26, 570–­580. https://doi. org/10.1080/01490​45090​2889080 Briggs, D. F. (2018). History of the Verde mining district, Jerome, Arizona. Arizona Geological Survey Contributed Report CR-­18-­D, 85. De Baar, H. J. W., German, C. R., Elderfield, H., & van Gaans, P. (1988). Rare earth element distribution in anoxic waters of the Cariaco Trench. Geochimica Et Cosmochimica Acta, 52, 1203–­1219. Broecker, W. S. (2010). The great ocean conveyer (p. 176). Princeton University Press. de Ronde, C. E. J., Hannington, M. D., Stoffers, P., Wright, I. C., Ditchburn, R. G., Reyes, A. G., Baker, E. T., Massoth, G. J., Lupton, J. E., Walker, S. L., Greene, R. R., Soong, C. W. R., Ishibashi, J., Lebon, G. T., Bray, C. J., & Resing, J. A. (2005). Evolution of a submarine magmatic-­ hydrothermal system: Brothers Volcano, southern Kermadec Arc, New Zealand. Economic Geology, 100, 1097–­1133. https://doi. org/10.2113/gseco​ngeo.100.6.1097 Buick, R. (1990). Microfossil recognition in Archean rocks: An appraisal of spheroids and filaments from a 3500 m.y. old chert-­barite unit at North Pole, Western Australia. Palaios, 5, 441–­459. https://doi. org/10.2307/3514837 Byrne, R. H., & Sholkovitz, E. R. (1996). Marine chemistry and geochem- istry of the lanthanides. In K. A. Gschneidner, & L. Eyring (Eds.), Handbook on the physics and chemistry of the rare earths (pp. 497–­593). Elsevier. De Ronde, C. E. J., Massoth, G. J., Baker, E. T., & Lupton, J. E. (2003). Submarine hydrothermal venting related to volcanic arcs. In S. F. Simmons, & I. Graham (Eds.), Volcanic, geothermal, and ore-­forming fluids: Rulers and witnesses of processes within the Earth (pp. 91–­110). Society of Economic Geologists Inc, Special Publication 10. Cady, S. L., Farmer, J. D., Grotzinger, J. P., Schopf, J. W., & Steele, A. (2003). Morphological biosignatures and the search for life on Mars. Astrobiology, 3, 351–­368. https://doi.org/10.1089/15311​07037​ 69016442 Canfield, D. E. (1998). A new model for Proterozoic ocean chemistry. Nature, 396, 450–­453. https://doi.org/10.1038/24839 Dekov, V. M., Lalonde, S. V., Kamenov, G. D., Bayon, G., Shanks, W. C. III, Fortin, D., Fouquet, Y., & Moscati, R. J. (2015). Beaulieu, S. E., Baker, E. T., German, C. R., & Maffei, A. (2013). An au- thoritative global database for active submarine hydrothermal vent fields. Geochemistry Geophysics Geosystems, 14, 4892–­4905. https:// doi.org/10.1002/2013G​C004998 Chi Fru, E., Ivarsson, M., Kilias, S. P., Bengtson, S., Belivanova, V., Marone, F., Fortin, D., Broman, C., & Stampanoni, M. (2013). Fossilized iron bacteria reveal a pathway to the biological origin of banded iron for- mations. Nature Communications, 4, 1–­7. Bekker, A., Holland, H. D., Wang, P. L., Rumble, D., Stein, H. J., Hannah, J. L., Coetzee, L. L., & Beukes, N. J. (2004). Dating the rise of atmo- spheric oxygen. Nature, 427, 117–­120. https://doi.org/10.1038/natur​ e02260 Chiu, B. K., Kato, S., McAllister, S. M., Field, E. K., & Chan, C. S. (2017). Novel pelagic iron-­oxidizing Zetaproteobacteria from the Chesapeake Bay oxic-­anoxic transition zone. Frontiers in Microbiology, 8, 1280. https://doi.org/10.3389/fmicb.2017.01280 Cloud, P. (1965). The significance of the Gunflint (Precambrian) micro- flora. Science, 148, 27–­35. Bekker, A., Krapež, B., & Karhu, J. A. (2020). Correlation of the stratigraphic cover of the Pilbara and Kaapvaal cratons record- ing the lead up to Paleoproterozoic Icehouse and the GOE. Earth Science Reviews, 211, 103389. https://doi.org/10.1016/j.earsc​ irev.2020.103389 Corliss, J. B., Dymond, J., Gordon, L. I., Edmond, J. M., von Herzen, R. P., Ballard, R. D., Green, K., Williams, D., Bainbridge, A., Crane, K., & van Andel, T. H. (1979). Submarine thermal springs on the Galápagos Rift. Science, 203, 1073–­1083. https://doi.org/10.1126/scien​ ce.203.4385.1073 Bekker, A., Slack, J. F., Planavsky, N., Krapež, B., Hofmann, A., Konhauser, K. O., & Rouxel, O. J. (2010). Iron formation: The sedimentary prod- uct of a complex interplay among mantle, tectonic, oceanic, and biospheric processes. Economic Geology, 105, 467–­508. https://doi. org/10.2113/gseco​ngeo.105.3.467 Crosby, C. H., Bailey, J. V., & Sharma, M. (2014). Fossil evidence of iron-­ oxidizing chemolithotrophy linked to phosphogenesis in the wake of the Great Oxidation Event. Geology, 42, 1015–­1018. https://doi. org/10.1130/G35922.1 Bennett, S. A., Toner, B. M., Barco, R., & Edwards, K. J. (2014). Carbon adsorption onto Fe oxyhydroxide stalks produced by a lithotro- phic iron-­oxidizing bacteria. Geobiology, 12, 146–­156. https://doi. org/10.1111/gbi.12074 Davis, R. E., & Moyer, C. L. (2008). Extreme spatial and temporal variabil- ity of hydrothermal microbial mat communities along the Mariana is- land arc and southern Mariana back-­arc system. Journal of Geophysical Research, 113, B08S15. https://doi.org/10.1029/2007J​B005413 Betts, H. C., Puttick, M. N., Clark, J. W., Williams, T. A., Donoghue, P. C., & Pisani, D. (2018). ACKNOWLEDGMENTS We are especially indebted to the late Paul Lindberg who provided guidance during fieldwork. CTSL thanks Simon Poulton for dis- cussions about Proterozoic and Archaean paleoceanography. The Research Council of Norway is acknowledged for support to the NTNU NanoLab (Trondheim) through the Norwegian Micro-­ and Nano-­Fabrication Facility, NorFab (197411/V30), and NORTEM infrastructure Grant 197405, TEM Gemini Centre, Norwegian University of Science and Technology (NTNU), Norway. TEM work was funded by the Bergen Research Foundation through a grant awarded to Nicola McLoughlin. Per Erik Vullum is thanked for invalu- able assistance with the FIB-­TEM analyses. Raman spectroscopy was funded through Swedish Research Council Contracts No. 2012-­4364 and 2017-­04129, and a Villum Investigator Grant to Don Canfield (No. 16518). We acknowledge the Paul Scherrer Institute, Villigen, Barghoorn, E. S., & Tyler, S. A. (1965). Microorganisms from the Gunflint Chert. Science, 147, 563–­577. Barlow, E., Van Kranendonk, M. J., Yamaguchi, K. E., Ikehara, M., & Lepland, A. (2016). Lithostratigraphic analysis of a new stromatolite-­thrombolite reef from across the rise of atmospheric oxygen in the Paleoproterozoic Turee Creek Group, Western Australia. Geobiology, 14, 317–­343. https://doi.org/10.1111/ gbi.12175 Bau, M. (1991). Rare-­earth element mobility during hydrothermal and metamorphic fluid-­rock interaction and the significance of the oxi- dation state of europium. Chemical Geology, 93, 219–­230. https://doi. org/10.1016/0009-­2541(91)90115​-­8 Bau, M. (1993). Effects of syn-­ and post-­depositional processes on the rare-­earth element distribution in Precambrian iron-­formations. European Journal of Mineralogy, 5, 257–­267. https://doi.org/10.1127/ ejm/5/2/0257 LITTLE et al. 245 Duhig, N. C., Davidson, G. J., & Stolz, J. (1992). Microbial involvement in the formation of Cambrian sea-­floor silica-­iron oxide deposits, Australia. Geology, 20, 511–­514. https://doi.org/10.1130/0091-­ 7613(1992)020<0511:MIITF​O>2.3.CO;2 Gustin, M. S. (1990). Stratigraphy and alteration of the host rocks, United Verde massive sulfide deposit, Jerome, Arizona. Economic Geology, 85, 29–­49. https://doi.org/10.2113/gseco​ngeo.85.1.29 Haley, B. A., Klinkhammer, G. P., & McManus, J. (2004). Rare earth elements in pore waters of marine sediments. Geochimica Et Cosmochimica Acta, 68, 1265–­1279. https://doi.org/10.1016/j. gca.2003.09.012 Edwards, K. J., Glazer, B. T., Rouxel, O. J., Bach, W., Emerson, D., Davis, R. E., Toner, B. M., Chan, C. S., Tebo, B. M., Staudigel, H., & Moyer, C. L. (2011). Ultra-­diffuse hydrothermal venting supports Fe-­oxidizing bacteria and massive umber deposition at 5000m off Hawaii. The ISME Journal, 5, 1748–­1758. Hallberg, R. O., & Broman, C. (2018). Microbial fossils in the 2.63 Ga Jeerinah Formation, Western Australia—­Evidence of micro- bial oxidation. Geomicrobiology Journal, 35, 255–­260. https://doi. org/10.1080/01490​451.2017.1348407 Emerson, D. (2009). Potential for iron-­reduction and iron-­ cycling in iron oxyhydroxide-­rich microbial mats at Loihi Seamount. Geomicrobiology Journal, 26, 639–­647. https://doi. org/10.1080/01490​45090​3269985 Hannington, M. D. (2014). Volcanogenic massive sulfide deposits. In S. D. Scott (Ed.), Geochemistry of mineral deposits. Treatise on geochemistry (2nd ed., vol. 13, pp. 463–­488). Elsevier. Emerson, D., & Moyer, C. L. (2002). Neutrophilic Fe-­oxidizing bacte- ria are abundant at the Loihi Seamount hydrothermal vents and play a major role in Fe oxide deposition. Applied and Environmental Microbiology, 68, 3085–­3093. https://doi.org/10.1128/ AEM.68.6.3085-­3093.2002 Hannington, M. D., Jonasson, I. R., Herzig, P. M., & Petersen, S. (1995). Physical and chemical processes of seafloor mineralization at mid-­ ocean ridges. In S. E. Humphris, R. A. Zierenberg, L. S. Mullineaux, & R. E. Thomson (Eds.) Seafloor hydrothermal systems: Physical, chem- ical, biological, and geological interactions (pp. 115–­157). American Geophysical Union. Geophysical Monograph 91. Emerson, D., Rentz, J. A., Lilburn, T. G., Davis, R. E., Aldrich, H., Chan, C., & Moyer, C. L. (2007). A novel lineage of Proteobacteria involved in formation of marine Fe-­oxidizing microbial mat communities. PLoS One, 2(8), e667. https://doi.org/10.1371/journ​al.pone.0000667 Hein, J. R., Clague, D. A., Koski, R. A., Embley, R. W., & Dunham, R. E. (2008). Metalliferous sediment and a silica-­hematite deposit within the Blanco Fracture Zone, northeast Pacific. Marine Georesources & Geotechnology, 26, 317–­339. https://doi.org/10.1080/10641​19080​ 2430986 Emerson, D., & Revsbech, N. P. (1994). Investigation of an iron-­oxidizing microbial mat community located near Aarhus, Denmark: Field stud- ies. Applied and Environmental Microbiology, 60, 4022–­4031. https:// doi.org/10.1128/AEM.60.11.4022-­4031.1994 Heising, S., & Schink, B. (1998). Phototrophic oxidation of ferrous iron by a Rhodomicrobium vannielii strain. Microbiology, 144, 2263–­2269. https://doi.org/10.1099/00221​287-­144-­8-­2263 Emerson, D., Scott, J. J., Leavitt, A., Fleming, E., & Moyer, C. (2017). In situ estimates of iron-­oxidation and accretion rates for iron-­oxidizing bacterial mats at Lō’ihi Seamount. Deep-­Sea Research (I), 126, 31–­39. https://doi.org/10.1016/j.dsr.2017.05.011 Holm, N. G. (1989). The 13C/12C ratios of siderite and organic matter of a modern metalliferous hydrothermal sediment and their impli- cations for banded iron formations. Chemical Geology, 77, 41–­45. https://doi.org/10.1016/0009-­2541(89)90013​-­2 Fadel, A., Lepot, K., Busigny, V., Addad, A., & Troadec, D. (2017). Iron mineralization and taphonomy of microfossils of the 2.45–­2.21 Ga Turee Creek Group, Western Australia. Precambrian Research, 298, 530–­551. https://doi.org/10.1016/j.preca​mres.2017.07.003 Hopkinson, L., Roberts, S., Herrington, R., & Wilkinson, J. (1998). Self-­organization of submarine hydrothermal siliceous deposits: Evidence from the TAG hydrothermal mound, 26°N Mid-­Atlantic Ridge. Geology, 26, 347–­350. https://doi.org/10.1130/0091-­ 7613(1998)026<0347:SOOSH​S>2.3.CO;2 Fleming, E. J., Davis, R., McAllister, S., Chan, C. S., Moyer, C. L., Tebo, B., & Emerson, D. (2013). Hidden in plain sight: Discovery of sheath forming, Fe-­oxidizing Zetaproteobacteria at Loihi Seamount. FEMS Microbial Ecology, 85, 116–­127. Huston, D. L., Pehrrson, S., Eglington, B. M., & Zaw, K. (2010). The geol- ogy and metallogeny of volcanic-­hosted massive sulphide deposits: Variations through geologic time and with tectonic setting. Economic Geology, 105, 571–­591. Forget, N., Murdock, S., & Juniper, S. (2010). Bacterial diversity in Fe-­rich hydro- thermal sediments at two south Tonga Arc submarine volcanoes. Geobiology, 8, 417–­432. https://doi.org/10.1111/j.1472-­4669.2010.00247.x Javaux, E. J., & Lepot, K. (2018). The Paleoproterozoic fossil record: Implications for the evolution of the biosphere during Earth's middle-­ age. Earth-­Science Reviews, 176, 68–­86. https://doi.org/10.1016/j. earsc​irev.2017.10.001 Fouquet, Y., Cambon, P., Etoubleau, J., Charlou, J. L., Ondréas, H., Barriga, F. J. A. S., Cherkashov, G., Semkova, T., Poroshina, I., Bohn, M., Donval, J. P., Henry, K., Murphy, P., & Rouxel, O. (2010). Geodiversity of hy- drothermal processes along the Mid-­Atlantic Ridge and ultramafic-­ hosted mineralization: A new type of oceanic Cu-­Zn-­Co-­Au volcano- genic massive sulfide deposit. In P. Rona (Ed.), Diversity of hydrothermal systems on slow-­spreading ocean ridges (pp. 321–­367). American Geophysical Union. Geophysical Monograph 188. Johannessen, K. C., McLoughlin, N., Vullum, P. E., & Thorseth, I. (2020). On the biogenicity of Fe-­oxyhydroxide filaments in silicified low-­ temperature hydrothermal deposits: Implications for the identifica- tion of Fe-­oxidizing bacteria in the rock record. Geobiology, 18, 31–­ 53. Geochemistry and mineralogy of a silica chimney from an inactive seafloor hydrother- mal field (East Pacific Rise, 18°S). Chemical Geology, 415, 126–­140. https://doi.org/10.1016/j.chemg​eo.2015.09.017 Canfield, D. E. (2005). The early history of atmospheric oxy- gen: Homage to Robert M. Garrels. Annual Review of Earth and Planetary Sciences, 33, 1–­36. https://doi.org/10.1146/annur​ ev.earth.33.092203.122711 Diamond, C. W., Planavsky, N. J., Wang, C., & Lyons, T. W. (2018). What the ∼1.4 Ga Xiamaling Formation can and cannot tell us about the mid-­Proterozoic ocean. Geobiology, 16, 219–­236. Canfield, D. E., Poulton, S. W., Knoll, A. H., Narbonne, G. M., Ross, G., Goldberg, T., & Strauss, H. (2008). Ferruginous conditions dominated later Neoproterozoic deep-­water chemistry. Science, 321, 949–­952. https://doi.org/10.1126/scien​ce.1154499 Dodd, M. S., Papineau, D., Grenne, T., Slack, J. F., Rittner, M., Pirajno, F., O’Neil, J., & Little, C. T. S. (2017). Evidence for early life in Earth’s oldest hydrothermal vent precipitates. Nature, 543, 60–­65. https:// doi.org/10.1038/natur​e21377 Chan, C. S., Emerson, D., & Luther, G. W. (2016). The role of microaero- philic Fe-­oxidizing micro-­organisms in producing banded iron forma- tions. Geobiology, 14, 509–­528. https://doi.org/10.1111/gbi.12192 Douville, E., Bienvenu, P., Charlou, J. L., Donval, J. P., Fouquet, Y., Appriou, P., & Gamo, T. (1999). Yttrium and rare earth elements in fluids from various deep-­sea hydrothermal systems. Geochimica Et Cosmochimica Acta, 63, 627–­643. https://doi.org/10.1016/S0016​ -­7037(99)00024​-­1 Chan, C. S., Fakra, S. C., Emerson, D., Fleming, E. J., & Edwards, K. J. (2011). Lithotrophic iron-­oxidizing bacteria produce organic stalks to control mineral growth: Implications for biosignature formation. The ISME Journal, 5, 717–­727. https://doi.org/10.1038/ismej.2010.173 Chan, C. S., McAllister, S. M., Leavitt, A. H., Glazer, B. T., Krepski, S. T., & Emerson, D. (2016). The architecture of iron microbial mats reflects the adaptation of chemolithotrophic iron oxidation in freshwater and marine environments. Frontiers in Microbiology, 7, 1–­18. https://doi. org/10.3389/fmicb.2016.00796 Doyle, K. A., Poulton, S. W., Newton, R. J., Podkovyrov, V. N., & Bekker, A. (2018). Shallow water anoxia in the Mesoproterozoic ocean: Evidence from the Bashkir Meganticlinorium, Southern Urals. Precambrian Research, 317, 196–­210. https://doi.org/10.1016/j.preca​ mres.2018.09.001 246 LITTLE et al. Earth’s earliest and deepest purported fossils may be iron-­mineralized chemical gardens. Proceedings of the Royal Society B, 286, 20192410. https://doi.org/10.1098/rspb.2019.2410 Krepski, S. T., Emerson, D., Hredzak-­Showalter, P. L., Luther, G. W. III, & Chan, C. S. (2013). Morphology of biogenic iron oxides records microbial physiology and environmental conditions: Toward in- terpreting iron microfossils. Geobiology, 11, 457–­471. https://doi. org/10.1111/gbi.12043 Meyer, K. M., & Kump, L. R. (2008). Oceanic euxinia in Earth his- tory: Causes and consequences. Annual Review of Earth and Planetary Sciences, 36, 251–­288. https://doi.org/10.1146/annur​ ev.earth.36.031207.124256 Mills, R. A., & Elderfield, H. (1995). Rare earth element geochemistry of hydrothermal deposits from the active TAG Mound, 26°N Mid-­ Atlantic Ridge. Geochimica Et Cosmochimica Acta, 59, 3511–­3524. https://doi.org/10.1016/0016-­7037(95)00224​-­N Langley, S., Igric, P., Takahashi, Y., Sakai, Y., Fortin, D., Hannington, M. D., & Schwarz-­Schampera, U. (2009). Preliminary characterization and biological reduction of putative biogenic iron oxides (BIOS) from the Tonga-­Kermadec Arc, southwest Pacific Ocean. Geobiology, 7, 35–­49. https://doi.org/10.1111/j.1472-­4669.2008.00180.x Möller, P., & Bau, M. (1993). Rare-­earth patterns with positive cerium anomaly in alkaline waters from Lake Van, Turkey. Earth and Planetary Science Letters, 117, 671–­676. https://doi.org/10.1016/0012-­ 821X(93)90110​-­U Laufer, K., Nordhoff, M., Halama, M., Martinez, R. E., Obst, M., Nowak, M., Stryhanyuk, H., Richnow, H. H., & Kappler, A. (2017). Microaerophilic Fe(II)-­oxidizing Zetaproteobacteria isolated from low-­Fe marine coastal sediments: Physiology and composition of their twisted stalks. Applied and Environmental Microbiology, 83, 1–­20. https://doi. org/10.1128/AEM.03118​-­16 Mulholland, D. S., Poitrasson, F., Shirokova, L. S., González, A. G., Pokrovsky, O. S., Boaventura, G. R., & Vieira, L. C. (2015). Iron iso- tope fractionation during Fe (II) and Fe (III) adsorption on cyano- bacteria. Chemical Geology, 400, 24–­33. https://doi.org/10.1016/j. chemg​eo.2015.01.017 Lawrence, M. G., & Kamber, B. S. (2006). The behaviour of the rare earth elements during estuarine mixing—­Revisited. Marine Chemistry, 100, 147–­161. https://doi.org/10.1016/j.march​em.2005.11.007 Ohmoto, H., Watanabe, Y., Ikemi, H., Poulson, S. R., & Taylor, B. E. (2006). Sulphur isotope evidence for an oxic Archaean atmosphere. Nature, 442, 909–­911. https://doi.org/10.1038/natur​e05044 Lepot, K., Addad, A., Knoll, A. H., Wang, J., Troadec, D., Béché, A., & Javaux, E. J. (2017). Iron minerals within specific microfos- sil morphospecies of the 1.88 Ga Gunflint Formation. Nature Communications, 8(1), 1–­11. https://doi.org/10.1038/ncomm​ s14890 Palandri, J. L., & Reed, M. H. (2004). Geochemical models of metasoma- tism in ultramafic systems: Serpentinization, rodingitization, and sea floor carbonate chimney precipitation. Geochimica Et Cosmochimica Acta, 68, 1115–­1133. https://doi.org/10.1016/j.gca.2003.08.006 Lewis, B. L., & Landing, W. M. (1991). Kamber, B. S., Webb, G. E., & Gallagher, M. (2014). The rare earth ele- ment signal in Archaean microbial carbonate: Information on ocean redox and biogenicity. Journal of the Geological Society of London, 171, 745–­763. https://doi.org/10.1144/jgs20​13-­110 at sea-­floor hydrothermal vents. Geomicrobiology Journal, 21, 415–­ 429. https://doi.org/10.1080/01490​45049​0485845 at sea-­floor hydrothermal vents. Geomicrobiology Journal, 21, 415–­ 429. https://doi.org/10.1080/01490​45049​0485845 Liu, H., Pourret, O., Guo, H., & Bonhoure, J. (2017). Rare earth elements sorption to iron oxyhydroxide: Model development and application to groundwater. Applied Geochemistry, 87, 158–­166. https://doi. org/10.1016/j.apgeo​chem.2017.10.020 Karl, D. M., McMurtry, G. M., Malahoff, A., & Garcia, M. O. (1988). Loihi Seamount, Hawaii: A mid-­plate volcano with a distinc- tive hydrothermal system. Nature, 335, 532–­535. https://doi. org/10.1038/335532a0 Marone, F., & Stampanoni, M. (2012). Regridding reconstruction algorithm for real-­time tomographic imaging. Journal of Synchrotron Radiation, 19, 1029–­1037. https://doi.org/10.1107/S0909​04951​2032864 Kelley, D. S., Karson, J. A., Früh-­Green, G. L., Yoerger, D. R., Shank, T. M., Butterfield, D. A., Hayes, J. M., Schrenk, M. O., Olson, E. J., Proskurowski, G., & Jakuba, M. (2005). A serpentinite-­hosted eco- system: The Lost City hydrothermal field. Science, 307, 1428–­1434. https://doi.org/10.1126/scien​ce.1102556 Martin, W., Rotte, C., Hoffmeister, M., Theissen, U., Gelius-­Dietrich, G., Ahr, S., & Henze, K. (2003). Early cell evolution, eukaryotes, anoxia, sulfide, oxygen, fungi first (?), and a tree of genomes revisited. IUBMB Life, 55, 193–­204. https://doi.org/10.1080/15216​54031​00014​1231 Kendall, B., Creaser, R. A., Gordon, G. W., & Anbar, A. D. (2009). Re-­ Os and Mo isotope systematics of black shales from the Middle Proterozoic Velkerri and Wollogorang formations, McArthur basin, northern Australia. Geochimica Et Cosmochimica Acta, 73, 2534–­ 2558. https://doi.org/10.1016/j.gca.2009.02.013 McAllister, S. M., Moore, R. M., Gartman, A., Luther, G. W. III, Emerson, D., & Chan, C. S. (2019). The Fe(II)-­oxidizing Zetaproteobacteria: Historical, ecological and genomic perspectives. FEMS Microbiology Ecology, 95, 1–­18. McAllister, S. M., Polson, S. W., Butterfield, D. A., Glazer, B. T., Sylvan, J. B., & Chan, C. S. (2020). Validating the Cyc2 neutrophilic iron oxida- tion pathway using meta-­omics of zetaproteobacteria iron mats at marine hydrothermal vents. mSystems, 5, e00553-­19. Konhauser, K. O., Planavsky, N. J., Hardisty, D. S., Robbins, L. J., Warchola, T. J., Haugaard, R., Lalonde, S. V., Partin, C. A., Oonk, P. B. H., Tsikos, H., Lyons, T. W., Bekker, A., & Johnson, C. M. (2017). Iron forma- tions: A global record of Neoarchaean to Palaeoproterozoic envi- ronmental history. Earth-­Science Reviews, 172, 140–­177. https://doi. org/10.1016/j.earsc​irev.2017.06.012 McMahon, S. (2019). https://doi.org/10.1111/gbi.12363 Garcia-­Ruiz, J. M., Melero-­García, E., & Hyde, S. T. (2009). Morphogenesis of self-­assembled nanocrystalline materials of barium carbonate and silica. Science, 323, 362–­365. https://doi.org/10.1126/scien​ ce.1165349 Johannessen, K. C., Vander Roost, J., Dahle, H., Dundas, S. H., Pedersen, R. B., & Thorseth, I. H. (2017). Environmental controls on biomineral- ization and Fe-­mound formation in a low-­temperature hydrothermal system at the Jan Mayen vent fields. Geochimica Et Cosmochimica Acta, 202, 101–­123. https://doi.org/10.1016/j.gca.2016.12.016 Glazer, B. T., & Rouxel, O. J. (2009). Redox speciation and distribu- tion within diverse iron-­dominated microbial habitats at Loihi Seamount. Geomicrobiology Journal, 26, 606–­622. https://doi. org/10.1080/01490​45090​3263392 Johannesson, K. H., & Lyons, W. B. (1994). The rare earth element geo- chemistry of Mono Lake water and the importance of carbonate complexing. Limnology and Oceanography, 39, 1141–­1154. https://doi. org/10.4319/lo.1994.39.5.1141 Grenne, T., & Slack, J. F. (2003). Bedded jaspers of the Ordovician Løkken ophiolite, Norway: Seafloor deposition and diagenetic maturation of hydrothermal plume-­derived silica-­iron gels. Mineralium Deposita, 38, 625–­639. https://doi.org/10.1007/s0012​ 6-­003-­0346-­3 Jones, B., de Ronde, C. E. J., & Renaut, R. W. (2008). Mineralized mi- crobes from Giggenbach submarine volcano. Journal of Geophysical Research, 113(B8, 13). https://doi.org/10.1029/2007J​B005482 Grenne, T., & Slack, J. F. (2005). Geochemistry of jasper beds from the Ordovician Løkken ophiolite, Norway: Origin of proximal and distal siliceous exhalites. Economic Geology, 100, 1511–­1527. Juniper, S. K., & Fouquet, Y. (1988). Filamentous iron silica deposits from modern and ancient hydrothermal sites. Canadian Mineralogist, 26, 859–­869. LITTLE et al. 247 J. (2019). Same, same, but different: Recent advances in our understanding of modern seafloor hydrothermal systems. Glasgow, Scotland, University of Glasgow, Proceedings of the 15th Biennial SGA Meeting, 1, 80–­82. oceanic mass balance of rhenium and implications for the extent of Proterozoic ocean anoxia. Geochimica Et Cosmochimica Acta, 227, 75–­ 95. https://doi.org/10.1016/j.gca.2018.01.036 Picard, A., Kappler, A., Schmid, G., Quaroni, L., & Obst, M. (2015). Experimental diagenesis of organo-­mineral structures formed by microaerophilic Fe(II)-­oxidizing bacteria. Nature Communications, 6, 6277. https://doi.org/10.1038/ncomm​s7277 Slack, J. F. (2012). Exhalites. In W. C. Shanks III, & R. Thurston (Eds.), Volcanogenic massive sulfide occurrence model. (pp. 154–­163). U.S. Geological Survey Scientific Investigations Report 2010–­5070−C. Slack, J. F., Grenne, T., & Bekker, A. (2009). Seafloor-­hydrothermal Si-­ Fe-­Mn exhalites in the Pecos greenstone belt, New Mexico, and the redox state of ca. 1720 Ma deep seawater. Geosphere, 5, 302–­314. Planavsky, N. J., McGoldrick, P., Scott, C. T., Li, C., Reinhard, C. T., Kelly, A. E., Chu, X., Bekker, A., Love, G. D., & Lyons, T. W. (2011). Widespread iron-­rich conditions in the mid-­Proterozoic ocean. Nature, 477, 448–­ 452. https://doi.org/10.1038/natur​e10327 Slack, J. F., Grenne, T., Bekker, A., Rouxel, O. J., & Lindberg, P. A. (2007). Suboxic deep seawater in the late Paleoproterozoic: Evidence from hematitic chert and iron formation related to seafloor-­hydrothermal sulfide deposits, central Arizona, USA. Earth and Planetary Science Letters, 255, 243–­256. https://doi.org/10.1016/j.epsl.2006.12.018 Planavsky, N., Rouxel, O., Bekker, A., Shapiro, R., Fralick, P., & Knudsen, A. (2009). Iron-­oxidizing microbial ecosystems thrived in late Paleoproterozoic redox-­stratified oceans. Earth and Planetary Science Letters, 286, 230–­242. https://doi.org/10.1016/j. epsl.2009.06.033 Sperling, E. A., Rooney, A. D., Hays, L., Sergeev, V. N., Vorob'eva, N. G., Sergeeva, N. D., Selby, D., Johnston, D. T., & Knoll, A. H. (2014). Redox heterogeneity of subsurface waters in the Mesoproterozoic ocean. Geobiology, 12, 373–­386. https://doi.org/10.1111/gbi.12091 Planavsky, N. J., Slack, J. F., Cannon, W. F., O'Connell, B., Isson, T. T., Asael, D., Jackson, J. C., Hardisty, D. S., Lyons, T. W., & Bekker, A. (2018). Evidence for episodic oxygenation in a weakly redox-­buffered deep mid-­Proterozoic ocean. Chemical Geology, 483, 581–­594. https://doi. org/10.1016/j.chemg​eo.2018.03.028 Spry, P. G., Peter, J. M., & Slack, J. F. (2000). Meta-­exhalites as explora- tion guides to ore. Reviews in Economic Geology, 11, 163–­201. Stampanoni, M., Groso, A., Isenegger, A., Mikuljan, G., Chen, Q., Bertrand, A., Henein, S., Betemps, R., Frommherz, U., Böhler, P., Meister, D., Lange, M., & Abela, R. (2006). Trends in synchrotron-­ based tomographic imaging: The SLS experience. Proceedings of SPIE, 6318, 63180M-­1-­63214. Posth, N. R., Konhauser, K. O., & Kappler, A. (2013). Microbiological pro- cesses in banded iron formation deposition. Sedimentology, 60, 1733–­ 1754. https://doi.org/10.1111/sed.12051 Poulton, S. W., & Canfield, D. E. (2011). Ferruginous conditions: A dom- inant feature of the ocean through Earth’s history. Elements, 7, 107–­ 112. https://doi.org/10.2113/gsele​ments.7.2.107 Sun, Z., Li, J., Huang, W., Dong, H., Little, C. T. S., & Li, J. (2015). Generation of hydrothermal Fe-­Si oxyhydroxide deposit on the Southwest Indian Ridge and its implication for the origin of ancient banded iron forma- tions. Journal of Geophysical Research: Biogeosciences, 120, 187–­203. https://doi.org/10.1002/2014J​G002764 Poulton, S. W., Fralick, P. W., & Canfield, D. E. (2004). The transition to a sulphidic ocean ~1:84 billion years ago. Nature, 431, 173–­177. Poulton, S. W., Fralick, P. W., & Canfield, D. E. (2010). Spatial variability in oceanic redox structure 1.8 billion years ago. Nature Geoscience, 3, 486–­490. Sun, Z., Zhou, H., Glasby, G. P., Sun, Z., Yang, Q., Yin, X., & Li, J. (2013). Mineralogical characterization and formation of Fe-­Si oxyhydrox- ide deposits from modern seafloor hydrothermal vents. American Mineralogist, 98, 85–­97. https://doi.org/10.2138/am.2013.4147 Read, R., & Pollard, R. (2017). An introduction to the physical ocean- ography of six seamounts in the southwest Indian Ocean. Deep Sea Research (II), 136, 44–­58. https://doi.org/10.1016/j.dsr2.2015.06.022 Tan, H., Verbeeck, J., Abakumov, A., & Van Tendeloo, G. (2012). Oxidation state and chemical shift investigation in transition metal oxides by EELS. Ultramicroscopy, 116, 24–­33. https://doi.org/10.1016/j.ultra​ mic.2012.03.002 Reinhard, C. T., Planavsky, N. J., Robbins, L. J., Partin, C. A., Gill, B. C., Lalonde, S. V., Bekker, A., Konhauser, K. O., & Lyons, T. W. (2013). Proterozoic ocean redox and biogeochemical stasis. Proceedings of the National Academy of Sciences, 110, 5357–­5362. https://doi. org/10.1073/pnas.12086​22110 Taylor, S. R., & McLennan, S. M. (1985). The continental crust: Its composi- tion and evolution (p. 312). Blackwell Scientific Publications. Rouxel, O., Toner, B., Germain, Y., & Glazer, B. (2018). Geochemical and iron isotopic insights into hydrothermal iron oxyhydroxide deposit formation at Loihi Seamount. Geochimica Et Cosmochimica Acta, 220, 449–­482. https://doi.org/10.1016/j.gca.2017.09.050 Tivey, M. K. (2007). Generation of seafloor hydrothermal vent fluids and associated mineral deposits. Oceanography, 20, 50–­65. https://doi. org/10.5670/ocean​og.2007.80 Toner, B. M., Berquo, T. S., Michel, F. M., Sorensen, J. V., Templeton, A. S., & Edwards, K. J. (2012). Mineralogy of iron microbial mats from Loihi Seamount. Frontiers in Microbiological Chemistry, 3, 1–­18. The biogeochemistry of man- ganese and iron in the Black Sea. Deep-­Sea Research, 38(Suppl. 2), S773–­S803. https://doi.org/10.1016/S0198​-­0149(10)80009​-­3 Partin, C. A., Bekker, A., Planavsky, N. J., Scott, C. T., Gill, B. G., Li, C., Podkovyrov, V., Maslov, A., Konhauser, K. O., Lalonde, S. V., Love, G. D., Poulton, S. W., & Lyons, T. W. (2013). Large-­scale fluctuations in Precambrian atmospheric and oceanic oxygen levels from the record of U in shales. Earth and Planetary Science Letters, 369–­370, 284–­293. https://doi.org/10.1016/j.epsl.2013.03.031 Li, J., Zhou, H., Peng, X., Wu, Z., Chen, S., & Fang, J. (2012). Microbial diversity and biomineralization in low-­temperature hydrother- mal iron-­silica-­rich precipitates of the Lau Basin hydrother- mal field. FEMS Microbiology Ecology, 81, 205–­216. https://doi. org/10.1111/j.1574-­6941.2012.01367.x Pedersen, R. B., Thorseth, I. H., Nygaard, T. E., Lilley, M. D., & Kelley, D. S. (2010). Hydrothermal activity at the Arctic mid-­ocean ridges. In P. A. Rona, C. W. Devey, J. Dyment, & B. J. Murton (Eds.), Diversity of hydrothermal systems on slow spreading ocean ridges (pp. 67–­89). American Geophysical Union. Geophysical Monograph 188. Lin, Y., Tang, D., Shi, X., Zhou, X., & Huang, K. (2019). Shallow-­marine ironstones formed by microaerophilic iron-­oxidizing bacteria in ter- minal Paleoproterozoic. Gondwana Research, 76, 1–­18. https://doi. org/10.1016/j.gr.2019.06.004 Peng, X., Ta, K., Chen, S., Zhang, L., & Xu, H. (2015). Coexistence of Fe(II)-­ and Mn(II)-­oxidizing bacteria govern the formation of deep sea umber deposits. Geochimica Et Cosmochimica Acta, 169, 200–­216. https://doi.org/10.1016/j.gca.2015.09.011 Lindberg, P. A. (2008). Early Proterozoic volcanogenic massive sulfide ore deposits, Jerome, Arizona, USA. Arizona Geological Society Digest, 22, 601–­610. Little, C. T. S., Glynn, S. E. J., & Mills, R. A. (2004). Four-­hundred-­and-­ ninety-­million-­year record of bacteriogenic iron oxide precipitation Petersen, S., Hannington, M. D., Hölz, S., Krätschell, A., Klischies, M., Graber, S., Anderson, M. O., Jamieson, J. W., Grant, H. L. J., & Murton, B. 248 LITTLE et al. | Proceedings of the National Academy of Sciences, 113, 1731–­1736. https://doi.org/10.1073/pnas.15234​49113 Yang, S., Kendall, B., Lu, X., Zhang, F., & Zheng, W. (2017). Uranium iso- tope compositions of mid-­Proterozoic black shales: Evidence for an episode of increased ocean oxygenation at 1.36 Ga and evalu- ation of the effect of post-­depositional hydrothermal fluid flow. Precambrian Research, 298, 187–­201. https://doi.org/10.1016/j.preca​ mres.2017.06.016 https://doi. org/10.3389/fmicb.2012.00118 Scott, C., Lyons, T. W., Bekker, A., Shen, Y., Poulton, S., Chu, X., & Anbar, A. (2008). Tracing the stepwise oxygenation of the Proterozoic bio- sphere. Nature, 452, 456–­459. Scott, J. J., Glazer, B. T., & Emerson, D. (2017). Bringing microbial diver- sity into focus: High-­resolution analysis of iron mats from the Lo‘ihi Seamount. Environmental Microbiology, 19, 301–­316. Tostevin, R., Wood, R. A., Shields, G. A., Poulton, S. W., Guilbaud, R., Bowyer, F., Penny, A. M., He, T., Curtis, A., Hoffmann, K. H., & Clarkson, M. O. (2016). Low-­oxygen waters limited habitable space for early animals. Nature Communications, 7(1), 1–­9. https://doi. org/10.1038/ncomm​s12818 Seewald, J. S., Reeves, E. P., Bach, W., Saccocia, P. J., Craddock, P. R., Shanks, W. C. III, Sylva, S. P., Pichler, T., Rosner, M., & Walsh, E. (2015). Submarine venting of magmatic volatiles in the eastern Manus Basin, Papua New Guinea. Geochimica Et Cosmochimica Acta, 163, 178–­199. https://doi.org/10.1016/j.gca.2015.04.023 Vander Roost, J., Daae, F. L., Steen, I. H., Thorseth, I. H., & Dahle, H. (2018). Distribution patterns of iron-­oxidizing Zeta and Beta-­ Proteobacteria from different environmental settings at the Jan Mayen vent fields. Frontiers in Microbiology, 9, 3008. Shang, M., Tang, D., Shi, X., Zhou, L., Zhou, X., Song, H., & Jiang, G. (2019). A pulse of oxygen increase in the early Mesoproterozoic ocean at ca. 1.57-­1.56 Ga. Earth and Planetary Science Letters, 527, 115797. https://doi.org/10.1016/j.epsl.2019.115797 Vander Roost, J., Thorseth, I. H., & Dahle, H. (2017). Microbial analy- sis of Zetaproteobacteria and co-­colonizers of iron mats in the Troll Wall vent field, Arctic mid-­ocean Ridge.PLoS One, 12(9), e0185008. https://doi.org/10.1371/journ​al.pone.0185008 Shapiro, R. S., & Konhauser, K. O. (2015). Hematite-­coated microfos- sils: Primary ecological fingerprint or taphonomic oddity of the Paleoproterozoic? Geobiology, 13, 209–­224. https://doi.org/10.1111/ gbi.12127 Wacey, D., McLoughlin, N., Kilburn, M. R., Saunders, M., Cliff, J. B., Kong, C., Barley, M. E., & Brasier, M. D. (2013). Nanoscale analysis of pyri- tized microfossils reveals differential heterotrophic consumption in the ∼1.9-­Ga Gunflint chert. Proceedings of the National Academy of Sciences of the United States of America, 110, 8020–­8024. Sheen, A. I., Kendall, B., Reinhard, C. T., Creaser, R. A., Lyons, T. W., Bekker, A., Poulton, S. W., & Anbar, A. D. (2018). A model for the LITTLE et al. 249 SUPPORTING INFORMATION Additional supporting information may be found online in the Zeng, Z., Ouyang, H., Yin, X., Chen, S., Wang, X., & Wu, L. (2012). Formation of Fe-­Si-­Mn oxyhydroxides at the PACMANUS hydro- thermal field, eastern Manus Basin: Mineralogical and geochemical evidence. Journal of Asian Earth Sciences, 60, 130–­146. https://doi. org/10.1016/j.jseaes.2012.08.009 Supporting Information section. How to cite this article: Little CTS, Johannessen KC, Bengtson S, et al. A late Paleoproterozoic (1.74 Ga) deep-­sea, low-­temperature, iron-­oxidizing microbial hydrothermal vent community from Arizona, USA. Geobiology. 2021;19:228–­ 249. https://doi.org/10.1111/gbi.12434 Zhang, K., Zhu, X., Wood, R. A., Shi, Y., Gao, Z., & Poulton, S. W. (2018). Oxygenation of the Mesoproterozoic ocean and the evolution of complex eukaryotes. Nature Geosciences, 11, 345–­350. https://doi. org/10.1038/s4156​1-­018-­0111-­y Zhang, S., Wang, X., Wang, H., Bjerrum, C. J., Hammarlund, E. U., Costa, M. M., Connelly, J. N., Zhang, B., Su, J., & Canfield, D. E. (2016). Sufficient oxygen for animal respiration 1,400 million years ago.
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https://www.biorxiv.org/content/biorxiv/early/2019/10/07/634568.full.pdf
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Automated data-intensive forecasting of plant phenology throughout the United States
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Automated data-intensive forecasting of 1 plant phenology throughout the United 2 States 3 Shawn D. Taylor1 (corresponding author), shawntaylor@weecology.org 4 Ethan P. White2, ethanwhite@ufl.edu 5 1 School of Natural Resources and Environment, University of Florida Gainesville, FL, United 6 States 7 2 Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, 8 United States 9 Running Head: Phenology Forecasting Methods 10 Automated data-intensive forecasting of 1 plant phenology throughout the United 2 States 3 Shawn D. Taylor1 (corresponding author), shawntaylor@weecology.org 4 Ethan P. White2, ethanwhite@ufl.edu 5 1 School of Natural Resources and Environment, University of Florida Gainesville, FL, United 6 States 7 2 Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, 8 United States 9 Running Head: Phenology Forecasting Methods 10 Automated data-intensive forecasting of 1 plant phenology throughout the United 2 States 3 Shawn D. Taylor1 (corresponding author), shawntaylor@weecology.org 4 Ethan P. White2, ethanwhite@ufl.edu 5 1 School of Natural Resources and Environment, University of Florida Gainesville, FL, United 6 States 7 2 Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, 8 United States 9 Running Head: Phenology Forecasting Methods 10 . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint States Running Head: Phenology Forecasting Methods 10 1 1 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint Abstract 11 Phenology - the timing of cyclical and seasonal natural phenomena such as flowering 12 and leaf out - is an integral part of ecological systems with impacts on human activities 13 like environmental management, tourism, and agriculture. As a result, there are 14 numerous potential applications for actionable predictions of when phenological events 15 will occur. However, despite the availability of phenological data with large spatial, 16 temporal, and taxonomic extents, and numerous phenology models, there has been no 17 automated species-level forecasts of plant phenology. This is due in part to the 18 challenges of building a system that integrates large volumes of climate observations 19 and forecasts, uses that data to fit models and make predictions for large numbers of 20 species, and consistently disseminates the results of these forecasts in interpretable 21 ways. Here we describe a new near-term phenology forecasting system that makes 22 predictions for the timing of budburst, flowers, ripe fruit, and fall colors for 78 species 23 across the United States up to 6 months in advance and is updated every four days. We 24 use the lessons learned in developing this system to provide guidance developing 25 large-scale near-term ecological forecast systems more generally, to help advance the 26 use of automated forecasting in ecology. 27 Keywords: climate, budburst, flowering, phenophase, ecology, decision making 28 2 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint Introduction 29 CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint extents, and at fine spatial resolutions. The only regularly updated phenology forecast in 56 current operation predicts only a single aggregated “spring index” that identifies when 57 early-spring phenological events occur at the level of the entire ecosystem (not 58 individual species) at a resolution of 1° lat/lon grid cells (Schwartz et al. 2013, Carrillo 59 et al. 2018). Forecasting individual species and multiple phenological events at higher 60 resolutions is challenging due to the advanced computational tools needed for building 61 and maintaining data-intensive automatic forecasting systems (White et al. 2018, Welch 62 et al. 2019). Automated forecasts requires building systems that acquire data, make 63 model-based predictions for the future, and disseminate the forecasts to end-users, all in 64 an automated pipeline (Dietze et al. 2018, White et al. 2018, Welch et al. 2019). This is 65 challenging even for relatively small-scale single site projects with one to several 66 species or response variables due to the need for advanced computational tools to 67 support robust automation (White et al. 2018, Welch et al. 2019). Building an 68 automated system to forecast phenology for numerous species at continental scales is 69 even more challenging due to the large-scale data intensive nature of the analyses. 70 Specifically, because phenology is sensitive to local climate conditions, phenology 71 modeling and prediction should be done at high resolutions (Cook et al. 2010). This 72 requires repeatedly conducting computationally intensive downscaling of seasonal 73 climate forecasts and making large numbers of predictions. To make 4 km resolution 74 spatially explicit forecasts for the 78 species in our study at continental scales requires 75 over 90 million predictions for each updated forecast. To make the forecasts actionable 76 these computational intensive steps need to be repeated in near real-time and 77 disseminated in a way that allows end-users to understand the forecasts and their 78 uncertainties (Dietze et al. 2018). 79 Here we describe an automated near-term phenology forecast system we developed to 80 k i l l f f 8 diff l i S i b 1 extents, and at fine spatial resolutions. Introduction 29 Plant phenology - the timing of cyclical and seasonal natural phenomena such as 30 flowering and leaf out - influences many aspects of ecological systems (Chuine and 31 Régnière 2017) from small scale community interactions (Ogilvie et al. 2017) to global 32 scale climate feedbacks (Richardson et al. 2012). Because of the central importance of 33 phenology, advanced forecasts for when phenological events will occur have numerous 34 potential applications including: 1) research on the cascading effects of changing plant 35 phenology on other organisms; 2) tourism planning related to flower blooms and 36 autumn colors; 3) planning for sampling and application of management interventions 37 by researchers and managers; and 4) agricultural decisions on timing for planting, 38 harvesting, and application of pest prevention techniques. However, due to the 39 challenges of automatically integrating, predicting, and disseminating large volumes of 40 data, there are limited examples of applied phenology forecast systems. 41 Numerous phenology models have been developed to characterize the timing of major 42 plant events and understand their drivers (Chuine et al. 2013). These models are based 43 on the idea that plant phenology is primarily driven by weather, with seasonal 44 temperatures being the primary driver at temperate latitudes (Basler 2016, Chuine and 45 Régnière 2017). Because phenology is driven primarily by weather, it is possible to 46 make predictions for the timing of phenology events based on forecasted weather 47 conditions. The deployment of seasonal climate forecasts (Weisheimer and Palmer 48 2014), those beyond just a few weeks, provides the potential to forecast phenology 49 months in advance. This time horizon is long enough to allow meaningful planning and 50 action in response to these forecasts. With well established models, widely available 51 data, and numerous use cases, plant phenology is well suited to serve as an exemplar for 52 near-term ecological forecasting. 53 For decision making purposes, the most informative plant phenology forecasts will 54 predict the response of large numbers of species and phenophases, over large spatial 55 3 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . Forecasting Pipeline 96 Welch et al. (2019) break down the process of developing tools for automated prediction 97 into four stages: 1) Acquisition, obtaining and processing the regularly updated data 98 needed for prediction; 2) Prediction, combining the data with models to estimate the 99 outcome of interest; 3) Dissemination, the public presentation of the predictions; and 4) 100 Automation, the tools and approaches used to automatically update the predictions 101 using the newest data on a regular basis. We start by describing our approach to 102 modeling phenology and then describe our approach to each of these stages. 103 Introduction 29 It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint forecasts for multiple phenophases and presents the resulting forecasts and their 83 uncertainty on a dynamic website, https://phenology.naturecast.org/. Since the majority 84 of plants complete budburst and/or flowering by the summer solstice in mid-June, this 85 results in lead times of up to six months. We describe the key steps in the system 86 construction, including: 1) fitting phenology models, 2) acquiring and downscaling 87 climate data; 3) making predictions for phenological events; 4) disseminating those 88 predictions; and 5) automating steps 2-4 to update forecasts at a sub-weekly frequency. 89 We follow Welch et al. (2019)’s framework for describing operationalized dynamic 90 management tools (ie. self-contained tools running automatically and regularly) and 91 describe the major design decisions and lessons learned from implementing this system 92 that will guide improvements to automated ecological forecasting systems. Due to the 93 data-intensive nature of forecasting phenology at fine resolutions over large scales this 94 system serves as a model for large-scale forecasting systems in ecology more broadly. 95 Introduction 29 The only regularly updated phenology forecast in 56 current operation predicts only a single aggregated “spring index” that identifies when 57 early-spring phenological events occur at the level of the entire ecosystem (not 58 individual species) at a resolution of 1° lat/lon grid cells (Schwartz et al. 2013, Carrillo 59 et al. 2018). Forecasting individual species and multiple phenological events at higher 60 resolutions is challenging due to the advanced computational tools needed for building 61 and maintaining data-intensive automatic forecasting systems (White et al. 2018, Welch 62 et al. 2019). Automated forecasts requires building systems that acquire data, make 63 model-based predictions for the future, and disseminate the forecasts to end-users, all in 64 an automated pipeline (Dietze et al. 2018, White et al. 2018, Welch et al. 2019). This is 65 challenging even for relatively small-scale single site projects with one to several 66 species or response variables due to the need for advanced computational tools to 67 support robust automation (White et al. 2018, Welch et al. 2019). Building an 68 automated system to forecast phenology for numerous species at continental scales is 69 even more challenging due to the large-scale data intensive nature of the analyses. 70 Specifically, because phenology is sensitive to local climate conditions, phenology 71 modeling and prediction should be done at high resolutions (Cook et al. 2010). This 72 requires repeatedly conducting computationally intensive downscaling of seasonal 73 climate forecasts and making large numbers of predictions. To make 4 km resolution 74 spatially explicit forecasts for the 78 species in our study at continental scales requires 75 over 90 million predictions for each updated forecast. To make the forecasts actionable 76 these computational intensive steps need to be repeated in near real-time and 77 disseminated in a way that allows end-users to understand the forecasts and their 78 uncertainties (Dietze et al. 2018). 79 Here we describe an automated near-term phenology forecast system we developed to 80 Here we describe an automated near-term phenology forecast system we developed to 80 make continental scale forecasts for 78 different plant species. Starting December 1st, 81 and updated every 4 days, this system uses the latest climate information to make 82 4 4 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. Phenology Modeling 104 Making large spatial scale phenology forecasts for a specific species requires species 105 level observation data from as much of its respective range as possible (Taylor et al. 106 5 . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint 2019). We used data from the USA National Phenology Network (USA-NPN), which 107 collects volunteer based data on phenological events and has amassed over 10 million 108 observations representing over 1000 species. The USA-NPN protocol uses status-based 109 monitoring, where observers answer ‘yes,’ ‘no,’ or ‘unsure’ when asked if an individual 110 plant has a specific phenophase present (Denny et al. 2014). Phenophases refer to 111 specific phases in the annual cycle of a plant, such as the presence of emerging leaves, 112 flowers, fruit, or senescing leaves. We used the “Individual Phenometrics” data product, 113 which provides pre-processed onset dates of individually monitored plants, for the 114 phenophases budburst, flowering, and fall colors for all species with data between 2009 115 and 2017 (USA National Phenology Network 2018). We only kept “yes” observations 116 where the individual plant also had a “no” observation within the prior 30 days and 117 dropped any records where a single plant had conflicting records for phenotype status or 118 more than one series of “yes” observations for a phenophase in a 12 month period. We 119 built models for species and phenophase combinations with at least 30 observations 120 (Figure 1, B) using daily mean temperature data at the location and time of each 121 observation from the PRISM 4km dataset (PRISM Climate Group 2004). We also 122 included contributed models of budburst, flowering, and/or fruiting for 5 species which 123 were not well represented in the USA-NPN dataset (see Appendix S1: Table S2; Janet S. 124 Prevéy, unpublished data, 2018, Prevéy et al. (In revision); Biederman et al. (2018)). Phenology Modeling 104 125 For each species and phenophase we fit an ensemble of four models using daily mean 126 temperature as the sole driver (Figure 1, C). The general model form assumes a 127 phenological event will occur once sufficient thermal forcing units accumulate from a 128 specified start day (Chuine et al. 2013, Chuine and Régnière 2017). The specification of 129 forcing units are model specific, but all are derived from the 24-hour daily mean 130 temperature. In a basic model a forcing unit is the maximum of either 0 or the mean 131 temperature above 0°C (ie. growing degree days). The amount of forcing units required, 132 and the date from which they start accumulating are parameterized for each species and 133 6 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint phenophase (see Appendix S1: Table S1). Ensembles of multiple models generally 134 improve prediction over any single model by reducing bias and variance, and in a 135 phenology context allow more accurate predictions to be made without knowing the 136 specific physiological processes for each species (Basler 2016, Yun et al. 2017, 137 phenophase (see Appendix S1: Table S1). Ensembles of multiple models generally 134 improve prediction over any single model by reducing bias and variance, and in a 135 phenology context allow more accurate predictions to be made without knowing the 136 specific physiological processes for each species (Basler 2016, Yun et al. 2017, 137 Dormann et al. 2018). We used a weighted ensemble of four phenology models. We 138 derived the weights for each model within the ensemble using stacking to minimize the 139 root mean squared error on held out test data (100 fold cross-validation) as described in 140 Dormann et al. (2018) (see Appendix S1: Sec. S1). Phenology Modeling 104 After determining the weights we 141 fit the core models a final time on the full dataset. Since individual process based 142 phenology models are not probabilistic they do not allow the estimation of uncertainty 143 in the forecasts. Therefore, we used the variance across the five climate models to 144 represent uncertainty (see Prediction). Finally, we also fit a spatially corrected Long 145 Term Average model for use in calculating anomalies (see Dissemination). This uses the 146 past observations in a linear model with latitude as the sole predictor (see Appendix S1: 147 Table S1). 148 In our pipeline 190 unique phenological models (one for each species and phenophase 149 combination, see see Appendix S1: Table S2) needed to be individually parameterized, 150 evaluated, and stored for future use. To consolidate all these requirements we built a 151 dedicated software package written in Python, pyPhenology, to build, save, and load 152 models, and also apply them to gridded climate datasets (Taylor 2018). The package 153 also integrates the phenological model ensemble so that the four sub-models can be 154 treated seamlessly as one in the pipeline. After parameterizing each model, its 155 specifications are saved in a text based JSON file that is stored in a git repository along 156 with a metadata file describing all models (Figure 1, D). This approach allows for the 157 tracking and usage of hundreds of models, allowing models to be easily synchronized 158 across systems, and tracking versions of models as they are updated (or even deleted). 159 7 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint Acquisition and Downscaling of Climate Data 160 It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint month (Figure 1, H). This downscaling model, at the scale of the continental U.S.A., is 187 used to downscale the most recent CFSv2 forecasts to a 4km resolution during the 188 automated steps. 189 We used specialized Python packages to overcome the computational challenges 190 inherent in the large CFSv2 climate dataset (Python Software Foundation 2003). The 191 climate forecast data for each phenology forecast update is 10-40 gigabytes, depending 192 on the time of year (time series are longer later in the year). While it is possible to 193 obtain hardware capable of loading this dataset into memory, a more efficient approach 194 is to perform the downscaling and phenology model operations iteratively by subsetting 195 the climate dataset spatially and performing operations on one chunk at a time. We used 196 the python package xarray (Hoyer and Hamman 2017), which allows these operations 197 to be efficiently performed in parallel through tight integration with the dask package 198 (Dask Development Team 2016). The combination of dask and xarray allows the 199 analysis to be run on individual workstations, stand alone servers, and high performance 200 computing systems, and to easily scale to more predictors and higher resolution data. 201 Acquisition and Downscaling of Climate Data 160 Since our phenology models are based on accumulated temperature forcing, making 161 forecasts requires information on both observed temperatures (from Nov. 30 of the prior 162 year up to the date a forecast is made) and forecast temperatures (from the forecast date 163 onward). For observed data we used 4km 24-hour daily mean temperature from PRISM, 164 a gridded climate dataset for the continental U.S.A. which interpolates on the ground 165 measurements and is updated daily (PRISM Climate Group 2004). These observed data 166 are saved in a netCDF file, which is appended with the most recent data every time the 167 automated forecast is run. For climate forecasts we used the Climate Forecast System 168 Version 2 (CFSv2; a coupled atmosphere-ocean-land global circulation model) 2-m 169 temperature data, which has a 6-hour timestep and a spatial resolution of 0.25 degrees 170 latitude/longitude (Saha et al. 2014). CFSv2 forecasts are projected out 9 months from 171 the issue date and are updated every 6 hours. The five most recent climate forecasts are 172 downloaded for each updated phenology forecast to accommodate uncertainty (see 173 Prediction). 174 Because the gridded climate forecasts are issued at large spatial resolutions (0.25 175 degrees), this data requires downscaling to be used at ecologically relevant scales (Cook 176 et al. 2010). A downscaling model relates observed values at the smaller scale to the 177 larger scale values generated by the climate forecast during a past time period. We 178 regressed these past conditions from a climate reanalysis of CFSv2 from 1995-2015 179 (Saha et al. 2010) against the 4km daily mean temperature from the PRISM dataset for 180 the same time period (PRISM Climate Group 2004) to build a downscaling model using 181 asynchronous regression (Figure 1, E-G). The CFSv2 data is first interpolated from the 182 original 0.25 degree grid to a 4km grid using distance weighted sampling, then an 183 asynchronous regression model is applied to each 4km pixel and calendar month 184 (Stoner et al. 2013, see see Appendix S1: Sec. S2). The two parameters from the 185 regression model for each 4 km cell are saved in a netCFD file by location and calendar 186 8 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. Prediction 202 The five most recent downscaled climate forecasts are each combined with climate 203 observations to make a five member ensemble of daily mean temperature across the 204 continental USA (Figure 1, L). These are used to make predictions using the phenology 205 model for each species and phenophase (Figure 1, M). Each climate ensemble member 206 is a 3d matrix of latitude × longitude × time at daily timesteps extending from Nov. 1 207 of the prior year to 9 months past the issue date. The pyPhenology package uses this 208 object to make predictions for every 4 km grid cell in the contiguous United States, 209 producing a 2d matrix (latitude × longitude) where each cell represents the predicted 210 Julian day of the phenological event. This results in approximately half a million 211 predictions for each run of each phenology model and 90 million predictions per run of 212 9 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint the forecasting pipeline. The output of each model is cropped to the range of the 213 respective species (US Geological Survey 1999) and saved as a netCDF file (Figure 1, 214 N) for use in dissemination and later evaluation. 215 the forecasting pipeline. The output of each model is cropped to the range of the 213 respective species (US Geological Survey 1999) and saved as a netCDF file (Figure 1, 214 N) for use in dissemination and later evaluation. 215 An important aspect of making actionable forecasts is providing decision makers with 216 information on the uncertainty of those predictions (Dietze et al. 2018). One major 217 component of uncertainty that is often ignored in near-term ecological forecasting 218 studies is the uncertainty in the forecasted drivers. Prediction 202 We incorporate information on 219 uncertainty in temperature, the only driver in our phenology models, using the CFSv2 220 climate ensemble (Figure 1, I; see Acquisition). The members of the climate ensemble 221 each produce a different temperature forecast due to differences in initial conditions 222 (Weisheimer and Palmer 2014). For each of the five climate members we make a 223 prediction using the phenology ensemble, and the uncertainty is estimated as the 224 variance of these predictions (see see Appendix S1: Sec. S1). This allows us to present 225 the uncertainty associated with climate, along with a point estimate of the forecast, 226 resulting in a range of dates over which a phenological event is likely to occur. 227 Dissemination 228 To disseminate the forecasts we built a website that displays maps of the predictions for 229 each unique species and phenophase (https://phenology.naturecast.org/; Figure 1 Q; 230 Figure 2). We used the Django web framework and custom JavaScript to allow the user 231 to select forecasts by species, phenophase, and issue date (Figure 2D). The main map 232 shows the best estimate for when the phenological event will occur for the selected 233 species (Figure 2A). Actionable forecasts also require an understanding of how much 234 uncertainty is present in the prediction (Dietze et al. 2018), because knowing the 235 expected date of an annual event such as flowering isn’t particularly useful if the 236 confidence interval stretches over several months. Therefore we also display a map of 237 uncertainty quantified as the 95% prediction interval, the range of days within which the 238 10 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint phenology event is expected to fall 95% of the time (Figure 2C). Finally, to provide 239 context to the current years predictions, we also map the predicted anomaly (Figure 2B). 240 The anomaly is the difference between the predicted date and the long term, spatially 241 corrected average date of the phenological event (Figure 1, O; see see Appendix S1: 242 Table S1). 243 Automation 244 CC-BY 4.0 International license a rtified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: oRxiv preprint successfully. This ensures that user of the website can always access the latest forecasts. 265 Software packages used throughout the system include, for the R language, ggplot2 266 (Wickham 2016), raster (Hijmans 2017), prism (Hart and Bell 2015), sp (Pebesma and 267 Bivand 2005), tidyr (Wickham and Henry 2018), lubridate (Grolemund and Wickham 268 2011), and ncdf4 (Pierce 2017). From the python language we also utilized xarray 269 (Hoyer and Hamman 2017), dask, (Dask Development Team 2016), scipy (Jones et al. 270 2001), numpy (Oliphant 2006), pandas (McKinney 2010), and mpi4py (Dalcin et al. 271 2011). All code described is available on a GitHub repository 272 (https://github.com/sdtaylor/phenology_forecasts). The code as well as 2019 forecasts 273 and observations (see Evaluation) are also permanently archived on Zenodo 274 (https://doi.org/10.5281/zenodo.2577452). 275 Automation 244 All of the steps in this pipeline, other than phenology and downscaling model fitting, are 245 automatically run every 4 days. To do this we use a cron job running on a local server. 246 Cron jobs automatically rerun code on set intervals. The cron job initiates a python 247 script which runs the major steps in the pipeline. First the latest CFSv2 climate 248 forecasts are acquired, downscaled, and combined with the latest PRISM climate 249 observations (Figure 1, I-L). This data is then combined with the phenology models 250 using the pyPhenology package to make predictions for the timing of phenological 251 events (Figure 1, M-N). These forecasts are then converted into maps and uploaded to 252 the website (Figure 1, O-Q). To ensure that forecasts continue to run even when 253 unexpected events occur it is necessary to develop pipelines that are robust to 254 unexpected errors and missing data, and are also informative when failures inevitably 255 do happen (Welch et al. 2019). We used status checks and logging to identify and fix 256 problems and separated the website infrastructure from the rest of the pipeline. Data are 257 checked during acquisition to determine if there are data problems and when possible 258 alternate data is used to replace data with issues. For example, members of the CFSv2 259 ensemble sometimes have insufficient time series lengths. When this is the case that 260 forecast is discarded and a preceding climate forecast obtained. With this setup 261 occasional errors in upstream data can be ignored, and larger problems identified and 262 corrected with minimal downtime. To prevent larger problems from preventing access 263 to the most recent successful forecasts the website is only updated if all other steps run 264 11 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . Evaluation 276 A primary advantage of near-term forecasts is the ability to rapidly evaluate forecast 277 proficiency, thereby shortening the model development cycle (Dietze et al. 2018). 278 Phenological events happen throughout the growing season, providing a consistent 279 stream of new observations to assess. We evaluated our forecasts (made from Dec. 1, 280 2018 thru May 1, 2019) using observations from the USA-NPN from Jan. 1, 2019 281 through May 8, 2019 and subset to species and phenophases represented in our system 282 (Figure 3; USA National Phenology Network (2019)). This resulted in 1581 283 phenological events that our system had forecasts for (588 flowering events, 991 284 budburst events, and 2 fall coloring across 65 species, see see Appendix S1: Table S3). 285 For each forecast issue date we calculated the root mean square error (RMSE) and 286 average forecast uncertainty for all events and all prior issue dates. We also assessed the 287 distribution of absolute errors (\ DOY −DOY ) for a subset of issue dates 288 (approximately two a month). 289 12 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint Forecast RMSE and uncertainty both decreased for forecasts with shorter lead time 290 (i.e. closer to the date the phenological event occurred), also known as the forecast 291 horizon (Fig. 4; Petchey et al. (2015)). Forecasts issued at the start of the year (on Jan. 292 5, 2019) had a RMSE of 20.9 days, while the most recent forecasts (on May 5, 2019) 293 had an RMSE of only 18.8 days. The average uncertainty for the forecasts were 7.6 and 294 0.2 days respectively for Jan. 5, and May 5. Errors were normally distributed with a 295 small over-prediction bias (MAE values of 6.8 - 12.1, Fig. 5). This bias also decreased 296 as spring progressed. Evaluation 276 These results indicate a generally well performing model, but also 297 one with significant room for improvement that will be facilitated by the iterative nature 298 of the forecasting system. 299 Discussion 300 Forecasts are updated every four days with the most recent climate observations and 303 forecasts, converted to static maps, and uploaded to a website for dissemination. We 304 used only open source software and data formats, and free publicly available data. 305 While a more comprehensive evaluation of forecast performance is outside the scope of 306 this paper, we note that the majority of forecasts provide realistic phenology estimates 307 across known latitudinal and elevational gradients (Figure 2), and forecast uncertainty 308 and error decreases as spring progresses (Figure 4). While there is a bias from 309 over-estimating phenological events, estimates were on-average within 2-3 weeks of the 310 true dates throughout the spring season. 311 Developing automated forecasting systems in ecology is important both for providing 312 decision makers with near real-time predictions and for improving our understanding of 313 biological systems by allowing repeated tests of, and improvements to, ecological 314 models (Dietze et al. 2018, White et al. 2018, Welch et al. 2019). To facilitate the 315 13 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint development of ecological forecasts, we need both active development, descriptions, 316 and discussion of a variety of forecasting systems. These discussions of the tools, 317 and discussion of a variety of forecasting systems. These discussions of the tools, 317 philosophies, and challenges involved in forecast pipeline development will advance our 318 understanding of how to most effectively build the systems, thereby lowering the entry 319 barrier of operationalizing ecological models for decision making. Active development 320 and discussion will also help us identify generalizable problems which can be solved 321 with standardized methods, data formats, and software packages. Tools such as this can 322 be used to more efficiently implement new ecological forecast systems, and facilitate 323 synthetic analyses and comparisons across a variety of forecasts. Discussion 300 324 Automated forecasting systems typically involve multiple major steps in a combined 325 pipeline. We found that breaking the pipeline into modular chunks made maintaining 326 this large number of components more manageable (White et al. 2018, Welch et al. 327 2019). For generalizable pieces of the pipeline we found that turning them into software 328 packages eased maintenance by decoupling dependencies and allowing independent 329 testing. Packaging large components also makes it easier for others to use code 330 developed for a forecasting system. The phenology modelling packge, pyPhenology, 331 was developed for the current system, but is generalized for use in any phenological 332 modelling study (Taylor 2018). We also found it useful to use different languages for 333 different pieces of the pipeline. Our pipeline involved tasks ranging from automatically 334 processing gigabytes of climate data to visualizing results to disseminating those results 335 through a dynamic website. In such a pipeline no single language will fit all 336 requirements, thus we made use of the strengths of two languages (Python and R) and 337 their associate package ecosystems. Interoperability is facilitated by common data 338 formats (csv and netCDF files), allowing scripts written in one language to 339 communicate results to the next step in the pipeline written in another language. 340 This phenology forecasting system currently involves 190 different ensemble models, 341 one for each species and phenological stage, each composed of 4 different phenology 342 14 14 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint sub-models and their associated weights for a total of 760 different models. This 343 necessitates having a system for storing and documenting models, and subsequently 344 updating them with new data and/or methods over time. We stored the fitted models in 345 JSON files (a open-standard text format). mutli-dimensional data and in our case are 300 times smaller than the csv files (50 370 MB/forecast). 371 mutli-dimensional data and in our case are 300 times smaller than the csv files (50 370 MB/forecast). 371 In addition to areas for improvement in the forecasting system itself, its development 372 has highlighted areas for potential improvement in phenology modeling. Other 373 well-known phenological drivers could be incorporated into the models, such as 374 precipitation and daylength. Precipitation forecasts are available from the CFSv2 375 dataset, though their accuracy is considerably lower than temperature forecasts (Saha et 376 al. 2014). Other large-scale phenological datasets, such as remotely-sensed spring 377 greenup could be used to constrain the species level forecasts made here (Melaas et al. 378 2016). Our system does not currently integrate observations about how phenology is 379 progressing within a year to update the models. USA-NPN data are available in near 380 real-time after they are submitted by volunteers, thus there is opportunity for data 381 assimilation of phenology observations. Making new forecasts with the latest 382 information not only on the current state of the climate, but also on the current state of 383 the plants themselves would likely be very informative (Luo et al. 2011, Dietze 2017). 384 For example, if a species is leafing out sooner than expected in one area it is likely that 385 it will also leaf out sooner than expected in nearby regions. This type of data 386 assimilation is important for making accurate forecasts in other disciplines including 387 meteorology (Bauer et al. 2015, Carrassi et al. 2018). However, process based plant 388 phenology models were not designed with data assimilation in mind (Chuine et al. 389 In addition to areas for improvement in the forecasting system itself, its development 372 has highlighted areas for potential improvement in phenology modeling. Other 373 well-known phenological drivers could be incorporated into the models, such as 374 precipitation and daylength. Precipitation forecasts are available from the CFSv2 375 dataset, though their accuracy is considerably lower than temperature forecasts (Saha et 376 al. 2014). Other large-scale phenological datasets, such as remotely-sensed spring 377 greenup could be used to constrain the species level forecasts made here (Melaas et al. 378 2016). Our system does not currently integrate observations about how phenology is 379 progressing within a year to update the models. Discussion 300 CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint Discussion 300 We used the version control system git to 346 track changes to these text based model specifications. While git was originally 347 designed tracking changes to code, it can also be leveraged for tracking data of many 348 forms, including our model specifications (Ram 2013, Bryan 2018, Yenni et al. 2019). 349 Managing many different models, including different versions of those models and their 350 associate provenance, will likely be a common challenge for ecological forecasting 351 (White et al. 2018) as one of the goals is iteratively improving the models. 352 The initial development of this system has highlighted several potential areas for 353 improvement. First, the data-intensive nature of this forecasting system provides 354 challenges and opportunities for disseminating results. Currently static maps show the 355 forecast dates of phenological events across each species respective range. However this 356 only answers one set of questions and makes it difficult for others to build on the 357 forecasts. Additional user interface design, including interactive maps and the potential 358 to view forecasts for a single location, would make it easier to ask other types of 359 questions such as “Which species will be in bloom on this date in a particular location?”. 360 User interface design is vital for successful dissemination, and tools such the python 361 package Django used here, or the R packages Shiny and Rmarkdown provide flexible 362 frameworks for implementation (White et al. 2018, Welch et al. 2019). In addition it 363 would be useful to provide access to the raw data underlying each forecast. The sheer 364 number of forecasts makes the bi-weekly forecast data relatively large, presenting some 365 challenges for dissemination through traditional ecological archiving services like 366 Dryad (https://datadryad.org) and Zenodo (https://zenodo.org). If stored as csv files 367 every forecast would have generated 15 GB of data. We addressed this by storing the 368 forecasts in compressed netCDF files, which are optimized for large-scale 369 15 15 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . transition dates as is currently done in this forecast system. 397 Using recent advances in open source software and large-scale open data collection we 398 have implemented an automated high resolution, continental scale, species-level 399 phenology forecast system. Implementing a system of this scale was made possible by a 400 new phenology data stream and new computational tools that facilitate large scale 401 analysis with limited computing and human resources. Most recent research papers 402 describing ecological forecast systems focus on only the modelling aspect (Chen et al. 403 2011, Carrillo et al. 2018, Van Doren and Horton 2018), and studies outlining 404 implementation methods and best practices are lacking (but see White et al. 2018, 405 Welch et al. 2019). Making a forecast system operational is key to producing applied 406 tools, and requires a significant investment in time and other resources for data logistics 407 and pipeline development. Major challenges here included the automated processing of 408 large meteorological datasets, efficient application of hundreds of phenological models, 409 and stable, consistently updated, and easy to understand dissemination of forecasts. By 410 discussing how we addressed these challenges, and making our code publicly available, 411 we hope to provide guidance for others developing ecological forecasting systems. 412 mutli-dimensional data and in our case are 300 times smaller than the csv files (50 370 MB/forecast). 371 It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint mutli-dimensional data and in our case are 300 times smaller than the csv files (50 370 MB/forecast). 371 USA-NPN data are available in near 380 real-time after they are submitted by volunteers, thus there is opportunity for data 381 assimilation of phenology observations. Making new forecasts with the latest 382 information not only on the current state of the climate, but also on the current state of 383 the plants themselves would likely be very informative (Luo et al. 2011, Dietze 2017). 384 For example, if a species is leafing out sooner than expected in one area it is likely that 385 it will also leaf out sooner than expected in nearby regions. This type of data 386 assimilation is important for making accurate forecasts in other disciplines including 387 meteorology (Bauer et al. 2015, Carrassi et al. 2018). However, process based plant 388 phenology models were not designed with data assimilation in mind (Chuine et al. 389 2013). Clark et al. (2014) built a bayesian hierarchical phenology model of budburst 390 which incorporates the discrete observations of phenology data. This could serve as a 391 starting point for a phenology forecasting model that incorporates data assimilation and 392 allows species with relatively few observations to borrow strength from species with a 393 large number of observations. The model from Clark et al. (2014) also incorporates all 394 2013). Clark et al. (2014) built a bayesian hierarchical phenology model of budburst 390 which incorporates the discrete observations of phenology data. This could serve as a 391 starting point for a phenology forecasting model that incorporates data assimilation and 392 allows species with relatively few observations to borrow strength from species with a 393 large number of observations. The model from Clark et al. (2014) also incorporates all 394 stages of the bud development process into a continuous latent state, thus there is also 395 potential for forecasting the current phenological state of plants, instead of just the 396 16 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. Acknowledgments 413 This research was supported by the Gordon and Betty Moore Foundation’s Data-Driven 414 Discovery Initiative through Grant GBMF4563 to E.P. White. We thank the USA 415 National Phenology Network and the many participants who contribute to its Nature’s 416 Notebook program. 417 17 17 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint References 418 Basler, D. 2016. Evaluating phenological models for the prediction of leaf-out dates in 419 six temperate tree species across central europe. Agricultural and Forest Meteorology 420 217:10–21. 421 Bauer, P., A. Thorpe, and G. Brunet. 2015. The quiet revolution of numerical weather 422 prediction. Nature 525:47–55. 423 Biederman, L., D. Anderson, N. Sather, J. Pearson, J. Beckman, and J. Prekker. 2018. 424 Using phenological monitoring in situ and historical records to determine environmental 425 triggers for emergence and anthesis in the rare orchid Platanthera praeclara Sheviak & 426 Bowles. Global Ecology and Conservation 16:e00461. 427 Bryan, J. 2018. Excuse me, do you have a moment to talk about version control? The 428 American Statistician 72:20–27. 429 Carrassi, A., M. Bocquet, L. Bertino, and G. Evensen. 2018. Data assimilation in the 430 geosciences: An overview of methods, issues, and perspectives. Wiley Interdisciplinary 431 Reviews: Climate Change 9:e535. 432 Carrillo, C. M., T. R. Ault, and D. S. Wilks. 2018. Spring onset predictability in the 433 north american multimodel ensemble. Journal of Geophysical Research: Atmospheres 434 123:5913–5926. 435 Chen, Y., J. T. Randerson, D. C. Morton, R. S. DeFries, G. J. Collatz, P. S. Kasibhatla, 436 L. Giglio, Y. Jin, and M. E. Marlier. 2011. Forecasting fire season severity in south 437 america using sea surface temperature anomalies. Science 334:787–791. 438 Chuine, I., and J. Régnière. 2017. Process-based models of phenology for plants and 439 animals. Annual Review of Ecology, Evolution, and Systematics 48:159–182. 440 Chuine, I., I. G. de Cortazar-Atauri, K. Kramer, and H. Hänninen. 2013. Plant 441 development models. Pages 275–293 in M. D. Schwartz, editor. Phenology: An 442 18 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint integrative environmental science. Springer Netherlands, Dordrecht. 443 Clark, J. S., C. Salk, J. Melillo, and J. Mohan. 2014. Dormann, C. F., J. M. Calabrese, G. Guillera-Arroita, E. Matechou, V. Bahn, K. Barto´n, 466 C. M. Beale, S. Ciuti, J. Elith, K. Gerstner, J. Guelat, P. Keil, J. J. Lahoz-Monfort, L. J. 467 C. M. Beale, S. Ciuti, J. Elith, K. Gerstner, J. Guelat, P. Keil, J. J. Lahoz-Monfort, L. J. 467 References 418 Tree phenology responses to 444 winter chilling, spring warming, at north and south range limits. Functional Ecology 445 28:1344–1355. 446 Cook, B. I., A. Terando, and A. Steiner. 2010. Ecological forecasting under climatic 447 data uncertainty: A case study in phenological modeling. Environmental Research 448 Letters 5:044014. 449 Dalcin, L. D., R. R. Paz, P. A. Kler, and A. Cosimo. 2011. Parallel distributed 450 computing using python. Advances in Water Resources 34:1124–1139. 451 Dask Development Team. 2016. Dask: Library for dynamic task scheduling. 452 Dask Development Team. 2016. Dask: Library for dynamic task scheduling. 452 Denny, E. G., K. L. Gerst, A. J. Miller-Rushing, G. L. Tierney, T. M. Crimmins, C. A. F. 453 Enquist, P. Guertin, A. H. Rosemartin, M. D. Schwartz, K. A. Thomas, and J. F. Weltzin. 454 2014. Standardized phenology monitoring methods to track plant and animal activity 455 for science and resource management applications. International Journal of 456 Biometeorology 58:591–601. 457 Dietze, M. C. 2017. Prediction in ecology: A first-principles framework. Ecological 458 Applications 27:2048–2060. 459 Dietze, M. C., A. Fox, L. M. Beck-Johnson, J. L. Betancourt, M. B. Hooten, C. S 0 Dietze, M. C., A. Fox, L. M. Beck-Johnson, J. L. Betancourt, M. B. Hooten, C. S. 460 Jarnevich, T. H. Keitt, M. A. Kenney, C. M. Laney, L. G. Larsen, H. W. Loescher, C. K. 461 Lunch, B. C. Pijanowski, J. T. Randerson, E. K. Read, A. T. Tredennick, R. Vargas, K. 462 C. Weathers, and E. P. White. 2018. Iterative near-term ecological forecasting: Needs, 463 opportunities, and challenges. Proceedings of the National Academy of Sciences 464 115:1424–1432. 465 Dormann, C. F., J. M. Calabrese, G. Guillera-Arroita, E. Matechou, V. Bahn, K. Barto´n, 466 C. M. Beale, S. Ciuti, J. Elith, K. Gerstner, J. Guelat, P. Keil, J. J. Lahoz-Monfort, L. J. 467 19 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. References 418 ; https://doi.org/10.1101/634568 doi: bioRxiv preprint Pollock, B. Reineking, D. R. Roberts, B. Schröder, W. Thuiller, D. I. Warton, B. A. 468 Wintle, S. N. Wood, R. O. Wüest, and F. Hartig. 2018. Model averaging in ecology: A 469 review of bayesian, information-theoretic, and tactical approaches for predictive 470 inference. Ecological Monographs 0:1–20. 471 Grolemund, G., and H. Wickham. 2011. Dates and times made easy with {lubridate}. 472 Journal of Statistical Software 40:1–25. 473 Hart, E. M., and K. Bell. 2015. Prism: Download data from the oregon prism project. 474 http://github.com/ropensci/prism. 475 Hijmans, R. J. 2017. Raster: Geographic data analysis and modeling. r package version 476 2.6-7. https://CRAN.R-project.org/package=raster. 477 Hoyer, S., and J. J. Hamman. 2017. Xarray: N-d labeled arrays and datasets in python. 478 Journal of Open Research Software 5. 479 Jones, E., T. Oliphant, P. Peterson, and Others. 2001. SciPy: Open source scientific 480 tools for python. http://www.scipy.org. 481 Luo, Y., K. Ogle, C. Tucker, S. Fei, C. Gao, S. LaDeau, J. S. Clark, and D. S. Schimel. 482 2011. Ecological forecasting and data assimilation in a data-rich era. Ecological 483 Applications 21:1429–1442. 484 McKinney, W. 2010. Data structures for statistical computing in python. Pages 51–56 in 485 Proceedings of the 9th python in science conference. SciPy, Austin, Texas, USA. 486 McKinney, W. 2010. Data structures for statistical computing in python. Pages 51–56 in 485 Proceedings of the 9th python in science conference. SciPy, Austin, Texas, USA. 486 Melaas, E. K., M. A. Friedl, and A. D. Richardson. 2016. Multiscale modeling of 487 spring phenology across Deciduous Forests in the Eastern United States. Global Change 488 Biology 22:792–805. 489 Melaas, E. K., M. A. Friedl, and A. D. Richardson. 2016. Multiscale modeling of 487 spring phenology across Deciduous Forests in the Eastern United States. Global Change 488 Biology 22:792–805. 489 Ogilvie, J. E., S. R. Griffin, Z. J. Gezon, B. D. Inouye, N. Underwood, D. W. Inouye, 490 and R. E. Irwin. 2017. Interannual bumble bee abundance is driven by indirect climate 491 20 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint effects on floral resource phenology. Ecology Letters 20:1507–1515. 492 Oliphant, T. 2006. References 418 CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint Schaefer, H. Tian, R. Vargas, H. Verbeeck, J. Xiao, and Y. Xue. 2012. Terrestrial 517 biosphere models need better representation of vegetation phenology: Results from the 518 north american carbon program site synthesis. Global Change Biology 18:566–584. 519 Schaefer, H. Tian, R. Vargas, H. Verbeeck, J. Xiao, and Y. Xue. 2012. Terrestrial 517 biosphere models need better representation of vegetation phenology: Results from the 518 north american carbon program site synthesis. Global Change Biology 18:566–584. 519 Saha, S., S. Moorthi, H.-L. Pan, X. Wu, J. Wang, S. Nadiga, P. Tripp, R. Kistler, J. 520 Woollen, D. Behringer, H. Liu, D. Stokes, R. Grumbine, G. Gayno, J. Wang, Y.-T. Hou, 521 H.-y. Chuang, H.-M. H. Juang, J. Sela, M. Iredell, R. Treadon, D. Kleist, P. Van Delst, 522 D. Keyser, J. Derber, M. Ek, J. Meng, H. Wei, R. Yang, S. Lord, H. van den Dool, A. 523 Kumar, W. Wang, C. Long, M. Chelliah, Y. Xue, B. Huang, J.-K. Schemm, W. 524 Ebisuzaki, R. Lin, P. Xie, M. Chen, S. Zhou, W. Higgins, C.-Z. Zou, Q. Liu, Y. Chen, Y. 525 Han, L. Cucurull, R. W. Reynolds, G. Rutledge, and M. Goldberg. 2010. The ncep 526 climate forecast system reanalysis. Bulletin of the American Meteorological Society 527 91:1015–1058. 528 Saha, S., S. Moorthi, H.-L. Pan, X. Wu, J. Wang, S. Nadiga, P. Tripp, R. Kistler, J. 520 Woollen, D. Behringer, H. Liu, D. Stokes, R. Grumbine, G. Gayno, J. Wang, Y.-T. Hou, 521 H.-y. Chuang, H.-M. H. Juang, J. Sela, M. Iredell, R. Treadon, D. Kleist, P. Van Delst, 522 D. Keyser, J. Derber, M. Ek, J. Meng, H. Wei, R. Yang, S. Lord, H. van den Dool, A. 523 Kumar, W. Wang, C. Long, M. Chelliah, Y. Xue, B. Huang, J.-K. Schemm, W. 524 Ebisuzaki, R. Lin, P. Xie, M. Chen, S. Zhou, W. Higgins, C.-Z. Zou, Q. Liu, Y. Chen, Y. 525 Han, L. Cucurull, R. W. Reynolds, G. Rutledge, and M. Goldberg. 2010. The ncep 526 climate forecast system reanalysis. Bulletin of the American Meteorological Society 527 91:1015–1058. 528 Saha, S., S. Moorthi, X. Wu, J. Wang, S. References 418 A guide to numpy. USA: Trelgol Publishing; Trelgol Publishing, 493 Provo, UT. 494 Pebesma, E. J., and R. S. Bivand. 2005. Classes and methods for spatial data in {R}. R 495 News 5:9–13. 496 Petchey, O. L., M. Pontarp, T. M. Massie, S. Kéfi, A. Ozgul, M. Weilenmann, G. M. 497 Palamara, F. Altermatt, B. Matthews, J. M. Levine, D. Z. Childs, B. J. McGill, M. E. 498 Schaepman, B. Schmid, P. Spaak, A. P. Beckerman, F. Pennekamp, and I. S. Pearse. 499 2015. The ecological forecast horizon, and examples of its uses and determinants. 500 Ecology Letters 18:597–611. 501 Pierce, D. 2017. Ncdf4: Interface to unidata netCDF (version 4 or earlier) format data 502 files}. 503 Prevéy, J., L. Parker, C. Harrington, C. Lamb, and M. Proctor. In revision. Climate 504 change shifts the habitat suitability and phenology of black huckleberry. Agricultural 505 and Forest Meteorology. 506 PRISM Climate Group. 2004. Oregon state university. http://prism.oregonstate.edu; 507 Oregon State University. 508 Python Software Foundation. 2003. Python language reference manual, version 3.6. 509 http://www.python.org. 510 Ram, K. 2013. Git can facilitate greater reproducibility and increased transparency in 511 science. Source Code for Biology and Medicine 8:7. 512 Richardson, A. D., R. S. Anderson, M. A. Arain, A. G. Barr, G. Bohrer, G. Chen, J. M. 513 Chen, P. Ciais, K. J. Davis, A. R. Desai, M. C. Dietze, D. Dragoni, S. R. Garrity, C. M. 514 Gough, R. Grant, D. Y. Hollinger, H. A. Margolis, H. McCaughey, M. Migliavacca, R. 515 K. Monson, J. W. Munger, B. Poulter, B. M. Raczka, D. M. Ricciuto, A. K. Sahoo, K. 516 Richardson, A. D., R. S. Anderson, M. A. Arain, A. G. Barr, G. Bohrer, G. Chen, J. M. 513 Chen, P. Ciais, K. J. Davis, A. R. Desai, M. C. Dietze, D. Dragoni, S. R. Garrity, C. M. 514 Gough, R. Grant, D. Y. Hollinger, H. A. Margolis, H. McCaughey, M. Migliavacca, R. 515 K. Monson, J. W. Munger, B. Poulter, B. M. Raczka, D. M. Ricciuto, A. K. Sahoo, K. 516 21 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . References 418 Nadiga, P. Tripp, D. Behringer, Y.-T. Hou, 529 H.-y. Chuang, M. Iredell, M. Ek, J. Meng, R. Yang, M. P. Mendez, H. van den Dool, Q. 530 Zhang, W. Wang, M. Chen, and E. Becker. 2014. The ncep climate forecast system 531 version 2. Journal of Climate 27:2185–2208. 532 Schwartz, M. D., T. R. Ault, and J. L. Betancourt. 2013. Spring onset variations and 533 trends in the continental United States: past and regional assessment using 534 temperature-based indices. International Journal of Climatology 33:2917–2922. 535 Stoner, A. M. K., K. Hayhoe, X. Yang, and D. J. Wuebbles. 2013. An asynchronous 536 regional regression model for statistical downscaling of daily climate variables. 537 I t ti l J l f Cli t l 33 2473 2494 regional regression model for statistical downscaling of daily climate variables. International Journal of Climatology 33:2473–2494. 538 Taylor, S. D. 2018. PyPhenology: A python framework for plant phenology modelling. 539 Journal of Open Source Software 3:827. 540 Taylor, S. D., J. M. Meiners, K. Riemer, M. C. Orr, and E. P. White. 2019. Comparison 541 of large-scale citizen science data and long-term study data for phenology modeling. 542 22 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint Ecology 100:e02568. 543 US Geological Survey. 1999. Digital representation of “Atlas of United States Trees” by 544 Elbert L. Little, Jr. US Geological Survey, Lakewood, CO. 545 USA National Phenology Network. 2018. Plant and animal phenology data. data type: 546 Individual phenometrics. 01/01/2008-12/31/2017 for region: 49.9375°, -66.4791667° 547 (ur); 24.0625°, -125.0208333° (ll). USA-NPN, Tucson, Arizona, USA. Data set 548 accessed 07/08/2018 at http://doi.org/10.5066/F78S4N1V. 549 USA National Phenology Network. 2019. Plant and animal phenology data. data type: 550 Individual phenometrics. 01/01/2019-05/08/2019 for region: 49.9375°, -66.4791667° 551 (ur); 24.0625°, -125.0208333° (ll). USA-NPN, Tucson, Arizona, USA. Data set 552 accessed 05/09/2019 at http://doi.org/10.5066/F78S4N1V. 553 USA National Phenology Network. 2019. Wickham, H., and L. Henry. 2018. Tidyr: Easily tidy data with ’spread()’ and ’gather()’ 566 Wickham, H., and L. Henry. 2018. Tidyr: Easily tidy data with ’spread()’ and ’ga 6 References 418 Plant and animal phenology data. data type: 550 Individual phenometrics. 01/01/2019-05/08/2019 for region: 49.9375°, -66.4791667° 551 (ur); 24.0625°, -125.0208333° (ll). USA-NPN, Tucson, Arizona, USA. Data set 552 accessed 05/09/2019 at http://doi.org/10.5066/F78S4N1V. 553 Van Doren, B. M., and K. G. Horton. 2018. A continental system for forecasting bird 554 migration. Science 361:1115–1118. 555 Weisheimer, A., and T. N. Palmer. 2014. On the reliability of seasonal climate forecasts. 556 Journal of The Royal Society Interface 11:20131162–20131162. 557 Welch, H., E. L. Hazen, S. J. Bograd, M. G. Jacox, S. Brodie, D. Robinson, K. L. Scales, 558 L. Dewitt, and R. Lewison. 2019. Practical considerations for operationalizing dynamic 559 management tools. Journal of Applied Ecology 56:459–469. 560 White, E. P., G. M. Yenni, S. D. Taylor, E. M. Christensen, E. K. Bledsoe, J. L. Simonis, 561 and S. K. Morgan Ernest. 2018. Developing an automated iterative near-term 562 and S. K. Morgan Ernest. 2018. Developing an automated iterative near-term 2 forecasting system for an ecological study. Methods in Ecology and Evolution. 563 Wickham, H. 2016. Ggplot2: Elegant graphics for data analysis. Springer-Verlag New 564 York. 565 Wickham, H., and L. Henry. 2018. Tidyr: Easily tidy data with ’spread()’ and ’gather()’ 566 23 23 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint functions. 567 functions. 567 Yenni, G. M., E. M. Christensen, E. K. Bledsoe, S. R. Supp, R. M. Diaz, E. P. White, 568 and S. K. M. Ernest. 2019. Developing a modern data workflow for regularly updated 569 data. PLOS Biology 17:e3000125. 570 Yenni, G. M., E. M. Christensen, E. K. Bledsoe, S. R. Supp, R. M. Diaz, E. P. White, 568 and S. K. M. Ernest. 2019. Developing a modern data workflow for regularly updated 569 data. PLOS Biology 17:e3000125. 570 n, K., J. Hsiao, M.-P. Jung, I.-T. Choi, D. M. Glenn, K.-M. Shim, and S.-H. Kim. 2017. Can a multi-model ensemble improve phenology predictions for climate change 572 studies? Ecological Modelling 362:54–64. 573 24 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint Figure Legends 574 It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint Figure Legends 574 Figure 1: Flowchart of initial model building and automated pipeline steps. Letters 575 indicate the associate steps discussed in the main text. 576 Figure 1: Flowchart of initial model building and automated pipeline steps. Letters 575 indicate the associate steps discussed in the main text. 576 Figure 2: Screenshot of the forecast presentation website 577 (http://phenology.naturecast.org) showing the forecast for the leaf out of Acer 578 saccharinum in Spring, 2019, issued on Feburary 21, 2019. The maps represent the 579 predicted date of leaf out (A), the anomaly compared to prior years (B), and the 95% 580 confidence interval (C). In the upper right is the interface for selecting different species, 581 phenophases, or forecast issue dates via drop down menus (D). 582 Figure 3: Locations of phenological events which have occurred between Jan. 1, 2019 583 and May 5, 2019 obtained from the USA National Phenology Network (blue circles), 584 and all sampling locations in the same dataset (red points). Four individual plants are 585 highlighted, with numbers indicating the USA National Phenology Network database 586 ID. The solid line indicates the predicted event date as well as the 95% confidence 587 interval for a specified forecast issue date, and the dashed line indicates the observed 588 event date. The x-axis corresponds to the date a forecast was issued, while the y-axis is 589 the date flowering or budburst was predicted to occur. For example: on Jan. 1, 2019 the 590 P. tremuloides plant was forecast to flower sometime between March, 29 and April, 24 591 (solid lines). The actual flowering date was March 18 (dashed line). 592 Figure 4: The root mean square error and the average uncertainty of forecasts issued 593 between Dec. 2, 2018 and May 5, 2019 for 1581 phenological events representing 65 594 species. 595 Figure 4: The root mean square error and the average uncertainty of forecasts issued 593 between Dec. 2, 2018 and May 5, 2019 for 1581 phenological events representing 65 594 species. 595 Figure 5: Distribution of absolute errors (prediction - observed) for 1581 phenological 596 events for 11 selected issue dates. Labels indicate the mean absolute error (MAE). 597 25 . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint Figures 598 Figure 1 599 599 26 . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint 600 Figure 2 27 27 . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint 602 Figure 3 603 28 28 . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint 604 Figure 4 605 604 Figure 4 605 29 . CC-BY 4.0 International license a ertified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: ioRxiv preprint . CC-BY 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. Figures 598 It is made available under The copyright holder for this preprint (which was not this version posted October 7, 2019. ; https://doi.org/10.1101/634568 doi: bioRxiv preprint 606 Figure 5 607 30
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Towards microalga-based superfoods: heterologous expression of zeolin in Chlamydomonas reinhardtii
Frontiers in plant science
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OPEN ACCESS Plant Sci. 14:1184064. doi: 10.3389/fpls.2023.1184064 © 2023 Perozeni, Pivato, Angelini, Maricchiolo, Pompa and Ballottari. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. KEYWORDS Chlamydomonas, protein expression, synthetic biology, microalgae, zein, phaseolin © 2023 Perozeni, Pivato, Angelini, Maricchiolo, Pompa and Ballottari. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Chlamydomonas, protein expression, synthetic biology, microalgae, zein, phaseolin TYPE Original Research PUBLISHED 09 May 2023 DOI 10.3389/fpls.2023.1184064 TYPE Original Research PUBLISHED 09 May 2023 DOI 10.3389/fpls.2023.1184064 KEYWORDS OPEN ACCESS EDITED BY Cyprien Verseux, University of Bremen, Germany REVIEWED BY Pannaga Pavan Jutur, International Centre for Genetic Engineering and Biotechnology, India Edmundo Lozoya-Gloria, Unidad Irapuato (CINVESTAV), Mexico *CORRESPONDENCE Matteo Ballottari matteo.ballottari@univr.it RECEIVED 10 March 2023 ACCEPTED 17 April 2023 PUBLISHED 09 May 2023 CITATION Perozeni F, Pivato M, Angelini M, Maricchiolo E, Pompa A and Ballottari M (2023) Towards microalga-based superfoods: heterologous expression of zeolin in Chlamydomonas reinhardtii. Front. Plant Sci. 14:1184064. doi: 10.3389/fpls.2023.1184064 REVIEWED BY Pannaga Pavan Jutur, International Centre for Genetic Engineering and Biotechnology, India Edmundo Lozoya-Gloria, Unidad Irapuato (CINVESTAV), Mexico Federico Perozeni 1, Matteo Pivato 1, Margherita Angelini 1, Elisa Maricchiolo 2, Andrea Pompa 2 and Matteo Ballottari 1* 1Dipartimento di Biotecnologie, Università degli Studi di Verona, Verona, Italy, 2Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino, Urbino, Italy Microalgae are unicellular photosynthetic organisms that can be grown in artificial systems to capture CO2, release oxygen, use nitrogen- and phosphorus-rich wastes, and produce biomass and bioproducts of interest including edible biomass for space exploration. In the present study, we report a metabolic engineering strategy for the green alga Chlamydomonas reinhardtii to produce high-value proteins for nutritional purposes. Chlamydomonas reinhardtii is a species approved by the U.S. Food and Drug Administration (FDA) for human consumption, and its consumption has been reported to improve gastrointestinal health in both murine models and humans. By utilizing the biotechnological tools available for this green alga, we introduced a synthetic gene encoding a chimeric protein, zeolin, obtained by merging the g- zein and phaseolin proteins, in the algal genome. Zein and phaseolin are major seed storage proteins of maize (Zea mays) and bean (Phaseolus vulgaris) that accumulate in the endoplasmic reticulum (ER) and storage vacuoles, respectively. Seed storage proteins have unbalanced amino acid content, and for this reason, need to be complemented with each other in the diet. The chimeric recombinant zeolin protein represents an amino acid storage strategy with a balanced amino acid profile. Zeolin protein was thus efficiently expressed in Chlamydomonas reinhardtii; thus, we obtained strains that accumulate this recombinant protein in the endoplasmic reticulum, reaching a concentration up to 5.5 fg cell-1, or secrete it in the growth medium, with a titer value up to 82 µg/L, enabling the production of microalga-based super-food. CITATION Perozeni F, Pivato M, Angelini M, Maricchiolo E, Pompa A and Ballottari M (2023) Towards microalga-based superfoods: heterologous expression of zeolin in Chlamydomonas reinhardtii. Front. 1 Introduction Zein are divided into four subfamilies based on their solubility and amino acid composition: a (22 and 19 kDa), b (15-kDa), g (50 kDa, 27 kDa, and 16 kDa), and d (18 kDa and 10 kDa) zeins (Holding, 2014), and these proteins are found in protein bodies (PBs) inside the endoplasmic reticulum (ER) (Lending and Larkins, 1989), accounting for more than 60% of the total stored proteins in the endosperm of maize kernels (Llop-Tous et al., 2010; Holding, 2014; Khan et al., 2019). Numerous studies have suggested that the packaging of zein and non-zein proteins into PBs has a peculiar role in maize endosperm development, influencing kernel properties (e.g., texture, functionality, and protein quality) (Guo et al., 2013; Holding, 2014). Due to reciprocal limitations in terms of amino acid composition, phaseolin and g-zein proteins were fused together to create a new recombinant protein, zeolin, characterized by a balanced amino acid content. The chimeric zeolin protein contained the entire phaseolin sequence, including the signal peptide, followed by the unstructured 15 amino acid linker (GGGGS)3 and 89 amino acids of mature g-zein (27 kDa), starting from the fifth residue after the g-zein signal peptide. The total number of amino acids was 525, including 24 residues of the N-terminal phaseolin signal peptide (Mainieri et al., 2004). When expressed in Nicotiana tabacum leaves, zeolin successfully accumulated, forming PBs in the ER (Mainieri et al., 2004). Zeolin is insoluble in the absence of reducing agents, whereas, phaseolin can be easily solubilized in the absence of reducing agents. This suggests that the protein interactions are different. Insolubility is also caused by disulfide bonds, a characteristic of g-zein (Vitale et al., 1982) which are transferred to zeolin. It was also observed that zein has a dominant effect on phaseolin intracellular traffic: the zein fragment prevents zeolin from being delivered to the vacuole and ER retention can be conferred to another protein by g-zein domains (Holding, 2014). nutrient recovery from wastes, and limited spaces. With increasing population, food demands, and desire for healthier lifestyles, alternative sources of functional foods are important for space exploration and terrestrial applications. In this context, photosynthetic microalgae cultivation could be an interesting opportunity because of their reduced water footprint compared to crops and the possibility of growing in different environmental conditions using wastewater as a nitrogen and phosphorous source. 1 Introduction The green alga Chlamydomonas reinhardtii is a model organism for microalgae and is one of the most used species for laboratory research purposes (fundamental and applied research) because it has fast growth, does not require expensive supplements or an elaborate system for cultivation, is capable of sexual reproduction, and is easily engineered by genetic manipulation of nuclear, chloroplast, and mitochondrial genomes. The rapid advancements in recombinant protein production in this host suggest that in the near future, it could have an important role in the production of compounds of interest for the pharmaceutical and nutraceutical industries (Masi et al., 2023). In addition, it has recently received the Generally Recognized As Safe (GRAS) certification from the FDA for food applications. Recently, C. reinhardtii was reported having a positive effect for gastrointestinal function when used as functional food ingredient in both murine and human models (Fields et al., 2020). Metabolic engineering approaches have been proposed to improve carbon storage in lipids; however, little effort has been made to improve carbon storage in proteins in C. reinhardtii. In this study, heterologous expression of zeolin was obtained in the green alga C. reinhardtii which could play an integral role in paving the way for the production of a microalgal superfood source. Zeolin gene, previously expressed in tobacco leaves (Mainieri et al., 2004), was here completely redesigned in order to optimize its expression in C. reinhardtii. Four different vectors were designed to express and accumulate the targeted or retained protein of interest in the endoplasmic reticulum of C. reinhardtii. The different expression vectors were characterized for having specific sequences at N and/or C terminus to achieve ER localization of zeolin: phaseolin or BIP signal peptide was used to target the protein inside the ER, while HDEL sequence was added as an ER retention sequence. Seed storage proteins accumulate at high levels in seeds as nitrogen, carbon, and sulfur reserves and are then used during seed germination. They do not have any enzymatic function and accumulate in the protein bodies (Krishnan and Coe, 2001). Seed storage proteins of legumes and cereals are two major sources of proteins for humans. From a nutritional perspective, they complement each other: the storage proteins from legumes are poor in sulfur amino acids, and those from cereals are poor in lysine and tryptophan. 1 Introduction Food production is one of the key challenges faced in supporting life in extra-terrestrial environments for space exploration. Several constraints are present when planning food production in spacecraft or in enclosed environments under harsh conditions, such as limited water and oxygen on the Moon or Mars, cosmic radiation, requirements for Frontiers in Plant Science 01 frontiersin.org Perozeni et al. 10.3389/fpls.2023.1184064 nutrient recovery from wastes, and limited spaces. With increasing population, food demands, and desire for healthier lifestyles, alternative sources of functional foods are important for space exploration and terrestrial applications. In this context, photosynthetic microalgae cultivation could be an interesting opportunity because of their reduced water footprint compared to crops and the possibility of growing in different environmental conditions using wastewater as a nitrogen and phosphorous source. The presence of carbon concentration mechanisms in microalgae and the absence of non-photosynthetic tissue, as in the case of vascular plants, allow microalgae to efficiently assimilate CO2, releasing oxygen as a byproduct of the photosynthetic process (Onyeaka et al., 2021). Moreover, the biomass produced by microalgae has considerable nutritional value and contains relatively high concentrations of proteins, polyunsaturated fatty acids, polysaccharides, pigments, vitamins, minerals, phenolic compounds and sterols (Camacho et al., 2019). Microalgae biomass has also been reported to be enriched in copper and iron, potentially matching 21% and 11% of the Required Daily Allowance (RDA) for these metals (Koyande et al., 2019). Therefore, microalgae could be considered to enhance CO2 sequestration, recover nutrients from waste, and produce edible biomass, with several species already approved as novel foods by the European Food Safety Association (EFSA) and the U.S. Food and Drug Administration (FDA) (Torres-Tiji et al., 2020; Mendes et al., 2022). 2016; Khan et al., 2019). Phaseolin, a glycoprotein belonging to the 7S vicilin class, is the major seed storage protein in the common bean. Each phaseolin polypeptide is cotranslationally glycosylated in the endoplasmic reticulum (ER) lumen (De La Fuente et al., 2012). being a trimeric high-mannose glycosylated protein of approximately 150 kDa, containing almost identical monomers with a molecular mass ranging from 45 to 51 kDa and isoelectric points of 5.6 to 5.8 (Sathe, 2016). Maize endosperm zein protein belongs to the prolamin family, which are the most abundant type of proteins stored in cereal seeds such as wheat, maize, sorghum, rice, and barley. Frontiers in Plant Science 2.2 Construction of transformation vectors, transformation, and mutant screening The zeolin-expressing vectors for C. reinhardtii transformation were prepared as follows. Starting from the amino acid sequence of zeolin (Supplementary Figure S1), the nucleotide sequence was optimized in silico, considering C. reinhardtii codon usage using Optimizer online tool (Puigbò et al., 2007). The mVenus (YFP) fluorescent coding sequence was added at the C-terminus of zeolin as an expression reporter for the selection of expression lines. A GSG- linker was also added between zeolin and YFP to allow the correct folding of the two proteins. To enhance protein expression and accumulation, RuBisCO introns were added to the coding sequence. Three rbcs2 intron 1 copies were inserted into the zeolin sequence, and rbcs2 intron 2 was added to the mVenus sequence according to the protocol designed by Baier et al. (Baier et al., 2018b). The optimized synthetic zeolin sequence is shown in Supplementary Figure S2. Additional peptides were then added at the N- or C-terminus to drive intracellular localization of zeolin: N terminus of the C. reinhardtii BiP1 protein (A8I7T8, herein named BiP) was used to drive ER localization, while HDEL ER retention sequence was added at the C-terminus (Rasala et al., 2014) as reported in the schematic diagram of the different vectors used in Figure 1. 2.1 Algal strains and culture conditions C. reinhardtii UVM4 (UV-mediated mutant 4) (Neupert et al., 2009) strain was used as the background for all the transformations. Algal cells were cultivated under mixotrophic conditions using Tris- acetate-phosphate (TAP) (Kropat et al., 2011)in shaker flasks at 25°C and 100–150 mmol photons m−2 s−1 of continuous white light, unless otherwise stated. Cultivation on solidified agar plates was performed under the same conditions. The different vectors were then used to transform the microalga C. reinhardtii; the UVM4 mutant strain, previously selected for efficient heterologous protein transformation, was adopted as the background (Neupert et al., 2009). Stable nuclear transformation was performed by glass beads agitation as previously described (Kindle, 1990). Transformants were selected on TAP agar plates supplied with 12 mg/mL of paromomycin for 6–7 days at a light intensity of 200 mmol photons m−2 s−1. Antibiotic-resistant colonies were cultivated in 96–well microtiter plates at a light intensity of 200 mmol photons m−2 s−1 until they were sufficiently dense. YFP fluorescence was measured using an Infinite PRO 200 plate reader (TECAN, Switzerland) with excitation at 509 ± 4.5 nm and emission at 540 ± 10 nm. Signals were normalized to 720 nm absorbance (cell scattering) to determine the highest expressing lines (Pivato et al., 2021). 2 Materials and methods 2.1 Algal strains and culture conditions 2 Materials and methods The synthesized nucleotide sequence (Thermo Scientific, USA) was BamHI-BglII cloned into a pOpt2 modified vector. This vector was modified from the original pOpt2 (Lauersen et al., 2015) containing a 10x H-tag instead of S-tag. Conversely, BIP sequence was amplified with specific primer from pCM0-056 vector included in MocloToolkit (Crozet et al., 2018) and NdeI-BamHI cloned into pOpt2_Zeolin_YFP_Paro vector while the HDEL sequence was inserted into pOpt2_Zeolin_YFP_Paro and pOpt2_BIP_Zeo lin_YFP_Paro by amplification of YFP with overhang primers and subsequent BglII-EcoRI cloning. 1 Introduction Among the different storage proteins, phaseolins and zeins have been extensively studied as the main seed storage proteins in legumes and cereals, respectively (Suárez-Martı́nez et al., 02 frontiersin.org Perozeni et al. 10.3389/fpls.2023.1184064 10.3389/fpls.2023.1184064 2.3 Total protein extraction, SDS-PAGE, and western blotting Total cells, exhaust growth media, and purified proteins were separated using SDS-PAGE (Laemmli, 1970). Separated proteins were stained using Coomassie Brilliant Blue solution or analyzed by immunodetection using an anti-GFP (Green Fluorescent Protein) antibody (Agrisera, Sweden). Protein accumulation over time in cells or supernatants was assessed by loading the same number of FIGURE 1 Zeolin expression vectors. Schematic overview of all expression vectors used in this work. All expression cassettes use the HSP70A-Rbcs2 hybrid promoter (containing rbcs2 intron 1 and its 5′ UTR), and coding sequence are in frame with mVenus (YFP) sequence to generate a fusion protein. BIP1 target peptide (blue) directs proteins into ER. HDEL sequence (red) is used to retain proteins into ER. All proteins expressed carry a 10x H-tag at the C-terminus (purple). Intron 1 (i1) and 2 (i2) of rbcs2 are depicted in grey color. FIGURE 1 Zeolin expression vectors. Schematic overview of all expression vectors used in this work. All expression cassettes use the HSP70A-Rbcs2 hybrid promoter (containing rbcs2 intron 1 and its 5′ UTR), and coding sequence are in frame with mVenus (YFP) sequence to generate a fusion protein. BIP1 target peptide (blue) directs proteins into ER. HDEL sequence (red) is used to retain proteins into ER. All proteins expressed carry a 10x H-tag at the C-terminus (purple). Intron 1 (i1) and 2 (i2) of rbcs2 are depicted in grey color. 03 Frontiers in Plant Science frontiersin.org Perozeni et al. 10.3389/fpls.2023.1184064 10.3389/fpls.2023.1184064 reported in detailed in the Materials and Methods section. Previous work demonstrated that the highest zeolin accumulation in tobacco leaves was obtained when the protein accumulated in the ER while chloroplast localization was not efficient; therefore, chloroplast localization was not considered in this study. Instead, ER was targeted for intracellular zeolin localization. The zeolin sequence used in this study included a phaseolin N-terminus signal peptide, which was reported in tobacco to drive protein accumulation in the ER (expression vector Zeolin_YFP). To ensure a higher probability of the protein being targeted into the ER, a vector with an N-terminus signal peptide of the HSP70 molecular chaperone BiP (BiP1) from C. reinhardtii (Rasala et al., 2014) was also prepared (expression vector BiP_Zeolin_YFP). Frontiers in Plant Science 2.3 Total protein extraction, SDS-PAGE, and western blotting Finally, because successful zeolin protein expression in Nicotiana tabacum was obtained when zeolin was retained in the ER-forming protein bodies, expression vectors containing an ER retention sequence at the C-terminus of zeolin were obtained using the HDEL sequence previously reported to improve the retention of proteins in this compartment in C. reinhardtii (Rasala et al., 2014). HDEL sequences were added at the C-terminus of zeolin either in presence (BiP_Zeolin_YFP_Erseq expression vector) or absence (Zeolin_YFP_Erseq expression vector) of BiP signal sequence at N-terminus. A scheme of the different vectors adopted in this study is shown in Figure 1. The different vectors were then used to transform the microalga C. reinhardtii; the UVM4 mutant strain, previously selected for efficient heterologous protein transformation, was adopted as the background (Neupert et al., 2009). cells and the equivalent volume of growth medium obtained after centrifugation to remove cells followed by concentration using membrane spin columns (GE Healthcare, USA). The cell density was measured using Countess 3 (Thermo Scientific, USA). Protein quantification was performed by densitometric analysis using ImageLab software and recombinant YFP produced in E.coli as standard. 2.4 Zeolin purification Zeolin_YFP was purified from BIP_Zeolin_YFP expressing lines, exploiting the presence of the H-tag at the C-terminus of the recombinant protein. After 4 days of cultivation, 1 L of culture was subjected to centrifugation to remove the cells, and the resulting supernatant containing secreted Zeolin_YFP was loaded onto an H- tag chromatographic affinity column. The elution was performed using 500 mM imidazole. 2.6 Confocal microscopy The subcellular localization of Zeolin_YFP was examined by confocal microscopy. Images were recorded using a Leica TCS-SP5 inverted confocal microscope (Leica Microsystems, Germany). mVenus (YFP) and chlorophyll were excited at 514 nm, and fluorescence emissions were detected at 522–572 nm and 680–720 nm for YFP and chlorophyll a, respectively as previously reported (Pivato et al., 2021). A B FIGURE 2 Fluorescence screening and Western blot analysis. (A) Fluorescence screening on putative BIP_Zeolin_YFP expressing lines (excitation: 509 ± 4.5 nm; emission: 540 ± 10 nm). (B) Western blot against YFP on putative BIP_Zeolin_YFP expressing lines (expected MW 85.5 kDa). A 2.5 Growth analysis Cell density was measured at 720 nm OD, and total dry biomass was evaluated by overnight lyophilization pellets followed by gravimetric determination as previously reported (Pivato et al., 2021). Cell dimension was measured by software analysis on microscope photos with n>70 (Perozeni et al., 2018). Statistical analysis was performed using a two-tailed t-test and compared with the UVM4. Putative transformant lines with the highest YFP fluorescence (at least 2-fold compared to the average YFP fluorescence emission of the screened lines) were then selected and investigated by western blotting (Figure 2). As reported in Figure 2 and Supplementary Figures S3–S5, positive signals at ~80 kDa were identified for all the expression vectors used (Table 1). Considering the expected molecular weight of ~85.5 kDa for the mature zeolin-YFP protein, the slightly lower molecular weight observed could be related to additional proteolysis of the protein. The lines with the 3.1 Zeolin expression in Chlamydomonas reinhardtii B Zeolin expression in C. reinhardtii was designed starting from the amino acid sequence previously expressed in tobacco (Mainieri et al., 2004) obtained by fusing T343 phaseolin from Phaseolus vulgaris L., including its signal peptide, with an unstructured 15 amino acids linker and 89 amino acids of mature g-zein from Zea mays (Supplementary Figure S1). Zeolin gene for heterologous expression in C. reinhardtii was synthetically redesigned by codon optimization and intron spreading to enhance transgene expression, as previously described (Baier et al., 2018b) and FIGURE 2 Fluorescence screening and Western blot analysis. (A) Fluorescence screening on putative BIP_Zeolin_YFP expressing lines (excitation: 509 ± 4.5 nm; emission: 540 ± 10 nm). (B) Western blot against YFP on putative BIP_Zeolin_YFP expressing lines (expected MW 85.5 kDa). FIGURE 2 Fluorescence screening and Western blot analysis. (A) Fluorescence screening on putative BIP_Zeolin_YFP expressing lines (excitation: 509 ± 4.5 nm; emission: 540 ± 10 nm). (B) Western blot against YFP on putative BIP_Zeolin_YFP expressing lines (expected MW 85.5 kDa). 04 frontiersin.org Perozeni et al. 10.3389/fpls.2023.1184064 TABLE 1 Numbers of lines screened by YFP fluorescence and western blotting. TABLE 1 Numbers of lines screened by YFP fluorescence and western blotting. Expression vector Transformant screened YFP positive lines Lines selected (YFP fluorescence) Zeolin-YFP expressing lines (western blot) Zeolin_YFP 192 45 8 5 BiP_Zeolin_YFP 96 39 6 1 Zeolin_YFP_ERseq_ 192 20 5 5 BiP_Zeolin_YFP_ERseq 168 83 5 1 ‘YFP positive lines’ refers to the transformant lines with an increase in YFP fluorescence of at least two-fold after normalization to the cell scattering at 720 nm, compared to the average of the 20 lines with the lowest YFP fluorescence emission per 720-nm cell scattering. The lines selected after YFP screening are those whose YFP fluorescence showed an increase of at least 3-fold compared to the average of the 20 lines with the lowest YFP fluorescence emission per 720-nm cell scattering. Expression vector Transformant screened YFP positive lines Lines selected (YFP fluorescence) Zeolin-YFP expressing lines (western blot) Zeolin_YFP 192 45 8 5 BiP_Zeolin_YFP 96 39 6 1 Zeolin_YFP_ERseq_ 192 20 5 5 BiP_Zeolin_YFP_ERseq 168 83 5 1 ‘YFP positive lines’ refers to the transformant lines with an increase in YFP fluorescence of at least two-fold after normalization to the cell scattering at 720 nm, compared to the average of the 20 lines with the lowest YFP fluorescence emission per 720-nm cell scattering. 3.1 Zeolin expression in Chlamydomonas reinhardtii The lines selected after YFP screening are those whose YFP fluorescence showed an increase of at least 3-fold compared to the average of the 20 lines with the lowest YFP fluorescence emission per 720-nm cell scattering. YFP positive lines’ refers to the transformant lines with an increase in YFP fluorescence of at least two-fold after normalization to the cell scattering at 720 nm, compared to the average of the 20 ines with the lowest YFP fluorescence emission per 720-nm cell scattering. The lines selected after YFP screening are those whose YFP fluorescence showed an increase of at least 3-fold compared o the average of the 20 lines with the lowest YFP fluorescence emission per 720-nm cell scattering. strongest accumulation of zeolin-YFP complex (D2.2 for Zeolin_YFP, F7 for BiP_Zeolin_YFP, E9.1, Zeolin_YFP_ER and B5.1 for BiP_Zeolin_YFP_ER, respectively) were then used for the following analysis. chloroplast localization. However, in some cases, the zeolin-YFP complex in Zeolin_YFP_ERseq transformant lines was found to be located in defined spherical structures with extremely high fluorescence, which can be reconducted to protein bodies, and the formation of protein bodies was reported in tobacco leaves to significantly increase the intracellular accumulation of zeolin (Mainieri et al., 2004). The variability observed in terms of protein body formation in Zeolin_YFP_ ERseq-expressing cells could be related to a different level of expression, with protein body formation where zeolin-YFP expression reached a certain level. Finally, the addition of both the BIP target peptide and the HDEL retention sequence gives confocal microscopy a hybrid picture. Proteins are both located in filaments around the nucleus but also in high-fluorescence circular bodies. 3.2 Zeolin localization The presence of YFP fused to zeolin allowed the investigation of the zeolin-YFP complex localization by confocal microscopy (Figure 3). In the case of cells transformed with the Zeolin_YFP vector, the YFP signal was measured around the nucleus and did not overlap with the chlorophyll fluorescence signal (second column), which can be reconducted to ER localization according to literature (Rasala et al., 2014). The same behavior was observed in BiP_Zeolin_ YFP-expressing lines, demonstrating that either phaseolin or BiP N- terminus signal peptides drive zeolin translation in the ER. In the case of Zeolin_YFP_ERseq, where the ER retention sequence HDEL was added at the C-terminus of the zeolin-YFP complex, the YFP fluorescence signal was again detected as a net around the nucleus, consisting of ER localization and excluding nucleus, cytosol, or 3.3 Zeolin influence on cell growth The influence of zeolin-YFP expression on cell growth and biomass productivity was analyzed by cultivating the transformed lines in mixotrophic conditions under high (500 µmol m-ss-1) or low light (80 µmol m-ss-1) conditions. Cell scattering at 720 nm was used to follow the growth kinetics of the zeolin-expressing lines and their background UVM4. As shown in Figure 4, similar growth kinetics were observed for cells grown under low or high light conditions. Under either low or high light conditions, a slightly reduced growth could be observed for zeolin-expressing lines compared to UVM4 on the first days of cultivation, but on the second day under low light or on the third day under high light, no significant difference could be observed between transformed lines and UVM4. The cell areas of the different lines grown at 80 or 500 µmol m-ss-1 were then measured. Similar values between the different genotypes were retrieved and investigated for cells grown under high or low light. Biomass dry weight was also measured at the end of the growth curves, as shown in Figure 4 Under high light conditions, increased biomass production was observed compared to low light conditions, likely a consequence of the increased light energy available. Under both low and high light conditions, the dry weights of the different zeolin-expressing lines were similar to those of UVM4, except for the Zeolin_YFP_ERseq transformant line, which was characterized by a slightly reduced dry weight compared to its background under both light conditions. Interestingly, the Zeolin_YFP_ERseq vector was the best condition for inducing zeolin accumulation in protein bodies, which could potentially have a minor negative effect on cell growth. FIGURE 3 Zeolin localization. Analysis of endogenous (first line) or additional (lines 2–5) Zeolin_YFP target peptide. YFP fluorescence (YFP), chlorophyll autofluorescence (Chl), and merger of these two channels are shown. Excitation for YFP was 514 nm and 633 nm for chlorophylls. Emission was detected at 522–572 nm for YFP and 670–690 nm for chlorophylls. Scale bar represents 5 µm. FIGURE 3 Zeolin localization. Analysis of endogenous (first line) or additional (lines 2–5) Zeolin_YFP target peptide. YFP fluorescence (YFP), chlorophyll autofluorescence (Chl), and merger of these two channels are shown. Excitation for YFP was 514 nm and 633 nm for chlorophylls. Emission was detected at 522–572 nm for YFP and 670–690 nm for chlorophylls. Scale bar represents 5 µm. FIGURE 3 Zeolin localization. 3.3 Zeolin influence on cell growth Analysis of endogenous (first line) or additional (lines 2–5) Zeolin_YFP target peptide. YFP fluorescence (YFP), chlorophyll autofluorescence (Chl), and merger of these two channels are shown. Excitation for YFP was 514 nm and 633 nm for chlorophylls. Emission was detected at 522–572 nm for YFP and 670–690 nm for chlorophylls. Scale bar represents 5 µm. frontiersin.org 05 Frontiers in Plant Science Perozeni et al. 10.3389/fpls.2023.1184064 A B C FIGURE 4 Expressing lines growth performance. Growth test was conducted in mixotrophy (TAP) in low (80 mmol photons m-2 s-2) or high (500 mmol photons m-2 s-2) light. 720 nm optical density (A), cell dimensions (B) as well as dry biomass (C) were evaluated. The significantly different values (P < 0.05) in panels B and C are indicated with different letters. For cell areas (B) n=70 while for dry weight values (C) n=3. A B A B B FIGURE 4 Expressing lines growth performance. Growth test was conducted in mixotrophy (TAP) in low (80 mmol photons m-2 s-2) or high (500 mmol photons m-2 s-2) light. 720 nm optical density (A), cell dimensions (B) as well as dry biomass (C) were evaluated. The significantly different values (P < 0.05) in panels B and C are indicated with different letters. For cell areas (B) n=70 while for dry weight values (C) n=3. Frontiers in Plant Science 3.4 Zeolin is retained in ER only in the presence of HDEL sequence In contrast, as shown in Figure 5, for the Zeolin_YFP transformed line, a double band at ~80 kDa was detected in cells harvested after 1 d of cultivation, which strongly decreased in the following days of cultivation, accompanied by an increase in the zeolin-YFP signal at higher molecular weight (~140 kDa) appearing in the supernatant, suggesting a possible secretion in dimeric form (see below for further details). The observation of a double band of the zeolin-YFP complex suggests the presence of partial protein degradation, as previously observed in the case of zeolin expressed in tobacco leaves (Mainieri et al., 2004), whereas the appearance of a clear band in the supernatants suggests zeolin-YFP protein secretion. Similar results were obtained for BiP_Zeolin_YFP, where most of the zeolin-YFP complexes were present in the supernatant after 3 or 4 d of cultivation. Completely different results were obtained in the case of Zeolin_YFP_ERseq transformant lines; in this case, YFP positive signals as a double band at ~80 kDa were observed only in cells for all four days of cultivation, while no zeolin-YFP could be detected in the growth medium. This result suggests that zeolin-YFP was successfully retained inside the cell and was not secreted in the presence of the HDEL sequence. In the case of the BIP_Zeolin_YFP_ERseq line, where both BiP and HDEL sequences were added to the N- and C- termini of the zeolin-YFP complex, a double band was detected at 80 kDa in the pellet samples, with the strongest protein signal observed on the second day in the pellet, whereas in the supernatant, a clear band appeared only on the fourth day. These results suggest that in the presence of both the BiP signal peptide and HDEL ER retention signal, the secretion of the protein is present yet delayed compared to when the HDEL sequence is absent (Zeolin_YFP and BiP_Zeolin_YFP). A possible explanation could be that the double signal peptide (the one contained in the zeolin sequence and the extra one from Bip) delays the folding of the protein, which is therefore retained in the ER for longer periods before being secreted, resulting in an intermediate phenotype compared to the case in which only one of the two sequences was added to the zeolin-YFP complex. A B D C FIGURE 5 Zeolin accumulation and distribution. 3.4 Zeolin is retained in ER only in the presence of HDEL sequence western blot analysis of cells and growth media was performed at different times of cultivation. UVM4 and zeolin-expressing lines were cultivated for up to 4 d in TAP medium at 200 µmol m-ss-1. At different cultivation times, cells were harvested by centrifugation, and pellets and supernatants were separately analyzed by western blotting using a-GFP antibody recognizing the zeolin-YFP complex. In the case of UVM4, no YFP bands were detected in Zeolin is retained in the ER of plant leaves. In the case of C. reinhardtii, proteins targeted to the ER were reported to be secreted in several locations and loaded in vesicles targeted to the plasma membrane. To monitor zeolin secretion in the expressing lines, 06 frontiersin.org Perozeni et al. 10.3389/fpls.2023.1184064 cultivation, while no zeolin-YFP could be detected in the growth medium. This result suggests that zeolin-YFP was successfully retained inside the cell and was not secreted in the presence of the HDEL sequence. In the case of the BIP_Zeolin_YFP_ERseq line, where both BiP and HDEL sequences were added to the N- and C- termini of the zeolin-YFP complex, a double band was detected at 80 kDa in the pellet samples, with the strongest protein signal observed on the second day in the pellet, whereas in the supernatant, a clear band appeared only on the fourth day. These results suggest that in the presence of both the BiP signal peptide and HDEL ER retention signal, the secretion of the protein is present yet delayed compared to when the HDEL sequence is absent (Zeolin_YFP and BiP_Zeolin_YFP). A possible explanation could be that the double signal peptide (the one contained in the zeolin sequence and the extra one from Bip) delays the folding of the protein, which is therefore retained in the ER for longer periods before being secreted, resulting in an intermediate phenotype compared to the case in which only one of the two sequences was added to the zeolin-YFP complex. cells or in the exhausted growth medium during the four days of sampling, as expected (Supplementary Figure S6). Frontiers in Plant Science 3.4 Zeolin is retained in ER only in the presence of HDEL sequence light energy to assimilate CO2 and inorganic nutrients into edible biomass without competing for land and water with other food crops. Moreover, the high photosynthetic efficiency of microalgae and their lower water footprint compared to crops make these organisms potential candidates to support life during space exploration as food and oxygen providers. The protein content of microalgae is species-related, but typically is very high, ranging from 30 to 60% of the total dry matter (Wang et al., 2021). The goal of this study was to further modify the protein content by introducing a storage protein with balanced amino acids, which could potentially accumulate in protein bodies. Zeolin localization in the ER was targeted because this compartment is a suitable organelle for protein accumulation, and previous studies in tobacco have shown that zeolin reaches a high concentration in the ER- forming inclusion body. Zeolin_YFP-expressing lines were stable and showed protein accumulation in the ER at the initial stage of cultivation, whereas zeolin-YFP secretion was observed in the mid-exponential and saturation phases. These results demonstrate that the N-terminus phaseolin signal peptide is recognized as an entry signal to the secretory pathway in C. reinhardtii. The secretion of zeolin-YFP further support the transient ER localization of the protein, being the translation in the ER required for the secretion of heterologous proteins in C. reinhardtii (Lauersen et al., 2013; Rasala et al., 2014; Baier et al., 2018a; Molino et al., 2018). Zeolin-YFP secretion is likely at the base of some discrepancy observed between YFP screening and western blot analysis of transformant lines (Figure 2; Supplementary Figures S3–5) because the cells were not synchronized for this screening procedure. In Nicotiana tabacum, zeolin forms protein bodies in the ER; however, considering that the two hosts have two different cell structures, it is reasonable that the mechanism is not conserved. The secretion of zeolin-YFP in the engineered strains described herein demonstrates that the mechanism of ER retention is different in zeolin-expressing tobacco leaves and C. reinhardtii cells. Alternatively, it is possible that YFP at the C-terminus of the recombinant zeolin-YFP complex negatively affects ER retention and protein body formation. HDEL addition at the C-terminus led to retention of the protein inside the ER. Even if we cannot exclude the possibility that a fraction of zeolin may be confined in the cytosol, interfering with ER import. 3.4 Zeolin is retained in ER only in the presence of HDEL sequence Western blot analysis showing protein accumulation at different days of cultivation in expressing lines either in the cell (inside) or secreted in the supernatant (outside). Data are referred to Zeolin_YFP (A), BIP_Zeolin_YFP (B), Zeolin_YFP_Erseq (C) and BIP_Zeolin_YFP_Erseq (D). The negative control is marked with (-) and is represented by UVM4 supernatant at day 4. A A B B C C D D D FIGURE 5 Zeolin accumulation and distribution. Western blot analysis showing protein accumulation at different days of cultivation in expressing lines either in the cell (inside) or secreted in the supernatant (outside). Data are referred to Zeolin_YFP (A), BIP_Zeolin_YFP (B), Zeolin_YFP_Erseq (C) and BIP_Zeolin_YFP_Erseq (D). The negative control is marked with (-) and is represented by UVM4 supernatant at day 4. Frontiers in Plant Science 07 07 frontiersin.org Perozeni et al. Perozeni et al. 10.3389/fpls.2023.1184064 10.3389/fpls.2023.1184064 The zeolin-YFP complex secreted in the expression lines Zeolin_YFP, BiP_Zeoin_YFP, and BIP_Zeolin_YFP_ERseq was detected at a higher molecular weight than the zeolin-YFP complex retained in the cells (Figure 5). The higher molecular weight of the secreted protein can be caused by a post-translational modification (i.e., N-glycosylation, as in phaseolin) or by interference in the electrophoretic pathway, caused by the salts contained in the growth medium or by the formation of complex aggregates in the secreted proteins. Another possibility is that the protein forms a dimer once it reaches the extracellular space, which would explain the molecular weight of approximately 150 kDa, which is exactly double the weight of the protein found inside the cells. To investigate the latter hypothesis, the secreted zeolin_YFP was purified from the growth medium by affinity chromatography owing to the presence of a His tag at the C-terminus. The purified zeolin-YFP was studied by western blot analysis. As shown in Supplementary Figure S7, a band of approximately 150 kDa was detected with the YFP antibody; these data are consistent with what was previously observed in western blot analysis of the supernatant. To clarify the nature of the 150 kDa band, western blot analysis was repeated by incubating the purified Zeolin-YFP complex at 100°C for 5 min to interrupt possible states of aggregation. Heat treatment resulted in a decrease in the molecular weight of the protein, while the intensity of the band remained the same, possibly indicating that the higher apparent molecular weight migration was due to the formation of zeolin-YFP dimers. 3.4 Zeolin is retained in ER only in the presence of HDEL sequence ER retention mediated by the HDEL sequence caused the formation of protein bodies, which were clearly visible by confocal microscopy. As previously suggested, zeolin protein bodies are likely too large to be packed in vesicles entering the secretion pathway (Mainieri et al., 2004). The simultaneous addition of the BiP signal peptide at the N- terminus and HDEL at the C-terminus led to an intermediate phenotype, with most zeolin-YFP retained in the cells even after two days of cultivation, whereas at the saturation phase (days 3 and 4), the chimeric protein was essentially secreted. According to these results, the presence of the BIP transit peptide strongly improved the ER localization of zeolin-YFP and its delivery in the secretion pathway, while the HDEL sequence at the C-terminus increased its retention in the ER. It is important to note that in plants, both KDEL and HDEL ER retention signals also promote protein delivery into the vacuole (Gomord et al., 1997): In the case of C. reinhardtii, HDEL sequence was reported to induce ER retention, The quantification of the zeolin accumulated in the cells or secreted into the medium is reported in Figure 6 and was calculated using isolated YFP as a standard. The maximum zeolin accumulation per cell was observed in the Zeolin_YFP_ERseq expressing line after two days of cultivation. The reduced content on the fourth day suggested that zeolin protein bodies accumulated in the Zeolin_YFP_ Erseq-expressing line were partially degraded and/or their biosynthesis was reduced during cell cultivation. Finally, the total protein content in the different zeolin-expressing lines was analyzed, as reported in Table 2. Similar total protein content was measured in all the different zeolin-expressing lines compared to the UVM4 background, even though a slight increase in the total protein fraction per cell could be observed in the case of Zeolin_YFP_Erseq compared to Zeolin_YFP and BiP_Zeoin_YFP transformant lines. Frontiers in Plant Science frontiersin.org 4 Discussion Seed storage proteins in legumes and cereals are the two main sources of protein for human nutrition. However, seed storage proteins from legumes are poor in sulfur amino acids, whereas cereal proteins are poor in Lysine and Tryptophan. Zeolin, the chimeric protein obtained by fusing phaseolin and zein, was proposed as a possible solution to provide a complete and balanced amino acid nutrition profile (Mainieri et al., 2004). In this study, we obtained heterologous expression of zeolin in the model organism for the green alga C. reinhardtii, which can be considered a novel sustainable protein source, with its ability to use 08 frontiersin.org 10.3389/fpls.2023.1184064 Perozeni et al. A B C FIGURE 6 Zeolin quantification. (A) Quantitative western blot of Zeolin accumulating lines both for cell (inside) and supernatant (outside). YFP used as standard is shown with the loaded amount. (B) Zeolin quantification inside cell for zeolin expressing lines at day 1 and 2. (C) Zeolin quantification into supernatant (outside) for zeolin expressing lines at day 4. Results represent mean values and standard deviation from biological triplicates (n = 3). The significantly differences (P < 0.05) between different genotype at the same time point and same localization (inside or outside the cells) are indicated with different letters. A A B C FIGURE 6 Zeolin quantification. (A) Quantitative western blot of Zeolin accumulating lines both for cell (inside) and supernatant (outside). YFP used as standard is shown with the loaded amount. (B) Zeolin quantification inside cell for zeolin expressing lines at day 1 and 2. (C) Zeolin quantification into B C B FIGURE 6 Zeolin quantification. (A) Quantitative western blot of Zeolin accumulating lines both for cell (inside) and supernatant (outside). YFP used as standard is shown with the loaded amount. (B) Zeolin quantification inside cell for zeolin expressing lines at day 1 and 2. (C) Zeolin quantification into supernatant (outside) for zeolin expressing lines at day 4. Results represent mean values and standard deviation from biological triplicates (n = 3). The significantly differences (P < 0.05) between different genotype at the same time point and same localization (inside or outside the cells) are indicated with different letters. TABLE 2 Protein content per dry weight of zeolin-YFP expressing lines. TABLE 2 Protein content per dry weight of zeolin-YFP expressing lines. Frontiers in Plant Science 4 Discussion UVM4 Zeolin_YFP BiP_Zeolin_YFP Zeolin_YFP_ERseq_ BiP_Zeolin_YFP_ERseq % protein/total weight 30.9 ± 4.7 a,b 23.8 ± 2.8 b 24.5 ± 2.0 b 35.9 ± 6.1 a,c 29.1 ± 1.1 a,c Total protein content in the different zeolin-expressing lines measured using micro BCA assay kit (Thermo Fisher). The significantly different values (P< 0.05) are indicated with different letters. protein body formation in the ER, which might induce the onset of protein degradation pathways. but we cannot exclude that zeolin-YFP with the HDEL sequence at the C-terminus might be partially delivered to other hydrolytic compartments in C. reinhardtii cells. The slightly reduced biomass accumulation observed in Zeolin_YFP_ERseq expressing lines raises the question of a possible negative effect on growth due to The Zeolin_YFP retained in the cell was detected by SDS-PAGE as a double band at ~80kDa. The expected molecular weight of the mature zeolin-YFP complex is 85.5 kDa: the lower apparent 09 frontiersin.org Perozeni et al. 10.3389/fpls.2023.1184064 molecular weight observed may be due to partial proteolysis of the protein. It is interesting to note that when retained in the cell, the protein was detected as a double band, as reported by Mainieri et. al., probably referring to the presence of two different proteolytic products. The secreted zeolin-YFP chimeric protein was detected at a higher molecular weight (~140 kDa) due to the presence of protein aggregates (dimers) that can be dissolved upon thermal treatment (Supplementary Figure S7). The nature of zein can explain its higher molecular weight; zein appears as a heterologous zein mix (disulfide-linked aggregates), in which g- zein is the starting point and is essential for protein body formation. Moreover, post-translational modifications are likely to occur, probably glycosylation, considering that in beans, phaseolin monomers are N-glycosylated and transported from the ER and Golgi complex to the protein storage vacuoles. such as antioxidants or omega-3 fatty acids (Nguyen et al., 2013). With the objective of obtaining a sustainable superfood with a high nutritional profile and the ability to convert CO2 and inorganic nutrients into edible biomass, zeolin expression in C. reinhardtii combined with metabolic engineering represents a possible solution. Funding This research was funded by CARIVERONA FOUNDATION (Grant No. 2019.0419.2019) to MB, by the Italian Ministry of University and Research (MUR, Grant PON Ricerca e Innovazione, Progetti-Progetti DM 1062) to FP, and by the Department of Biomolecular Sciences “ food safety” University of Urbino Carlo Bo (Grant DISB_POMPA_PROG_ SIC_ALIMENTARE). Publisher’s note All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher. In conclusion, we obtained heterologous expression of a chimeric seed storage protein in a model organism for green alga, C. reinhardtii. Using the ER retention sequence HDEL, it was possible to induce zeolin accumulation as protein bodies in the ER, even with low expression efficiency. It is interesting to note that C. reinhardtii has already been recognized as safe for human consumption by the FDA, and previous work has demonstrated the possibility of inducing the accumulation of other compounds important for human nutrition, Frontiers in Plant Science Author contributions Zeolin production yield by engineered strains was quite low, reaching values of ~6 fg/cell when retained in the ER, whereas a concentration of ~82 µg/L was obtained when zeolin-YFP was secreted. Several reasons can explain why the production is low. A negative effect could be related to the presence of YFP and His tags and the C-terminus; it is well known that different tags could have different impacts on protein expression in both prokaryotic and eukaryotic cells (Baier et al., 2018a; Koppl et al., 2022). Moreover, we cannot exclude the possibility that the protein could accumulate and degrade without forming protein bodies. It is important to note that zeolin retention in the ER is facilitated by the formation of Cys- bound in its C-terminus region. In our zeolin-YFP chimeric protein, the C-terminus contains YFP, a 27-kDa protein with a well-defined secondary structure that can interfere with the formation of Cys bonds and thus, ER retention. A strategy to fully exploit the zeolin potential is represented by the expression of zeolite alone, without any fluorophore. With the exception of the zeolin-YFP variant presenting the HDEL sequence at the C-terminus, the recombinant chimeric protein was secreted, excluding possible feedback inhibition due to protein accumulation. A further possible explanation could be the correlation between zeolin-YFP production and acetate availability (carbon source in TAP medium), indicating that depletion of the carbon source in the first two days causes a decrease in zeolin-YFP biosynthesis. To study this hypothesis and test C level as a limiting factor, further experiments must be performed under autotrophy conditions (CO2 as a C source) or constant acetate supplementation. In addition to the random nature of gene insertion, expression is affected by the position effect; thus, by screening a large number of lines, it is possible to obtain lines with higher accumulation. Moreover, insertion of multiple gene copies could have a positive effect on protein accumulation. Finally, we cannot exclude the possibility that other growth conditions may have different effects on protein production and accumulation. MB and AP conceived of the study. MB and AP supervised experiments. FP and MA performed or contributed to all experiments reported herein. MP performed confocal microscopy analysis. MB, FP, and AP wrote the manuscript with contributions from all authors. All authors discussed the results, contributed to data interpretation, and commented on the manuscript. All authors contributed to the article and approved the submitted version. Conflict of interest The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Data availability statement The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding author. References Lending, C. R., and Larkins, B. A. (1989). Changes in the zein composition of protein bodies during maize endosperm development. Plant Cell 1 (10), 1011–1023. doi: 10.1105/tpc.1.10.1011 Baier, T., Kros, D., Feiner, R. C., Lauersen, K. J., Muller, K. M., and Kruse, O. (2018a). Engineered fusion proteins for efficient protein secretion and purification of a human growth factor from the green microalga chlamydomonas reinhardtii. ACS Synth Biol. 7 (11), 2547–2557. doi: 10.1021/acssynbio.8b00226 Llop-Tous, I., Madurga, S., Giralt, E., Marzabal, P., Torrent, M., and Ludevid, M. D. (2010). Relevant elements of a maize gamma-zein domain involved in protein body biogenesis. J. Biol. Chem. 285 (46), 35633–35644. doi: 10.1074/jbc.M110.116285 Baier, T., Wichmann, J., Kruse, O., and Lauersen, K. J. (2018b). Intron-containing algal transgenes mediate efficient recombinant gene expression in the green microalga chlamydomonas reinhardtii. Nucleic Acids Res. 46 (13), 6909–6919. doi: 10.1093/nar/ gky532 Mainieri, D., Rossi, M., Archinti, M., Bellucci, M., De Marchis, F., Vavassori, S., et al. (2004). Zeolin. a new recombinant storage protein constructed using maize gamma- zein and bean phaseolin. Plant Physiol. 136 (3), 3447–3456. doi: 10.1104/pp.104.046409 Camacho, F., Macedo, A., and Malcata, F. (2019). Potential industrial applications and commercialization of microalgae in the functional food and feed industries: a short review. Mar. Drugs 17 (6). doi: 10.3390/md17060312 Masi, A., Leonelli, F., Scognamiglio, V., Gasperuzzo, G., Antonacci, A., and Terzidis, M. A. (2023). Chlamydomonas reinhardtii: a factory of nutraceutical and food supplements for human health. Molecules 28 (3), 1185. doi: 10.3390/ molecules28031185 Crozet, P., Navarro, F. J., Willmund, F., Mehrshahi, P., Bakowski, K., Lauersen, K. J., et al. (2018). Birth of a photosynthetic chassis: a MoClo toolkit enabling synthetic biology in the microalga chlamydomonas reinhardtii. ACS Synthetic Biol. 7 (9), 2074– 2086. doi: 10.1021/acssynbio.8b00251 Mendes, M. C., Navalho, S., Ferreira, A., Paulino, C., Figueiredo, D., Silva, D., et al. (2022). Algae as food in Europe: an overview of species diversity and their application. Foods 11 (13), 1871. doi: 10.3390/foods11131871 De La Fuente, M. D., López-Pedrouso, M., Alonso, J., Santalla, M., De Ron, A. M., Á lvarez, G., et al. (2012). In-depth characterization of the phaseolin protein diversity of common bean (Phaseolus vulgaris l.) based on two-dimensional electrophoresis and mass spectrometry. Food Technol. Biotechnol. 50 (3), 315–325. doi: 10.3390/ su11195443 Molino, J. V. D., de Carvalho, J. C. M., and Mayfield, S. P. (2018). References Comparison of secretory signal peptides for heterologous protein expression in microalgae: expanding the secretion portfolio for chlamydomonas reinhardtii. PloS One 13 (2), e0192433. doi: 10.1371/journal.pone.0192433 Fields, F. J., Lejzerowicz, F., Schroeder, D., Ngoi, S. M., Tran, M., McDonald, D., et al. (2020). Effects of the microalgae chlamydomonas on gastrointestinal health. J. Funct. Foods 65, 103738. doi: 10.1016/j.jff.2019.103738 Neupert, J., Karcher, D., and Bock, R. (2009). Generation of chlamydomonas strains that efficiently express nuclear transgenes. Plant J. 57 (6), 1140–1150. doi: 10.1111/ j.1365-313X.2008.03746.x Gomord, V., Denmat, L. A., Fitchette-Lainé, A. C., Satiat-Jeunemaitre, B., Hawes, C., and Faye, L. (1997). The c-terminal HDEL sequence is sufficient for retention of secretory proteins in the endoplasmic reticulum (ER) but promotes vacuolar targeting of proteins that escape the ER. Plant J. 11 (2), 313–325. doi: 10.1046/j.1365- 313x.1997.11020313.x Nguyen, H. M., Cuiné, S., Beyly-Adriano, A., Légeret, B., Billon, E., Auroy, P., et al. (2013). The green microalga chlamydomonas reinhardtii has a single w-3 fatty acid desaturase that localizes to the chloroplast and impacts both plastidic and extraplastidic membrane lipids. Plant Physiol. 163 (2), 914–928. doi: 10.1104/ pp.113.223941 Guo, X., Yuan, L., Chen, H., Sato, S. J., Clemente, T. E., and Holding, D. R. (2013). Nonredundant function of zeins and their correct stoichiometric ratio drive protein body formation in maize endosperm. Plant Physiol. 162 (3), 1359–1369. doi: 10.1104/ pp.113.218941 Onyeaka, H., Miri, T., Obileke, K., Hart, A., Anumudu, C., and Al-Sharify, Z. T. (2021). Minimizing carbon footprint via microalgae as a biological capture. Carbon Capture Sci. Technol. 1, 100007. doi: 10.1016/j.ccst.2021.100007 Perozeni, F., Stella, G. R., and Ballottari, M. (2018). LHCSR expression under HSP70/RBCS2 promoter as a strategy to increase productivity in microalgae. Int. J. Mol. Sci. 19 (1). doi: 10.3390/ijms19010155 Holding, D. R. (2014). Recent advances in the study of prolamin storage protein organization and function. Front. Plant Sci. 5. doi: 10.3389/fpls.2014.00276 Khan, N. U., Sheteiwy, M., Lihua, N., Khan, M. M. U., and Han, Z. (2019). An update on the maize zein-gene family in the post-genomics era. Food Production Process. Nutr. 1 (1), 13. doi: 10.1186/s43014-019-0012-5 Pivato, M., Perozeni, F., Licausi, F., Cazzaniga, S., and Ballottari, M. (2021). Heterologous expression of cyanobacterial orange carotenoid protein (OCP2) as a soluble carrier of ketocarotenoids in chlamydomonas reinhardtii. Algal Res. 55, 102255. doi: 10.1016/j.algal.2021.102255 Kindle, K. L. (1990). High-frequency nuclear transformation of chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. U.S.A. 87 (3), 1228–1232. Supplementary material The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fpls.2023.1184064/ full#supplementary-material 10 frontiersin.org 10.3389/fpls.2023.1184064 Perozeni et al. Perozeni et al. References doi: 10.1073/pnas.87.3.1228 Puigbò, P., Guzmán, E., Romeu, A., and Garcia-Vallvé, S. (2007). OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. Nucleic Acids Res. 35 (suppl_2), W126–W131. doi: 10.1093/nar/gkm219 Koppl, C., Lingg, N., Fischer, A., Kross, C., Loibl, J., Buchinger, W., et al. (2022). Fusion tag design influences soluble recombinant protein production in escherichia coli. Int. J. Mol. Sci. 23 (14). doi: 10.3390/ijms23147678 Rasala, B. A., Chao, S.-S., Pier, M., Barrera, D. J., and Mayfield, S. P. (2014). Enhanced genetic tools for engineering multigene traits into green algae. PloS One 9 (4), e94028. doi: 10.1371/journal.pone.0094028 Koyande, A. K., Chew, K. W., Rambabu, K., Tao, Y., Chu, D.-T., and Show, P.-L. (2019). Microalgae: a potential alternative to health supplementation for humans. Food Sci. Hum. Wellness 8 (1), 16–24. doi: 10.1016/j.fshw.2019.03.001 Sathe, S. K. (2016). “Beans, overview,” in Reference module in food science (Elsevier). doi: 10.1016/B978-0-08-100596-5.00033-0 Krishnan, H. B., and Coe, E. H. (2001). “Seed storage proteins,” in Encyclopedia of genetics. Eds. S. Brenner and J. H. Miller (New York: Academic Press). Suárez-Martı́nez, S. E., Ferrı́z-Martı́nez, R. A., Campos-Vega, R., Elton-Puente, J. E., de la Torre Carbot, K., and Garcı́a-Gasca, T. (2016). Bean seeds: leading nutraceutical source for human health. CyTA - J. Food 14, 131–137. doi: 10.1080/ 19476337.2015.1063548 Kropat, J., Hong-Hermesdorf, A., Casero, D., Ent, P., Castruita, M., Pellegrini, M., et al. (2011). A revised mineral nutrient supplement increases biomass and growth rate in chlamydomonas reinhardtii. Plant J. 66 (5), 770–780. doi: 10.1111/j.1365-313X.2011.04537.x Laemmli, U. K. (1970). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227 (5259), 680–685. doi: 10.1038/227680a0 Torres-Tiji, Y., Fields, F. J., and Mayfield, S. P. (2020). Microalgae as a future food source. Biotechnol. Adv. 41, 107536. doi: 10.1016/j.biotechadv.2020.107536 Lauersen, K. J., Berger, H., Mussgnug, J. H., and Kruse, O. (2013). Efficient recombinant protein production and secretion from nuclear transgenes in chlamydomonas reinhardtii. J. Biotechnol. 167 (2), 101–110. doi: 10.1016/j.jbiotec.2012.10.010 Vitale, A., Smaniotto, E., Longhi, R., and Galante, E. (1982). Reduced soluble proteins associated with maize endosperm protein bodies. J. Exp. Bot. 33 (3), 439– 448. doi: 10.1093/jxb/33.3.439 Lauersen, K. J., Kruse, O., and Mussgnug, J. H. (2015). Targeted expression of nuclear transgenes in chlamydomonas reinhardtii with a versatile, modular vector toolkit. Appl. Microbiol. Biotechnol. 99 (8), 3491–3503. doi: 10.1007/s00253-014-6354-7 Wang, Y., Tibbetts, S. M., and McGinn, P. J. (2021). References Microalgae as sources of high- quality protein for human food and protein supplements. Foods 10 (12). doi: 10.3390/ foods10123002 Frontiers in Plant Science 11 frontiersin.org
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La situación en Afganistán y su impacto regional La situación en Afganistán y su impacto regional Silvana Lorena Barrios1 Contribución en la Sección Debates Internacionales Resumen: Luego de veinte años de la presencia de tropas occidentales, tanto estadounidenses como de la OTAN, la inestabilidad en Afganistán ha sido constante y en consecuencia el balance de dos décadas de presencia internacional ha sido un fracaso, dado que no se ha conseguido estabilizar mínimamente al país. Desde hace una década atrás, las potencias occidentales vislumbran la necesidad de retirarse de un teatro de operaciones sin salida, pero los costos políticos de esa decisión, de la que nadie quería hacerse cargo, hizo que la retirada se demorara hasta la actualidad. Dicha situación ha obligado a los países de mayoría musulmana a reconfigurar su postura frente al conflicto afgano, así como también a las potencias regionales e intermedias en abierta oposición y/o competencia con occidente. Desde el principio de la operación, tras los atentados del 11 de septiembre de 2001, los objetivos de Estados Unidos y de la OTAN no han sido claros, es decir, no fue definido si se trataba de luchar contra el terrorismo y capturar a Osama bin Laden o de establecer una Constitución y construir un Estado democrático en una nación multiétnica como Afganistán. La consecuencia fue la ejecución de una operación que aunó cuestiones diferentes (Burnard, 2021). El resultado, en tanto, fue la construcción de un estado ficticio (Bernabé, 2021). Introducción Desde el principio de la operación, tras los atentados del 11 de septiembre de 2001, los objetivos de Estados Unidos y de la OTAN no han sido claros, es decir, no fue definido si se trataba de luchar contra el terrorismo y capturar a Osama bin Laden o de establecer una Constitución y construir un Estado democrático en una nación multiétnica como Afganistán. La consecuencia fue la ejecución de una operación que aunó cuestiones diferentes (Burnard, 2021). El resultado, en tanto, fue la construcción de un estado ficticio (Bernabé, 2021). Afganistán se constituye en una preocupación para Asia Central y del Sur El retorno del régimen Talibán al poder en Afganistán, el 15 de agosto de este año, devuelve a la región la importancia de ciertos actores estatales obligados a convivir en el 1 Universidad de Buenos Aires, Grupo de Trabajo sobre Asia del Sur, Comité de Asuntos Asiáticos, Consejo Argentino para las relaciones Internacionales. Correo electrónico: silvanabarrios@gmail.com pág. 170 ISSN 2362-194X Journal de Ciencias Sociales Año 10 N° 18 vecindario, que resultan fundamentales al momento de asegurar la estabilidad. Desde su perspectiva, mantener estable al país se convierten en una prioridad y por ende en un interés común de esos diversos países, que posibilita también la conciliación de objetivos, incluso entre países enfrentados en otros contextos, como el caso de Irán y Estados Unidos, por ejemplo. Central a este proceso es la figura y actuación de Pakistán, que obró de mediador en las conversaciones entre Estados Unidos y el movimiento Talibán en Qatar desde su inicio. Este país comparte la frontera más extensa con Afganistán y registra disputas internas, al tiempo que precisa garantizar profundidad estratégica frente a la India. Su posición desde la Conferencia de Bonn de 2001 es aquella de que no hay una solución militar al problema de Afganistán sino una solución política. Precisamente India, que ya ha dado cuenta oficial de contactos con el Talibán y ha tenido relación estrecha con el anterior gobierno afgano, ha buscado contar con Afganistán como un aliado que permita disuadir a Pakistán desde su retaguardia, teme el resurgimiento de la violencia en distintos frentes (Cachemira, reclutamientos yihadistas, terrorismo) y al igual que Pakistán, se encuentra frente a la necesidad de replantear sus políticas de enfrentamiento tradicionales (Ruiz Arévalo, 2020). Ambos países (Pakistán e India) han sufrido diversos impactos del conflicto en Afganistán, a lo largo de los años, que se traducen en inestabilidad y una situación de inseguridad, las muertes por actos terroristas y la población desplazada que llega a sus territorios. Pakistán parece ser el más beneficiado si es que el gobierno Talibán le brindase más influencia y ventajas en Kabul y así podría convertirse en un fuerte aliado en la región, alineado con sus valores islámicos. Paradójicamente, también podría ser el gran perjudicado si el resurgir Talibán envalentona a los grupos islamistas radicales de Pakistán (Roth et al. 2021). Aunque es cierto que sus Fuerzas Armadas han sabido prepararse para la guerra contrainsurgente en el flanco occidental y para un conflicto tradicional con India, en el flanco oriental, por ello estarían en capacidad de dar batalla en caso que esta segunda hipótesis se convierta en realidad. Por su parte, China, declaró su respeto a la independencia de Afganistán y a su soberanía territorial y criticó el retiro apresurado y desordenado de las fuerzas extranjeras, manifestó su voluntad de conservar relaciones con las nuevas autoridades afganas y mantuvo abierta su embajada en el país (Srinivasan, 2021). Al mismo tiempo han expresado públicamente su voluntad de mantener buenas relaciones con China, como ha sucedido en el pasado. pág. 171 La situación en Afganistán y su impacto regional Además, hay que recordar que China, Rusia, Pakistán, Qatar, y una pequeña misión de Indonesia son los únicos países que han decidió mantener abiertas sus embajadas en Kabul. Los Talibán esperan apoyo económico de China (de hecho, en la reunión de Ministros de Relaciones Exteriores de los países que limitan con Afganistán, el Canciller chino, Wang Yi anunció la donación de 31 millones de dólares en ayudas a ese país), al tiempo que China busca evitar que Afganistán se convierta en un santuario para los separatistas de la Región Autónoma Uigur de Xinjiang, o para los grupos rebeldes de la región de Baluchistán, que han atacado ya intereses chinos en Pakistán. Sin embargo, la victoria de Talibán no es clara para China, que aún desconfía del grupo islamista, dado que no cumplieron completamente el acuerdo con Estados Unidos y podrían actuar de manera similar con ellos. Además, China no tiene experiencia en mediar en luchas políticas internas de larga data en un país extranjero, por ende, se estima que todavía está trazando su curso de acción (Brar, 2021). Rusia, por otro lado, adoptó una actitud que podría denominarse conciliadora hacia el Talibán, reconociendo la victoria de estos, pero pidiendo un "diálogo nacional" para formar un gobierno representativo. Aun así, continúa considerando a los Talibán como un grupo terrorista y teme por la seguridad de las antiguas repúblicas soviéticas de Asia central, limítrofes con Afganistán (Turkmenistán, Uzbekistán y Tayikistán), frente al posible resurgimiento de grupos islamistas, con apoyo en ese país, al mismo tiempo que teme por un desplazamiento masivo de población afgana que busca escapar de la difícil situación socioeconómica, y la posible escalada en tráfico de drogas. En consecuencia, Moscú se está preparando para una mayor inestabilidad en la región, que queda evidenciado en las maniobras militares que ha realizado recientemente con Uzbekistán y Tayikistán, además de ejercicios militares con China (Roth et al. 2021). Existen también otras cuestiones afectadas, como podría ser un posible ataque y/o parálisis de la construcción de un gasoducto que compromete intereses de Pakistán, India y Turkmenistán, a pesar de que los Talibán han señalado que garantizarían la seguridad de ese gasoducto. No obstante, se prevé que Rusia estaría dispuesta a defender sus intereses, dicha afirmación se sostiene en que en 2012 Tayikistán le cedió a este país hasta 2042, la Base 201ª que está en la capital Dushanbe para ayudar a vigilar la frontera con Afganistán. La misma fue creada en 2005, tiene 3 instalaciones independientes y cuenta con 5.500 efectivos (Alarabiya News, 2021). Finalmente, Qatar, ha jugado un papel rol positivo en torno de la retirada estadounidense de Afganistán y constituyó un apoyo para la colaboración con aquellos que pág. 172 ISSN 2362-194X Journal de Ciencias Sociales Año 10 N° 18 intentaban abandonar el país. Suma a su fuerza económica, la militar y de poder blando (siendo Al Jazeera una referencia internacional en noticias). Como sede de la oficina del movimiento Talibán afgano, realiza un movimiento arriesgado, que puede tener un alto costo si el gobierno islamista promueve el terrorismo en la región. La importancia que juegan estos países en el actual contexto es de tal relevancia para el grupo Talibán, que invitaron a China, Rusia, Pakistán y Qatar a participar de la ceremonia de anuncio del nuevo gobierno realizada el 7 de septiembre, además de Turquía e Irán, citando a Al Jazeera, la cadena oficial de información utilizada por el grupo islamista. En reciprocidad, Pakistán ha sido el primer país que reanudó los vuelos de aerolíneas comerciales con el aeropuerto de Kabul, reconstruido por los Talibán. También hay que mencionar que una aerolínea afgana, reactivó los vuelos locales casi inmediatamente después de la toma de Kabul por el grupo radical. Por su parte, Qatar nunca ha dejado de realizar vuelos con carácter humanitario hacía dicho país. Irán, en tanto, continúa abogando por un gobierno de inclusión en Afganistán y se espera que continúen las buenas relaciones y el apoyo mientras no ataquen a la minoría de confesión shiita de habla darí, que habita el país. Asimismo, cabe considerar que tanto Qatar como Turquía se han ofrecido a operar el aeropuerto internacional de Kabul, pero aún no se ha definido quien se encargará de hacerlo. Si bien, todo apuntaría a que la balanza se incline hacia Qatar, dado el mayor compromiso que ha demostrado con la situación de Afganistán hasta el momento. Afganistán, mientras tanto, sufre la interna entre los sectores más radicales y los más pragmáticos de los miembros del grupo Talibán, aunque ello parece no constituir una real amenaza hasta el momento a su intento de consolidar su poder, legitimarse y efectivamente abordar los grandes desafíos políticos que tienen. Por otra parte, frente a la actitud expectante de las Naciones Unidas y el resto de los países, desde los cuales ha habido reclamos en pro de los derechos de las mujeres, los líderes Talibán anunciaron que permitirán que las mujeres estudien en la universidad, pero deberán hacerlo de manera separada de los hombres y observando normas estrictas de vestimenta y su impacto regional, tal como lo indica la interpretación que ellos hacen de la shairia (ley islámica). Conclusión Los gobiernos vecinos a Afganistán confían en que los Talibán en el poder actualmente, son diferentes a los que dirigió el mulá Mohammed Omar, ahora se les considera más pragmáticos, porque han entendido la importancia de ganar influencia política, pág. 173 La situación en Afganistán y su impacto regional y son optimistas en que hayan entendido la preocupación de la comunidad internacional y que protejan los derechos de las minorías, de las mujeres, de los niños, etc. También son conscientes que esta percepción puede ser errónea, pero esperan no equivocarse. Los factores mencionados hacen evidente, la necesidad de que la comunidad internacional reconozca la situación en Afganistán como una situación que tendrá profundas repercusiones en la estabilidad y la paz en Asia meridional y Asia central y urgentemente actúe en consecuencia. Es poco probable que el mero gobierno del Talibán mitigue el desastre humanitario que se está desarrollando, sin ayuda internacional. Referencias Alarabiya News (julio de 2021). Russia holds military drills in Tajikistan amid Taliban’s Afghanistan offensive. https://english.alarabiya.net/News/world/2021/07/14/Russia-holds-military-drillsin-Tajikistan-amid-Taliban-s-Afghanistan-offensive Bernabé, M. (agosto de 2021). Afganistán, crónica de una ficción. https://es.ara.cat/internacional/afganistan-cronica-ficcion_129_4087015.html Brar, A. (18 de agosto de 2021). Chinese people debating Taliban on Weibo but Beijing still hesitating on Afghanistan. The Print. https://theprint.in/opinion/eye-onchina/chinese-people-debating-taliban-on-weibo-but-beijing-still-hesitating-onafghanistan/717180/ Burnard, F. (18 de agosto de 2021). Pierre Centlivres: “Pakistán tiene las llaves de Afganistán” https://www.swissinfo.ch/spa/pierre-centlivres---pakist%C3%A1ntiene-las-llaves-de-afganist%C3%A1n-/46874382 Ruiz Arévalo, J. (2020). El papel de los actores regionales en el proceso de paz afgano. Revista Instituto Español de Estudios Estratégicos, (16), 221-250. Roth, A., Ellis-Petersen, H., Ni, V. (17 de agosto de 2021). Los "ganadores" de la vuelta de los talibanes: China, Pakistán y Rusia aumentarán su influencia. ElDiario.es. https://www.eldiario.es/internacional/theguardian/ganadores-vuelta-talibaneschina-pakistan-rusia-aumentaran-influencia_1_8226463.html Srinivasan, R. (16 de agosto de 2021). Between the Devil and the Deep Sea: China's Options in Afghanistan. Chennai Centre for China Studies (C3S). https://www.c3sindia.org/defence-security/between-the-devil-and-the-deep-seachinas-options-in-afghanistan-by-gp-capt-dr-r-srinivasan/ pág. 174
https://openalex.org/W4385829593
https://rbc.inca.gov.br/index.php/revista/article/download/3866/2707
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Mortalidade por Câncer Ginecológico no Rio de Janeiro (ex-Estado da Guanabara) 1965/ 73
Revista Brasileira de Cancerologia
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Trabalho realizado para o xi congresso Brasileiro de Ginecologia e Obstetrícia, Rio, 31 de agosto a 6 de setembro de 1975. Professor Adjunto da Escola Nacional de Saúde Pública - Fundação Oswaldo cruz. Rio de Janeiro. Bolsista da Escola Nacional de Saúde Pública - FIOCRUZ - Rio de Janeiro. Assessora de Epidemiologia da Secretaria de Saúde do Rio de Janeiro. Médico do Serviço de Bioestat(stica da Secretaria de Saúde do Rio de Janeiro. Mortalidade por Câncer Ginecológico no Rio de Janeiro (ex-Estado da Guanabara) 1965/ 73 (1) Eduardo de Azeredo Costa (2) Carlos Henrique Klein (3) Alys Bittencourt Furtado (4) Marcos Fernandes da Silva Moreira (5) Eduardo de Azeredo Costa (2) Carlos Henrique Klein (3) Alys Bittencourt Furtado (4) Marcos Fernandes da Silva Moreira (5) INTRODUÇÃO servado na tabela 1, responsáveis por cerca de lO°/o do total de óbitos ocorri- dos nos grupos etários de 35 a 64 anos Nos grupos etários de 25 a 64 anos mais de 40% dos óbitos por neoplasias eram desse grupo de causas. A mortalidade por neoplasias malignas no Rio de Janeiro tem crescido nos últimos anos. De 1950 a 1972 o coeficiente por 100 000 habitantes passou de 77,4 para 117,5. Esse aumento, no entanto, foi maior no sexo masculino do que no feminino: os respectivos coeficientes no mesmo pe- ríodo de tempo passaram de 75,7 para 134,7 e de 79,0 para 101,6. g p A magnitude do problema, pois, nos esti- mulou a fazer um estudo descritivo da mortalidade por câncer ginecológico, acionando no Rio um esforço cooperati- vo entre a Escola de Saúde Pública e a Secretaria de Saúde a área de análise de dados de registro. O acréscimo verificado no sexo feminino bem pode estar creditado ao envelheci- mento da população e maior cobertura de serviços de saúde no período. A "força" de mortalidade estaria, pois, em relativa estabilidade. Isso, no entanto, não signi- fica que se trata de um problema de pou- ca importância, já que 13% dos óbitos ocorridos em mulheres do Rio de Janei- ro foram devidos a neoplasias malignas. No grupo etário de 35 a 74 anos essa pro- porção foi de 21°/o. Os tumores malignos da mama e órgãos genitais femininos que corresponderam a 4,55% do total de óbitos no período 1965/72 e 34,83% dos óbitos por neopla- sias malignas, foram, como pode ser ob- REVISTA BRASILEIRA DE CANCEROLOGIA NOVEMBRO/DEZEMBRO, 1976 42 rias uterinas elas se equivalem. Na figura 2 apresentamos a situação da mortalidade por câncer ginecológico no Rio de Janeiro em relação às cidades in- cluídas na Investigação Interamericana de Mortalidade Urbana (10). Note-se que as populações foram padronizadas por idade e que o triênio de que dispúnha- mos para o Rio não é o mesmo das ou- tras cidades, embora bastante próximo. interessante que o Rio vai se situar en- tre as cidades de taxas de câncer de ma ma elevadas e de útero baixas, com um quadro muito semelhante ao de São Paulo, ainda que no nosso caso não se tenha dado peso para causas associadas. Esse fato julgamos ajudar a validar os dados que apresentamos. MÉTODOS Os óbitos ocorridos no ex-Estado da Gua- nabara são reqularmente codificados. A causa básica de morte é classificada se- gundo a Classificação Internacional de Doenças (CID), tendo sido utilizada a 73 Revisão até 1967 e a partir daí @ 8. p Os óbitos do período 1965/73 já haviam sido transferidos para cartões perfura- dos. Os tumores ginecológicos malignos de todas as categorias constantes da CID que se mantiveram individualizados nas duas revisões foram apurados, sendo, no entanto, posteriormente, reagrupados em função da localização, quando o número de óbitos era limitado. Ao pé da tabela 2 apresentamos esses grupos e os núme- ros dos códigos correspondentes. De to- dos os demais itens codificados, julga- mos importante apurar a distribuição por grupo etário, cor, estado civil, região ad- ministartiva da residência e local do óbi- to. Um dado que desse informação sobre situação sócio-econômica, como ocupa- ção, não pôde ser processado por falta de código e classificação adequados. A seguir comentaremos os resultados por categoria estudada. Tumor Maligno de Mama (170 - 7. revi- são e 174 - 8.8 revisão) Tumor Maligno de Mama (170 - 7. revi- são e 174 - 8.8 revisão) ) A par da leve tendência a aumento já re- ferida, observou-se uma peculiar distri- buição etária (figuras 3 e 4). No gráfico semi-logarítmico, como já observara Li- lienfeld, a curva apresenta rápida eleva- ção entre os grupos etários de 25 a 34 anos e de 35 a 44 (4). A partir daí sofre inflexão, diminuindo o ritmo de incremen- to nas idades mais avançadas. Isso, no entanto, como pode ser visto na figura 4, é decorrência de sua função de cresci- mento ser linear, isto é, há um cresci- mento constante do tipo aritmético dos 25 anos em diante, que aliás se traduz por uma reta em qualquer dos triênios estudados. Geradas as tabelas, as taxas foram cal- cutadas a partir de estimativas da popu- lação baseadas nos censos de 1960 e 1970, e projetadas pelo método geomé- trico. Pela natureza descritiva do estudo não houve preocupação de maior análise es- tatística, porém, foram utilizados testes de hipótese e padronização dos coeficien- tes, quando oportuno. RESULTADOS E COMENTÁRIOS A figura 1 e a tabela 2 mostram as taxas de mortalidade por 100 000 mulheres por ano com a posição relativa das várias ca- tegorias que utilizamos para classificar os casos de câncer ginecológico. Embora o período de observação seja muito pe- queno, parece haver uma ligeira tendên- cia a aumento do câncer de mama e do câncer do corpo uterino, enquanto que o de colo tenderia a declinar. A localização mamária é que apresenta as maiores ta- xas, mas se somarmos todas as catego- A tabela 3 mostra uma taxa, ainda que padronizada por idade, maior em não brancas do que em brancas, porém, devi- do ao fato das estimativas por cor serem pouco precisas, já que essa característi- ca não foi incluída no censo de 1970, são de pouca confiança. Melhor analisada, então, pela proporção de câncer de ma- mo sobre o total de câncer ginecoógico, a mortalidade proporcional foi significan- temente maior em brancas do que em NOVEMBRO/DEZEMBRO 1976 REVISTA BRASILEIRA DE CANCEROLOGIA 43 não brancas (tabela 4). não brancas (tabela 4). aleatórias são, pois, grandes. A distribuição por região administrativa (figura 11) mostrou um aspecto peculiar importante: as taxas mais baixas estão na zona de condições sócio-econômicas melhores (Santa Tereza, Botafogo, Copa- cabana, Tijuca, Vila Izabel) e as mais al- tas em áreas pobres com grandes con- centrações populacionais, no já referido "corredor epidemiológico" de doenças in- fecciosas do Rio de Janeiro, ou em áreas de até há poucos anos alta incidência de meretrício de baixo padrão econômico (Portuária, Rio Comprido, São Cristóvão, Ramos, Penha, rajá). Em relação ao estado civil (tabelas 5 e 6) observa-se que, uma vez ajustadas por idade, a maior taxa recaiu entre soltei- ras. As demais categorias apresentaram riscos muito semelhantes. Esse achado é concordante com o de outros estudos e traduziria um efeito "protetor" da pari- dade precoce, com a qual o estado civil apresentaria, mesmo na sociedade mo- derna, ainda algum grau de correlação, como também o apresenta em relação a outros fatores que podem ser intervenien- tes em termos de causalidade, como pa- ridade, lactação e vida sexual ativa. (4, 5,6,7,8,9 e 12). Esses dados concordam com observações que levaram a crer que o câncer de colo está relacionado, possivelmente, com uma causa exógena, possivelmente um vírus transmitido por contato venéreo, cujo candidato mais importante é o Her- pes tipo II (HSVIl). RESULTADOS E COMENTÁRIOS Se isso não for ver- dade, pelo menos parece certo que se constitui em doença que está relaciona- da com promiscuidade sexual, vida se- xual precoce, número de gestações, núme- ro de abortos, etc. (1,2,3,11 e 12). A distribuição por região administrativa mostra que as iegiões com mais altas taxas são as áreas de maior proporção de classe média ou alta, tais como: Cen- tro, Botafogo, Copacabana, Lagoa, Tijuca, Vila Izabel e Engenho Novo, caindo em gradiente na direção de Santa Cruz e Campo Grande (figura 10). Tumor Maligno de Colo Uterino (171 - 7." revisão e 180 - 8." revisão) Tumor Maligno de Colo Uterino (171 - 7." revisão e 180 - 8." revisão) Além da ligeira tendência a declinar, já assinalada anteriormente, o câncer de co- lo apresenta uma distribuição etária que, embora muito semelhante à do câncer de mama até o grupo etário de 35 a 44 anos, sofre a partir daí um processo de dimi- nuição do ritmo de incremento (figura 3). Já a figura 5 mostra que na verdade a aceleração inicial é retomada a partir dos 65 anos. Tumor Maligno de Corpo Uterino (172 - 7." revisão e 182.0 8." revisão) Sendo uma localização pouco freqüente, é difícil afirmar se a leve tendência a su- bir verificada no período é significativa. Esse tumor não mostrou padrão claro em relação à cor e ao estado civil. Já em relação à idade, verifica-se que a mortalidade só começa a ser significati- va no grupo etário de 35 a 45 anos, subin- do a partir daí de modo contínuo, lem- brando, com uma década etária de atra- so, em que pesem flutuações nos triê- nios e taxas de nível mais baixo, a curva do câncer de mama (figuras 3 e 6). A distribuição por Região Administrati- va também lembra a do câncer de mama com maiores taxas nas zonas de melho res condições sócio-econômicas (figura 12). Tumor Maligno de Corpo Uterino (172 - 7." revisão e 182.0 8." revisão) Sendo uma localização pouco freqüente, é difícil afirmar se a leve tendência a su- bir verificada no período é significativa. Esse tumor não mostrou padrão claro em relação à cor e ao estado civil. RESULTADOS E COMENTÁRIOS Já em relação à idade, verifica-se que a mortalidade só começa a ser significati- va no grupo etário de 35 a 45 anos, subin- do a partir daí de modo contínuo, lem- brando, com uma década etária de atra- so, em que pesem flutuações nos triê- nios e taxas de nível mais baixo, a curva do câncer de mama (figuras 3 e 6). A distribuição por Região Administrati- va também lembra a do câncer de mama com maiores taxas nas zonas de melho res condições sócio-econômicas (figura 12). Tumor Maligno de Corpo Uterino (172 - 7." revisão e 182.0 8." revisão) Sendo uma localização pouco freqüente, é difícil afirmar se a leve tendência a su- bir verificada no período é significativa. Esse tumor não mostrou padrão claro em relação à cor e ao estado civil. Já em relação à idade, verifica-se que a mortalidade só começa a ser significati- va no grupo etário de 35 a 45 anos, subin- do a partir daí de modo contínuo, lem- brando, com uma década etária de atra- so, em que pesem flutuações nos triê- nios e taxas de nível mais baixo, a curva do câncer de mama (figuras 3 e 6). Em relação à cor, verificou-se que a taxa entre não brancas é duas vezes maior do que entre brancas, porém, vale a mesma restrição feita em relação ao câncer de mama (tabela 3). A proporção de câncer de colo sobre o total de câncer ginecoló- gico mostrou-se significativamente me- nor entre brancas do que não brancas (tabela 4). A distribuição por Região Administrati- va também lembra a do câncer de mama com maiores taxas nas zonas de melho res condições sócio-econômicas (figura 12). Em relação ao estado civil, encontramos apenas uma taxa padronizada (tabela 6) mais baixa em desquitados, porém, esse grupo é muito pequeno e as variações Tais características poderiam estar rela- cionadas à menor acessibilidade diagnós. REVISTA BRASILEIRA DE CANCEROLOGIA NOVEMBRO/DEZEMBRO. 1976 44 grupos ('ovário" e "demais") (figura 1) é bastante semelhante e oposta, permi- tindo supor que possa haver um balanço entre as duas que mais possivelmente dependeria da quantidade de tumores ovarianos não especificados que seriani incluídos entre os "restantes". tica desse tumor, favorecendo sua detec- ção mais tardia na vida e em classes mais favorecidas em termos de assistência médica. RESULTADOS E COMENTÁRIOS Outros Tumores Malignos do Útero Es- pecificados, Inclusive o Corioepitelioma, e não Especificados (173 e 174 - 7. re- visão e 181 e 182.9 - 8. Revisão) Outros Tumores Malignos do Útero Es- pecificados, Inclusive o Corioepitelioma, e não Especificados (173 e 174 - 7. re- visão e 181 e 182.9 - 8. Revisão) É um grupo de difícil análise porque seu conteúdo maior é constituído de neopla- sias de localização uterina não especifi- cada No entanto, a curva etária de ambos é bem diversa, diversa aliás dos outros grupos já analisados. O tumor de ovário tem aparição precoce no grupo etário menor de 15 anos. A partir do grupo etá- rio de 25 a 35 anos, aumenta exponen- cialmente, diminuindo o ritmo a partir do grupo etário de 55 a 65 anos, dando a impressão de haver três fases ou três formas distintas dessa patologia. Já os "demais" ou "restantes", com poucos casos presentes em menores de 15 anos, sobem exponencialmente e consistente- mente até o grupo etário de 75 anos e mais. (figuras 3, 8 e 9). É um grupo de difícil análise porque seu conteúdo maior é constituído de neopla- sias de localização uterina não especifi- cada. A distribuição por cor e estado civil, bem como a distribuição geográfica (tabela 13) lembram a distribuição do tumor do colo uterino, o que faz pensar que esse seja o tumor mais presente nas declara- ções de óbito sem especificação quanto à natureza do tumor. A mortalidade por grupo etário (figuras 3 e 7), apesar de mostrar semelhanças importantes com o câncer de colo nas idades mais jovens, passa a st compor- tar, a partir do grupo etário de 35 a 45 'anos, de maneira semelhante à curva dos tumores malignos do corpo uterino, ainda que com taxas bem maiores. Pare- ce, pois, que, especialmente nas idades mais avançadas, há uma contribuição im- portante de tumores de corpo uterino não especificados nas declarações de óbitos e que aí são classificados. A distribuição por região administrativa da mortalidade por câncer de ovário é su- perponível à do câncer de mama, isto é, com taxas mais elevadas nas áreas mais ricas, enquanto que o padrão do grupo "restantes", embora semelhante, apre- senta discrepâncias se dirigindo mais a uma distribuição do tipo da apresentada pelo câncer do colo uterino. Tumor Maligno de ovário (175.0 - 7.1 re- visão e 183.0 - 8. RESULTADOS E COMENTÁRIOS revisão) e Demais Tumores Malignos (Não especificados co- mo mamários, uterinos ou de ovário) - (183.1,183.9 e 184 da 7." revisão e 175.1, 175.8, 175.9 e 176 da 8." revisão). AGRADECIMENTO Os autores agradecem a colaboração de Lauro de Oliveira e Silva e de Luiz Paulo Fiares Avelino da Divisão de Processa- p RESUMO E CONCLUSÕES O t li Os autores realizaram um estudo descri- tivo da mortalidade por câncer ginecoló- gico na cidade do Rio de Janeiro (Ex-Es- tado da Guanabara) no período 1965/73, analisando os dados de valor epidemioló- gico constantes do atestado de óbito. O tumor de ovário apresenta-se como a terceira causa, em ordem de magnitude, de mortalidade por cânceres ginecológi- cos. Em função da Classificação Internacional de Doenças da O.M.S. e do número de óbitos de cada item da mesma, utilizaram as seguintes categorias de estudo: tumor maligno de mama (170 - 7." Revisão e 173 - 8. Revisão); tumor maligno de colo uterino (171 - 7." Revisão e 180 - 8." Revisão); tumor maligno de corpo ute- rino (172— 7." Revisão e 182.0 - 8. Re- visão); outros tumores malignos do úte- Parece estar em relativa estabilidade no período observado, ainda que haja um decréscimo em 1972, ano que surpreen- dentemente apresenta um acréscimo dos "demais" tumores ginecológicos e gran- de proporção de localizações não espe- cificadas. Na verdade, a evolução temporal dos dois NOVEMBRO/DEZEMBRO. 1976 REVISTA BRASILEIRA DE CANCEROLOGIA 45 ro (173 e 174— 7. Revisão e 181 e 182.9 - 8.a Revisão); e demais tumores gine- cológicos malignos (183.1, 183.9 e 184 - 7. Revisão e 175.1, 175.8, 175.9 e 176 da 8. Revisão). ro (173 e 174— 7. Revisão e 181 e 182.9 - 8.a Revisão); e demais tumores gine- cológicos malignos (183.1, 183.9 e 184 - 7. Revisão e 175.1, 175.8, 175.9 e 176 da 8. Revisão). A mortalidade por outros tumores ma- lignos do útero é de difícil análise por- que em sua maioria é constituída por óbi- tos classificados como de localização não especificada do útero. Suas caracte- rísticas levaram os autores a julgar que essa categoria inclui em sua maioria tu- mores malignos de colo nas idades mais jovens (até 45 anos) e a partir daí há pre- domínio de câncer de corpo uterino; Além de discutir a peculiar distribuição etária de cada uma dessas categorias o trabalho mostrou que: 1 . p RESUMO E CONCLUSÕES O t li A mortalidade por câncer de mama foi a mais elevada das categorias e esteve associada à cor (nas brancas é maior), ao estado civil (nas solteiras é maior) e ao local de residência (no sentido de que nas Regiões Administrativas de melho- res condições sócio-econômicas é maior, caindo em direção às áreas de tipo rural); A mortalidade por câncer de colo se- guiu-se em magnitude, apresentando-se associada à cor (é mais elevada em não brancas) e ao local de residência, no sentido de que as taxas mais elevadas ocorreram em áreas de condições sócio- econômicas piores; A mortalidade por câncer de ovário foi a terceira em freqüência quando con- siderados os itens individualizados de Classificação Internacional de Doenças. Foi também um pouco mais freqüente entre brancas, solteiras e em regiões me- lhores do ponto de vista sócio-econômi- co. Sua peculiar distribuição etária suge- re a existência de três fases ou tipos da doença: uma com predominância até os 25 anos, outra daí até aos 55 anos e a terceira daí em diante. A mortalidade pelos demais cânce- res ginecológicos parece ter um compor- tamento de equilíbrio quantitativo com o câncer de ovário. Suas características de estado civil, cor e local de residência também coincidiram. Porém, a distribui- ção etária é divergente apresentando um crescimento constante durante a vida. A mortalidade por câncer do corpo de útero foi a mais baixa das categorias es- tudadas. Não apresentou associação ní- tida com estado civil e cor. A distribui- ção por região administrativa mostrou predominância nas áreas de melhores condições sócio-econômicas; mento de Dados da Secretaria de Saúde do Rio de Janeiro. mento de Dados da Secretaria de Saúde do Rio de Janeiro. REFERÊNCIAS BIBLIOGRÁFICAS ADELSTEIN, A.M. et ai. - Mortality from Carcinoma of the Uterus. An interventional cohort study. Br, J. Prev. Soc. Med. 25 (4) 186-91. 1971. MIRRA, A.P., et ai. - Estudo epidemiológico do cancer de mama numa área de alta pari- dade: São Paulo, Brasil, - Rev, Assoc. Med. Bras. 18 (9): 357-364, 1972. BERAL, V. - Cancer of the Cervix: A Se- xuaiiy Transmitted Infection? The Lancet, May 25, 1974 (pp. 1037-1040). PASCUA, M. - Trends of female mortality frçm cancer of the breast and cancer of the genital organs. Buii. Wid. Hith. Org., 15: 5-41, 1956. KALLNER, G. et ai. - Site Misassignement of Cervical Cancer. In Cancer Morbidity and Mortality in Israei: 1950-1961. Part II. Wld. Hlth. Org. Genebra, 1966. PUFFER, E.R. & Griffith, G.W. - Caracteris- ticas de ia Mortaiidad .Urbana. Organização Panamericana de Saúde, Publicação Científi- ca n.' 151 - Washington, 1968. LILIENFELD, A.M. - The relationship of con- cer of the femaie breast to Artificial Meno- pause and Marital Status. Cancer 9: 927-934, 1956. SELLERS, A.H. & McLerie, E.E. - A Note on Trends in Mortality from Cancer of the Cer- vix, Ontario an British Coiumbia, 1950-1971 - Canadian J. of P. Heaith. 64: 364-367, 1973. LOWE, C. R. & Mac Mahon, B. - Breast Can- cer and Reproductive History of Women in South Wales. Lancet, 1: 153, 1970. MAC MAHON et ai. - Lactation and Cancer of the Breast. Summary of an international study. Buli. Wid. Hith. Org., 42: 185, 1970. 12. STOCKS, P. - Statistical Investigation Con- cerning the Causation of Various Forms of Human Cancer. In Cancer, vol. 3: 116-172, de Ravan, R.W. ed. - Butterworth and Co, Lon- don, 1958. 12. STOCKS, P. - Statistical Investigation Con- cerning the Causation of Various Forms of Human Cancer. In Cancer, vol. 3: 116-172, de Ravan, R.W. ed. - Butterworth and Co, Lon- don, 1958. MAC MAHON, et ai. - Age at first birth and breast risk. Buli. Wiid. Hith. Org., 43, 209, 1970. MAC MAHON, et ai. - Age at first birth and breast risk. Buli. Wiid. Hith. Org., 43, 209, 1970. SUMMAAY A descriptive study on mortality by gyne- cological cancer based on death certifi- cates of the former State of Guanabara during the period 1965/73 was perfor- med. tional Classification of Causes of Death. Apart from the peculiar age distribution of each gynecological malignant growth, interesting patterns were observed in re- Iation to marital status and geographical distribution revealing, particularly, clus- tering in the poorer areas for cancer of the cervix and, in the richer aeras, for breast cancer Age, marital status and residency at death were analysed in relation to the site of cancer, according to the Interna- REVISTA BRASILEIRA DE CANCEROLOGIA NOVEMBRO/DEZEMBRO, 1976 46 REFERÊNCIAS BIBLIOGRÁFICAS TABELA 1 ÓBITOS POR TODAS AS CAUSAS, POR CÂNCER DE TODAS AS LOCALIZAÇÕES E POR CÂNCER GINECOLÓGICO EM MULHERES NO RIO DE JANEIRO (EX-ESTADO DA GUANABARA) - PERÍODO 1965/72 - CÂNCER GINECOLÓGICO GRUPOETÁRIO NPDEOBITOS NPDEOBITOS - (ANOS) POR TODAS PORCÂNCER AS CAUSAS EM GERAL N9deObitos Sobre Total do Total de Obi- de Obitos tos por Câncer O - 14 29.554 422 20 0,07 4,74 15-24 4,267 268 42 0,98 15,67 25-34 6.342 627 259 6,07 41,31 35-44 9.644 1.923 957 9,92 49,77 45-54 12.087 3.121 1.468 12,14 47,04 55 - 64 17.062 3.958 1.451 8,50 36,66 65-74 22.470 3.894 1.114 4,96 28,61 75emais 31.656 3.139 742 2,34 23,64 Totai 133.082 17.352 6.053 4,55 34,88 REVISTA BRASILEIRA DE CANCEROLOGIA NOVEMBRO/DEZEMBRO, 1976 47 N LO (O 0) N OS LO LO N LO LO LO LO (') C') C') C') C') C') C') C') (') N - N (') LO 0) N 0) ( .cz: N O cq 0), L CN C"J C') C') — ClJ N m N m N LO 11:t m C') LO LO r- LO LO ' LO LO LO c0rN- C'C)LO N N LO C') LO LO N' LO LO r LO N. N- LO 112- ciLO LO LO LO LO LO LO N. LO LO 0 w z uJ o 0 0 z (1) USI w 1 -J O O c') O LO O LO 0) 00 O-o U) 0 <E x w < o - - (ci: w , <0< wO z o 0 E- Lii ci 0w 0w a - w cn '0 00 u, 00 f_J (J)j ui LU wo (1) > o o 0' N -J o o -J w 1- o o C') o a O O N O O o LO LO N- LO 0) O CN C') LO LO co LO LO r-. N N- r-. 9 9 01 0) 0) 0)0)0)0) o z a) E o o a o o 'a) o E o e - a) o o . REFERÊNCIAS BIBLIOGRÁFICAS --o o a) a 00 - o 00 'a) 0 o 00 a) o "O E 0,2 co II o NO) > (ora) r-co o CL - o 0 0 - o 0.0 (0 't E r-co 9' a)E LÜ D co o, a 0a co o S 0 0 0 000 ° , r- co 2' icic'j ao E c co o' o' - "E r- co o,,,, o.o. 0.0. 0.0. 0.0. a 0.0. 0.0. O 00 CC CC CC CC CC ii 1 II II -° g ii 00 00 00 00 00 00 ' ' •9' • ' ' ' •9, >> >> >> a) a) >> - .E >> >> -- Q))1) a)Q, C °' Q) a) a) a).a). a).a). a).a). a).a). o r- co NO r-co r-co ocç r- co r- co 0a) ii Eo II li Eo 00 00 00 00 F- - 00 00 I- , IE I N LO (O 0) N OS LO LO N LO LO LO LO (') C') C') C') C') C') C') C') (') N - N (') LO 0) N 0) ( .cz: N O cq 0), L CN C"J C') C') — ClJ N m N m N LO 11:t m C') LO LO r- LO LO ' LO LO LO c0rN- C'C)LO N N LO C') LO LO N' LO LO r LO N. N- LO 112- ciLO LO LO LO LO LO LO N. LO LO 0 w z uJ o 0 0 z (1) USI w 1 -J O O c') O LO O LO 0) 00 O-o U) 0 <E x w < o - - (ci: w , <0< wO z o 0 E- Lii ci 0w 0w a - w cn '0 00 u, 00 f_J (J)j ui LU wo (1) > o o 0' N -J o o -J w 1- o o C') o a O O N O O o LO LO N- LO 0) O CN C') LO LO co LO LO r-. N N- r-. 9 9 01 0) 0) 0)0)0)0) o z ° , r- c co o.o. 0.0. 0.0 00 CC C ii 1 I 00 00 0 >> >> > a) Q))1) a).a). a).a). REFERÊNCIAS BIBLIOGRÁFICAS a).a r- co NO r-c ii 00 00 0 REVISTA BRASILEIRA DE CANCEROLOGIA NOVEMBRO/DEZEMBRO, 1976 48 o 2 q c a CV) CN C'•4 > o o io co CC) o O (3) CN 1 O) E- d- d O o CN — co o (O CV) h 0 N ('3 o - ('3 o 4-' (('3 o Z E- , O O q 0 1- 0j 0 0 <CV) N wOl 0 Lo )I(3) -:1 DCC) ZO) w < C'I oI (30 Oci, - 0 I w 1 (ocr - a. 'uJ 1 << 0 z< < (0< (> << N CV) NO — < zo 00 - - UJ cr< < O OH cr < <(') O Q LU (OX <O E- (5 -, '0 w -JO 0 00 -0 Ir (1) 0 w w O -J o E- o o o Ir — (1) o OCO oqo O o LO z o dod OCO o O —, e e e e w O o - E o - - co o q'& -'J O LO LO CV) LO o o- o o o -J CCV) E < CO CO lzt O) > ::: O) WLC) o co CC) CC) CV- ZC) — O) - (5 CC LO 0< zcr CV) c'J.- Oh (c cq o co ,- (00(0 (O < w < -J O z LU < cr o E-O E- C)c' co 00 LU ( C (OC' csicV) CC) r' E- - ____ w o - b C"J 0) (Oh 0) co - '0 0- o - co - co N co - '— cli CN N -J o LO N-.-- N LO co (J) O) CV) cz '< o > '< / O N / v o / 1< < / 0 cr o 0/ -/ °- o / ti o c cu 0 / '3) - O 1- CV) LO CC) - CV) REVISTA BRASILEIRA DE CANCEROLOGIA NOVEMBRO/DEZEMBRO, 1976 49 o o Q o co cli co co o:r) cn <o - co co co-c' - co r-. REFERÊNCIAS BIBLIOGRÁFICAS O) r — 0 - -Ir) 0 0 0 w_ o jNC'4 C'D co - o: V) w CQV)< CN'-O)-- C-'J UJ0 Ci 0- W Lii 0< zo: 3< Oco V)Z o - o: 0(D0 çrco (D Cl, o 0> C")CNO)LC) ' 0 - cNcoo) LO DE- N4 '- oC co Z&) Lfl<LLJ - O N'C')C) cli - r -J < o WH o o: LI) z o W E O) co rc'c') Ir) LO (V) c) -J E- o OCLO <u-J d2 o: 00 o 6 -c-- O)0O) o, 'OZ — uJ cn O)coco r- o:o 'LflC) ("1 0< o CI' 2 Lii Diii O -j <.1 O 0_J < - o: -c cu > o- cu - - o m - o.- - ai 0(/)>0 E- , O O) <NV) -W 0OO) g (/)_Jl0 - cocoor- - - E-- 00 i (r W w w o o j< cn a0- '-O) qo C')C4O Z< <Wo Do: 0< DLI) u)3 <0 1< cr- 0- > coo L- lq c co O) o CV)LOC)O ZW N 0 - co LC) O) co lo O) ci co LU -J O r- ZZ <0< 0 W < o o: o w E <o: i_ ( '3 0 -J 0< 0w O co or- O)LOCN cor- - 0 rj cr Po LU Z< -co 0'- < ro)coLr) o:w wO - ou) Zw 0w 0-J O o o -J - 00 < - :5c cu E- LU ru -a .- > O 0 o 0u>O co O) c) co CN C) C) O) o 1-o (4) c-'J 4-' o 1- REVISTA BRASILEIRA DE CANCEROLOGIA NOVEMBRO/DEZEMBRO, 1976 50 FIGURA A MORTALIDADE POR CANCER EM GERAL E POR CANCER GINECOLOGICO POR 100000 MULHERES DO RIO DE JANEIRO (EX-ESTA000G GUANABARA) PERI000 1965/1973 COEF/ 100000 MULHERES 150 110 100 CANCEREMGERAL 90 80 70 60 50 :: • . 20 A CANCER DE MAMA CANCER DE IíTER0-TOTAL(A+8+C) 10 9 8 OUTROS CNCERESDEITER0 (C) 7 6 ------a,---- . CANCER DE COLO UTERINO (A) 5 4 3 CANCER DE OVA'RIO DEMAIS LOCALIZACÕES E SEM ESPECIFICACSO --e' a,-- e CNCER DE CORPO UTERINO (B) 1 /fr 0,9 / 0,9 07 _. REFERÊNCIAS BIBLIOGRÁFICAS -------aí 0,6 -- 0,4 0,3 1965 66 67 68 69 70 71 72 73 74 ANO CANCEREMGERAL e CNCER DE CORPO UTERINO (B) NOVEMBRO/DEZEMBRO, 1976 REVISTA BRASILEIRA DE CANCEROLOGIA 52 FIGURA 3 A MORTALIDADE POR CANCER GIMECOLOGICO POR GRUPO ETARIO -RIO DE JANEIRO (EX-ESTADO DA GUANABARA) PER(000 1965 /1973 100 MAMA v OUTROS DE ATERO / COLODEÚTERO / OVRIO / - / --- / // •___ •/__--- RESTANTES 10 // // 2 / / A Á/ 1/ /• / / /,' •// i/ '- - 1 / 0,1 / .. GE(ANOS) O 15 25 35 45 55 65 75 1 NOVEMBRO/DEZEMBRO, 1976 REVISTA BRASILEIRA DE CANCEROLOGIA 51 e o o o o o w 1- o o (1) 1h o D 1- 1h o 1- o z o r- .-d o -j o o 1h W o o o o z z _I J o o D : 1- 1- iii o o o Id, o e e REVISTA BRASILEIRA DE CANCEROLOGIA NOVEMBRO/DEZEMBRO, 1976 51 (1) uJ uJ— ILiJ -iz uJ O o oQ ouJ ui -J o- o -J -J o o WW ZO C'J (flZ LiJ cp •0 ca 0W o uJ 00 o 0 - 3- (n Ct)W oz o (1,0 UJ LiJ 00 o W O (fl h L * ,- -; o a. o O i o * * o x — 1•- ij J i o u) w o - E ° o w CO (1) J (1) O (1) C13 O ..J O C'J cp NOVEMBRO/DEZEMBRO, 1976 REVISTA BRASILEIRA DE CANCEROLOGIA 53 FIGURA 4 MORTALIDADE POR CÂNCER DE MAMA POR GRUPO ETRIO'RIO DE JANEIRO (Ex-ESTADO DA G1JANABARA) PER(000 1965/1973 114 uJ ix uJ 1 -J o o o o- o ir tu o d o -J 1- o ui tu 1-• z tu o LL tu o o FIGURA 4 MORTALIDADE POR CÂNCER DE MAMA POR GRUPO ETRIO'RIO DE JANEIRO (Ex-ESTADO DA G1JANABARA) PER(000 1965/1973 114 uJ ix uJ 1 -J o o o o- o ir tu o d o -J 1- o ui tu 1-• z tu o LL tu o o NOVEMBRO/DEZEMBRO, 1976 REVISTA BRASILEIRA DE CANCEROLOGIA 54 FIGURA 5 A MORTALIDADE POR CANCER DE COLO DE UJTERO POR G. ETRIO•RIO DE JANEIRO (EX-ESTADO DA GUANABARA) PERÍODO 1965 /1973 (1) ui ir 1 -J o o o o 2 ir o a- uJ 1- z uJ U. o U i3 55 45 55 65 75 (anos)G.E. (anos)G.E. REVISTA BRASI LEIRA DE CANCEROLOGIA NOVEMBRO/DEZEMBRO, 1976 55 FIGURA 6 1' MORTALIDADE POR CANCER DE CORPO DE ÚTERO POR G.ETA'RIO•RIO DE JANEIRO (EX-ESTADO DA GUANABARA) PERI'ODO 19 65/1973 (1) uJ 1 -J o o o 8 o a- uJ 1•- 7 o o o EVISTA BRASI LEIRA DE CANCEROLOGIA NOVEMBRO/DEZEMBRO, 1976 55 FIGURA 6 1' MORTALIDADE POR CANCER DE CORPO DE ÚTERO POR G.ETA'RIO•RIO DE JANEIRO (EX-ESTADO DA GUANABARA) PERI'ODO 19 65/1973 (1) uJ 1 -J o o o 8 o a- uJ 1•- 7 o o o O 15 25 35 45 55 65 75 (anos) SE. REVISTA BRASI LEIRA DE CANCEROLOGIA NOVEMBRO/DEZEMBRO, 1976 55 75 (anos) SE. O NOVEMBRO/DEZEMBRO, 1976 REVISTA BRASILEIRA DE CANCEROLOGIA 56 NOVEMBRO/DEZEMBRO, 1976 REVISTA BRASILEIRA DE CANCEROLOGIA FIGURA 7 MORTALIDADE POR TUMORES MALIGNOS DO ÚTERO NAO ESPECIFICADOS OU ESPECIFICADOS,MAS NAO DE COLO OU CORPOS POR GRUPO ETRIO NO RO DE JANEIRO (-FrAnr nA ri IArIAftPA) PFRICIBfl 1RR O 15 25 35 45 55 65 75 (onos) G.E. LSJ uJ 1 -J o 8 o o o a. 1- z IJ o uJ o o 56 NOVEMBRO/DEZEMBRO, 1976 REVISTA BRASILEIRA DE CANCEROLOGIA FIGURA 7 MORTALIDADE POR TUMORES MALIGNOS DO ÚTERO NAO ESPECIFICADOS OU ESPECIFICADOS,MAS NAO DE COLO OU CORPOS POR GRUPO ETRIO NO RO DE JANEIRO (-FrAnr nA ri IArIAftPA) PFRICIBfl 1RR LSJ uJ 1 -J o 8 o o o a. 1- z IJ o uJ o o (onos) G.E. NOVEMBRO/DEZEMBRO, 1976 REVISTA BRASILEIRA DE CANCEROLOGIA 57 REVISTA BRASILEIRA DE CANCEROLOGIA NOVEMBRO/DEZEMBRO, 1976 57 FIGURA 8 A MORTALIDADE POR CANCER DE OV/RIO POR GRUPO ETLRIO'RIO DE JANEIRO (Ex-ESTADO DA GUANABARA) PERI'ODO 19 65 /1973 co fc Ici x —J o 8 ac o o o- tcJ o 4 o —J 4 1— o w o LcJ z w c-) U. o o O 15 25 35 45 55 65 75 (anos) G.E. FIGURA 8 A MORTALIDADE POR CANCER DE OV/RIO POR GRUPO ETLRIO'RIO DE JANEIRO (Ex-ESTADO DA GUANABARA) PERI'ODO 19 65 /1973 co fc Ici x —J o 8 ac o o o- tcJ o 4 o —J 4 1— o w o LcJ z w c-) U. o o FIGURA 8 A MORTALIDADE POR CANCER DE OV/RIO POR GRUPO ETLRIO'RIO DE JANEIRO (Ex-ESTADO DA GUANABARA) PERI'ODO 19 65 /1973 co fc Ici x —J o 8 ac o o o- tcJ o 4 o —J 4 1— o w o LcJ z w c-) U. o o x —J o 8 ac o o o- tcJ o 4 o —J 4 1— o w o LcJ z w c-) U. o o O 15 25 35 45 55 65 75 (anos) G.E. O O 15 (anos) G.E. (anos) G.E. 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A semi-empirical model to predict excess pore pressure generation in partially saturated sand
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1 Introduction skeleton, np is porosity of soil, and Kf is the bulk stiffness of pore fluid. The induced volumetric strains in soil is highly affected by induced shear strains, soil type and density, and number of loading cycles, among other factors [9]. Seismic loadings such as earthquakes induce cyclic shear strains resulting in rearrangement and densification of soils to a more stable condition. Because the pore space of saturated soils is filled with a relatively incompressible fluid like water, the pore fluid resists against densification under an undrained condition, which leads to pore pressure build-up. This generation of pore pressure is the main mechanism in seismically induced liquefaction. In addition, pore pressure generation can significantly affect the overall seismic response including wave propagation (i.e. site response), seismic settlement, and stability; even if it does not lead to liquefaction [1-2]. The bulk stiffness of pore fluid is very sensitive to the existence of gas and is related to soil’s degree of saturation, Sr as follows: 1 1 f r r w g K S S K K = − + (2) 1 1 f r r w g K S S K K = − + (2) (2) where Kw is the bulk stiffness of water (Kw ≈2.2 GPa) and Kg is the bulk stiffness of gas (Kg ≈142 kPa). Figure 1 presents the evolution of fluid bulk stiffness with degree of saturation. Only a small reduction in degree of saturation of a fully saturated soil significantly reduces the fluid bulk stiffness and consequently the excess pore pressure generation according to Fig. 1 and Eq. 1. Experimental studies have also confirmed the significant effect of desaturation on pore pressure generation and liquefaction resistance of soils [10-14]. These facts strongly suggest that induced partial saturation can show promise as an effective measure for liquefaction mitigation. The pore pressure generation mechanisms during dynamic loadings and factors governing its amplitude have been studied for many years [3-7]. 1 Introduction Previous research indicated that the excess pore pressure generation (∆u) is mainly governed by induced volumetric strains and soil and fluid stiffness characteristics, and can be estimated using the following equation [5, 7, 8]: 1 vd p r f u n E K ε ∆ ∆= + (1) 1 vd p r f u n E K ε ∆ ∆= + (1) (1) In recent years, quite extensive research has been conducted on development of effective techniques to induce partial saturation in soils and understanding their effect on their liquefaction resistance. However, development of a framework for estimation of excess where ∆u is the excess pore pressure, ∆εvd is soil volumetric strains, Er is rebound modulus of soil * Corresponding author: majid.ghayoomi@unh.edu A semi-empirical model to predict excess pore pressure generation in partially saturated sand Sayedmasoud Mousavi1, and Majid Ghayoomi2,* 1Graduate Student, University of New Hampshire, Dept. of Civil and Environmental Engineering, Durham, NH, USA 2Associate Professor, University of New Hampshire, Dept. of Civil and Environmental Engineering, Durham, NH, USA Abstract. Past studies revealed that excess pore pressure generation due to cyclic loading is highly governed by induced strains, volumetric deformation potential of soil, number of cycles, and bulk stiffness of pore fluid. It is well established that partial saturation can significantly reduce bulk stiffness of pore fluid and consequently excess pore pressure generation during seismic loading. On the basis of that, a number of researchers have investigated induced partial saturation as an effective soil improvement technique to increase the liquefaction resistance of fully saturated soils. This paper focuses on development of a semi- empirical model to interpret the effects of partial saturation on the excess pore pressure generation in sands. In this regard, an existing strain based excess pore pressure ratio (ru) prediction model originally developed for fully saturated soils was modified to incorporate the effect of partial saturation on the excess pore pressure generation. The literature data as well as data from a series of strain-controlled direct simple shear test were used to evaluate the reliability of the proposed equation in predicting the excess pore pressure ratio in partial saturation condition. © The Authors, published by EDP Sciences. This is an open access article distributed under the terms of the Creative Commons Attribution License 4.0 (http://creativecommons.org/licenses/by/4.0/). ciences. This is an open access article distributed under the terms of the Creative Commons Attribution License 4.0 y/4 0/) https://doi.org/10.1051/e3sconf/202019502026 https://doi.org/10.1051/e3sconf/202019502026 E3S Web of Conferences 195, 02026 (2020) E-UNSAT 2020 * Corresponding author: majid.ghayoomi@unh.edu © The Authors, published by EDP Sciences. This is an open access article distributed under the terms of the Creative Commons Attribution License 4.0 (http://creativecommons.org/licenses/by/4.0/). E3S Web of Conferences 195, 02026 (2020) E-UNSAT 2020 https://doi.org/10.1051/e3sconf/202019502026 , ( ) 1 ( ) s tvp u N s tvp p f N F r f N F γ γ γ γ × × × × − = + × × × − (3) pore pressure generation in partially saturated soil has received little attention. This paper focuses on development of a semi-empirical model to interpret the effects of partial saturation on the excess pore pressure generation in sands. In this regard, an existing strain based excess pore pressure generation prediction model originally developed for fully saturated soils was modified to incorporate the effect of partial saturation on the excess pore pressure generation. The literature data as well as data from a series of strain-controlled direct simple shear test were used to evaluate the reliability of the proposed equation in predicting the excess pore pressure ratio in partial saturation condition. (3) where ru,N is the excess pore pressure ratio at Nth cycle of loading, defined as the ratio of the excess pore pressure to vertical effective stress, σ’ v (∆u/ σ’ v). γ is the induced shear strain. f is dimensionality factor and can be assumed as 1 or 2, depending on whether pore pressures is induced by one-or two-directional shaking. F, p, and s are fitting parameters which depend on volumetric deformation potential of soils and can be obtained by laboratory data-based fitting attempts. The model’s fitting parameters can also be derived by empirical equations. The parameter F is reversely proportional to the shear wave velocity of soil and takes the following functional form [16]: Fig. 1. Effect of soil saturation on the bulk stiffness of pore fluid. 0 30000 60000 90000 120000 150000 0 20 40 60 80 100 Fluid bulk stifness, Κf (kPa) Degree of saturation (%) 1.55 3810 s F V − = × (4) (4) where Vs is the shear wave velocity of soils in fully saturated condition. The fitting parameter s is proportional to soil’s fine content (FC) and can be presented as follows [16]: 0.1252 ( 1) s FC = + (5) (5) Laboratory data on different types and relative densities of sands indicated that values for parameter p varies between ±7.1% of 1 [17]. Fig. * Corresponding author: majid.ghayoomi@unh.edu 1. Effect of soil saturation on the bulk stiffness of pore fluid. 3 Proposed model A number of methodologies have been developed to quantitatively estimate the excess pore pressure generation in fully saturated soils. The methods can be generally categorized as (1) stress-based [4] and (2) strain-based [3] models. Theoretical and experimental studies indicate that the generation of excess pore pressure is mainly controlled by induced volumetric strain (Eq. 1), and that induced volumetric strain is mainly governed by the level of induced shear strains [3, 9]. Thus, strain-based models provide a more fundamental basis for estimation of pore pressure generation in soils. Although Eq. (3) has shown to be capable of estimating ru in fully saturated soils, it does not directly consider the effect of degree of saturation on excess pore pressure generation; even though this was considered in the theoretical formulation by Martin et al. [5]. In their theoretical formulation (Eq. 1), Martin et al. [5] showed that excess pore pressure generation is proportional to bulk stiffness of pore fluid. As discussed earlier, the bulk stiffness of pore fluid is highly governed by soil degree of saturation (Eq. 2 and Fig. 1). To capture the effect of partial saturation on the excess pore pressure generation, Eq. 3 was modified by implementing the effect of fluid bulk stiffness in partially saturated condition into Eq. 3. In this regard, a semi-empirical equation for prediction of ru in partially saturated condition can be obtained by implementing the ratio of pore fluid bulk stiffness in partially saturated condition to fully saturated condition into Eq. 3 as follows: Dobry [15] compiled data from seven series of undrained cyclic strain-controlled direct simple shear, cyclic triaxial, and cyclic torsional shear tests on undisturbed as well as remolded samples at varying effective confining stresses from 25 to 200 kPa and relative densities from 20-80%. Results suggested a clear trend between induced shear strain and excess pore pressure generation in sands [15]. The results also indicated the existence of a strain level below which no significant pore pressure develops. This stain level is referred to as threshold shear strain, γtvp and is around 0.01 to 0.02% for most sands [3]. On the basis of the laboratory observations and Martin et al. 3 Proposed model [5] theoretical model, Dobry [15] proposed a strain-based methodology to predict pore pressure generation in fully saturated sands, as follows: 0 0 , ( ) ( ) 1 ( ) ( ) f s tvp f u N f s tvp f K p f N F K r K f N F K γ γ γ γ × × × × × − = + × × × × − (6) 0 0 , ( ) ( ) 1 ( ) ( ) f s tvp f u N f s tvp f K p f N F K r K f N F K γ γ γ γ × × × × × − = + × × × × − (6) (6) where Kf,0 is the initial pore fluid bulk stiffness at which the fitting parameters are obtained (i.e. fully saturated 2 https://doi.org/10.1051/e3sconf/202019502026 E3S Web of Conferences 195, 02026 (2020) E-UNSAT 2020 https://doi.org/10.1051/e3sconf/202019502026 condition) and Kf is the bulk stiffness of pore fluid in partially saturated condition, which can be calculated from Eq. 2. used in the model. Parameter F was obtained using the shear wave measurements reported by Eseller-Bayat et al. [12]. The shear wave velocity of a fully saturated sample at the bottom of the sample (σ’v=9.6 kPa) was approximately 70 m/s. Since the shear wave velocity is proportional to soil’s effective stress [16], its value varied from 0 at soil surface to 70 m/s at the bottom of sample. Therefore, an average shear wave velocity of 35 m/s was considered to obtain parameter F. For clean sand tested in Eseller-Bayat et al. [12], parameter s= 1 was used in the model. Finally, a value of p=1.07 was used to fit Eq. 3 to the experimental measurements. Table 1 presents a summary of model parameters for prediction of ru in fully saturated sand. Using these parameters, the model was found to provide an acceptable prediction of ru data at different strain values and number of cycles (Fig. 2). q The methodology to obtain these parameters within the proposed equation’s relies on undrained stain- controlled test on saturated samples or empirical correlations discussed in previous section. 4.1. Literature data The experimental measurements by Eseller-Bayat et al. [12] were identified from literature for which ru data on both fully saturated and induced partially saturated soil were available. They utilized a cyclic simple shear liquefaction box to perform a series of strain-controlled simple shear tests on saturated and induced partially saturated sands [12]. The induced partial saturation was achieved by wet pluviation of sodium perborate monohydrate mixed with Ottawa sand where the reaction of the sodium perborate with pore water reduced degree of saturation by releasing oxygen bubbles. Sand specimens with different degrees of saturation were subjected to constant cyclic strains at various levels. Fig. 2. Comparison of the predicted excess pore pressure ratio data of fully saturated samples with those measured experimentally by Eseller-Bayat et al. [12]. Fig. 3 presents ru data obtained from cyclic tests on sand samples at various degrees of saturation, N=2 and 10, and γ = 0.1%. Regardless of number of cycles of loading, initial liquefaction did not occur in partially saturated samples. The ru versus degree of saturation curves showed a dramatic reduction in excess pore pressure ratio with reduction in degree of saturation up to around 72%. The ru was less affected by lowering the Sr from 72% to 60%. This behaviour is very similar to trends observed in fluid bulk stiffness versus Sr curves, which confirms the significant impact of Kf on pore pressure response of soils. Fig. 2 represents ru data obtained from cyclic tests on fully saturated sand samples at relative density Dr= 30- 40%, average effective stress, σ’v=2.5 kPa, and 2 and 10 number of cycles, N [12]. Regardless of magnitude of induced shear strain, the data shows higher values of ru at 10 cycles of loading than N=2. The excess pore pressure data shows a clear trend with shear strain level, increasing as the shear strain increases. Although the excess pore pressure data at shear strains lower than 0.005% was not reported, threshold shear strain is expected to be lower than 0.005% and was assumed to be 0.002%. This value appears to be considerably lower than the typical range (0.01% to 0.02%) for sands reported in previous studies. This may be due to very low effective stress at which the specimens were subjected to cyclic loadings. 3 Proposed model Overall, the parameters required to estimate the evolution of ru during constant-strain cyclic loading include the fitting parameters (p, F, s) and the threshold shear strain value obtained from cyclic tests on saturated samples at various shear strain amplitude as well as the Kf and Kf0 calculated from Eq. 2. Since the direct measurement of degree of saturation in a nearly saturated sample is difficult, the initial bulk stiffness of pore fluid can be indirectly calculated from B-value measurements. 4 Model validation Table 1. A summary of model parameters. Parameter f p s F value 1 1.07 1 16 Fig. 2. Comparison of the predicted excess pore pressure ratio data of fully saturated samples with those measured experimentally by Eseller-Bayat et al. [12]. 0 0.2 0.4 0.6 0.8 1 0.001 0.01 0.1 Excess pore pressure ratio, ru Induced shear strain, γ (%) N = 2 R2=0.93 N = 10 R2=0.60 Prediction (N=2) Prediction (N=10) σ'v = 2.5 kPa Sr = 100% Table 1. A summary of model parameters. In order to examine the applicability of the proposed equation for prediction of ru in a partially saturated state, the model was first calibrated by strain-controlled test results on saturated sands available in literature as well as data from this study and then estimated values from the proposed model was compared with the data obtained from tests on induced partially saturated soils. 0 0.2 0.4 0.6 0.8 1 0.001 0.01 0.1 Excess pore pressure ratio, ru Induced shear strain, γ (%) N = 2 R2=0.93 N = 10 R2=0.60 Prediction (N=2) Prediction (N=10) σ'v = 2.5 kPa Sr = 100% 4.2.1 Tested material and Experimental procedures The soil used in this study were reconstituted F-75 Ottawa sand samples. The sand was a fine silica sand classified as poorly graded sand (SP) according to Unified Soil Classification System (USCS). Table 2 describes a summary of physical and geoetechnical properties of the sand tested in this study. Fig. 3. Comparison of the predicted pore pressure ratio data of induced partially saturated sand with those measured experimentally by Eseller-Bayat et al. [12]. 0 0.2 0.4 0.6 0.8 1 40 50 60 70 80 90 100 Excess pore pressure ratio, ru Degree of saturation, Sr (%) σ'v = 2.5 kPa γ=0.1% N = 2 R2=0.86 N = 10 R2=0.69 Prediction curve 0 0.2 0.4 0.6 0.8 1 40 50 60 70 80 90 100 Excess pore pressure ratio, ru Degree of saturation, Sr (%) σ'v = 2.5 kPa γ=0.1% N = 2 R2=0.86 N = 10 R2=0.69 Prediction curve Table 2. A summary of physical and geotechnical properties of the Ottawa sand. Table 2. A summary of physical and geotechnical properties of the Ottawa sand. Property value Coefficient of curvature, Cc 1.74 Coefficient of uniformity, Cu 1.08 D50 (mm) 0.19 D10 (mm) 0.12 Specific gravity, Gs 2.65 Void ratio limits, emin, emax 0.49, 0.8 Fig. 3. Comparison of the predicted pore pressure ratio data of induced partially saturated sand with those measured experimentally by Eseller-Bayat et al. [12]. The model was found to provide a good prediction of excess pore pressure generation ratio reported by Eseller-Bayat et al. [12]. The model predicted a dramatic drop in the excess pore pressure ratio as the degree of saturation decreases which followed by a gradual decrease in ru with further reduction in the degree of saturation; a behavior which was found consistent with the experimental results as presented in Fig. 3. However, a considerable discrepancy was found between the model prediction and reported ru values at Sr= 80%. Two reasons may explain the discrepancies observed between the model prediction and ru values : 1) very low effective stress at wich samples were tested; the effective stress varied from 0 to 9.6 kPa and any shaking could result in large deformation of soil particles at soil surface level. 2) application of several cyclic test on one sample ; previous experiments have revealed that re-shearing the specimens significantly influence their volumetric deformation and pore pressure response [17-18]. Thus, although reported data by Eseller-Bayat et al. 4.2.1 Tested material and Experimental procedures [12] revealed the significance of induced partial saturation on pore pressure response, further laboratory data is required in order to examine the adequancy of the proposed model for excess pore pressure prediction. The DSS apparatus utilized in this study includes a Swedish Geotechnical Institute (SGI) configuration soil cell with a stack of Teflon coated aluminum rings. Dry pluviation method was employed in order to prepare cylindrical sand with identical relative density Dr ≈ 55%. Carbon dioxide (CO2) permeation and backpressure methods were used to ensure full saturation of samples. Pore pressure parameter (B-value) was recorded at the end of saturation process and specimens were consolidated at 50 kPa vertical effective stress. Induced partial saturation was achieved by using microbial induced partial saturation (MIPS) via denitrification. This process utilizes microbial anaerobic respiration to reduce nitrate to nitrogen gas. The generated nitrogen gas then exsolve in pore fluid and form tiny gas bubbles within the pore space. Mousavi and Ghayoomi [21] showed that the degree of saturation in this method can be adjusted by adjusting the initial concentration of nitrate. In order to desaturate samples using MIPS process, saturated soil samples were flushed by a solution medium containing a mixture of Paracoccus denitrificans (ATCC 17741) bacteria and a nutrient medium that had mineral salts and ethanol and nitrate at different concentrations. The solution volume was at least three times volume of the soil samples’ pore volume. The degree of saturation at the end of this process was calculated by measuring the volume of expelled water from sample as a result of gas formation in the soil pores. Details of MIPS process using denitrification process are elaborated in Mousavi and Ghayoomi [21]. 4.1. Literature data In order to examine the suitability of the proposed model to predict excess pore pressure ratio in partially saturated condition, predicted ru values using Eq. 6 were plotted along with the experimental measurements by Eseller-Bayat et al. [12] in Fig. 3. The fluid bulk stiffness at different saturation levels were estimated using Eq. 2. It is noteworthy that since the existence of The parameters in Eq. 6 were calibrated using the empirical methodology described in section 2. Since the cyclic tests were conducted in one dimension, f= 1 was 3 E3S Web of Conferences 195, 02026 (2020) E-UNSAT 2020 https://doi.org/10.1051/e3sconf/202019502026 this device were described in detail by Mousavi and Ghayoomi [19-20] and are briefly described here. dissolved gas can influence the fluid bulk stiffness of a saturated soil, Kf,0 is not always equal to that of de-aired water. The initial pore fluid bulk stiffness must be calculated based on initial B-value of soil sample in saturated condition. Since the B-value measurements were not available, Kf,0= 30 MPa was assumed, in order to fit the model to the experimental data. This value suggests that the degree of saturation in saturated samples was approximately 99.5%. 4.2. Experimental investigation To further examine the adequacy of the proposed model for prediction of ru in a partially saturated state, the model was fit to data points obtained from an experimental program using a Direct Simple Shear (DSS) test setup. The testing setup and procedures for Strain-controlled tests were performed at 0.1 Hz frequency for 20 cycles of loading at a constant shear level. All tests were conducted in an undrained condition 4 E3S Web of Conferences 195, 02026 (2020) E-UNSAT 2020 https://doi.org/10.1051/e3sconf/202019502026 and the excess pore pressure ratio were calculated by recording the pore pressure during cyclic loading. and the excess pore pressure ratio were calculated by recording the pore pressure during cyclic loading. 4.2.3 Model calibration and verification The proposed model parameters were obtained by fitting the predicted values of Eq 6. to the experimental ru data points of fully saturated tests using a least square fitting method. Table 3 presents a summary of the fitting parameters’ values. Using these parameters, the model yielded a very well prediction of the experimental data obtained in this study. 4.2.2 Experimental results Experimental results from undrained strain-controlled DSS tests are presented in terms of excess pore pressure ratio with induced shear strain. Fig. 4 shows the excess pore pressure ratio of Ottawa sand samples subjected to various shear strain levels. This figure shows a clear dependency of the magnitude of excess pore pressure on number of cycles and induced shear strain level. The results also indicate that the threshold shear strain falls between 0.005 and 0.025%. The magnitude of threshold shear strain was assumed to be 0.012% based on the observed trends in ru versus γ curves. This value agrees well with the reported ranges for clean sands. Table 3. A summary of model parameters. Table 3. A summary of model parameters. Table 3. A summary of model parameters. Parameter f p s F value 1 1.07 1 16 Fig. 6. Comparison of model prediction with the experimental excess pore pressure ratio data for fully saturated tests. 0 0.2 0.4 0.6 0.8 1 0.001 0.01 0.1 1 Excess pore pressure ratio, ru Induced shear strain, γ (%) N = 5 N = 10 N = 15 N = 20 Prediction curve σv = 50 kPa Sr = 100% R2= 0.99 0 0.2 0.4 0.6 0.8 1 0.001 0.01 0.1 1 Excess pore pressure ratio, ru Induced shear strain, γ (%) N = 5 N = 10 N = 15 N = 20 Prediction curve σv = 50 kPa Sr = 100% R2= 0.99 Fig. 4. Excess pore pressure ratio of fully saturated sand samples versus induced shear strain. 0 0.2 0.4 0.6 0.8 1 0.001 0.01 0.1 1 Excess pore pressure ratio, ru Induced shear strain, γ (%) N = 5 N = 10 N = 15 N = 20 σv = 50 kPa Sr = 100% Fig. 6. Comparison of model prediction with the experimental excess pore pressure ratio data for fully saturated tests. Fig. 4. Excess pore pressure ratio of fully saturated sand samples versus induced shear strain. Fig. 7. Comparison of model prediction with the experimental excess pore pressure ratio for partially saturated specimens. 5 Conclusion 9. P.M. Duku, J.P. Stewart, D.H. Whang, E. Yee. Volumetric strains of clean sands subject to cyclic loads. J. geotech. and geoenvir. Eng., 134, 8 (2008) The excess pore pressure generation in cyclically loaded partially saturated soils is a topic that has received little attention and deserves further investigation. A new semi- empirical model was presented in this study to represent the impact of partial saturation on the excess pore pressure generation of partially saturated soils. In this regard, an existing strain-based model generally developed for fully saturated soils was modified to capture the impacts of fluid bulk stiffness reduction due to desaturation on the excess pore pressure response of soils subjected to cyclic loading. A methodology also was presented to calibrate the proposed model’s parameters. The new model was found to fit well for the ru measurements reported in the literature as well as the experimental results in this study. The results presented in this study reflected considerable impacts of Sr on the excess pore pressure generation of sands. However, further testing of partially saturated soils with different types and initial conditions (e.g. density and effective stress) is needed to assess the capability of the proposed model to characterize the pore pressure response of soils in partially saturated conditions. 10. R.C. Chaney. Saturation effects on the cyclic strength of sands. In From Vol. I Earthquake Eng. Soil Dyn. -Proc. ASCE Geotech. Eng. Div. Spec. Conf., June (1978), Pasadena, California. 11. M. Okamura, K. Noguchi. Liquefaction resistances of unsaturated non-plastic silt. Soils and Found., 49, 2, (2009). 12. S. Mousavi, M. Ghayoomi. Dynamic shear modulus of microbial induced partially saturated sand. Proc. Int. Symp. Bio-mediated Bio-inspired Geotech., Atlanta, in press. 13. S. Mousavi, M. Ghayoomi. Liquefaction mitigation of silty sands via microbial induced partial saturation. In Geo-Congress 2019: Earthquake Engineering and Soil Dynamics. (2019) 14. E. Eseller-Bayat, M.K. Yegian, A. Alshawabkeh, S. Gokyer. Liquefaction response of partially saturated sands. I: Experimental results. J. Geotech. Geoenviron. Eng., 139, 6 (2013). 15. R. Dobry. Liquefaction of soils during earthquakes. Rep. No. CETS-EE-001, National Res. Council NRC, Committee on Earthquake Engineering, Washington, D.C. (1985) 4.2.2 Experimental results 0 0.2 0.4 0.6 0.8 1 70 80 90 100 Excess pore pressure ratio, ru Degree of saturation, Sr (%) R2=0.98 σ'v = 50 kPa γ=0.3%, N=10 γ=0.3%, N=20 γ=0.1%, N=10 γ=0.1%, N=20 prediction curves 0 0.2 0.4 0.6 0.8 1 70 80 90 100 Excess pore pressure ratio, ru Degree of saturation, Sr (%) R2=0.98 σ'v = 50 kPa γ=0.3%, N=10 γ=0.3%, N=20 γ=0.1%, N=10 γ=0.1%, N=20 prediction curves Fig. 5 illustrates the excess pore pressure generation ratio of MIPS treated samples at different degrees of saturation and N= 10 and N= 20. Regardless of induced shear strain level, the ru-Sr curves showed a dramatic drop in ru values when the degree of saturation decreased to 90%. The excess pore pressure magnitude was less influenced by desaturation for saturation levels lower than 90%. This behavior is very similar to theoretical trends of fluid bulk stiffness observed in Fig. 1. Fig. 5. Excess pore pressure ratio versus sample’s degree of saturation. 0 0.2 0.4 0.6 0.8 1 70 80 90 100 Excess pore pressure ratio, ru Degree of saturation, Sr (%) γ = 0.1% γ = 0.3% N = 20 N = 10 σv = 50 kPa 0 0.2 0.4 0.6 0.8 1 70 80 90 100 Excess pore pressure ratio, ru Degree of saturation, Sr (%) γ = 0.1% γ = 0.3% N = 20 N = 10 σv = 50 kPa 80 Degree of saturation, Sr (%) Degree of saturation, Sr (%) Fig. 7. Comparison of model prediction with the experimental excess pore pressure ratio for partially saturated specimens. The fitting parameters obtained for fully saturated tests were used to examine the Eq. 6 suitability to predict the experimental ru data for samples in a partially saturated condition (Fig. 7). The model successfully captured the dramatic drop in the excess pore pressure ratio of MIPS treated samples with reduction in degree of saturation from full saturation to Sr≈ 90%. The model prediction showed a gradual reduction in excess pore pressure ration with degree of saturation reduction to values lower than 90%; a behavior which was found consistent with the experimental results as presented in Degree of saturation, Sr (%) Fig. 5. Excess pore pressure ratio versus sample’s degree of saturation. 5 https://doi.org/10.1051/e3sconf/202019502026 E3S Web of Conferences 195, 02026 (2020) E-UNSAT 2020 Fig. 7. 4.2.2 Experimental results The model’s adequacy to predict the experimental ru data was also evaluated by calculating the coefficient of determination (R2). Results indicated R2 value of approximately 0.98 for the data points which indicates very good consistency of the predicted ru values from the model with the experimental measurements. 7. W.L. Finn, P.M. Byrne, G.R. Martin. Seismic response and liquefaction of sands. J. Geotech. Geoenviron. Eng. Dev. 102. (1976) 8. S. Mousavi, M. Ghayoomi. Liquefaction mitigation of sands with non-Plastic fines via microbial induced partial saturation. J. of Geotech. and Geoenvir. Eng.- Under review (2019) References 1. K. Hazirbaba, E.M. Rathje, E. M. Pore pressure generation of silty sands due to induced cyclic shear strains. J. Geotech. Geoenviron. Eng., 135, 12, (2009) 16. Carlton, B. (2014). “An Improved Description of the Seismic Response of Sites with High Plasticity Soils, Organic Clays, and Deep Soft Soil Deposits.” PhD Thesis. University of California, Berkeley. 2. M. Mirshekari, M. Ghayoomi. Effects of shaking intensity on seismic response of unsaturated sand layers. In Vol. 1 of Proc., 7th Int. Conf. on Unsaturated Soils, (2018) 17. Y.M.A Hashash. DEEPSOIL V3.5 1-D nonlinear and equivalent linear wave propagation analysis program for geotechnical seismic site response analysis of soil deposits. User Man. and Tut., (2006) 3. R. Dobry, R. Ladd, F. Yokel, R. Chung, D. Powell. Prediction of pore water pressure build-up and liquefaction of sands during earthquakes by the cyclic strain method. NBS Building Science Series 138 (1982) 18. H.B. Seed, R.T. Wong, I.M. Idriss, K. Tokimatsu. Moduli and damping factors for dynamic analyses of cohesionless soils. J. Geotech. Eng., 112, 11 (1986). 19. H.B. Seed, K. Mori, and C.K. Chan. Influence of seismic history on liquefaction of sands. J. Geotech. Engrg. Div., 103 (1977) 4. H.B. Seed, I.M. Idriss, F. Makidisi, N. Banerjee. The generation and dissipation of pore water pressures during soil liquefaction. Rep. No. EERC 75-26, Univ. of California, Berkeley, Calif. (1975). 20. E. Yee, P.M. Duku, J.P. Stewart. Cyclic volumetric strain behavior of sands with fines of low plasticity. Journal of Geotechnical and Geoenvironmental Engineering, 140, 4 (2013). 5. G.R. Martin, W.D.L. Finn, Seed H.B. Fundamentals of liquefaction under cyclic loading. J. Geotech. Engrg. Div., 101, 5 (1975) 21. S. Mousavi, M. Ghayoomi, S.H. Jones. Compositional and Geo-Environmental Factors in Microbial Induced Partial Saturation. Environ. Geotech. (2019) 6. C.P. Polito, R.A. Green, and J. Lee. Pore pressure generation models for sands and silty soils subjected to cyclic loading. Journal of Geotechnical and Geoenvironmental Engineering 134, 10 (2008) 6
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Filter Effects and Filter Artifacts in the Analysis of Electrophysiological Data
Frontiers in psychology
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1The EEGLAB “Basic FIR filter” function is based on the firls (least square fitting of FIR coefficients) MATLAB function (in the current version 11.0.2.1b as of writing this commentary). Filter length is defined independently of transition-band width. This can result in various adverse effects from sub-optimal stop-band attenuation, over filter artifacts, to leakage in the transition-band (the infamous “band-pass filter bug”). The problem is incre- ased by the property of the firls function that transition-bands are defined as “do not care” regions. In a warning message it is announced in the current EEGLAB version that firls based filters are no longer recommended and fir1 should be used instead and will be the default setting in a future version. In its current implementation this change will not solve the problem as filter length and transition-band width are still defined independently. The filter actually generated by the fir1 function will deviate from the requested and reported transition-band width. Filter effects vs. filter artifacts unity gain at DC (the step response never returns to one). These artifacts are due to a known misconception in FIR filter design in EEGLAB1. The artifacts are further ampli- fied by filtering twice, forward and back- ward, to achieve zero-phase. Andreas Widmann* and Erich Schröger Institute of Psychology, University of Leipzig, Leipzig, Germany *Correspondence: widmann@uni-leipzig.de Signal-to noise ratio The signal-to-noise ratio chosen by VanRullen for the simulated dataset is implausibly high (+26  dB at single trial level, +43 dB averaged) as signal-to-noise ratios smaller than one are common in real electrophysiological data. This assumption biases the conclusion on the detectability of the signal without filtering and overesti- mates the impact of filter ringing artifacts. i g The causality in filtering is not directly related to the symmetry of filter coefficients as implied in Figure 1 in Rousselet’s (2012) comment. That is, the FIR filter labeled “non- causal” can also be applied in a causal way by not compensating the filter’s delay (by not filtering the signal backward and not “left- shifting” the signal by the group delay). In order to reduce this filter delay in causal fil- tering, asymmetric “causal” FIR filters, more often referred to as minimum-phase filters, can be used. However, as FIR filter coef- It is correct that any band limitation in the frequency domain necessarily affects the signal in the time domain resulting in reduced precision and artifacts (cf. e.g., Luck, 2005). Nevertheless, here, we will discuss that the problem is overesti- mated by about an order of magnitude by the assumptions and analysis parameters used in VanRullen’s simulated dataset and advertise the cautious usage of carefully designed filters to be able to also detect small signals. At more realistic signal-to-noise ratios no significant impact of the filter arti- facts is observed (but only effects of tran- sient smoothing by low-pass filtering; see Figure 1 and Appendix). The precision that can be achieved in the measurement of the response onset latency is limited by signal- to-noise ratio. Thus, the trade-off between filter effects versus the signal-to-noise ratio gain by filtering must be considered. Causal filtering I In a recent review, VanRullen (2011) con- cludes that electrophysiological data should not be filtered at all when one is interested in the temporal dynamics or onset latencies of the electrophysiological responses. This conclusion was based on the observation that response onset latency was “smeared out in time for several tens or even hun- dreds of milliseconds” (p. 6) in a simulated dataset. In a commentary on VanRullen, Rousselet (2012) suggested to use “causal” filtering to solve the problem of signal onset latency underestimation due to smoothing. This is a valid recommendation, which has already been given (e.g., Luck, 2005). However, it should have been made explicit that the sug- gested type of “causal” filtering comes at the cost of a distortion of phase information also with FIR filters (cf., Figure A1 in Appendix). A commentary on We also recommend to distinguish between filter effects, that is, the obligatory effects any filter with equivalent properties – cutoff frequency, roll-off, ripple, and attenuation – would have on the data (e.g., smoothing of transients as demonstrated by the filter’s step response), and filter artifacts, that is, effects which can be minimized by selection of filter type and parameters (e.g., ringing). Four conceptual fallacies in mapping the time course of recognition by VanRullen, R. (2011). Front. Psychol. 2:365. doi: 10.3389/fpsyg.2011.00365 With more appropriate filters the under- estimation of signal onset latency due to the smoothing effect of low-pass filtering could be narrowed down to about 4–12 ms in the simulated dataset (see Figure 1 and Appendix for a simulation), that is, about an order of magnitude smaller than assumed. Does filtering preclude us from studying ERP time-courses? Does filtering preclude us from studying ERP time-courses? by Rousselet, G. A. (2012). Front. Psychol. 3:131. doi: 10.3389/fpsyg.2012.00131 by Rousselet, G. A. (2012). Front. Psychol. 3:131. doi: 10.3389/fpsyg.2012.00131 www.frontiersin.org Filter selection h fil l d 0 0.05 0.1 0.15 0.2 10 20 30 40 50 -14 dB SNR 0 0.05 0.1 0.15 0.2 10 20 30 40 50 +6 dB SNR Trial 0 0.05 0.1 0.15 0.2 10 20 30 40 50 Trial 0 0.05 0.1 0.15 0.2 10 20 30 40 50 Gaussian fltered 0 0.05 0.1 0.15 0.2 10 20 30 40 50 Trial 0 0.05 0.1 0.15 0.2 0 0.05 0.1 Amplitude Averaged (+17 dB SNR) 0 0.05 0.1 0.15 0.2 Unfltered EEGLAB frls Windowed sinc Discrete gaussian Minimum−phase Time 0 0.05 0.1 0.15 0.2 0 0.05 0.1 Unfltered EEGLAB frls Windowed sinc Discrete gaussian Minimum−phase 0 0.05 0.1 0.15 0.2 0 0.05 0.1 Amplitude Averaged (+17 dB SNR) 0 0.05 0.1 0.15 0.2 0 0.05 0.1 0 0.05 0.1 0.15 0.2 Time 0 0.05 0.1 0.15 0.2 Unfltered EEGLAB frls Windowed sinc Discrete gaussian Minimum−phase Time 0 0.05 0.1 0.15 0.2 Time Figure 1 | Impact of filter type and signal-to-noise ratio (SNR) on the time course of the averaged signal and the detected signal onset latency in the simulated dataset (sampling frequency 500 Hz; step signal; signal onset 150–180 ms) as defined by VanRullen (2011). The simulated dataset was filtered with the EEGLAB firls based filter, a windowed sinc FIR filter (Widmann, 2006), a discrete Gaussian kernel filter (Lindeberg, 1990), and a minimum-phase converted version of the Gaussian filter (causal; see Figure A1 in Appendix for a detailed description of the filters). Single trial signal-to-noise ratio was reduced in 20 dB-steps from +26 dB (original dataset; left column) to −14 dB (right column). The Gaussian filtered single trials (second row) and the averaged trials (third row) are displayed. Signal onset latency was measured by a running one-sided t-test (bottom row; gray bars) and jack-knifing with a relative 20%-criterion (black lines; Kiesel et al., 2008). ficients ­necessarily must be symmetric (or antisymmetric) for the filter to have linear- phase characteristic (Rabiner and Gold, 1975; Ifeachor and Jervis, 2002), this reduction of filter delay comes at the cost of a non-linear phase response and the introduction of a sys- tematic delay in the signal (which can not eas- ily be compensated due to non-linear phase). The recommendation for minimum-phase causal FIR filtering, thus, should be strictly limited to the detection of onset latencies and applications where causality is required for theoretical considerations. Frontiers in Psychology  |  Perception Science Filter selection h fil l d In its application it should be considered that the systematic delay and the non-linear phase response could also affect response onset information. However, in most situations filtering will nevertheless be necessary to appropriately analyze electrophysiological data. In these situations it is essential to know and under- stand the effects of filtering on the data and cautiously adjust filter settings (cutoff fre- quencies, roll-off, attenuation, and ripple) to the signal of interest and the particular application, e.g., by evaluating the effects of different filters on the data. Especially the high-pass filtering of slow ERP components or blinks, as commonly observed in the lit- erature, might seriously affect ERP time course and amplitudes (see, Luck, 2005, for a detailed discussion). Furthermore, we rec- ommend not using default filter settings, in In the first paragraph of the appendix Rousselet (2012) suggests that the causal filtered signal could be left-shifted by the group delay to achieve zero-phase. We do not agree with this recommendation: First, this would re-introduce non-causality. Second, this statement is wrong as only linear-phase (anti-/symmetric FIR) filters can be made zero-phase by left-shifting the signal. Filter selection h fil l d The filter selected in VanRullen’s simulation was a bad choice as it results in artifacts not related to filtering per se. The FIR filter gen- erated by EEGLAB (Delorme et al., 2011) with default settings exhibits excessive filter ringing (cf., Figure A1 in Appendix), and excessive pass-band ripple including non- July 2012  | Volume 3  |  Article 233  |  1 www.frontiersin.org Widmann and Schröger Filter effects and filter artifacts Trial 0 0.05 0.1 0.15 0.2 10 20 30 40 50 Trial 0 0.05 0.1 0.15 0.2 10 20 30 40 50 0 0.05 0.1 0.15 0.2 0 0.05 0.1 Amplitude 0 0.05 0.1 0.15 0.2 10 20 30 40 50 0 0.05 0.1 0.15 0.2 10 20 30 40 50 0 0.05 0.1 0.15 0.2 0 0.05 0.1 0 0.05 0.1 0.15 0.2 10 20 30 40 50 0 0.05 0.1 0.15 0.2 10 20 30 40 50 0 0.05 0.1 0.15 0.2 0 0.05 0.1 Unfltered EEGLAB frls Windowed sinc Discrete gaussian Minimum−phase +26 dB SNR -14 dB SNR +6 dB SNR Unfltered Gaussian fltered Averaged (+17 dB SNR) 0 0.05 0.1 0.15 0.2 Unfltered EEGLAB frls Windowed sinc Discrete gaussian Minimum−phase Time 0 0.05 0.1 0.15 0.2 Time 0 0.05 0.1 0.15 0.2 Time Figure 1 | Impact of filter type and signal-to-noise ratio (SNR) on the time course of the averaged signal and the detected signal onset latency in the simulated dataset (sampling frequency 500 Hz; step signal; signal onset 150–180 ms) as defined by VanRullen (2011). The simulated dataset was filtered with the EEGLAB firls based filter, a windowed sinc FIR filter (Widmann, 2006), a discrete Gaussian kernel filter (Lindeberg, 1990), and a minimum-phase converted version of the Gaussian filter (causal; see Figure A1 in Appendix for a detailed description of the filters). Single trial signal-to-noise ratio was reduced in 20 dB-steps from +26 dB (original dataset; left column) to −14 dB (right column). The Gaussian filtered single trials (second row) and the averaged trials (third row) are displayed. Signal onset latency was measured by a running one-sided t-test (bottom row; gray bars) and jack-knifing with a relative 20%-criterion (black lines; Kiesel et al., 2008). Conclusion I h l i In the analysis of electrophysiological data signal-to-noise ratio has to be improved by all adequate means. Priority should be given to the collection of higher numbers of trials and reduction of noise in data recording. Frontiers in Psychology  |  Perception Science July 2012  | Volume 3  |  Article 233  |  2 Filter effects and filter artifacts Widmann and Schröger Rousselet, G. A. (2012). Does filtering preclude us from studying ERP time-courses? Front. Psychol. 3, 365. doi: 10.3389/fpsyg.2011.00365 particular when using EEGLAB, but rather to manually and carefully select filter type and parameters to minimize filter artifacts. Filtering can result in considerable dis- tortions of the time course (and amplitude) of a signal as demonstrated by VanRullen (2011). Thus, filtering should not be used lightly. However, if effects of filtering are cautiously considered and filter artifacts are minimized, a valid interpretation of the temporal dynamics of filtered electrophysi- ological data is possible and signals missed otherwise can be detected with filtering. the German Research Foundation (DFG; a Reinhart-Koselleck grant awarded to Erich Schröger). particular when using EEGLAB, but rather to manually and carefully select filter type and parameters to minimize filter artifacts. VanRullen, R. (2011). Four common conceptual falla- cies in mapping the time course of recognition. Front. Psychol. 2, 365. doi: 10.3389/fpsyg.2011.00365 Filtering can result in considerable dis- tortions of the time course (and amplitude) of a signal as demonstrated by VanRullen (2011). Thus, filtering should not be used lightly. However, if effects of filtering are cautiously considered and filter artifacts are minimized, a valid interpretation of the temporal dynamics of filtered electrophysi- ological data is possible and signals missed otherwise can be detected with filtering. References Widmann, A. (2006). Firfilt EEGLAB Plugin, Version 1.5.1. Leipzig: University of Leipzig. Delorme, A., Mullen, T., Kothe, C., Akalin Acar, Z., Bigdely-Shamlo, N., Vankov, A., and Makeig, S. (2011). EEGLAB, SIFT, NFT, BCILAB, and ERICA: new tools for advanced EEG processing. Comput. Intell. Neurosci. 2011, 130714. Received: 14 June 2012; accepted: 19 June 2012; published online: 09 July 2012. Received: 14 June 2012; accepted: 19 June 2012; published online: 09 July 2012. Citation: Widmann A and Schröger E (2012) Filter effects and filter artifacts in the analysis of electrophysi- ological data. Front. Psychology 3:233. doi: 10.3389/ fpsyg.2012.00233 This article was submitted to Frontiers in Perception Science, a specialty of Frontiers in Psychology. Copyright © 2012 Widmann and Schröger. This is an open- access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribu- tion and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc. Ifeachor, E. C., and Jervis, B. W. (2002). Digital Signal Processing: A Practical Approach. Edinburgh: Pearson. Ifeachor, E. C., and Jervis, B. W. (2002). Digital Signal Processing: A Practical Approach. Edinburgh: Pearson. Kiesel, A., Miller, J., Jolicoeur, P., and Brisson, B. (2008). Measurement of ERP latency differences: a compari- son of single-participant and jackknife-based scoring methods. Psychophysiology 45, 250–274. Citation: Widmann A and Schröger E (2012) Filter effects and filter artifacts in the analysis of electrophysi- ological data. Front. Psychology 3:233. doi: 10.3389/ fpsyg.2012.00233 Kiesel, A., Miller, J., Jolicoeur, P., and Brisson, B. (2008). Measurement of ERP latency differences: a compari- son of single-participant and jackknife-based scoring methods. Psychophysiology 45, 250–274. Received: 14 June 2012; accepted: 19 June 2012; published online: 09 July 2012. Citation: Widmann A and Schröger E (2012) Filter effects and filter artifacts in the analysis of electrophysi- ological data. Front. Psychology 3:233. doi: 10.3389/ fpsyg.2012.00233 This article was submitted to Frontiers in Perception Science, a specialty of Frontiers in Psychology. Copyright © 2012 Widmann and Schröger. This is an open- access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribu- tion and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc. July 2012  | Volume 3  |  Article 233  |  3 Acknowledgments Lindeberg, T. (1990). Scale-space for discrete signals. IEEE Trans. Pattern Anal. Mach. Intell. 12, 234–254. We are grateful to Burkhard Maess for the extensive discussion and helpful com- ments and to Nicole Wetzel for her help- ful comments on the manuscript. The research was supported by a grant from Luck, S. J. (2005). An Introduction to the Event-Related Potential Technique. Cambridge, MA: MIT Press. Rabiner, L. R., and Gold, B. (1975). Theory and Application of Digital Signal Processing. Englewood Cliffs, NJ: Prentice-Hall. July 2012  | Volume 3  |  Article 233  |  3 www.frontiersin.org www.frontiersin.org Filter effects and filter artifacts Widmann and Schröger filters were significantly reduced (non-unity DC gain is still noticeable with the EEGLAB firls filter). No significant ringing artifacts were observed with the windowed sinc FIR filters. Importantly, at −14 dB single trial signal-to-noise ratio the signal could no longer be reliably detected without filter- ing and thus no signal onset latency could be determined. With non-causal and causal filtering the signal was detectable and the onset latency was overestimated by 4–6 and 18 ms, respectively (0 and 14 ms as esti- mated by jack-knifing). −14 dB single trial signal-to-noise ratio would be considered a good value in many electrophysiological measurements as, e.g., in electroencepha- lography (EEG). Averaging the 50 trials improved signal-to-noise ratio by +17 dB. Filtering further improved signal-to-noise ratio by about +12 dB allowing the reliable detection of the signal. Signal-to-noise ratio dd l l In two additional analyses we reduced single trial signal-to-noise ratio in the simulated dataset in steps of −20 dB to +6 dB and −14 dB by reducing the signal amplitude from 1 to 0.1 and 0.01, respectively (Figure 1, columns two and three). At +6 dB signal-to- noise ratio the differences in onset latency underestimation between the linear-phase We would like to note that ringing arti- facts must be considered in relation to noise level. In non-simulated electrophysiological Impulse response Step response Magnitude response Phase response Linear phase flters Minimum phase flter −20 0 20 −0.05 0 0.05 0.1 0.15 Amplitude −20 0 20 −0.2 0 0.2 0.4 0.6 0.8 1 Amplitude 0 100 200 −60 −40 −20 0 Magnitude (dB) −20 0 20 0 0.05 0.1 Sample Amplitude −20 0 20 −0.2 0 0.2 0.4 0.6 0.8 1 Sample Amplitude 0 100 200 −60 −40 −20 0 Frequency (Hz) Magnitude (dB) 0 100 200 −2 − 0 Frequency (Hz) Phase (rad) EEGLAB frls Windowed sinc Discrete gaussian Figure A1 | Prototypical low-pass linear-phase filters’ impulse, step, magnitude, and phase responses (top row; sampling frequency = 500 Hz, cutoff frequency 30 Hz). The EEGLAB “Basic FIR filter” (red, 49 points, default settings, EEGLAB v11.0.2.1b; Delorme et al., 2011) exhibiting excessive ringing artifacts (“ripples” in the time domain observed if filtering a non-oscillating input, e.g., a step signal, yields an oscillating output) is shown in comparison to a windowed sinc (green, 49 points, firfilt EEGLAB plugin; Widmann, 2006) and a discrete Gaussian kernel filter (σ = 6.18 ms, based on a modified Bessel function; Lindeberg, 1990). The minimum-phase converted version of the discrete Gaussian kernel filter (bottom row; “causal” filter converted by means of Hilbert transform) shows a considerably non-linear phase response but does not show a response before signal onset. Appendix Filter selection observed with the windowed sinc filter, in particular undershoot before signal onset (see Figure  1, left column, third row). Additionally, we re-analyzed the dataset by means of a causal filtering with a min- imum-phase converted discrete Gaussian kernel filter as suggested by Rousselet (2012). The signal onset latency was over- estimated by 4 ms due to the systematic delay introduced by causal filtering (16 ms as estimated by jack-knifing). However, the morphology of the signal was considerably affected by the non-linear phase response of the filter. We re-analyzed the simulated dataset as defined by VanRullen by means of a 49 point Hamming windowed sinc FIR filter (same length as the “default” EEGLAB gen- erated filter; Widmann, 2006), and a dis- crete Gaussian kernel filter (σ = 6.18 ms; see Figure A1 for impulse, step, magni- tude, and phase responses). The signal onset latency was underestimated by about 4 (windowed sinc) to 12 ms (discrete Gaussian) relative to unfiltered data com- pared to 42 ms when applying the EEGLAB firls default filter by one-sided t-tests (see Figure 1, bottom row; with non-simulated data more appropriate methods as, e.g., cluster-based non-parametric analysis, Maris and Oostenveld, 2007, could have been employed). No signal onset latency underestimation was observed using a jack-knifing technique with a rela- tive 20%-criterion (Kiesel et  al., 2008). Significant ringing artifacts could still be Signal-to-noise ratio dd l l Frontiers in Psychology  |  Perception Science July 2012  | Volume 3  |  Article 233  |  4 Impulse response Linear phase flters −20 0 20 −0.05 0 0.05 0.1 0.15 Amplitude A li d Magnitude response Phase response 0 100 200 −60 −40 −20 0 Magnitude (dB) EEGLAB frls Windowed sinc Discrete gaussian Step response −20 0 20 −0.2 0 0.2 0.4 0.6 0.8 1 Amplitude Magnitude (dB) Amplitude Minimum phase flter −20 0 20 0 0.05 0.1 Sample Amplitude Amplitude −20 0 20 −0.2 0 0.2 0.4 0.6 0.8 1 Sample Amplitude M it d (dB) 0 100 200 −60 −40 −20 0 Frequency (Hz) Magnitude (dB) Ph ( d) 0 100 200 −2 − 0 Frequency (Hz) Phase (rad) −20 0 20 −0.2 0 0.2 0.4 0.6 0.8 1 Sample Amplitude 0 100 200 −60 −40 −20 0 Frequency (Hz) Magnitude (dB) Ph ( d) Minimum phase flter Magnitude (dB) Amplitude Phase (rad) Figure A1 | Prototypical low-pass linear-phase filters’ impulse, step, magnitude, and phase responses (top row; sampling frequency = 500 Hz, cutoff frequency 30 Hz). The EEGLAB “Basic FIR filter” (red, 49 points, default settings, EEGLAB v11.0.2.1b; Delorme et al., 2011) exhibiting excessive ringing artifacts (“ripples” in the time domain observed if filtering a non-oscillating input, e.g., a step signal, yields an oscillating output) is shown in comparison to a Figure A1 | Prototypical low-pass linear-phase filters’ impulse, step, magnitude, and phase responses (top row; sampling frequency = 500 Hz, cutoff frequency 30 Hz). The EEGLAB “Basic FIR filter” (red, 49 points, default settings, EEGLAB v11.0.2.1b; Delorme et al., 2011) exhibiting excessive ringing artifacts (“ripples” in the time domain observed if filtering a non-oscillating input, e.g., a step signal, yields an oscillating output) is shown in comparison to a windowed sinc (green, 49 points, firfilt EEGLAB plugin; Widmann, 2006) and a discrete Gaussian kernel filter (σ = 6.18 ms, based on a modified Bessel function; Lindeberg, 1990). The minimum-phase converted version of the discrete Gaussian kernel filter (bottom row; “causal” filter converted by means of Hilbert transform) shows a considerably non-linear phase response but does not show a response before signal onset. windowed sinc (green, 49 points, firfilt EEGLAB plugin; Widmann, 2006) and a discrete Gaussian kernel filter (σ = 6.18 ms, based on a modified Bessel function; Lindeberg, 1990). Signal-to-noise ratio dd l l The minimum-phase converted version of the discrete Gaussian kernel filter (bottom row; “causal” filter converted by means of Hilbert transform) shows a considerably non-linear phase response but does not show a response before signal onset. July 2012  | Volume 3  |  Article 233  |  4 Frontiers in Psychology  |  Perception Science Filter effects and filter artifacts Widmann and Schröger filters, e.g., the Remez-exchange (equirip- ple) algorithm, preferable for arbitrary frequency responses not very common in the analysis of electrophysiological data (McClellan et al., 1973). The authors have good experiences with windowed sinc FIR filters, also commonly referred to as “ideal” filters due to the rectangular shape of the sinc function in the frequency domain. Implementations for the analysis of elec- trophysiological data can be found, e.g., in EEProbe software package (ANT, Enschede, The Netherlands) and the open-source firfilt EEGLAB plugin (Widmann, 2006). For a widely accessible introduction to windowed sinc FIR filter design see, e.g., Smith (1999). Windowed sinc FIR filter’s stop-band attenuation (and pass-band rip- ple) can be precisely controlled by selection of window type; the filters’ transition-band width is a function of filter order/length (and window type), thus, filter length can be estimated (as with Remez-exchange FIR filters) or computed (with Kaiser windows), and high-pass filters can be easily optimized for excellent DC attenuation. If filter ringing is assumed to have an impact on a particular application, non-oscillating FIR filters, as, e.g., Gaussian kernel FIR filters, should be considered. filters, e.g., the Remez-exchange (equirip- ple) algorithm, preferable for arbitrary frequency responses not very common in the analysis of electrophysiological data (McClellan et al., 1973). The authors have good experiences with windowed sinc FIR filters, also commonly referred to as “ideal” filters due to the rectangular shape of the sinc function in the frequency domain. Implementations for the analysis of elec- trophysiological data can be found, e.g., in EEProbe software package (ANT, Enschede, The Netherlands) and the open-source firfilt EEGLAB plugin (Widmann, 2006). For a widely accessible introduction to windowed sinc FIR filter design see, e.g., Smith (1999). Windowed sinc FIR filter’s stop-band attenuation (and pass-band rip- ple) can be precisely controlled by selection of window type; the filters’ transition-band width is a function of filter order/length (and window type), thus, filter length can be estimated (as with Remez-exchange FIR filters) or computed (with Kaiser windows), and high-pass filters can be easily optimized for excellent DC attenuation. Signal-to-noise ratio dd l l If filter ringing is assumed to have an impact on a particular application, non-oscillating FIR filters, as, e.g., Gaussian kernel FIR filters, should be considered. roll-off) should be preferred over nar- rower ones where possible. Cutoff fre- quencies and transition-bands should be separated from the signal of interest in the frequency domain to minimize dis- tortion of the signal by filter artifacts and undesired filter effects. The filter should be as short as possible in order to mini- mize temporal smearing. Low-pass filters can sometimes be omitted in favor of later analysis steps introducing additional fil- tering as, e.g., computing time window mean values (representing low-pass filters as well). Balancing transition-band width and cutoff frequency is a particular chal- lenge for high-pass filter design as the transition-band is limited by DC on the one hand but cutoff frequency should be low in order not to distort slow compo- nents on the other hand. Extreme cutoff frequencies <0.1 Hz as found sometimes in the literature should be avoided as filters usually become very long. data ringing artifacts are not expected to have a major impact due to the high noise level on the one hand and the absence of ultra-sharp transients on the other hand. July 2012  | Volume 3  |  Article 233  |  5 Recommendations for selection of filter type and parameters Unfortunately there cannot be given a ubiquitously valid recommendation for the selection of optimal filter settings, type, and parameters. They have to be individually adjusted to each application. Infinite impulse response (IIR) filters are often considered as computationally more efficient compared to FIR filters as they are shorter. However, it should be considered, that the signal has to be filtered twice – for- ward and backward – to achieve zero-phase (possibly introducing artifacts with DC off- sets at signal boundaries and squaring the frequency response); a larger number of computations is necessary with IIR filters due to recursive operation (relative to the IIR filter’s shorter length); numerical errors can be accumulated due to the infinitive impulse response; and they are more dif- ficult to control and can be unstable. References Maris, E., and Oostenveld, R. (2007). Non-parametric statistical testing of EEG- and MEG-data. J. Neurosci. Methods 164, 177–190. For FIR filters, only symmetric linear- phase filters should be considered for most applications in electrophysiology as they can be easily made zero-phase by left- shifting the signal by the filters group delay. There are various methods to design FIR McClellan, J. H., Parks, T. W., and Rabiner, L. R. (1973). A computer program for designing optimum FIR lin- ear phase digital filters. IEEE Trans. Acoust. AU-21, 509–526. As rule of thumb, stop-band attenu- ation should be selected only as high as necessary, wider transition-bands (slow Smith, S. W. (1999). The Scientist and Engineer’s Guide to Digital Signal Processing. San Diego, CA: California Technical Publishing. July 2012  | Volume 3  |  Article 233  |  5 www.frontiersin.org www.frontiersin.org
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Nucleoside Analogues as Antibacterial Agents
Frontiers in microbiology
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Nucleoside Analogues as Antibacterial Agents Jessica M. Thomson and Iain L. Lamont* Department of Biochemistry, University of Otago, Dunedin, New Zealand The rapid increase in antibiotic-resistant bacteria has emphasized the urgent need to identify new treatments for bacterial infections. One attractive approach, reducing the need for expensive and time-consuming clinical trials, is to repurpose existing clinically approved compounds for use as antibacterial agents. Nucleoside analogues are commonly used for treating viral and fungal infections, as well as for treating cancers, but have received relatively little attention as treatments for bacterial infections. However, a significant number of clinically approved derivatives of both pyrimidines and purines including halogenated, thiolated, and azolated compounds have been shown to have antibacterial activity. In the small number of studies carried out to date, such compounds have shown promise in treating bacterial infections. Here, we review the mechanisms of action and antibacterial activities of nucleoside analogues that can potentially be repurposed for treating infections as well as considering possible limitations in their usage. Edited by: Rustam Aminov, University of Aberdeen, United Kingdom Keywords: repurposed antibiotics, antibiotic resistance, pyrimidine analogues, purine analogues, multidrug-resistant bacteria, antibacterial agents, antimicrobial Reviewed by: Babita Agrawal, University of Alberta, Canada Steven W. Polyak, University of South Australia, Australia REVIEW published: 22 May 2019 doi: 10.3389/fmicb.2019.00952 published: 22 May 2019 doi: 10.3389/fmicb.2019.00952 INTRODUCTION The introduction of antibiotics into clinical use heralded a new age for medicine. However, less than a century later, the therapeutic efficacy of antibiotics is becoming limited owing to the rise of resistance in pathogenic bacteria (Lewis, 2013). Once a problem largely limited to hospital environments, antibiotic-resistant strains of pathogens have progressively become more prevalent in the community, and their spread has been unrestricted (Rice, 2009). It has been estimated that there are at least 700,000 deaths a year worldwide due to infections by antibiotic- resistant bacteria and in the absence of new treatment strategies this figure could rise to 10 million deaths a year by 2050 (O’Neill, 2014). Despite an urgent need for new antibiotics to combat resistant pathogens, there have been very few novel antibiotics to make it into clinical practice. Indeed, the majority of antibiotics in use today belong to classes discovered before the 1970s (Lewis, 2013). There are a number of factors contributing to the issue of failing antibiotic discovery, including declining interest in discovery by pharmaceutical companies due to the high costs of bringing drugs to market and limited approaches to identify lead compounds (Livermore, 2011). However, some promising approaches to antibiotic discovery do exist. Recently, novel methods of screening environmental microbes have yielded promising antibiotic compounds (Gavrish et al., 2014; Ling et al., 2015). While such screening techniques hold promise for discovery of novel compounds, it will be  a number of years before any discovered compounds are sufficiently studied to be  used clinically. Thus, a different approach to discovery, namely drug repurposing, may identify compounds with antibiotic activity and *Correspondence: Iain L. Lamont iain.lamont@otago.ac.nz Specialty section: This article was submitted to Antimicrobials, Resistance and Chemotherapy, a section of the journal Frontiers in Microbiology Received: 29 January 2019 Accepted: 15 April 2019 Published: 22 May 2019 Citation: Thomson JM and Lamont IL (2019) Nucleoside Analogues as Antibacterial Agents. Front. Microbiol. 10:952. doi: 10.3389/fmicb.2019.00952 Specialty section: This article was submitted to Antimicrobials, Resistance and Chemotherapy, a section of the journal Frontiers in Microbiology Specialty section: This article was submitted to Antimicrobials, Resistance and Chemotherapy, a section of the journal Frontiers in Microbiology Received: 29 January 2019 Accepted: 15 April 2019 Published: 22 May 2019 Received: 29 January 2019 Accepted: 15 April 2019 Published: 22 May 2019 Gemcitabine Modifications to nucleobases include halogenation and addition of azido groups, and modifications of the sugar component include ring opening, halogenation, methylation, and hydroxylation or dehydroxylation (Jordheim et al., 2013). It is worth noting that a class of drugs called nucleoside antibiotics has also been studied for potential clinical use as antibacterials. Nucleoside antibiotics typically consist of parts of natural nucleosides conjugated with additional complex structures such as amino acids or fatty acids, with the combination having antibacterial properties. In bacteria, nucleoside antibiotics primarily target cell-wall biosynthesis (Winn et  al., 2010; Niu and Tan, 2015). The potential use of various nucleoside antibiotics has been extensively reviewed elsewhere (Winn et  al., 2010; Carter and McDonald, 2014; Niu and Tan, 2015) and is beyond the scope of this review.h Gemcitabine has been the subject of various repurposing studies. In a study that explored the efficacy of various nucleoside analogues against clinical isolates from different bacteria genera, gemcitabine was identified as having antibacterial activity (Sandrini et al., 2007b). Gemcitabine had a potent antibacterial effect on Gram-positive bacteria, including important pathogenic species from genera Listeria, Bacillus, Enterococcus, and Staphylococcus, although it was ineffective against Gram-negative bacteria. A murine infection model was used to investigate whether gemcitabine was useful as an antibiotic in vivo (Sandrini et  al., 2007a). Mice were infected with Streptococcus pyogenes AP1, a virulent strain responsible for causing the majority of severe S. pyogenes infections. Of the mice infected with a potentially fatal dose of S. pyogenes AP1, those treated with the control had a 100% mortality rate, whereas those treated with gemcitabine had only a 17% mortality rate. This demonstrated that gemcitabine had potent activity against S. pyogenes in  vivo.h This review will cover nucleoside analogues that have shown clinical potential for repurposing as antibacterials. A summary of the metabolism of the relevant compounds is shown in Figure 1. First, their usage and modes of action in treating cancer or viral infections, along with studies validating their antibiotic activity against bacteria, will be  outlined. Second, studies on the metabolism of nucleoside analogues and their mechanism of action in bacteria will be  discussed. Finally, limitations of nucleoside analogues as antibiotics including potential for toxicity and development of resistance will be  considered. S. These studies showed gemcitabine to be  a good candidate for repurposing as an antibiotic. Jordheim et al. Gemcitabine Gemcitabine (2′,2′-difluoro-2′-deoxycytidine) is an analogue of deoxycytidine and has two fluorine atoms in place of hydrogen atoms on the 2′ carbon of the sugar component (Figure 2A). Gemcitabine was first developed as an antiviral drug but has since been used exclusively as an anticancer drug (Mini et al., 2006). Gemcitabine is used alone or in combination with other drugs for various types of cancers, including metastatic pancreatic cancer (Burris et  al., 1997; Ishii et  al., 2005). Gemcitabine is a prodrug, which is taken up into eukaryotic cells, phosphorylated to gemcitabine monophosphate by deoxycytidine kinase, and converted to the active metabolites gemcitabine di- and triphosphate (Heinemann et al., 1988; Mini et al., 2006). Once activated, gemcitabine is incorporated into growing DNA (Figure  1), ultimately resulting in termination of strand elongation. After incorporation of gemcitabine, the DNA polymerase adds one additional deoxynucleotide and DNA synthesis then ceases; the additional deoxynucleotide may mask gemcitabine from proof-reading exonucleases, preventing its removal (Huang and Plunkett, 1995). It is unclear why only one nucleotide is added after gemcitabine, but it may be  that the drug induces DNA conformation changes, preventing the addition of further nucleotides (Plunkett et al., 1995). Gemcitabine can also potently inhibit ribonucleotide reductase (Figure 1; Huang and Plunkett, 1995). There is evidence that a metabolite of gemcitabine can be  incorporated into RNA, although the identity of this metabolite and the impact this has on cells are unclear (Figure 1; Vanhaperen et  al., 1993). One class of drugs that are important from a clinical perspective is nucleoside analogues, a pharmacologically diverse class of drugs that arose from chemically modified natural ribose or 2′-deoxyribose nucleosides (Koszytkowska-Stawinska and Buchowicz, 2014). Nucleoside analogues are among the most important drugs in the clinical setting and are used widely as both anticancer and antiviral agents (Jordheim et al., 2013). Nucleoside analogues mimic endogenous nucleosides, exploiting cellular metabolism and becoming incorporated into both DNA and RNA. This property makes nucleoside analogues effective at inhibiting viral replication and stopping cancer cell proliferation. However, although there have been some studies on the efficacy of nucleoside analogues as antibacterial agents, the potential use of these compounds in treating bacterial infections has been relatively neglected. For the purposes of this review, a nucleoside analogue is defined as a nucleobase linked to a sugar, where the nucleobase or the sugar component is altered such that the molecule becomes distinct from those found naturally. Abbreviations: dNK, Deoxyribonucleoside kinase; HPRT, Hypoxanthine-guanine phosphoribosyl transferase; TK, Thymidine kinase. Citation: Thomson JM and Lamont IL (2019) Nucleoside Analogues as Antibacterial Agents. Front. Microbiol. 10:952. doi: 10.3389/fmicb.2019.00952 May 2019 | Volume 10 | Article 952 1 Frontiers in Microbiology | www.frontiersin.org Nucleoside Analogues as Antibacterial Agents Thomson and Lamont PYRIMIDINE ANALOGUES represents a way to fast track them into clinical use (Brown, 2015; Rangel-Vega et  al., 2015; Miro-Canturri et  al., 2019). The concept behind repurposing is that almost all drugs in clinical use exhibit various pharmacological activities secondary to their main activity. Screening these compounds for side activities, and optimizing activity if required, could represent a way to identify new antibiotics. As the safety profiles of the drugs are known, clinical trials could be  less extensive, thus reducing costs associated with approval and allowing drugs to be  used clinically more rapidly than completely novel drugs. Gemcitabine (2012) performed additional in vitro preclinical studies to investigate the potential of gemcitabine, especially its efficacy against clinically important multidrug-resistant strains of Staphylococcus aureus. Gemcitabine was found to be active against 19 different strains of methicillin- resistant S. aureus. Gemcitabine was effective against glycopeptide- intermediate S. aureus, a strain resistant to all glycopeptide antibiotics, including vancomycin. Resistance to gemcitabine May 2019 | Volume 10 | Article 952 Frontiers in Microbiology | www.frontiersin.org 2 Nucleoside Analogues as Antibacterial Agents Thomson and Lamont A B FIGURE 1  |  Pathways by which pyrimidine and purine analogues are metabolized and become incorporated into DNA and RNA. Inhibition of enzymes by nucleoside analogues and their metabolites is also shown (⊣). (A) Pyrimidine analogues. (B) Purine analogues. Abbreviations: HPRT, hypoxanthine-guanine phosphoribosyl transferase; IMP, inosine monophosphate; RNR, ribonucleotide reductase; TK, thymidylate kinase; TMK, deoxythymidine monophosphate kinase; TS, thymidylate synthase; UDP-GlcNAc, uridine diphosphate N-acetylglucosamine; XMP, xanthosine monophosphate. A A B B FIGURE 1  |  Pathways by which pyrimidine and purine analogues are metabolized and become incorporated into DNA and RNA. Inhibition of enzymes by nucleoside analogues and their metabolites is also shown (⊣). (A) Pyrimidine analogues. (B) Purine analogues. Abbreviations: HPRT, hypoxanthine-guanine phosphoribosyl transferase; IMP, inosine monophosphate; RNR, ribonucleotide reductase; TK, thymidylate kinase; TMK, deoxythymidine monophosphate kinase; TS, thymidylate synthase; UDP-GlcNAc, uridine diphosphate N-acetylglucosamine; XMP, xanthosine monophosphate. polymerase (Furman et  al., 1986). However, zidovudine has still been found to be  incorporated into the DNA of patients taking the drug, and there is evidence that at high doses, zidovudine can lead to various toxicities, including mitochondrial toxicity and cardiomyopathy (Lewis et  al., 1992, 2000).i could develop in treated S. aureus (Jordheim et  al., 2012). However, gemcitabine was found to have synergistic activity with gentamicin, and if used in combination, emergence of resistance to these drugs may be slowed (Jordheim et al., 2012). Frontiers in Microbiology | www.frontiersin.org Zidovudine Zidovudine was first found to have antibacterial activity in the late 1980s. Zidovudine had antimicrobial activity against various Enterobacteriaceae, including Salmonella species (Elwell et  al., 1987). Zidovudine was activated in these bacteria by thymidine kinase (TK), and incorporation of activated zidovudine into bacterial DNA resulted in DNA chain termination (Figure 1; Elwell et  al., 1987). Subsequently, zidovudine has been demonstrated to have potent activity against many pathogenic Gram-negative bacteria, including Escherichia coli, Salmonella typhimurium, Klebsiella pneumoniae, Shigella flexneri, and Haemophilus influenzae and including isolates resistant to conventional antibiotics (Keith et al., 1989; Sandrini et al., 2007a,b; Zidovudine [3′azido-3′-deoxythymidine, AZT] is a thymidine analogue with an azido group in place of the hydroxyl group at the 3′ carbon of the deoxyribose ring (Figure 2B). Zidovudine is an antiretroviral agent and is used clinically as therapy for HIV/AIDS. Once activated to its triphosphorylated form, zidovudine inhibits viral replication. The azido group of zidovudine prevents phosphodiester bond formation and results in DNA chain termination (Furman et  al., 1986; Cooper and Lovett, 2011). Zidovudine is effective as an antiretroviral because it has an affinity for the viral reverse transcriptase that is approximately 100-fold greater than its affinity for human DNA May 2019 | Volume 10 | Article 952 Frontiers in Microbiology | www.frontiersin.org 3 Nucleoside Analogues as Antibacterial Agents Thomson and Lamont A B C D FIGURE 2  |  Structures of pyrimidines, purines, and their analogues, with substituted atoms highlighted. (A) Deoxycytidine and its analogue. (B) Thymidine and its analogues. (C) Cytosine, uracil, and fluorinated pyrimidines. (D) Hypoxanthine, guanine, and their analogues. A A B B B B A C C C D D C FIGURE 2  |  Structures of pyrimidines, purines, and their analogues, with substituted atoms highlighted. (A) Deox analogues. (C) Cytosine, uracil, and fluorinated pyrimidines. (D) Hypoxanthine, guanine, and their analogues. FIGURE 2  |  Structures of pyrimidines, purines, and their analogues, with substituted atoms highlighted. (A) Deoxycytidine and its analogue. (B) Thymidine and its analogues. (C) Cytosine, uracil, and fluorinated pyrimidines. (D) Hypoxanthine, guanine, and their analogues. patients (Casado et  al., 1999). These in vivo findings suggest that zidovudine has potential application as an antibacterial agent. Zidovudine has also been the subject of modification studies, which aim to improve its therapeutic efficacy and resolve issues like short half-life of the drug. Research has gone into creating zidovudine derivatives that retain antiviral activity while having improved bactericidal activity (Moroni et  al., 2002). Zidovudine Such derivatives may be  particularly useful for HIV/AIDS patients; HIV/AIDS patients are susceptible to opportunistic bacterial infections, and improved bactericidal profile of these derivatives would be  a beneficial side activity. Doleans-Jordheim et  al., 2011; Peyclit et  al., 2018). It also acts synergistically with conventional antibiotics, enhancing their effectiveness (Wambaugh et  al., 2017; Ng et  al., 2018; Falagas et  al., 2019; Hu et  al., 2019). Zidovudine is ineffective against Gram-positive bacteria such as Listeria species, Bacillus species, Staphylococci, and Enterococcus faecalis as well as against Mycobacteria species and Pseudomonas aeruginosa (Elwell et  al., 1987; Sandrini et  al., 2007a).h Doleans-Jordheim et  al., 2011; Peyclit et  al., 2018). It also acts synergistically with conventional antibiotics, enhancing their effectiveness (Wambaugh et  al., 2017; Ng et  al., 2018; Falagas et  al., 2019; Hu et  al., 2019). Zidovudine is ineffective against Gram-positive bacteria such as Listeria species, Bacillus species, Staphylococci, and Enterococcus faecalis as well as against Mycobacteria species and Pseudomonas aeruginosa (Elwell et  al., 1987; Sandrini et  al., 2007a).h The antibacterial activity of zidovudine has been demonstrated both in vitro and in vivo. Herrmann and Lagrange (1992) used a macrophage cell line to demonstrate that zidovudine inhibited intracellular growth of S. typhimurium. Zidovudine had potent in vivo activity. Zidovudine prevented lethal infections in mice with pyelonephritis caused by E. coli infection, being as effective as either trimethoprim or ampicillin (Keith et  al., 1989). It also inhibited growth of antibiotic-resistant E. coli and K. pneumoniae in a murine peritoneal infection model, acting synergistically with colistin (Hu et  al., 2019). When administered subcutaneously, zidovudine also prevented lethal salmonellosis in calves infected with S. dublin (Keith et  al., 1989). Zidovudine has therapeutic potential for humans as well; zidovudine given as an antiretroviral to HIV/AIDS patients also had the additional protective effect of lowering the recurrence of Salmonella bacteremia, a significant problem for HIV/AIDS Frontiers in Microbiology | www.frontiersin.org Idoxuridine Idoxuridine (5-iodo-2′-deoxyuridine; Figure 2B) was the first antiviral drug introduced to the clinic (Kaufman, 1962); nowadays, it is mostly used in the therapy of herpetic simplex keratitis (Wilhelmus, 2010). At high concentrations, idoxuridine is cytotoxic because it competitively inhibits various enzymes, including TK, and when triphosphorylated can become incorporated into DNA (Figure 1; Prusoff et  al., 1979). The exact effect of the incorporation of triphosphorylated idoxuridine into DNA is unknown. Idoxuridine alone had no antimicrobial properties against a range of clinically important pathogens tested (Zander et al., 2010a). However, when used in conjunction with SXT, a combination of trimethoprim and sulfamethoxazole that inhibits tetrahydrofolic acid synthesis, idoxuridine significantly enhanced the antimicrobial properties of SXT against most of the bacterial species tested, including K. pneumoniae, S. aureus, and S. pyogenes (Zander et al., 2010a,b). Tetrahydrofolic acid is a critical bacterial cofactor of thymidine synthesis, and thus, DNA synthesis (Sköld, 2009) and inhibition of TK by idoxuridine evidently enhanced the effects of SXT in inhibiting DNA synthesis. This was the case even in the presence of extracellular thymidine, which would be  present during infections and ameliorate the effects of SXT (Zander et  al., 2010a,b). l The possible application of fluorinated pyrimidines as antibacterials has been tested in vivo (Walz et  al., 2010; Imperi et al., 2013; Kirienko et al., 2016). 5-Fluorouracil was demonstrated to be a clinically useful antibacterial agent by Walz et al. (2010). In a phase III clinical trial, Walz and colleagues studied the efficacy of central venous catheters coated with 5-fluorouracil in decreasing catheter-related bloodstream infections and reducing colonization of catheters by bacteria. Nearly 1,000 patients were randomized into two groups, one receiving a catheter coated with 5-fluorouracil and the other group receiving standard catheters coated with chlorhexidine-silver sulfadiazine (Walz et  al., 2010). The catheters coated with 5-fluorouracil were as effective at preventing bacterial colonisation as the standard chlorhexidine- silver sulfadiazine catheters. The frequency of adverse events was comparable between the two groups. The dose of 5-fluorouracil used to coat the catheter was very low, and in a small tissue While the combination of idoxuridine and SXT has promise for clinical application, extensive clinical studies will need to be  performed. Fluorinated Pyrimidines 5-Fluorocytosine itself is not active; antifungal activity is dependent upon uptake of 5-fluorocytosine into fungal cells and subsequent deamination to 5-fluorouracil (Figure 1; Bennett, 1977). In turn, 5-fluorouracil is converted to floxuridine mono-, di-, and tri-phosphate. Metabolites of 5-fluorouracil and floxuridine can become incorporated into DNA and RNA and can also inhibit thymidylate synthase, preventing de novo formation of deoxythymidine monophosphate (Figure 1; Bennett, 1977). sample obtained from the location of catheterization, no toxicity was observed in patients receiving 5-fluorouracil-coated catheters (Walz et al., 2010). These data suggest that if widespread resistance to compounds currently impregnated in standard catheters were to arise, then 5-fluorouracil impregnated catheters could be  clinically useful as an alternative. It is also encouraging that the 5-fluorouracil coating the catheters did not cause any toxicity or significant side effects.l if While 5-fluorouracil has been shown to be  a potentially effective antimicrobial, the drug does not specifically target bacteria and is also toxic to eukaryotic cells (Alvarez et  al., 2012). Conversely, 5-fluorocytosine is a prodrug and is only converted to 5-fluorouracil by susceptible cells. Human cells lack the enzymes required to convert 5-fluorocytosine to 5-fluorouracil; therefore, the drug is less toxic than 5-fluorouracil to patients. The potential of 5-fluorocytosine as an antibacterial was identified from a drug repurposing screen. 5-Fluorocytosine was identified as a compound that inhibited production of a number of virulence factors of P. aeruginosa (Imperi et al., 2013, 2019). 5-Fluorocytosine suppressed P. aeruginosa pathogenicity in a mouse model of pulmonary infection (Imperi et al., 2013) as well as in a Caenorhabditis elegans infection model (Kirienko et  al., 2016). 5-Fluorocytosine needs to be  deaminated to 5-fluorouracil to inhibit virulence factor production of P. aeruginosa (Imperi et  al., 2013, 2019). Compounds from the fluorinated pyrimidine family have antibacterial activity. Various fluorinated pyrimidines could inhibit the growth of the human pathogen Ureaplasma urealyticum (Carnrot et  al., 2003). Floxuridine had a strong effect in vitro, inhibiting the growth of U. urealyticum for up to 72  h. This finding was supported by a later study (Wehelie et  al., 2004). Subsequently, various Gram-positive and Gram-negative bacteria were found to be  susceptible to floxuridine (Sandrini et  al., 2007a,b; Zander et  al., 2010a). Gram-positive bacteria, such as various streptococci, S. aureus and Bacillus species, were more sensitive than the Gram-negative bacteria tested. Floxuridine has also been found to have synergistic effects when used in combination with zidovudine (Wambaugh et  al., 2017). Fluorinated Pyrimidines 5-Fluorouracil has been reported to decrease virulence of P. aeruginosa by disrupting biofilm formation (Ueda et al., 2009) and also has activity against Mycobacterium tuberculosis and a number of oral microbes including the pathogen S. pyogenes (Singh et al., 2015; Vanlancker et al., 2016). Floxuridine and trifluridine both affected the growth of Mycoplasma pneumoniae, with trifluridine strongly inhibiting growth in vitro (Sun and Wang, 2013). These studies highlight the antibacterial activity of fluorinated pyrimidines. Frontiers in Microbiology | www.frontiersin.org Fluorinated Pyrimidines Originally synthesized as antitumor drugs (Heidelberger et al., 1957), fluorinated pyrimidines have also been used widely as antifungals (Vermes et  al., 2003), have some use as antivirals (Wilhelmus, 2010), and show promise as antibacterials. The fluorinated pyrimidine family was first synthesized after the observation that tumor cells preferentially utilized uracil for nucleic acid biosynthesis (Rutman et  al., 1954; Heidelberger et al., 1957). From this large family of compounds, the nucleobase 5-fluorouracil and the nucleoside floxuridine (5-fluoro- 2′deoxyuridine, Figure 2C) are frequently used for the treatment of various cancers (Galmarini et al., 2002; Alvarez et al., 2012). May 2019 | Volume 10 | Article 952 Frontiers in Microbiology | www.frontiersin.org 4 Nucleoside Analogues as Antibacterial Agents Thomson and Lamont While these compounds are effective anticancer drugs and are taken up more rapidly by cancerous cells, they also affect non-cancerous cells, and their use is associated with a number of side effects, such as bone marrow depression (Galmarini et  al., 2002). Trifluridine (Figure 2C) is used as an antiviral and is a therapy for herpetic simplex virus epithelial keratitis (Wilhelmus, 2010). 5-Fluorocytosine (Figure 2C), a prodrug of 5-fluorouracil, is used as an antifungal agent. 5-Fluorocytosine is most commonly used in combination therapy with other antifungals, typically amphotericin B, as resistance to 5-fluorocytosine arises readily (Bennett, 1977; Francis and Walsh, 1992; Ghannoum and Rice, 1999). 5-Fluorocytosine itself is not active; antifungal activity is dependent upon uptake of 5-fluorocytosine into fungal cells and subsequent deamination to 5-fluorouracil (Figure 1; Bennett, 1977). In turn, 5-fluorouracil is converted to floxuridine mono-, di-, and tri-phosphate. Metabolites of 5-fluorouracil and floxuridine can become incorporated into DNA and RNA and can also inhibit thymidylate synthase, preventing de novo formation of deoxythymidine monophosphate (Figure 1; Bennett, 1977).l While these compounds are effective anticancer drugs and are taken up more rapidly by cancerous cells, they also affect non-cancerous cells, and their use is associated with a number of side effects, such as bone marrow depression (Galmarini et  al., 2002). Trifluridine (Figure 2C) is used as an antiviral and is a therapy for herpetic simplex virus epithelial keratitis (Wilhelmus, 2010). 5-Fluorocytosine (Figure 2C), a prodrug of 5-fluorouracil, is used as an antifungal agent. 5-Fluorocytosine is most commonly used in combination therapy with other antifungals, typically amphotericin B, as resistance to 5-fluorocytosine arises readily (Bennett, 1977; Francis and Walsh, 1992; Ghannoum and Rice, 1999). Thiopurines In contrast to pyrimidines, for which halogenated analogues have been characterized, purine analogues with potential application as antimicrobials are predominantly thio-derivatives. Currently, the predominant clinical uses for thiopurines are as anticancer, immunosuppressant, and anti-inflammatory agents. In particular, they are important therapeutic agents for acute leukemias and for inflammatory bowel disease (Galmarini et al., 2002; Cooper and Brown, 2015; Hanauer et al., 2019). Compounds from the thiopurine family (Figure 2D) have antibacterial activity. As mercaptopurine has in vitro activity against Mycobacterium avium subspecies paratuberculosis and Corynebacterium species (Greenstein et  al., 2007; Shin and Collins, 2008; Liu et al., 2017), 6-thioguanosine 5′-triphosphate (thio-dGTP) can inhibit spore germination of Bacillus anthracis in an infected macrophage cell line (Akoachere et  al., 2007; Alvarez et  al., 2010), and thioguanine can inhibit in vitro growth of Mycoplasma pneumoniae (Sun and Wang, 2013). Idoxuridine The use of idoxuridine is severely limited because of its cytotoxicity, and its use is largely limited to topical applications, where toxicity is not significant (Boston Interhospital Virus Study Group and NIAID-Sponsored Cooperative Antiviral Clinical Study, 1975; Yolton and Haesart, 2008). May 2019 | Volume 10 | Article 952 5 Nucleoside Analogues as Antibacterial Agents Thomson and Lamont (Akoachere et  al., 2007). Thio-dGTP was the only compound identified as being effective at preventing spore germination. The ability of thio-dGTP to prevent necrosis in murine macrophages infected with B. anthracis was subsequently tested (Alvarez et  al., 2010). Thio-dGTP and its parent compound 6-thioguanine were the most effective analogues and were able to protect cells from necrosis even after the time point at which 100% cell death normally occurs (Alvarez et  al., 2010). While the activity of thio-dGTP as an antigerminant is promising, spore germination in vivo is a complex process dependent upon numerous factors, and further studies of the efficacy of thio-dGTP are required. Although idoxuridine was effective against S. aureus in  vitro at concentrations below those known to be cytotoxic (Zander et al., 2010a), it is unclear whether such low concentrations would improve the bactericidal effect of drugs like SXT in vivo. Frontiers in Microbiology | www.frontiersin.org METABOLISM AND MECHANISMS OF ACTION OF NUCLEOSIDE ANALOGUES IN BACTERIA Pyrimidine and purine analogues utilize the same pathways as their natural counterparts and therefore compete for both uptake and metabolism (Sun and Wang, 2013). Typically, nucleobase and nucleoside analogues enter bacterial cells through membrane transporters and then are cycled through the nucleotide salvage pathway, where they are activated by deoxyribonucleoside kinases (dNKs). dNKs perform the first committed reaction in the salvage pathway, namely the phosphorylation of deoxyribonucleosides (Figure 1). In bacteria, the metabolism and mechanism of action of pyrimidine and purine analogues have significant differences and will be further discussed separately. g y p p g Mercaptopurine is an analogue of hypoxanthine, and thioguanine is an analogue of guanine. Mercaptopurine and thioguanine require phosphorylation before they can exert their therapeutic effects. Both mercaptopurine and thioguanosine are metabolized intracellularly to the active thio-dGTP (Lennard, 1992), although mercaptopurine is also metabolized to other nucleoside derivatives. Thio-dGTP exerts its cytotoxic effect on cells primarily by becoming incorporated into DNA (Figure 1), resulting in local changes to the DNA structure, largely because it forms an unstable base pair with deoxycytidine (Somerville et  al., 2003; de Boer et  al., 2007; Karran and Attard, 2008). This change in structure can lead to DNA breaks and also inhibition of DNA replication (Somerville et  al., 2003). Thiopurine derivatives can also inhibit enzymes involved in de novo purine synthesis (Figure 1; Galmarini et  al., 2002). In eukaryotic cells, thio-dGTP is also known to interfere with secondary messengers and energy carrying processes, competing with natural guanosine triphosphate (de Boer et  al., 2007). Pyrimidine Analogues Early work on the metabolism and mechanism of action of pyrimidine analogues in bacteria demonstrated the importance of the enzymes that metabolize them, such as dNKs. Thymidine kinase (TK), a dNK, was shown to be necessary for activation of zidovudine in bacteria and subsequent incorporation of activated zidovudine into the DNA (Elwell et  al., 1987). Since the identification of TK as being important for the activity of zidovudine, the involvement of dNKs and other enzymes on the metabolism and activity of pyrimidine analogues has been demonstrated. dNK genes are differentially distributed among different bacterial species (Saito and Tomioka, 1984; Sandrini et  al., 2007b; Konrad et  al., 2012), and this differential distribution explains in part species-specific susceptibilities to nucleoside analogues. For example, P. aeruginosa lacks TK activity and is not susceptible to many pyrimidine analogues that have activity against other Gram-negative bacteria. Additionally, the presence of different dNKs in different species explains differences in responses to gemcitabine, which is found to be  effective predominantly against Gram-positive bacteria. E. coli that lacks deoxyadenosine kinase is not usually susceptible to gemcitabine but is sensitive to this compound when expressing deoxyadenosine kinases from Gram-positive bacteria such as S. aureus, S. pyogenes, and B. cereus (Sandrini et  al., 2007a,b). M. avium ssp. paratuberculosis may be  an environmental trigger for Crohn’s disease or even a causative agent of the disease (Greenstein and Collins, 2004). Mercaptopurine is commonly used to induce and maintain remission of Crohn’s disease. The effect of mercaptopurine on the growth of M. avium ssp. paratuberculosis was therefore tested, and the drug was found to inhibit growth in vitro (Greenstein et  al., 2007; Shin and Collins, 2008), although in vivo experiments have yet to be  carried out. Inosine is an important germinant of B. anthracis in  vitro. Inosine analogues and guanosine analogues were tested for their ability to block in vitro germination of spores May 2019 | Volume 10 | Article 952 6 Nucleoside Analogues as Antibacterial Agents Thomson and Lamont Zidovudine is effective against some Gram-negative but not Gram-positive species (Sandrini et  al., 2007a). The basis for this was explored using an E. coli mutant lacking TK. This mutant was resistant to zidovudine but became sensitized when transformed with TK genes from either Gram-negative species or zidovudine-resistant Gram-positive species such as Bacillus cereus and Listeria monocytogenes (Elwell et al., 1987; Sandrini et  al., 2007a,b). Toxicity While the safety profiles of clinically used nucleoside analogues are generally favorable, some of these drugs do have side effects. Nucleoside analogues, especially those used as anticancer agents, are often not specific for their target cells and also affect healthy human cells. Therefore, the use of this class of drugs is associated with a number of side effects. Many side effects are mild and do not require cessation of treatment, but some side effects are severe. For example, some analogues such as trifluridine and idoxuridine are only used topically as they have severe side effects when used systemically. While severe side effects as a result of treatment with nucleoside analogues are generally rare, they will need to be  considered if nucleoside analogues are to have clinical application as antibiotics.if ll y y y y An important part of the mechanism of action of nucleoside analogues in cancers and viruses is the incorporation of their metabolites into nucleic acids. There is evidence that this incorporation is important in bacteria as well. Metabolites of 5-fluorouracil become incorporated into E. coli RNA and to a lesser extent DNA (Warner and Rockstroh, 1980). The proportion of fluorinated uracil derivatives in the DNA increased significantly when the enzymes responsible for the removal of deoxyuridine triphosphate (UTP) from DNA were absent, indicating that this mechanism has a role in the removal of fluorinated UTP from DNA (Warner and Rockstroh, 1980). Fluorinated metabolites were also detected in the nucleic acids of Mycobacterium tuberculosis (Singh et  al., 2015). In M. tuberculosis, treatment with 5-fluorouracil also led to an upregulation of DNA damage response genes proposed to be a result of DNA breakages caused by incorporation of fluorinated UTP (Singh et  al., 2015). pp One of the most common significant side effects of nucleoside analogues is myelosuppression. Myelosuppression is a decrease in the production of blood cells in bone marrow and can affect all types of blood cells. A serious type of myelosuppression caused by chemotherapy is neutropenia, which is the reduction of leukocytes. Neutropenia predisposes patients to infections and is the dose-limiting factor in many therapeutic regimens with nucleoside analogues, including gemcitabine, 5-fluorouracil, and floxuridine, and the thiopurines (Galmarini et  al., 2002). Myelosuppression is also a dose-limiting toxicity in the use of 5-fluorocytosine as an antifungal agent. Pyrimidine Analogues These findings suggest that resistance in the Gram-positive species is not a result of lack of TK activity toward zidovudine, but instead that the monophosphate form of zidovudine resulting from the action of TK is a poor substrate for subsequent enzymes such as thymidylate kinase (Sandrini et  al., 2007a). TKs are also important for the activity of other fluorinated pyrimidines such as floxuridine in U. urealyticum (Carnrot et al., 2003). Floxuridine and trifluridine are substrates for U. urealyticum TK and are converted to the monophosphate forms that may be  further metabolized and incorporated into DNA (Sun and Wang, 2013). The monophosphate forms of floxuridine and trifluridine may also inhibit thymidylate synthase. inhibited activity of M. pneumoniae HPRT with either of its natural substrates, hypoxanthine and guanosine (Figure 1). Thioguanosine inhibited M. pneumoniae HPRT much more effectively than human HPRT. This likely reflects structural differences between humans and M. pneumoniae HPRT leading to differences in binding of thioguanosine; these differences may allow for designing pathogen-specific HPRT inhibitors (Sun and Wang, 2013). Toxicity Even though 5-fluorocytosine is a prodrug and human cells lack the enzyme needed to convert it to 5-fluorouracil, when serum concentration of 5-fluorocytosine reaches 100  μg/ml or higher, toxicities similar to those seen in patients taking 5-fluorouracil can occur (Kauffman and Frame, 1977; Harris et  al., 1986). Why these toxicities occur is unclear, although there is evidence that the host gut microbiota may convert 5-fluorocytosine to 5-fluorouracil, which can cause myelosuppression (Harris et al., 1986; Vermes et  al., 2003). Of the drugs discussed in this review, idoxuridine highlights the problem myelosuppression may cause when nucleoside analogues are used as antibiotics. While idoxuridine is used to treat herpetic simplex keratitis of the eye, it has been found to worsen and slow healing of bacterial infections of the eye (Yamaguchi et  al., 1979). Thus, nucleoside analogues that need to be  administered at doses that cause myelosuppression may be  contraindicated for use against bacterial infections.f An effect of fluorinated pyrimidines independent of nucleic acid incorporation has also been observed. Treatment with 5-fluorouracil caused E. coli to become osmotically sensitive, leading to a rapid loss of bacterial viability (Tomasz and Borek, 1959), an effect proposed to be due to metabolites of 5-fluorouracil affecting UDP-linked cell-wall precursors (Tomasz and Borek, 1960, 1962). 5-Fluorouracil partially inhibited peptidoglycan biosynthesis in S. aureus, leading to accumulation of fluorinated cell-wall precursors (Rogers and Perkins, 1960; Stickgold and Neuhaus, 1967). Accumulation of fluorinated cell-wall precursors also occurred in 5-fluorouracil-treated Mycobacterium tuberculosis (Singh et  al., 2015). Frontiers in Microbiology | www.frontiersin.org Purine Analoguesi One of the first enzymes in the purine salvage pathway is hypoxanthine guanine phosphoribosyl transferase (HPRT) (Figure 1). Thioguanosine strongly inhibited the growth of M. pneumoniae, and HPRT is a target of this analogue (Sun and Wang, 2013). Thioguanosine strongly inhibited uptake of hypoxanthine and guanosine and their subsequent incorporation into DNA and RNA. Thioguanosine also strongly Another side effect is pulmonary toxicity, commonly associated with gemcitabine use. Gemcitabine causes a range of pulmonary Frontiers in Microbiology | www.frontiersin.org May 2019 | Volume 10 | Article 952 7 Nucleoside Analogues as Antibacterial Agents Thomson and Lamont toxicities, from those that are mild and do not require stopping treatment, to rare but severe side effects, like pulmonary fibrosis and respiratory distress syndrome (Chi et al., 2012). It is unclear why gemcitabine has this effect, but it has been proposed that pulmonary toxicity occurs more frequently in patients who have underlying pulmonary disease or in patients who are concomitantly taking therapeutics that can also cause pulmonary toxicity (Gupta et al., 2002). The concentrations of gemcitabine that inhibited the growth of S. aureus in vitro were lower than the plasma concentrations of gemcitabine in cancer patients, suggesting that lower doses than are used in oncology may be  effective in treating infections, potentially reducing side effects of gemcitabine (Jordheim et  al., 2012). mutations in E. coli (Doleans-Jordheim et  al., 2011). Because of the apparent importance of TK on the metabolism of zidovudine (Sandrini et  al., 2007a,b), Doleans-Jordheim et  al. (2011) compared the sequence of the TK-encoding gene from resistant strains and susceptible strains. All 10 strains analyzed had changes to the sequences of the gene that would result in changes to the TK protein, including amino acid changes and premature stop codons. In addition to zidovudine resistance via a non-functional TK enzyme, there appears to be another mechanism of resistance. Some resistant bacteria, like staphylococci, do have functional TK enzymes (Lewin et  al., 1990a). The reason why these bacterial strains are zidovudine resistant is not clear, but it is possible that in such strains, zidovudine does not act as a substrate for TK or DNA polymerase and is thus not incorporated into nucleic acids (Lewin et  al., 1990a). Resistance As found for classical antibiotics, resistance can arise when using nucleoside analogues as antibiotics. Resistance to zidovudine and gemcitabine has been studied in detail. After short-term exposure to zidovudine, Salmonella and E. coli strains have been found develop stable high-level resistance both in vitro and in vivo (Lewin et  al., 1990a,b; Doleans-Jordheim et  al., 2011). Zidovudine-resistant E. coli has been isolated from HIV/ AIDS patients taking zidovudine as antiretroviral therapy, whereas E. coli isolated from control samples was susceptible (Lewin et  al., 1990b, 1991).i Purine Analoguesi While it is proposed that nucleoside analogues would be  effective against bacteria at concentrations that make them unlikely to cause myelosuppression or other serious side effects (Walz et al., 2010; Zander et al., 2010a; Jordheim et al., 2012), toxicity remains a serious consideration that must be  resolved before these drugs can be  used as antibacterials. Treatment of bacterial infections with compounds, which at high serum concentrations can have immunomodulatory or toxic effects, could potentially result in the drug exacerbating the infection it was intended to treat. The examples described above highlight the fact that a significant amount of investigation into the safety of nucleoside analogues as antibiotics will have to be  performed to ensure bacterial infections are not worsened by administration of analogues.f Resistance to gemcitabine has also been observed. Jordheim et  al. (2012) observed regrowth of S. aureus treated with gemcitabine, even at concentrations significantly above the determined minimum inhibitory concentration values. Mutational frequencies were found to be similar to those found for classical antibiotics. Most of the resistant mutants had mutations in the gene encoding deoxyadenosine kinase that is thought to activate gemcitabine (Jordheim et  al., 2012). It was concluded that mutations of deoxyadenosine kinase were important for conferring resistance to gemcitabine, although as some resistant mutants had no mutations in the dNK genes, there are likely to be  other mechanisms involved. The induced resistance was found to be  highly stable (Jordheim et  al., 2012). A potential way to overcome any toxic effects is to search for nucleoside analogues that are more specific for their bacterial targets. Characterization of the substrate specificities of different bacterial dNKs, which are responsible for the activation of many nucleoside analogues in bacteria, suggests that it may be  possible to design analogues specific for bacterial dNKs (Sandrini et  al., 2007a; Doleans-Jordheim et  al., 2011). While resistance to both zidovudine and gemcitabine arises readily, this could be  prevented at least in part either by coadministering with other drugs or possibly by modifying the drug itself. Zidovudine has been shown to have synergistic activity with gentamicin and amikacin (Doleans-Jordheim et al., 2011). Gemcitabine has synergy with gentamicin, and combinations of drugs may help slow the emergence of resistance (Jordheim et  al., 2012). Frontiers in Microbiology | www.frontiersin.org REFERENCES Cooper, S. L., and Brown, P. A. (2015). Treatment of pediatric acute lymphoblastic leukemia. Pediatr. Clin. N. Am. 62, 61–73. doi: 10.1016/j.pcl.2014.09.006 Akoachere, M., Squires, R. C., Nour, A. M., Angelov, L., Brojatsch, J., and Abel- Santos, E. (2007). Identification of an in vivo inhibitor of Bacillus anthracis spore germination. J. Biol. Chem. 282, 12112–12118. doi: 10.1074/jbc.M611432200 Cooper, D. L., and Lovett, S. T. (2011). Toxicity and tolerance mechanisms for azidothymidine, a replication gap-promoting agent, in Escherichia coli. DNA Repair 10, 260–270. doi: 10.1016/j.dnarep.2010.11.007 de Boer, N. K. H., Van Bodegraven, A. A., Jharap, B., de Graaf, P., and Mulder, C. J. J. (2007). Drug insight: pharmacology and toxicity of thiopurine therapy in patients with IBD. Nat. Clin. Pract. Gastroenterol. Hepatol. 4, 686–694. doi: 10.1038/ncpgasthep1000 Alvarez, Z., Lee, K., and Abel-Santos, E. (2010). Testing nucleoside analogues as inhibitors of Bacillus anthracis spore germination in vitro and in macrophage cell culture. Antimicrob. Agents Chemother. 54, 5329–5336. doi: 10.1128/ AAC.01029-10 Alvarez, P., Marchal, J. A., Boulaiz, H., Carrillo, E., Velez, C., Rodriguez-Serrano, F., et al. (2012). 5-Fluorouracil derivatives: a patent review. Expert Opin. Ther Pat. 22, 107–123. doi: 10.1517/13543776.2012.661413 Doleans-Jordheim, A., Bergeron, E., Bereyziat, F., Ben-Larbi, S., Dumitrescu, O., Mazoyer, M. A., et al. (2011). Zidovudine (AZT) has a bactericidal effect on enterobacteria and induces genetic modifications in resistant strains. Eur. J. Clin. Microbiol. Infect. Dis. 30, 1249–1256. doi: 10.1007/ s10096-011-1220-3 Bennett, J. E. (1977). Flucytosine. Ann. Intern. Med. 86, 319–322. doi: 10.7326/0003-4819-86-3-319 Elwell, L. P., Ferone, R., Freeman, G. A., Fyfe, J. A., Hill, J. A., Ray, P. H., et  al. (1987). Antibacterial activity and mechanism of action of 3′-azido-3′-deoxythymidine (Bw-A509u). Antimicrob. Agents Chemother. 31, 274–280. doi: 10.1128/AAC.31.2.274i Boston Interhospital Virus Study Group and NIAID-Sponsored Cooperative Antiviral Clinical Study (1975). Failure of high dose 5-iodo-2′-deoxyuridine in the therapy of herpes simplex virus encephalitis. Evidence of unacceptable toxicity. N. Engl. J. Med. 292, 599–603. doi: 10.1056/NEJM197503202921201i Brown, D. (2015). Antibiotic resistance breakers: can repurposed drugs fill the antibiotic discovery void? Nat. Rev. Drug Discov. 14, 821–832. doi: 10.1038/ nrd4675 Falagas, M. E., Voulgaris, G. L., Tryfinopoulou, K., Giakkoupi, P., Kyriakidou, M., Vatopoulos, A., et al. (2019). Synergistic activity of colistin with azidothymidine against colistin-resistant Klebsiella pneumoniae clinical isolates collected from inpatients in Greek hospitals. Int. J. Antimicrob. Agents. doi: 10.1016/j. ijantimicag.2019.02.021l Burris, H. A., Moore, M. J., Andersen, J., Green, M. R., Rothenberg, M. L., Madiano, M. R., et al. (1997). CONCLUSIONS AND FUTURE PERSPECTIVES Nucleoside analogues are widely used as effective therapeutics for a variety of diseases and thus make an interesting focus on repurposing studies. Studies to date have yielded promising data on the efficacy of analogues as antibacterial agents, highlighting their potential for use in treating bacterial infections. This potential will become increasingly important as the numbers of multidrug-resistant bacteria continue to rise. Nonetheless, to the best of our knowledge, no nucleoside analogues are currently approved for treating bacterial infections, and so they are not used even in cases where no other options are available. A mechanism for resistance to zidovudine was first proposed by Lewin et al. (1990a). It was found that zidovudine-resistant strains of E. coli and S. typhimurium were unable to incorporate radiolabeled thymidine into their chromosomal DNA, and that this incorporation was still prevented in the presence of a membrane permeabilizer. This suggested that in these bacteria, resistance was due not to inhibition of uptake but rather to loss of TK activity (Lewin et  al., 1990a). As TKs have been shown to be important for conversion of nucleoside analogues into their active forms, this may provide an explanation for the observed resistance. Zidovudine has been found to induce What are the gaps in current knowledge that are barriers to the use of nucleoside analogues in treating bacterial infections? First and foremost, our review highlights the paucity of studies investigating the effectiveness of nucleoside analogues in treating infections in animal models, information that is needed to May 2019 | Volume 10 | Article 952 May 2019 | Volume 10 | Article 952 8 Nucleoside Analogues as Antibacterial Agents Thomson and Lamont determine doses that would be  needed to treat infections. This information is particularly crucial for nucleoside analogues that commonly have adverse side effects when used at higher doses, such as in cancer therapy. Second, although the nucleoside analogues discussed here are approved for use in people, clinical trials will be  necessary to test their effectiveness in treating bacterial infections and costs are associated with these. Third, the antibacterial modes of action of many nucleoside analogues are not fully understood. Overcoming this knowledge gap may facilitate strategies for better targeting nucleoside analogues as inhibitors of infection while minimizing toxicity to patients. CONCLUSIONS AND FUTURE PERSPECTIVES Lastly, although investigations of resistance to nucleoside analogues have been carried out in a few cases, a comprehensive picture is lacking and it is not known how readily resistance might arise during infection. Examples described here of the use of nucleoside analogues in combination with other antibiotics, or as inhibitors of virulence rather than of bacterial growth, suggest strategies that may minimize the development of resistance. treating bacterial infections. The research reviewed here highlights the potential for use of nucleoside analogues in situations where classical antibiotics fail. With the current requirement for more antibiotics, it will be  very important to fill the knowledge gaps described above, so that nucleoside antibiotics can provide a clinically usable tool in the treatment of bacterial infections. AUTHOR CONTRIBUTIONS JT and IL reviewed the literature. JT prepared the figures. JT and IL wrote the manuscript. JT and IL reviewed the literature. JT prepared the figures. JT and IL wrote the manuscript. FUNDING JT was the recipient of a PhD scholarship from the University of Otago. Research in the authors’ laboratory is supported by the Otago Medical Research Foundation (grant AG330), the New Zealand Health Research Council (17/372), Cure Kids New Zealand (3574), and Cystic Fibrosis New Zealand. JT was the recipient of a PhD scholarship from the University of Otago. Research in the authors’ laboratory is supported by the Otago Medical Research Foundation (grant AG330), the New Zealand Health Research Council (17/372), Cure Kids New Zealand (3574), and Cystic Fibrosis New Zealand. The increasing emergence of multidrug-resistant bacteria capable of causing severe, life-threatening infections provides a hugely powerful imperative to develop new approaches for REFERENCES A new antibiotic kills pathogens without detectable resistance. Nature 517, 455–459. doi: 10.1038/nature14098 Hu, Y., Liu, Y., and Coates, A. (2019). Azidothymidine produces synergistic activity in combination with colistin against antibiotic-resistant Enterobacteriaceae. Antimicrob. Agents Chemother. 63:e01630-18. doi: 10.1128/ AAC.01630-18 Liu, F., Ma, R., Riordan, S. M., Grimm, M. C., Liu, L., Wang, Y., et al. (2017). Azathioprine, mercaptopurine, and 5-aminosalicylic acid effect the growth of IBD-associated campylobacter species and other enteric microbes. Front. Microbiol. 8:527. doi: 10.3389/fmicb.2017.00527 Huang, P., and Plunkett, W. (1995). Induction of apoptosis by gemcitabine. Semin. Oncol. 22, 19–25. Livermore, D. M. (2011). Discovery research: the scientific challenge of finding new antibiotics. J. Antimicrob. Chemother. 66, 1941–1944. doi: 10.1093/jac/ dkr262 Imperi, F., Fiscarelli, E. V., Visaggio, D., Leoni, L., and Visca, P. (2019). Activity and impact on resistance development of two antivirulence fluoropyrimidine drugs of Pseudomonas aeruginosa. Front. Cell. Infect. Microbiol. 9:49. doi: 10.3389/fcimb.2019.00049 Mini, E., Nobili, S., Caciagli, B., Landini, I., and Mazzei, T. (2006). Cellular pharmacology of gemcitabine. Ann. Oncol. 17, V7–V12. doi: 10.1093/annonc/ mdj941 Imperi, F., Massai, F., Facchini, M., Frangipani, E., Visaggio, D., Leoni, L., et  al. (2013). Repurposing the antimycotic drug flucytosine for suppression of Pseudomonas aeruginosa pathogenicity. Proc. Natl. Acad. Sci. USA 110:16693. doi: 10.1073/pnas.1222706110 Miro-Canturri, A., Ayerbe-Algaba, R., and Smani, Y. (2019). Drug repurposing for the treatment of bacterial and fungal infections. Front. Microbiol. 10:41. doi: 10.3389/fmicb.2019.00041 Ishii, H., Furuse, J., Nagase, M., and Yoshino, M. (2005). Impact of gemcitabine on the treatment of metastatic pancreatic cancer. J. Gastroenterol. Hepatol. 20, 62–66. doi: 10.1111/j.1440-1746.2004.03487.x Moroni, G. N., Bogdanov, P. M., and Brinon, M. C. (2002). Synthesis and in vitro antibacterial activity of novel 5′-O-analog derivatives of zidovudine as potential prodrugs. Nucleosides Nucleotides Nucleic Acids 21, 231–241. doi: 10.1081/NCN-120003288 Jordheim, L. P., Ben Larbi, S., Fendrich, O., Ducrot, C., Bergeron, E., Dumontet, C., et al. (2012). Gemcitabine is active against clinical multiresistant Staphylococcus aureus strains and is synergistic with gentamicin. Int. J. Antimicrob. Agents 39, 444–447. doi: 10.1016/j.ijantimicag.2012.01.019 Ng, S. M. S., Sioson, J. S. P., Yap, J. M., Ng, F. M., Ching, H. S. V., Teo, J. W. P., et al. (2018). Repurposing Zidovudine in combination with Tigecycline for treating carbapenem-resistant Enterobacteriaceae infections. Eur. J. Clin. Microbiol. Infect. Dis. 37, 141–148. doi: 10.1007/s10096-017-3114-5 Jordheim, L. P., Durantel, D., Zoulim, F., and Dumontet, C. (2013). Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases. Nat. Rev. REFERENCES (2007). On the action of methotrexate and 6-mercaptopurine on M. avium subspecies paratuberculosis. PLoS One 2:e161. doi: 10.1371/journal.pone.0000516 Koszytkowska-Stawinska, M., and Buchowicz, W. (2014). Multicomponent reactions in nucleoside chemistry. Beilstein J. Org. Chem. 10, 1706–1732. doi: 10.3762/bjoc.10.179h Lennard, L. (1992). The clinical-pharmacology of 6-mercaptopurine. Eur. J. Clin. Pharmacol. 43, 329–339. doi: 10.1007/BF02220605 Gupta, N., Ahmed, I., Steinberg, H., Patel, D., Nissel-Horowitz, S., and Mehrotra, B. (2002). Gemcitabine-induced pulmonary toxicity–case report and review of the literature. Am. J. Clin. Oncol. 25, 96–100. doi: 10.1097/00000421-200202000-00021 Lewin, C. S., Allen, R. A., and Amyes, S. G. B. (1990a). Mechanisms of Zidovudine Resistance in Bacteria. J. Med. Microbiol. 33, 235–238. doi: 10.1099/00222615-33-4-235 Hanauer, S. B., Sandborn, W. J., and Lichtenstein, G. R. (2019). Evolving considerations for thiopurine therapy for inflammatory bowel diseases-a clinical practice update: commentary. Gastroenterology 156, 36–42. doi: 10.1053/j.gastro.2018.08.043 Lewin, C. S., Watt, B., and Naden, M. (1991). Zidovudine resistance in clinically significant bacterial isolates from aids patients. J. Antimicrob. Chemother. 28, 778–780. doi: 10.1093/jac/28.5.778 Harris, B., Manning, B., Federle, T., and Diasio, R. (1986). Conversion of 5-fluorocytosine to 5-fluorouracil by human intestinal microflora. Fed. Proc. 45:443. doi: 10.1128/AAC.29.1.44 Lewin, C. S., Watt, B., Paton, R., and Amyes, S. G. B. (1990b). Isolation of zidovudine resistant Escherichia coli from AIDS patients. FEMS Microbiol. Lett. 70, 141–144. doi: 10.1111/j.1574-6968.1990.tb13967.x Heidelberger, C., Chaudhuri, N. K., Danneberg, P., Mooren, D., Griesbach, L., Duschinsky, R., et al. (1957). Fluorinated pyrimidines, a new class of tumour- inhibitory compounds. Nature 179, 663–666. doi: 10.1038/179663a0 Lewis, K. (2013). Platforms for antibiotic discovery. Nat. Rev. Drug Discov. 12, 371–387. doi: 10.1038/nrd3975 Heinemann, V., Hertel, L. W., Grindey, G. B., and Plunkett, W. (1988). Comparison of the cellular pharmacokinetics and toxicity of 2′,2′-difluorodeoxycytidine and 1-beta-D-arabinofuranosylcytosine. Cancer Res. 48, 4024–4031. Lewis, W., Gonzalez, B., Chomyn, A., and Papoian, T. (1992). Zidovudine induces molecular, biochemical, and ultrastructural-changes in rat skeletal- muscle mitochondria. J. Clin. Investig. 89, 1354–1360. doi: 10.1172/JCI115722 Lewis, W., Grupp, I. L., Grupp, G., Hoit, B., Morris, R., Samarel, A. M., et  al. (2000). Cardiac dysfunction occurs in the HIV-1 transgenic mouse treated with zidovudine. Lab. Investig. 80, 187–197. doi: 10.1038/labinvest.3780022 Herrmann, J. L., and Lagrange, P. H. (1992). Intracellular activity of zidovudine (3′-azido-3′-deoxythymidine, Azt) against Salmonella typhimurium in the macrophage cell line-J774-2. Antimicrob. Agents Chemother. 36, 1081–1085. doi: 10.1128/AAC.36.5.1081 Ling, L. L., Schneider, T., Peoples, A. J., Spoering, A. L., Engels, I., Conlon, B. P., et al. (2015). REFERENCES Improvements in survival and clinical benefit with gemcitabine as first-line therapy for patients with advanced pancreas cancer: a randomized trial. J. Clin. Oncol. 15, 2403–2413. doi: 10.1200/ JCO.1997.15.6.2403 Francis, P., and Walsh, T. J. (1992). Evolving role of flucytosine in immunocompromised patients  - new insights into safety, pharmacokinetics, and antifungal therapy. Clin. Infect. Dis. 15, 1003–1018. doi: 10.1093/clind/15.6.1003 Furman, P. A., Fyfe, J. A., Stclair, M. H., Weinhold, K., Rideout, J. L., Freeman, G. A., et al. (1986). Phosphorylation of 3′-azido-3′-deoxythymidine and selective interaction of the 5′-triphosphate with human-immunodeficiency- virus reverse-transcriptase. Proc. Natl. Acad. Sci. USA 83, 8333–8337. doi: 10.1073/pnas.83.21.8333 Carnrot, C., Wehelie, R., Eriksson, S., Bolske, G., and Wang, L. Y. (2003). Molecular characterization of thymidine kinase from Ureaplasma urealyticum: nucleoside analogues as potent inhibitors of mycoplasma growth. Mol. Microbiol. 50, 771–780. doi: 10.1046/j.1365-2958.2003.03717.x Carter, G. T., and McDonald, L. (2014). “Uridyl peptide antibiotics: developments in biosynthesis and medicinal chemistry” in Antimicrobials. eds. F. Marinelli, and O. Genilloud (Berlin: Springer-Verlag), 177–191. doi: 10.1007/978-3-662-45786-3_9 Galmarini, C. M., Mackey, J. R., and Dumontet, C. (2002). Nucleoside analogues and nucleobases in cancer treatment. Lancet Oncol. 3, 415–424. doi: 10.1016/ S1470-2045(02)00788-X Casado, J. L., Valdezate, S., Calderon, C., Navas, E., Frutos, B., Guerrero, A., et al. (1999). Zidovudine therapy protects against Salmonella bacteremia recurrence in human immunodeficiency virus-infected patients. J. Infect. Dis. 179, 1553–1556. doi: 10.1086/314749 Gavrish, E., Sit, C. S., Cao, S. G., Kandror, O., Spoering, A., Peoples, A., et  al. (2014). Lassomycin, a ribosomally synthesized cyclic peptide, kills Mycobacterium tuberculosis by targeting the ATP-dependent protease ClpC1P1P2. Chem. Biol. 21, 509–518. doi: 10.1016/j.chembiol.2014.01.014 Chi, D. C., Brogan, F., Turenne, I., Zelonis, S., Schwartz, L., and Saif, M. W. (2012). Gemcitabine-induced Pulmonary Toxicity. Anticancer Res. 32, 4147–4149. Ghannoum, M. A., and Rice, L. B. (1999). Antifungal agents: mode of action, mechanisms of resistance, and correlation of these mechanisms with bacterial resistance. Clin. Microbiol. Rev. 12, 501–517. doi: 10.1128/CMR.12.4.501 May 2019 | Volume 10 | Article 952 Frontiers in Microbiology | www.frontiersin.org 9 Nucleoside Analogues as Antibacterial Agents Thomson and Lamont Greenstein, R. J., and Collins, M. T. (2004). Emerging pathogens: is Mycobacterium avium subspecies paratuberculosis zoonotic? Lancet 364, 396–397. doi: 10.1016/ S0140-6736(04)16781-0 Konrad, A., Yarunova, E., Tinta, T., Piskur, J., and Liberles, D. A. (2012). The global distribution and evolution of deoxyribonucleoside kinases in bacteria. Gene 492, 117–120. doi: 10.1016/j.gene.2011.10.039 Greenstein, R. J., Su, L., Haroutunian, V., Shahidi, A., and Brown, S. T. REFERENCES J., and Dankert, J. (2003). An in vitro study on the active conversion of flucytosine to fluorouracil by microorganisms in the human intestinal microflora. Chemotherapy 49, 17–23. doi: 10.1159/000069784 j Rutman, R. J., Cantarow, A., and Paschkis, K. E. (1954). The catabolism of uracil in vivo and in  vitro. J. Biol. Chem. 210, 321–329.h Walz, J. M., Avelar, R. L., Longtine, K. J., Carter, K. L., Mermel, L. A., Heard, S. O., et al. (2010). Anti-infective external coating of central venous catheters: a randomized, noninferiority trial comparing 5-fluorouracil with chlorhexidine/silver sulfadiazine in preventing catheter colonization. Crit. Care Med. 38, 2095–2102. doi: 10.1097/CCM.0b013e3181f265ba Saito, H., and Tomioka, H. (1984). Thymidine kinase of bacteria–activity of the enzyme in actinomycetes and related organisms. J. Gen. Microbiol. 130, 1863–1870. doi: 10.1099/00221287-130-7-1863 Sandrini, M. P. B., Clausen, A. R., On, S. L. W., Aarestrup, F. M., Munch- Petersen, B., and Piskur, J. (2007a). Nucleoside analogues are activated by bacterial deoxyribonucleoside kinases in a species-specific manner. J. Antimicrob. Chemother. 60, 510–520. doi: 10.1093/jac/dkm240 Wambaugh, M. A., Shakya, V. P. S., Lewis, A. J., Mulvey, M. A., and Brown, J. C. S. (2017). High-throughput identification and rational design of synergistic small-molecule pairs for combating and bypassing antibiotic resistance. PLoS Biol. 15:e2001644. doi: 10.1371/journal.pbio.2001644 Sandrini, M. P. B., Shannon, O., Clausen, A. R., Bjorck, L., and Piskur, J. (2007b). Deoxyribonucleoside kinases activate nucleoside antibiotics in severely pathogenic bacteria. Antimicrob. Agents Chemother. 51, 2726–2732. doi: 10.1128/AAC.00081-07 Warner, H. R., and Rockstroh, P. A. (1980). Incorporation and excision of 5-fluorouracil from deoxyribonucleic acid in Escherichia coli. J. Bacteriol. 141, 680–686. Shin, S. J., and Collins, M. T. (2008). Thiopurine drugs azathioprine and 6-mercaptopurine inhibit Mycobacterium paratuberculosis growth in  vitro. Antimicrob. Agents Chemother. 52:1208. doi: 10.1128/AAC.00125-08 Wehelie, R., Eriksson, S., and Wang, L. Y. (2004). Effect of fluoropyrimidines on the growth of Ureaplasma urealyticum. Nucleosides Nucleotides Nucleic Acids 23, 1499–1502. doi: 10.1081/NCN-200027714 Singh, V., Brecik, M., Mukherjee, R., Evans, J. C., Svetlikova, Z., Blasko, J., et  al. (2015). The complex mechanism of antimycobacterial action of 5-fluorouracil. Chem. Biol. 22, 63–75. doi: 10.1016/j.chembiol.2014.11.006 Wilhelmus, K. R. (2010). Antiviral treatment and other therapeutic interventions for herpes simplex virus epithelial keratitis. Cochrane Database Syst. Rev. 8:CD002898. doi: 10.1002/14651858.CD002898.pub4 l Sköld, O. (2009). “Sulfonamides and trimethoprim” in Antimicrobial drug resistance. ed. D. L. Mayers (New York City: Humana Press), 259–269. doi: 10.1007/978-1-59745-180-2_23 Winn, M., Goss, R. J. M., Kimura, K., and Bugg, T. D. H. REFERENCES Drug Discov. 12, 447–464. doi: 10.1038/ nrd4010 Niu, G. Q., and Tan, H. R. (2015). Nucleoside antibiotics: biosynthesis, regulation, and biotechnology. Trends Microbiol. 23, 110–119. doi: 10.1016/j.tim.2014.10.007 Karran, P., and Attard, N. (2008). Thiopurines in current medical practice: molecular mechanisms and contributions to therapy-related cancer. Nat. Rev. Cancer 8, 24–36. doi: 10.1038/nrc2292f O’Neill, J.C. (2014). Review on antimicrobial resistance. Antimicrobial resistance: tackling a crisis for the health and wealth of nations. (United Kingdom Government Report). (Accessed March 21, 2019).i Peyclit, L., Baron, S. A., Yousfi, H., and Rolain, J. M. (2018). Zidovudine: a salvage therapy for mcr-1 plasmid-mediated colistin-resistant bacterial infections? Int. J. Antimicrob. Agents 52, 11–13. doi: 10.1016/j.ijantimicag.2018.03.012 Kauffman, C. A., and Frame, P. T. (1977). Bone-marrow toxicity associated with 5-fluorocytosine therapy. Antimicrob. Agents Chemother. 11, 244–247. doi: 10.1128/AAC.11.2.244 Kaufman, H. E. (1962). Clinical cure of herpes simplex keratitis by 5-iodo-2- deoxyuridine. Proc. Soc. Exp. Biol. Med. 109, 251–252. doi: 10.3181/00379727-109-27169 Plunkett, W., Huang, P., and Gandhi, V. (1995). Preclinical characteristics of gemcitabine. Anti-Cancer Drugs 6, 7–13. doi: 10.1097/00001813- 199512006-00002 Keith, B. R., White, G., and Wilson, H. R. (1989). Invivo efficacy of zidovudine (3′-azido-3′-deoxythymidine) in experimental gram-negative-bacterial infections. Antimicrob. Agents Chemother. 33, 479–483. doi: 10.1128/ AAC.33.4.479 Prusoff, W. H., Chen, M. S., Fischer, P. H., Lin, T. S., Shiau, G. T., Schinazi, R. F., et al. (1979). Antiviral iodinated pyrimidine deoxyribonucleosides: 5-iodo-2′- deoxyuridine; 5-iodo-2′-deoxycytidine; 5-iodo-5′-amino-2′,5′-dideoxyuridine. Pharmacol. Ther. 7, 1–34. doi: 10.1016/0163-7258(79)90023-8 harmacol. Ther. 7, 1–34. doi: 10.1016/0163-7258(79)90023-8 Kirienko, D. R., Revtovich, A. V., and Kirienko, N. V. (2016). A high-content, phenotypic screen identifies fluorouridine as an inhibitor of pyoverdine biosynthesis and Pseudomonas aeruginosa virulence. mSphere 1:e00217-16. doi: 10.1128/mSphere.00217-16 Rangel-Vega, A., Bernstein, L. R., Mandujano-Tinoco, E. A., Garcia-Contreras, S. J., and Garcia-Contreras, R. (2015). Drug repurposing as an alternative for the treatment of recalcitrant bacterial infections. Front. Microbiol. 6:282. doi: 10.3389/fmicb.2015.00282 May 2019 | Volume 10 | Article 952 Frontiers in Microbiology | www.frontiersin.org 10 Nucleoside Analogues as Antibacterial Agents Thomson and Lamont Rice, L. B. (2009). The clinical consequences of antimicrobial resistance. Curr. Opin. Microbiol. 12, 476–481. doi: 10.1016/j.mib.2009.08.001 Vanlancker, E., Vanhoecke, B., Smet, R., Props, R., and Van De Wiele, T. (2016). 5-fluorouracil sensitivity varies among oral micro-organisms. J. Med. Microbiol. 65, 775–783. doi: 10.1099/jmm.0.000292 Rogers, H. J., and Perkins, H. R. (1960). 5-Fluorouracil and mucopeptide biosynthesis by Staphylococcus aureus. Biochem. J. 77, 448–459. doi: 10.1042/ bj0770448 Vermes, A., Kuijper, E. J., Guchelaar, H. REFERENCES (2010). Antimicrobial nucleoside antibiotics targeting cell wall assembly: recent advances in structure-function studies and nucleoside biosynthesis. Nat. Prod. Rep. 27, 279–304. doi: 10.1039/B816215H Somerville, L., Krynetski, E. Y., Krynetskaia, N. F., Beger, R. D., Zhang, W. X., Marhefka, C. A., et al. (2003). Structure and dynamics of thioguanine- modified duplex DNA. J. Biol. Chem. 278, 1005–1011. doi: 10.1074/jbc. M204243200 Yamaguchi, K., Okumoto, M., Stern, G., Friedlaender, M., and Smolin, G. (1979). Idoxuridine and bacterial corneal infection. Am J. Ophthalmol. 87, 202–205. doi: 10.1016/0002-9394(79)90143-0 Stickgold, R. A., and Neuhaus, F. C. (1967). On the initial stage in peptidoglycan synthesis. Effect of 5-fluorouracil substitution on phospho-N-acetylmuramyl- pentapeptide translocase (uridine 5′-phosphate). J. Biol. Chem. 242, 1331–1337. Yolton, D. P., and Haesart, S. P. (2008). “Anti-infective drugs” in Clinical ocular pharmacology. 2nd Edn, ed. J. D. Bartlett. (St Louis, MO: Butterworth-Heinemann), 175–220. doi: 10.1016/B978-0-7506-7576-5.50016-1 Zander, J., Besier, S., Ackermann, H., and Wichelhaus, T. A. (2010a). Synergistic antimicrobial activities of folic acid antagonists and nucleoside analogs. Antimicrob. Agents Chemother. 54, 1226–1231. doi: 10.1128/AAC.00705-09 Sun, R., and Wang, L. Y. (2013). Inhibition of Mycoplasma pneumoniae growth by FDA-approved anticancer and antiviral nucleoside and nucleobase analogs. BMC Microbiol. 13:184. doi: 10.1186/1471-2180-13-184 Tomasz, A., and Borek, E. (1959). An early phase in the bactericidal action of 5-fluorouracil on E. coli K12. Osmotic imbalance. Proc. Natl. Acad. Sci. USA. 45, 929–932. doi: 10.1073/pnas.45.7.929h Zander, J., Besier, S., Faetke, S., Saum, S. H., Muller, V., and Wichelhaus, T. A. (2010b). Antimicrobial activities of trimethoprim/sulfamethoxazole, 5-iodo-2′- deoxyuridine and rifampicin against Staphylococcus aureus. Int. J. Antimicrob. Agents 36, 562–565. doi: 10.1016/j.ijantimicag.2010.08.007 Tomasz, A., and Borek, E. (1960). The mechanism of bacterial fragility produced by 5-fluorouracil: the accumulation of cell wall precursors. Proc. Natl. Acad. Sci. USA 46, 324–327. doi: 10.1073/pnas.46.3.324h Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Tomasz, A., and Borek, E. (1962). The mechanism of an osmotic instability induced in E. coli K-12 by 5-fluorouracil. Biochemistry 1, 543–552. doi: 10.1021/bi00910a001l Ueda, A., Attila, C., Whiteley, M., and Wood, T. K. (2009). Uracil influences quorum sensing and biofilm formation in Pseudomonas aeruginosa and fluorouracil is an antagonist. Microb. Biotechnol. 2, 62–74. doi: 10.1111/j.1751-7915.2008.00060.x Copyright © 2019 Thomson and Lamont. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). Frontiers in Microbiology | www.frontiersin.org REFERENCES The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Vanhaperen, V. W. T. R., Veerman, G., Vermorken, J. B., and Peters, G. J. (1993). 2′,2′-difluoro-deoxycytidine (gemcitabine) incorporation into RNA and DNA of tumor-cell lines. Biochem. Pharmacol. 46, 762–766. doi: 10.1016/0006-2952(93)90566-F May 2019 | Volume 10 | Article 952 Frontiers in Microbiology | www.frontiersin.org 11
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The niche matters: origin, function and fate of CNS-associated macrophages during health and disease
Acta neuropathologica
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The niche matters: origin, function and fate of CNS‑associated macrophages during health and disease Adrià Dalmau Gasull1   · Martina Glavan2,3 · Sai K. Reddy Samawar4 · Kishan Kapupara4 · Joe Kelk5 · Marina Rubio2 · Stefano Fumagalli5 · Lydia Sorokin4 · Denis Vivien2,6 · Marco Prinz1,7 Received: 14 November 2023 / Revised: 13 December 2023 / Accepted: 22 December 2023 © The Author(s) 2024 * Marco Prinz marco.prinz@uniklinik-freiburg.de * Adrià Dalmau Gasull adria.dalmau.gasull@uniklinik-freiburg.de Acta Neuropathologica (2024) 147:37 https://doi.org/10.1007/s00401-023-02676-9 Acta Neuropathologica (2024) 147:37 https://doi.org/10.1007/s00401-023-02676-9 REVIEW REVIEW Abstract There are several cellular and acellular structural barriers associated with the brain interfaces, which include the dura, the leptomeninges, the perivascular space and the choroid plexus epithelium. Each structure is enriched by distinct myeloid populations, which mainly originate from erythromyeloid precursors (EMP) in the embryonic yolk sac and seed the CNS during embryogenesis. However, depending on the precise microanatomical environment, resident myeloid cells differ in their marker profile, turnover and the extent to which they can be replenished by blood-derived cells. While some EMP-derived cells seed the parenchyma to become microglia, others engraft the meninges and become CNS-associated macrophages (CAMs), also referred to as border-associated macrophages (BAMs), e.g., leptomeningeal macrophages (MnMΦ). Recent data revealed that MnMΦ migrate into perivascular spaces postnatally where they differentiate into perivascular macrophages (PvMΦ). Under homeostatic conditions in pathogen-free mice, there is virtually no contribution of bone marrow-derived cells to MnMΦ and PvMΦ, but rather to macrophages of the choroid plexus and dura. In neuropathological conditions in which the blood–brain barrier is compromised, however, an influx of bone marrow-derived cells into the CNS can occur, potentially contributing to the pool of CNS myeloid cells. Simultaneously, resident CAMs may also proliferate and undergo transcriptional and proteomic changes, thereby, contributing to the disease outcome. Thus, both resident and infiltrating myeloid cells together act within their microenvironmental niche, but both populations play crucial roles in the overall disease course. Here, we summarize the current understanding of the sources and fates of resident CAMs in health and disease, and the role of the microenvironment in influencing their maintenance and function. Abstract Keywords  Macrophages · CNS · Development · Disease Keywords  Macrophages · CNS · Development · Disease Vol.:(0123456789) * Adrià Dalmau Gasull adria.dalmau.gasull@uniklinik-freiburg.de * Marco Prinz marco.prinz@uniklinik-freiburg.de 1 Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany 2 Normandie University, UNICAEN, INSERM UMR-S U1237, Physiopathology and Imaging of Neurological Disorders (PhIND), GIP Cyceron, Institut Blood and Brain @ Caen-Normandie (BB@C), 14000 Caen, France 3 Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, USA 4 Institute of Physiological Chemistry and Pathobiochemistry and Cells in Motion Interfaculty Centre (CIMIC), University of Münster, Münster, Germany 5 Laboratory of Stroke and Vascular Dysfunctions, Department of Acute Brain and Cardiovascular Injury, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy 6 Department of Clinical Research, Caen-Normandie University Hospital, CHU, Avenue de La Côte de Nacre, Caen, France 7 Signalling Research Centres BIOSS and CIBSS‑Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany * Adrià Dalmau Gasull adria.dalmau.gasull@uniklinik-freiburg.de * Marco Prinz marco.prinz@uniklinik-freiburg.de 1 Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany 2 Normandie University, UNICAEN, INSERM UMR-S U1237, Physiopathology and Imaging of Neurological Disorders (PhIND), GIP Cyceron, Institut Blood and Brain @ Caen-Normandie (BB@C), 14000 Caen, France 3 Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, USA 4 Institute of Physiological Chemistry and Pathobiochemistry and Cells in Motion Interfaculty Centre (CIMIC), University of Münster, Münster, Germany 5 Laboratory of Stroke and Vascular Dysfunctions, Department of Acute Brain and Cardiovascular Injury, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy 6 Department of Clinical Research, Caen-Normandie University Hospital, CHU, Avenue de La Côte de Nacre, Caen, France 7 Signalling Research Centres BIOSS and CIBSS‑Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany 4 Institute of Physiological Chemistry and Pathobiochemistry and Cells in Motion Interfaculty Centre (CIMIC), University of Münster, Münster, Germany * Marco Prinz marco.prinz@uniklinik-freiburg.de 5 Laboratory of Stroke and Vascular Dysfunctions, Department of Acute Brain and Cardiovascular Injury, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy 1 Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany 6 Department of Clinical Research, Caen-Normandie University Hospital, CHU, Avenue de La Côte de Nacre, Caen, France 2 Normandie University, UNICAEN, INSERM UMR-S U1237, Physiopathology and Imaging of Neurological Disorders (PhIND), GIP Cyceron, Institut Blood and Brain @ Caen-Normandie (BB@C), 14000 Caen, France 7 Signalling Research Centres BIOSS and CIBSS‑Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany 3 Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, USA (012 3456789) Acta Neuropathologica (2024) 147:37 Page 2 of 13 Acta Neuropathologica 37 day (E)9.5 [52], while in humans, the first microglia have been described at 4.5 weeks post-conception [70]. Abstract Upon entry into the CNS, the myeloid progenitor cells undergo extensive proliferation and differentiation within their respective niches. While microglial precursors seed the CNS parenchyma, CAM precursors seed CNS interfaces, giving rise first to leptomeningeal macrophages (MnMΦ) and choroid plexus macrophages (cpMΦ) [35]. In fact, recent data found that human microglia and CAMs are transcriptionally distinct already at 5 weeks post-concep- tion [91]. Recent research in mice revealed that MnMΦ populate the perivascular spaces postnatally, subsequently differentiating into perivascular macrophages (PvMΦ) [61]. The leptomeningeal and perivascular niches differ Introduction Central nervous system (CNS) resident macrophages are comprised of two main groups: parenchymal microglia and extra-parenchymal, CNS-associated macrophages (CAMs). Recent research has shown that CNS endogenous mac- rophages share a common origin, as both microglia and CAMs originate from embryonic yolk sac (YS) progenitors [34, 35] (Fig. 1). These precursors give rise to a pool of immature macrophages that migrate via blood vessels to colonize different regions of the developing CNS before the formation of the blood–brain barrier (BBB) [105]. In mice, CNS seeding of microglia occurs around embryonic Fig. 1   CNS resident macrophages during development, homeostasis, and Alzheimer’s disease (AD). During embryogenesis, erythromye- loid precursors (EMP) from the yolk sac differentiate to an intermedi- the perivascular spaces postnatally, differentiating into perivascu- lar macrophages (PvMΦ). The PvMΦ are sandwiched between the endothelial basement membrane (BM) and the glia limitants In the Fig. 1   CNS resident macrophages during development, homeostasis, and Alzheimer’s disease (AD). During embryogenesis, erythromye- loid precursors (EMP) from the yolk sac differentiate to an intermedi- ate immature population (A1) which transition into pre-macrophages progenitors (A2). These immature macrophages migrate through the developing blood vessels and start to invade the neural tube by E9.5. While some ­CD206+ A2 progenitors seed the parenchyma to become microglia, others engraft 1) the dura to become dural macrophages (dmMΦ), 2) the choroid plexus (ChP) to become epiplexus or stro- mal choroid plexus macrophages (cpMΦ), and 3) the leptomeninges to become leptomeningeal macrophages (MnMΦ). MnMΦ populate the perivascular spaces postnatally, differentiating into perivascu- lar macrophages (PvMΦ). The PvMΦ are sandwiched between the endothelial basement membrane (BM) and the glia limitants. In the developed CNS, microglia, MnMΦ, PvMΦ, and epiplexus cpMΦ are long-lived and self-maintain. Instead, dmMΦ and stromal cpMΦ are slowly replaced by bone marrow-derived Monocytes. During AD context, not only microglia, but also PvMΦ and MnMΦ have a criti- cal role in the clearance of vascular and parenchymal amyloid beta (Aβ) plaques. The maintenance of blood–brain barrier integrity, along with the possible contribution of monocyte-derived cells in clearing plaques, remains unclear the perivascular spaces postnatally, differentiating into perivascu- lar macrophages (PvMΦ). The PvMΦ are sandwiched between the endothelial basement membrane (BM) and the glia limitants. In the developed CNS, microglia, MnMΦ, PvMΦ, and epiplexus cpMΦ are long-lived and self-maintain. Instead, dmMΦ and stromal cpMΦ are slowly replaced by bone marrow-derived Monocytes. Origin and fate It was long believed that microglia and CAMs constitute ontogenically distinct myeloid populations [44]. However, this concept was based on studies in bone marrow chimeric mice, where bone marrow-derived cells were detected in CNS perivascular spaces [8, 125]. These results were poten- tially due to the artificial disruption of the BBB and con- comitant induction of aberrant chemoattractant signals in the CNS caused by whole-body irradiation [68]. The break- through came in 2016 when Goldmann et al., [35] employed fate-mapping mouse lines to demonstrate that CAMs and microglia both originate from the YS’s early erythromyeloid progenitors (EMPs). Differentiation into tissue-resident mac- rophages begins with a shift from EMPs to an intermedi- ate immature population so-called A1, which then transi- tions into A2 pre-macrophages progenitors [34, 35, 52, 61, 113, 114] (Fig. 1). Based on Mrc1 gene expression (which encodes CD206), two transcriptionally and phenotypically distinct A2 subpopulations were identified in the YS of E9.5 mice. As CD206 expression is limited to CAMs in the adult mouse CNS, this led to the assumption that ­CD206neg A2 cells are microglia progenitors and ­CD206+ A2 cells are CAM progenitors [113]. However, this may not be the case, since tamoxifen induction in pregnant Mrc1CreERT2/ CreERT2R26tdTomato/tdTomato mice at E9.0 resulted in not only ­tdTomato+ CAMs but also ­tdTomato+ microglia in post- natal (P)14 brains [61]. This substantiates that microglia and CAMs share the same progenitor cells and, only once within their niche, do local factors determine their terminal differentiation. Besides their ontogeny, microglia and CAMs share some transcriptomic signatures including the expression of ion- ized calcium-binding adaptor molecule (Iba) 1, fractalkine receptor (Cx3cr1), and colony-stimulating factor (Csf) 1 receptor. Only the recent development of new technolo- gies, such as single-cell RNA sequencing (scRNA-seq), has resulted in the identification of transcriptomic profiles that permit segregation of microglia and CAMs. For exam- ple, hexosaminidase subunit beta (Hexb), P2Y purinergic receptor (P2ry) 12, transmembrane protein (Tmem) 119, spalt-like transcription factor (Sall) 1, sialic acid binding Ig-like lectin (Siglec) h, are enriched in microglia, whereas mannose receptor (Mrc) 1 (or CD206), membrane-spanning 4-domains subfamily A member (Ms4a)7, platelet factor (Pf)4 are preferentially expressed by CAMs [35, 49, 126]. scRNA-seq has further revealed transcriptomic heteroge- neity in CAMs located at different brain interfaces [114]. Specifically, MnMΦ were shown to be distinct from dural macrophages (dmMΦ) in the meninges. Introduction During AD context, not only microglia, but also PvMΦ and MnMΦ have a criti- cal role in the clearance of vascular and parenchymal amyloid beta (Aβ) plaques. The maintenance of blood–brain barrier integrity, along with the possible contribution of monocyte-derived cells in clearing plaques, remains unclear Page 3 of 13  37 Acta Neuropathologica (2024) 147:37 in their cellular and extracellular matrix characteristics [40], thereby, imparting niche-specific signatures to the resident myeloid populations that include transcriptional profile, morphology, motility, self-maintenance capacity, and function [49, 53, 71, 98, 114]. Although microglial functions during homeostasis and disease have been long studied in depth [19, 82], the role of CAMs in physio- logical and disease conditions has just begun to be elu- cidated. So far, few studies have addressed this topic and have implicated CAMs in cerebrospinal fluid (CSF) flow dynamics [25], as well as in neurodegenerative [42, 95], cerebrovascular [77, 101], and neuroinflammatory diseases [22, 49, 78, 88, 90]. in their cellular and extracellular matrix characteristics [40], thereby, imparting niche-specific signatures to the resident myeloid populations that include transcriptional profile, morphology, motility, self-maintenance capacity, and function [49, 53, 71, 98, 114]. Although microglial functions during homeostasis and disease have been long studied in depth [19, 82], the role of CAMs in physio- logical and disease conditions has just begun to be elu- cidated. So far, few studies have addressed this topic and have implicated CAMs in cerebrospinal fluid (CSF) flow dynamics [25], as well as in neurodegenerative [42, 95], cerebrovascular [77, 101], and neuroinflammatory diseases [22, 49, 78, 88, 90]. microglia or CAMs [12, 50, 61–63]. The use of such innova- tive and promising mouse lines in models of neuroinflamma- tion and/or neurodegeneration now provides the possibility of defining functions of specific CAM populations in brain homeostasis and pathologies and their potential as thera- peutic targets. Origin and fate This is not surpris- ing given that, despite collectively constituting the meninges that surround and protect the CNS, the leptomeninges and dura matter comprise distinct layers. The dura, positioned as the outermost layer, possesses unique characteristics such as high vascularity and abundance of collagen fibers, resem- bling more a connective tissue. Because the dura does not establish a BBB, it enables an exchange of blood-derived cells and molecules [4]. Consequently, these distinct niches are associated with unique CAM signatures. Similarly to meningeal macrophages, within the population of cpMΦ stromal- and epiplexus-located cells were shown to have distinct transcriptomic profiles. A recent study suggested the existence of more than one PvMΦ population, defined by presence or absence of CX3CR1 expression. A ­CX3CR1neg population was identified, the function of which remains to be determined [101]. Importantly, comparison between human and mouse CAMs transcriptomic profiles highlighted the conservation of evolutionary markers in these cells [91]. The identification of differentially expressed genes in dif- ferent myeloid populations has provided valuable knowledge i f To seed the developing brain at E9.5, progenitor popula- tions travel within the bloodstream of the developing vas- culature [105]. NCX1-deficient embryos, that lack a heart- beat and hence blood circulation, have normal numbers of YS pre-macrophage progenitors at E9.5 but lack microglia, indicating that blood circulation is required for seeding of the CNS [34]. The first A2 pre-macrophage progenitors are detectable in the mesenchyme surrounding the developing CNS at E9.0 and colonize the neural tube by E9.5 [60, 96]. Two recent studies have used ex-vivo time-lapse imaging on brain slices to investigate the CNS seeding of microglia pro- genitors, but with contradictory results. One study suggested that ­CD206+ A2 progenitors migrate from the mesenchyme first into the ventricle and subsequently into the developing The identification of differentially expressed genes in dif- ferent myeloid populations has provided valuable knowledge for generation of novel mouse lines that specifically target Acta Neuropathologica (2024) 147:37 Acta Neuropathologica Page 4 of 13 37 37 all CNS interfaces, each displaying different engraftment rates. Remarkably, a time-dependent increase in engraftment was observed, with the highest exchange occurring in the choroid plexus, followed by the dura, and the slowest in the brain parenchyma—a pattern consistent with pre-clinical studies. Furthermore, transcriptional analysis unveiled a sus- tained activated profile of the engrafted myeloid cells. Molecular cues for myeloid precursor recruitment to specific niches PU.1 (or SPFI) is an essential transcription factor for the differentiation of macrophage progenitors into CNS resident cells. PU.1−/− mice have diminished A1 and A2 progenitor populations and, consequently, no microglia or CAMs [35]. Another important transcription factor is interferon regula- tory factor 8 (IRF8). Depletion of IRF8 in mice impairs A2, but not A1 progenitor cells, reducing the number of micro- glia and MnMΦ but not cpMΦ [52]. Neither the depletion of the chemokine receptor CX3CR1 nor of transcription factors such as Myb and Batf3 in late embryonic stages affect CNS resident macrophages numbers [35, 52]. Mice lacking C–C chemokine receptor 2 (CCR2), crucial for myeloid recruit- ment into the inflamed CNS [67, 85, 87], do not show any differences in microglia, MnMΦ and PvMΦ abundance, sug- gesting that CCR2 is not required for CNS seeding during embryogenesis. By contrast, CCR2−/− adult mice showed a reduced number of cpMΦ, further supporting their continu- ous replenishment by peripheral monocytes [35]. p Importantly, during pathological conditions marked by physical damage to brain vasculature, there is a significant infiltration and active recruitment of peripheral monocytes [1, 22, 49, 71]. However, once the inflammation subsides, monocyte-derived cells usually not persist as residents in the CNS parenchyma [1, 49]. In contrast, it seems that methods depleting CNS myeloid cells create both accessi- ble and available niches contributing to efficient monocyte engraftment and colonization [99, 121]. In a study where chronic partial microglia depletion was accomplished with- out disruption of the BBB, recruited cells were able to enter and engraft the CNS parenchyma while maintaining dis- tinct transcriptional profiles from resident microglia [20]. Similarly, it has been suggested that in pathological states PvMΦ can also be replenished by the infiltration of circulat- ing monocytes into perivascular spaces [59]. Interestingly, it has been proposed that dmMΦ turnover does not depend on blood circulating monocytes, but rather on engraftment from monocytes derived from calvarial bone marrow [21]. The latter topic is controversial as most of these studies are based on highly invasive imaging techniques that include skulls transplants or thinning of the skull bone, which may result in an inflamed condition. Recently, Sankowski et al. [91] assessed the engraftment of bone marrow-derived myeloid cells within the distinct compartments of the human CNS. Origin and fate These findings suggest peripheral blood stem cell transplantation as a potential CAM replacement therapy for CAM-related disorders. brain parenchyma at E12.5. These cells then lose CD206 expression and acquire a microglia phenotype [41]. In con- trast, the other study imaged slices of Csf1r-EGFP embryos and showed migration of ­Iba1+ cells from the developing parenchyma into the ventricle at E11, suggesting that these cells thereafter become cpMΦ [72]. These results indicate an opposite directionality at E11 compared to E12.5, which could be attributed to differences in cellular composition and thickness of the ventricle wall. Once within their niche, microglia, MnMΦ, PvMΦ, and epiplexus cpMΦ are long-lived and self-maintain, thereby, retaining their YS origin, while dmMΦ and stromal cpMΦ are slowly replaced by circulating cells [35, 113, 114] (Fig. 1). These differences in population maintenance seem to be niche-dependent, since the dura mater and the choroid plexus stroma offer greater accessibility from the periph- ery compared to the other brain interfaces. In an attempt to further dissect the replacement of CAMs, Brioschi et al. [11] used a constitutive Crybb1-Cre line to label embry- onic microglia and CAMs. As expected, microglia main- tained their embryonic origin, but both MnMΦ and PvMΦ were suggested to be a mixture of embryonic and mono- cyte-derived populations that differed in CD38 and MHC2 expressions. Unfortunately, the authors did not address the turnover of cpMΦ or dmMΦ. Vascular cues for erythromyeloid progenitor differentiation Studies done in mice showed that a primitive, yet functional, BBB is formed by E15.5 and already contains some mac- rophage niches, structures where CAM differentiation pro- ceeds to mature perivascular macrophages (PvMΦ), as dis- cussed above. The full maturation of the perivascular space with arterioles containing smooth muscle cells and associ- ated CAMs continues up to 2 weeks after birth, when PvMΦ start to appear [61]. The fact that other cellular components of the brain vascular barrier, like perivascular fibroblasts, appear between postnatal day P5 and P14 [48], suggests that the first two postnatal weeks are a critical period for exten- sive expansion of the cerebral capillaries [18]. The PvMΦ are sandwiched between glial and vascu- lar basement membranes, a spatially restricted location which probably determines their limited motility and typi- cal elongated shape, along the vessels. Spatial constraints could also affect the PvMΦ phenotype as previous in vitro studies have reported that forcing the elongation of cul- tured macrophages using narrow lines of substrate, such as fibronectin, upregulates arginase-1, Ym1 and the typical PvMΦ marker CD206 [64]. CD206 is a membrane-bound mannose receptor. Together with other glycans, including N-acetylglucosamine, glucose, fucose, sialic acid and hep- aran sulfate, mannose is present in the glycoproteins lining the luminal surface of blood vessels, contributing to the gly- cocalyx. Depending on vessel type, the glycocalyx has sev- eral physiological functions—it supports vascular tone and integrity, provides mechanotransduction signals, interacts with cytokines and growth factors, and regulates immune cell adhesion and rolling [69]. While this latter function has been studied in pathological contexts where immune cell recruitment supports inflammation [16], there are lit- tle data on CNS development. The glycocalyx appears as soon as blood flow is initiated in the embryo and is involved in normal vessel development [37, 43]. In this regard, the Microglia and CAMs originate from EMPs, which dif- fer from angiopoietic progenitors from which the brain vasculature is derived. In general, each brain cell type is derived from a specific subset of progenitor cells, follow- ing a defined spatiotemporal pattern of differentiation that spans from the yolk sac to the first postnatal weeks. How- ever, endothelial cells can share a common erythromyeloid lineage with CNS resident macrophages. Plein et al. Molecular cues for myeloid precursor recruitment to specific niches Employing autopsies from female patients who had under- gone sex-mismatched peripheral blood stem cell transplanta- tion, revealing the presence of donor-derived Y + cells across It has been proposed that in the developing CNS, micro- glia entry into the ventricular and subventricular zones is mediated by CXCR4 interaction with CXCL12 expressed in the developing cortex [5]. Global deletion of Cxcr4, condi- tional deletion of its ligand Cxcl12 in Gfap-expressing cells or injection of CXCR4 antagonist, reduced the amount of cortical microglia in mice [5, 112]. Accordingly, condi- tional deletion of Cxcr4 in Cx3cr1-expressing cells at E10.5 reduced microglial cell numbers in ventricular and subven- tricular zones at E18.5 [112]. However, others have reported no expression of Cxcr4 in microglia and normal microglia distributions in Cxcl12−/− and Cxcr4−/− embryos at E13.5 and E16.5, respectively [116]. This could be due to differ- ences in embryonic time points or brain regions analyzed. Little is known about the molecular mechanisms of CAM recruitment to their distinct niches during development. Recently, the migration of MnMΦ into the perivascular spaces early after birth was shown to be integrin-signaling dependent [61], suggesting a role for the unique extracel- lular matrix of the leptomeningeal and perivascular niches Page 5 of 13  37 Acta Neuropathologica (2024) 147:37 37 [39, 40]. Deletion of the gene encoding talin-1, Tln1, an important activator of β-integrin binding activity [13, 106], resulted in a normal distribution of microglia and MnMΦ in the embryonic CNS, but a 50% reduction of PvMΦ at P14 [61]. This implies an involvement of the extracellular matrix in MnMΦ migration into the perivascular niche. A functional role of mural cells was recently identified, which express several extracellular matrix molecules, since PvMΦ were highly reduced in Notch3−/− animals that have defec- tive maturation of arterial smooth muscle actin-positive cells [61]. The complex mutual interplay between perivascular cells, the extracellular matrix and associated factors, and the developing PvMΦ still requires elucidation. membrane glycoprotein neuropilin functions as a co-receptor for vascular endothelial growth factor receptor (VEGFR)2 and guides developmental angiogenesis [32]. The early for- mation of the glycocalyx could potentially affect the migra- tion and recruitment of A2 pre-macrophage progenitors to the developing brain, an important step in the maturation of the cerebral vasculature [27]. Molecular cues for myeloid precursor recruitment to specific niches Brain vessels are, therefore, key players in the ontogeny of CAMs, mediating the migration of the immature mac- rophages to the developing CNS and their placement in spe- cific differentiation niches. Microglia seeding occurs around E9.5, when the BBB has not yet developed. In rodents, clusters of vascular endothelial-like cells are present in the developing CNS at E7.5–E8.5 [115] and start to organ- ize into a branched vascular network by E9.5 [109], which correlates with microglia seeding of the CNS. Microglia exploit the forming vascular structures as paths to infiltrate into the CNS [6] and colonize the CNS in a heterogene- ous spatiotemporal pattern, with transient accumulation in selected hotspots, i.e., the cortico-striatal-amygdalar bound- ary, before distributing throughout the brain and develop- ing site-specific morphological and phenotypical features [10]. As discussed above, mature microglia have a typi- cal gene profile, with Hexb, P2ry12, Tmem119, Sall1 and Siglech representing homeostatic markers [62]. However, some of these genes may vary in expression according to the developmental stage [9] or reactive states of microglia [65]. Embryonic or postnatal microglia are best visualized through Cx3cr1-linked reporters. Studies with transgenic mice expressing fluorescent reporters under the control of the Cx3cr1 promotor have helped describe microglia activ- ity during brain development, i.e., the sculpting of postnatal neuronal networks through complement C3-mediated synap- tic pruning [93]. There is less information on whether micro- glia can affect the formation of the brain vasculature during CNS development. However, liposomal clodronate-mediated depletion of microglia has been reported to impair retinal vessel formation [17] and to alter the vascular architecture and capillary diameter via transforming growth factor beta 1 (TGFβ1)-dependent paracrine signaling [24, 26, 47]. CAMs in homeostasis Under homeostatic conditions, CAMs play an important role in maintaining the integrity of the CNS barriers as well as regulating the exchange of metabolites and antigens with the periphery [53]. It has been shown that the production of VEGF by PvMΦ impacts endothelial cell function, thereby modifying vascular permeability [46]. Furthermore, despite their limited motility, PvMΦ are potentially able to extend their processes along the perivascular space into the vascular lumen and sense molecular signals within the bloodstream [7, 35, 53]. Similarly, two-photon in vivo imaging of dmMΦ and MnMΦ suggests that these macrophages continuously scavenge their environment [94]. In fact, studies using injec- tions of the tracer ferritin directly into the CSF have shown the phagocytic capacity of PvMΦ and epiplexus cpMΦ [15, 33, 53, 73]. Consistent with this, single-cell phenotyp- ing of CAMs has associated them with various biological processes, such as phagocytosis, antigen presentation, and cytokine production in mice [2, 49, 71, 95, 114] and recently in humans [51, 91, 124]. Altogether, this emphasizes the piv- otal role of CAMs as immune surveillants, clearing poten- tially harmful substances and contributing to the mainte- nance of CNS homeostasis. g Due to their specific anatomical location, PvMΦ and MnMΦ have been suggested to have an important role in the surveillance and control of flow dynamics of the CSF [25]. Conveniently, the injection of clodronate-containing liposomes into the cisterna magna or cerebral ventricles effectively depletes these CAM populations, albeit with sig- nificant changes in the CSF volume and osmolarity which may have collateral effects [79]. Nevertheless, such clo- dronate-liposome depletion studies in different mouse mod- els of AD are associated with reduced clearance of vascular and parenchymal Aβ plaques [25, 42] (Fig. 1), potentially by PvMΦ and MnMΦ where the scavenger receptor class B type I (SR-BI) seems to play a role [111]. Yet, another depletion study showed that the expression of CD36 and Nox2 by PvMΦ and MnMΦ leads to the generation of reac- tive oxygen species (ROS) and consequent cerebrovascu- lar dysfunction in Tg2576 mice [76]. In addition, anti-Aβ immunotherapy in a mouse model of AD has been shown to activate PvMΦ, which exhibit a higher association with vascular Aβ plaques, ultimately inducing microhemorrhages and an increased monocyte infiltration [110]. Vascular cues for erythromyeloid progenitor differentiation [80] traced EMPs in Csf1r-Egfp mouse embryos, reporting that at E8.5 the EMPs protrude into the vascular lumen, acquir- ing the typical elongated shape of the endothelial cells and expressing the VEGFR2. The EMP-derived endothelial cells are transcriptomically identical to the neighboring ones of Page 6 of 13 Acta Neuropathologica (2024) 147:37 Acta Neuropathologica 37 37 are significantly enriched or uniquely expressed in myeloid cells such as microglia [83]. angiopoietic origin, and lack the expression of genes of dif- ferentiated myeloid cells. Also, these cells are long-lived after their integration into the vessel wall. Thus, a new source of endothelial cells is revealed, suggesting that the embryonic blood vascular endothelium expands in a dual mechanism involving both the proliferation of pre-existing endothelial cells and the incorporation of endothelial cells derived from hematopoietic precursors [80]. The BBB plays a crucial role in regulating both protein diffusion and leukocyte migration, and these functions are intricately regulated. In its response to CNS inflammation, the BBB is able to regulate leukocyte migration without con- current protein leakage, and vice versa. This underscores the precision and regulatory mechanisms governing these pro- cesses. The maintenance of BBB integrity in neurodegen- erative disorders [reviewed in 116], along with the possible contribution of monocyte-derived cells in clearing plaques, remains unclear. This is due to the difficulty in distinguish- ing CNS resident macrophages and infiltrating myeloid populations, since in situ they show similar morphologies and phenotypes [84]. The proximity of monocyte-derived cells to Aβ plaques and their engulfment of Aβ was proposed in a recent study where Ms4a3CreR26tdTomato bone marrow was transplanted into 5×FAD mice, a mouse model of AD [100]. Similarly, Flt3Cre constitutive fate mapping of bone marrow-derived cells labeled 6% of plaque-associated mac- rophages in APP/PS1 AD mice [123]. Conflicting earlier results showed that, in the absence of brain irradiation, using inducible Ccr2CreERT2 and Cx3cr1CreERT2 fate-mapping on a 5×FAD background, no myeloid cell infiltration is detected [89]. Similarly, in the inducible KitMerCreMerR26Eyfp on an ­APPNL−G−F background, no replacement by bone marrow- derived monocytes was observed neither in microglia nor CAM populations [118]. Despite conflicting results, in vivo two-photon imaging of APP/PS1 mice reveled that patrolling Ly6C low monocytes are attracted to the luminal walls of Aβ-positive veins where they phagocyte Aβ before circulat- ing back into the bloodstream [66]. CAMs in neurodegenerative diseases The study of CAMs and their impact on CNS diseases is a rapidly developing field of research. Although the pre- cise role of CAM perturbation in CNS homeostasis is far from understood, recent studies have shed some light on their involvement in neurodegenerative and cerebrovascular diseases. Alzheimer’s disease (AD) and Parkinson’s disease (PD) are both characterized by local microgliosis, neuronal death and the appearance of protein aggregates. While in AD, these aggregates mainly include amyloid beta (Aβ) plaques and/or tau neurofibrillary tangles [3], in PD, they are known as Lewy bodies and are primarily composed of α-synuclein (α-syn) [104]. Importantly, genome-wide association studies (GWAS) have identified genetic variants associated with an increased risk of neurodegenerative disease, many of which Page 7 of 13  37 Acta Neuropathologica (2024) 147:37 Acta Neuropathologica 37 responsible for the excessive production of ROS via Nox2 in mouse models of hypertension [28, 92]. The accumulation of ROS compromises BBB function and is associated with neurovascular and cognitive defects, which are mitigated by clodronate-mediated CAM depletion [28, 92]. Accordingly, in animal models of permanent ischemic stroke, elevated numbers of ­CD163+ CAMs have been reported near the lesion in rats [77, 86] and of ­Lyve1+ CAMs in mice [101]. These PvMΦ express VEGF, which may compromise vas- cular barrier function and, thereby, granulocyte recruitment [77]. Transplantation of ­Cx3cr1gfpCCR2rfp bone marrow into wild-type hosts revealed that peripheral monocytes infiltrate and repopulate the perivascular spaces 4 days after ischemic stroke [86]. These results are consistent with a pre- vious study in mice suffering from experimental autoim- mune encephalomyelitis (EAE), which reported that CAM proliferation occurs alongside the infiltration of monocytes [49]. These monocyte-derived cells only transiently colonize the parenchyma but are not integrated into the microglia pool and remain functionally distinct to microglia [1, 49]. Additionally, there is clinical evidence supporting the accu- mulation of ­CD163+ PvMΦ in autopsied brains of patients with cerebral ischemia [45], as well as of PvMΦ-like cells in patients with brain arteriopathies [122]. Indeed, these data need to be interpreted with caution, since microglia and bone marrow-derived macrophages may upregulate CD163 and other CAM markers under certain conditions [97]. For this reason, to specifically distinguish and target each myeloid population in the context of disease, the use of fate-mapping mouse models is indispensable. The limited data on the role of human CAMs in cerebrovascular diseases underscore the importance of future research in this area. CAMs in cerebrovascular diseases Cerebrovascular diseases are medical conditions that influ- ence the blood flow in the vessels supplying the brain, with ischemic stroke being the best-known and most studied pathology [14]. Lack of adequate blood supply causes brain damage and induces a pro-inflammatory immune response as well as an excessive production of ROS, which compro- mises BBB functional integrity. Considering their anatomi- cal location at the CNS interfaces, it seems rational that CAMs play a role in such conditions. Consistent with this hypothesis, it has been suggested that in homeostatic con- ditions, Lyve-1+ perivascular macrophages prevent arterial stiffness in mouse aorta by influencing collagen expression by vascular smooth muscle cells [57].i CAMs in neurodegenerative diseases A potential role of CAMs in AD has become more evi- dent with a recent single-nucleus RNAseq study of the human brain vasculature. This study unveiled that many of the top GWAS genes were not only expressed by microglia but also by PvMΦ [124]. Interestingly, a novel scRNA-seq study in a mouse model of PD reported that CAMs, rather than microglia, play an essential role as antigen-presenting cells and mediate α-synuclein-related neuroinflammation [30, 95]. While mice lacking the antigen-presenting mol- ecule MHCII specifically in microglia showed no differences in the recruitment of peripheral immune cells, clodronate- mediated depletion of CAMs significantly decreased infil- trating CD4 T cells and monocytes [74, 95]. Extensive research has underscored the crucial role of microglia in the human pathogenesis of neurodegenerative diseases. Immunostainings of autopsy tissues have revealed that under such conditions, microglia undergo activation and engage on the phagocytosis of protein aggregates. The advent of new single-cell technologies has allowed for a more detailed and intricate characterization of microglial states in neurodegenerative diseases, exposing a spectrum of subtypes and providing insights into their distinct gene expression profiles [74, 81]. Yet, despite the expected involvement of CAMs in human neurodegenerative condi- tions, data on their specific role remain scarce. Emerging vascular mechanisms of myeloid cell brain infiltration In patients with acute heart failure syndromes, circulating levels of heparan sulfate proteoglycan degradation products derived from the glycocalyx were found to be elevated com- pared to aged-matched healthy controls and were associated with increased CD14 levels, a marker of monocyte activation [38]. Evidence of monocyte activation by products of glyco- calyx disruption was reported in lipopolysaccharide (LPS)- treated mice and linked to the activation of Toll-like receptor 4 (TLR4) [29]. Heparan sulfate-rich vascular domains are particularly involved in the regulation of thrombo-inflam- matory events, presenting binding sites for different growth factors, cytokines and chemokines [69]. Chemokines, like the monocyte chemoattractant protein (MCP) 1, and the macrophage inflammatory peptides (MIP) 1α and β inter- act with the glycocalyx to generate a local concentration of chemokines (‘chemokine-cloud’), facilitating leukocyte acti- vation and amplifying pro-inflammatory signals [36, 54]. At present, how the glycocalyx is modified in different diseased brain conditions, and how this may affect monocyte recruit- ment is not fully understood. Glycans shed from the injured endothelium could potentially bind and modulate inflamma- tory molecules systemically [108], but also the modification of endothelial cell surface-exposed sugars may direct mono- cyte interaction with the endothelium, as recently hypoth- esized in a murine model of ischemic stroke [75]. Two subsets of monocytes have been identified based on their ability to extravasate ­(Ly6ChighCCR2highCXCR1low) or to patrol the vessels ­(Ly6ClowCCR2lowCXCR1high) [31]. These phenotypes represent the extremes of a range of phenotypes that are defined by environmental factors that also control bone marrow-derived monocyte migration, dif- ferentiation, and tissue entry. Brain resident myeloid cell replacement by monocytes during homeostasis is limited and restricted to dura and choroid plexus macrophages only [80]. By contrast, tissue-resident macrophages located in other organs are more frequently replenished [120] through a mechanism involving both the endothelial cells and their underlying basement membrane. This latter structure has been recently reported as a critical cue for monocyte dif- ferentiation into macrophages in the intestine, with a spe- cific role of laminin proteins [56]. The two main endothelial laminins, laminin 411 and 511, are constituents of vascular basement membranes of arteries, arterioles and capillaries, with progressively less laminin 511 in postcapillary ven- ules, venules and veins. Postcapillary venules which have low or no laminin 511 are the preferred sites for leukocyte and monocyte extravasation in both the brain and periph- eral organs [56, 102, 103, 117]. Emerging vascular mechanisms of myeloid cell brain infiltration In neurodegenerative and cerebrovascular diseases, blood- borne myeloid cells may have access to the brain, where they can differentiate into mature macrophages. This process differs from that regulating myeloid cell seeding and dif- ferentiation during CNS development, due to the presence of a defined, but damaged, vascular barrier. Whether mac- rophages derived from such infiltrating monocytic cells are functionally equivalent to the long-term resident populations is not yet resolved. Hypertension, or high blood pressure, is a significant risk factor that can lead to various vascular diseases, includ- ing ischemic stroke. It is widely recognized that microglia respond rapidly and become activated in the presence of BBB leakages. Interestingly, studies have shown that in cases of vascular injury, microglia activation occurs promptly, accumulating around vasculature even before detectable BBB damage takes place [107]. Similarly, hyper- tension is associated with increased PvMΦ numbers along the cerebral vasculature [58]. Interestingly, consistent with findings from AD studies, PvMΦ have been suggested to be The recruitment of myeloid cells largely depends on pro- teins expressed on the endothelium of postcapillary ven- ules, including adhesion molecules controlling monocyte rolling, arrest and extravasation [reviewed in 22]. There are two emerging mechanisms to explain regulation of mono- cyte entry into the brain, i.e., glycocalyx-associated vascu- lar-immune cell interactions and an endothelial basement Acta Neuropathologica (2024) 147:37 Acta Neuropathologica Page 8 of 13 37 37 extravascular cellular and basement membrane components. That the glycocalyx forms a CNS barrier was demonstrated by Kutuzov et al. [55] who intravenously injected fluor- conjugated wheat-germ agglutin into mice to selectively label N-acetylglucosamine and sialic acid, components of the glycocalyx. In addition, mice were injected with sul- forhodamine 101 to label the astrocytic endfeet, and 40 or 150 kDa MWt fluorescein isothiocyanate (FITC)-dextran. Diffusion of FITC-dextran across the BBB was followed by live in vivo two-photon microscopy, revealing accumulation in the glycocalyx which was 44% of the signal intensity in the blood. By modeling a partition coefficient, the authors concluded that the glycocalyx is one of the three structures, including the endothelium and the extravascular compo- nents, forming a sequence of diffusional constraints that was termed the tripartite BBB [55]. It is, therefore, not surprising that disruption of the glycocalyx, as occurs in inflamma- tion and disease conditions, compromises BBB function. Moreover, proteins shed from the glycocalyx provide solu- ble damage-associated molecular patterns (DAMPs), further enhancing inflammation and immune cell recruitment [69]. Emerging vascular mechanisms of myeloid cell brain infiltration In patients with acute heart failure syndromes, circulating levels of heparan sulfate proteoglycan degradation products derived from the glycocalyx were found to be elevated com- pared to aged-matched healthy controls and were associated with increased CD14 levels, a marker of monocyte activation [38]. Evidence of monocyte activation by products of glyco- calyx disruption was reported in lipopolysaccharide (LPS)- treated mice and linked to the activation of Toll-like receptor 4 (TLR4) [29]. Heparan sulfate-rich vascular domains are particularly involved in the regulation of thrombo-inflam- matory events, presenting binding sites for different growth factors, cytokines and chemokines [69]. Chemokines, like the monocyte chemoattractant protein (MCP) 1, and the macrophage inflammatory peptides (MIP) 1α and β inter- act with the glycocalyx to generate a local concentration of chemokines (‘chemokine-cloud’), facilitating leukocyte acti- vation and amplifying pro-inflammatory signals [36, 54]. At present, how the glycocalyx is modified in different diseased brain conditions, and how this may affect monocyte recruit- ment is not fully understood. Glycans shed from the injured endothelium could potentially bind and modulate inflamma- tory molecules systemically [108], but also the modification of endothelial cell surface-exposed sugars may direct mono- cyte interaction with the endothelium, as recently hypoth- esized in a murine model of ischemic stroke [75] membrane (laminin)-driven infiltration and differentiation into macrophages.i extravascular cellular and basement membrane components. That the glycocalyx forms a CNS barrier was demonstrated by Kutuzov et al. [55] who intravenously injected fluor- conjugated wheat-germ agglutin into mice to selectively label N-acetylglucosamine and sialic acid, components of the glycocalyx. In addition, mice were injected with sul- forhodamine 101 to label the astrocytic endfeet, and 40 or 150 kDa MWt fluorescein isothiocyanate (FITC)-dextran. Diffusion of FITC-dextran across the BBB was followed by live in vivo two-photon microscopy, revealing accumulation in the glycocalyx which was 44% of the signal intensity in the blood. By modeling a partition coefficient, the authors concluded that the glycocalyx is one of the three structures, including the endothelium and the extravascular compo- nents, forming a sequence of diffusional constraints that was termed the tripartite BBB [55]. It is, therefore, not surprising that disruption of the glycocalyx, as occurs in inflamma- tion and disease conditions, compromises BBB function. Moreover, proteins shed from the glycocalyx provide solu- ble damage-associated molecular patterns (DAMPs), further enhancing inflammation and immune cell recruitment [69]. References 1. Ajami B, Bennett JL, Krieger C, McNagny KM, Rossi FMV (2011) Infiltrating monocytes trigger EAE progression, but do not contribute to the resident microglia pool. Nat Neurosci 14:1142–1149. https://​doi.​org/​10.​1038/​nn.​2887 The use of animal models that specifically target CAMs as well as the development of new state-of-the-art techniques that allow precise characterization of both CAMs and their interaction with other brain resident cells holds great prom- ise for understanding CAM functionality and their potential as therapeutic targets. Given the pivotal role of these cells in neurodegenerative, cerebrovascular and neuroinflammatory diseases, more studies that specifically interrogate CAMs in these pathogenesis are needed. While new technologies have facilitated the identification of markers distinguishing microglia and CAMs, aiding in the dissection of their dis- tinct functionalities, a deeper characterization of individual CAM populations will enable the study of their precise niche functions in both homeostasis and CNS perturbation. This is of special interest in human studies, where the complexity of CAM subsets is just starting to be unveiled. Moreover, a more comprehensive understanding of myeloid cell engraft- ment in the CNS parenchyma and interfaces, particularly now that it has been suggested in humans, opens up promis- ing avenues for potential CAM and microglia replacement therapies. 2. Ajami B, Samusik N, Wieghofer P, Ho PP, Crotti A, Bjornson Z et al (2018) Single-cell mass cytometry reveals distinct popula- tions of brain myeloid cells in mouse neuroinflammation and neurodegeneration models. Nat Neurosci 21:541–551. https://​ doi.​org/​10.​1038/​s41593-​018-​0100-x 3. Alonso AC, Grundke-Iqbal I, Iqbal K (1996) Alzheimer’s disease hyperphosphorylated tau sequesters normal tau into tangles of filaments and disassembles microtubules. Nat Med 2:783–787. https://​doi.​org/​10.​1038/​nm0796-​783 4. Amann L, Masuda T, Prinz M (2023) Mechanisms of mye- loid cell entry to the healthy and diseased central nervous system. Nat Immunol 24:393–407. https://​doi.​org/​10.​1038/​ s41590-​022-​01415-8 5. Arnò B, Grassivaro F, Rossi C, Bergamaschi A, Castiglioni V, Furlan R et al (2014) Neural progenitor cells orchestrate micro- glia migration and positioning into the developing cortex. Nat Commun 5:5611. https://​doi.​org/​10.​1038/​ncomm​s6611 6. Arnoux I, Hoshiko M, Mandavy L, Avignone E, Yamamoto N, Audinat E (2013) Adaptive phenotype of microglial cells during the normal postnatal development of the somatosensory “Barrel” cortex. Glia 61:1582–1594. https://​doi.​org/​10.​1002/​glia.​22503 7. Barkauskas DS, Evans TA, Myers J, Petrosiute A, Silver J, Huang AY (2013) Extravascular CX3CR1+ cells extend intravascular dendritic processes into intact central nervous system vessel lumen. Microsc Microanal 19:778–790. Conclusions adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​creat​iveco​mmons.​ org/​licen​ses/​by/4.​0/. adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​creat​iveco​mmons.​ org/​licen​ses/​by/4.​0/. Although the origin of CAMs has been recently elucidated in mice, the specific niche factors that facilitate their proper development, migration, engraftment, and long-term main- tenance in the distinct CNS compartments remain largely unknown. Data suggest that the brain vasculature and the extracellular matrix constituting the microenvironment are likely to provide the cues to maintain CAM phenotype and functions, once they are established within their niches. Encouragingly, recent studies have begun elucidating the role of CAMs in CNS development, homeostasis and per- turbations. Nevertheless, further studies are needed to fully comprehend the intricate networks through which CAMs contribute to disease pathogenesis.i Emerging vascular mechanisms of myeloid cell brain infiltration Laminin 511 together with the endothelium provide a cue for monocyte differentia- tion, as observed in the intestine of endothelial cell-specific laminin 511 knockout mice (Tek-cre:Lama5−/−), which show reduced proportions of mature macrophages—identified as ­Ly6ClowMHCIIhigh—compared to wild type or laminin 411 depleted (Lama4−/−) mice despite higher numbers of infiltrating ­Ly6Chigh/MHCIIlow monocytes. By contrast, Lama4−/− mice which have a high expression of laminin 511 have less extravasation of immature ­(Ly6ChighMHCIIlow) and maturing ­(LY6ChighMHCIIhigh) monocytes but higher proportions of differentiated macrophages [56]. The data suggest that laminin 411 in the postcapillary venule base- ment membrane supports immature monocyte extravasation, while laminin 511 together with the endothelium promotes their differentiation into macrophages. In the brain, the dif- ferential expression of laminins 411 and 511 in endothelial basement membranes have also been shown to modulate the pathogenicity of infiltrating T cells during neuroinflamma- tion [127]. Taken together these data suggest that laminins 411 and 511 may also control monocyte recruitment and differentiation during neuroinflammation. As discussed above the endothelial glycocalyx a nega fl As discussed above, the endothelial glycocalyx—a nega- tively charged, carbohydrate-rich structure—is a major regulator of immune cell trafficking. Being exposed on the luminal surface of the endothelium, glycoproteins are accessible to circulating cells and proteins. In physiological conditions, the glycocalyx contributes to the barrier func- tion of the BBB, together with the endothelium and the Acta Neuropathologica (2024) 147:37 Page 9 of 13  37 Acta Neuropathologica References Campbell BCV, De Silva DA, Macleod MR, Coutts SB, Schwamm LH, Davis SM et al (2019) Ischaemic stroke. Nat Rev Dis Primer 5:70. https://​doi.​org/​10.​1038/​s41572-​019-​0118-8 rimer 5:70. https://​doi.​org/​10.​1038/​s41572-​019-​0118-8 15. Carpenter SJ, McCarthy LE, Borison HL (1970) Electron micro- scopic study on the epiplexus (Kolmer) cells of the cat choroid plexus. Z Für Zellforsch Mikrosk Anat 110:471–486. https://​doi.​ org/​10.​1007/​BF003​30099l 30. Frosch M, Amann L, Prinz M (2023) CNS-associated mac- rophages shape the inflammatory response in a mouse model of Parkinson’s disease. Nat Commun 14:3753. https://​doi.​org/​10.​ 1038/​s41467-​023-​39061-9 16. Chappell D, Dörfler N, Jacob M, Rehm M, Welsch U, Conzen P et al (2010) Glycocalyx protection reduces leukocyte adhe- sion after ischemia/reperfusion. Shock Augusta Ga 34:133–139. https://​doi.​org/​10.​1097/​SHK.​0b013​e3181​cdc363 31. Fumagalli S, Perego C, Pischiutta F, Zanier ER, De Simoni M-G (2015) The ischemic environment drives microglia and mac- rophage function. Front Neurol 6:81. https://​doi.​org/​10.​3389/​ fneur.​2015.​00081 17. Checchin D, Sennlaub F, Levavasseur E, Leduc M, Chemtob S (2006) Potential role of microglia in retinal blood vessel forma- tion. Invest Ophthalmol Vis Sci 47:3595–3602. https://​doi.​org/​ 10.​1167/​iovs.​05-​1522 32. Gelfand MV, Hagan N, Tata A, Oh W-J, Lacoste B, Kang K-T et al (2014) Neuropilin-1 functions as a VEGFR2 co-receptor to guide developmental angiogenesis independent of ligand bind- ing. eLife 3:e03720. https://​doi.​org/​10.​7554/​eLife.​03720 18. Coelho-Santos V, Berthiaume A-A, Ornelas S, Stuhlmann H, Shih AY (2021) Imaging the construction of capillary networks in the neonatal mouse brain. Proc Natl Acad Sci 118:e2100866118. https://​doi.​org/​10.​1073/​pnas.​21008​66118 33. Gingras MC, Lapillonne H, Margolin JF (2001) CFFM4: a new member of the CD20/FcepsilonRIbeta family. Immunogenetics 53:468–476. https://​doi.​org/​10.​1007/​s0025​10100​345 19. Colonna M, Butovsky O (2017) Microglia function in the central nervous system during health and neurodegeneration. Annu Rev Immunol 35:441–468. https://​doi.​org/​10.​1146/​annur​ev-​immun​ ol-​051116-​052358 34. Ginhoux F, Greter M, Leboeuf M, Nandi S, See P, Gokhan S et al (2010) Fate mapping analysis reveals that adult microglia derive from primitive macrophages. Science 330:841–845. https://​doi.​ org/​10.​1126/​scien​ce.​11946​37 35. Goldmann T, Wieghofer P, Jordão MJC, Prutek F, Hagemeyer N, Frenzel K et al (2016) Origin, fate and dynamics of macrophages at central nervous system interfaces. Nat Immunol 17:797–805. https://​doi.​org/​10.​1038/​ni.​3423 20. Cronk JC, Filiano AJ, Louveau A, Marin I, Marsh R, Ji E et al (2018) Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia. J Exp Med 215:1627–1647. https://​doi.​org/​10.​1084/​ jem.​20180​247 36. Graham GJ, Handel TM, Proudfoot AEI (2019) Leukocyte adhe- sion: reconceptualizing chemokine presentation by glycosamino- glycans. Trends Immunol 40:472–481. https://​doi.​org/​10.​1016/j.​ it.​2019.​03.​009fi 21. References Cugurra A, Mamuladze T, Rustenhoven J, Dykstra T, Beroshvili G, Greenberg ZJ et al (2021) Skull and vertebral bone marrow are myeloid cell reservoirs for the meninges and CNS paren- chyma. Science 373:eabf7844. https://​doi.​org/​10.​1126/​scien​ce.​ abf78​44 37. Griffin ME, Sorum AW, Miller GM, Goddard WA, Hsieh-Wilson LC (2021) Sulfated glycans engage the Ang/Tie pathway to regu- late vascular development. Nat Chem Biol 17:178–186. https://​ doi.​org/​10.​1038/​s41589-​020-​00657-7 22. De Vlaminck K, Van Hove H, Kancheva D, Scheyltjens I, Pombo Antunes AR, Bastos J et al (2022) Differential plasticity and fate of brain-resident and recruited macrophages during the onset and resolution of neuroinflammation. Immunity 55:2085-2102. e9. https://​doi.​org/​10.​1016/j.​immuni.​2022.​09.​005 38. Grushko OG, Cho S, Tate AM, Rosenson RS, Pinsky DJ, Haus JM et al (2022) Glycocalyx disruption triggers human monocyte activation in acute heart failure syndromes. Cardiovasc Drugs Ther. https://​doi.​org/​10.​1007/​s10557-​022-​07390-4 23. Denes A, Hansen CE, Oezorhan U, Figuerola S, de Vries HE, Sorokin L et al (2024) Endothelial cells and macrophages as allies in the healthy and diseased brain. Acta Neuropathol. https://​doi.​org/​10.​1007/​s00401-​024-​02695-0 39. Hallmann R, Hannocks M-J, Song J, Zhang X, Di Russo J, Luik A-L et al (2020) The role of basement membrane laminins in vascular function. Int J Biochem Cell Biol 127:105823. https://​ doi.​org/​10.​1016/j.​biocel.​2020.​105823 p g 24. Dixon MA, Greferath U, Fletcher EL, Jobling AI (2021) The contribution of microglia to the development and maturation of the visual system. Front Cell Neurosci 15:659843. https://​doi.​ org/​10.​3389/​fncel.​2021.​659843 40. Hannocks M-J, Pizzo ME, Huppert J, Deshpande T, Abbott NJ, Thorne RG et al (2018) Molecular characterization of perivascu- lar drainage pathways in the murine brain. J Cereb Blood Flow Metab Off J Int Soc Cereb Blood Flow Metab 38:669–686. https://​doi.​org/​10.​1177/​02716​78X17​749689 25. Drieu A, Du S, Storck SE, Rustenhoven J, Papadopoulos Z, Dykstra T et al (2022) Parenchymal border macrophages regulate the flow dynamics of the cerebrospinal fluid. Nature 611:585– 593. https://​doi.​org/​10.​1038/​s41586-​022-​05397-3l 41. Hattori Y, Kato D, Murayama F, Koike S, Asai H, Yamasaki A et al (2023) CD206+ macrophages transventricularly infiltrate the early embryonic cerebral wall to differentiate into micro- glia. Cell Rep 42:112092. https://​doi.​org/​10.​1016/j.​celrep.​2023.​ 112092 p g 26. Dudiki T, Meller J, Mahajan G, Liu H, Zhevlakova I, Stefl S et al (2020) Microglia control vascular architecture via a TGFβ1 dependent paracrine mechanism linked to tissue mechanics. Nat Commun 11:986. https://​doi.​org/​10.​1038/​s41467-​020-​14787-y 42. Hawkes CA, McLaurin J (2009) Selective targeting of perivas- cular macrophages for clearance of beta-amyloid in cerebral amyloid angiopathy. References https://​doi.​org/​10.​1017/​ S1431​92761​30004​82 Acknowledgements  This work is supported by the research funds from the European Union’s Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie Grant Agreement No. 813294 (ENTRAIN). MP is supported by the Sobek Foundation, the Ernst-Jung Foundation, the Klaus Faber Foundation, the Novo Nordisk Foundation, the German Research Foundation (SFB 992 Project ID192904750, SFB 1160, SFB 1479 Project ID441891347, TRR 359 Project ID491676693, SFB/TRR167 Project ID259373024 “NeuroMac”, Gottfried Wilhelm Leibniz Prize) and by the DFG under Germany’s Excellence Strategy (CIBSS—EXC-2189—Project ID390939984). LS is supported by the Advanced ERC funding and by the ERANET project DeCoDis. SF is supported by Fondazione Regionale per la Ricerca Biomedica (Regione Lombardia), project ID 1739635. 8. Barr CM, Manning J, Lewis CAB, Rossi FMV, Krieger C (2015) Submyeloablative conditioning with busulfan permits bone mar- row-derived cell accumulation in a murine model of Alzheimer’s disease. Neurosci Lett 588:196–201. https://​doi.​org/​10.​1016/j.​ neulet.​2015.​01.​023 9. Bennett ML, Bennett FC, Liddelow SA, Ajami B, Zamanian JL, Fernhoff NB et al (2016) New tools for studying microglia in the mouse and human CNS. Proc Natl Acad Sci USA 113:E1738- 1746. https://​doi.​org/​10.​1073/​pnas.​15255​28113 10. Bridlance C, Thion MS (2023) Multifaceted microglia dur- ing brain development: models and tools. Front Neurosci 17:1125729. https://​doi.​org/​10.​3389/​fnins.​2023.​11257​29 11. Brioschi S, Belk JA, Peng V, Molgora M, Rodrigues PF, Nguyen KM et al (2023) A Cre-deleter specific for embryo-derived brain macrophages reveals distinct features of microglia and border macrophages. Immunity 56:1027-1045.e8. https://​doi.​org/​10.​ 1016/j.​immuni.​2023.​01.​028 Funding  Open Access funding enabled and organized by Projekt DEAL. Open Access  This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, 12. Buttgereit A, Lelios I, Yu X, Vrohlings M, Krakoski NR, Gau- tier EL et al (2016) Sall1 is a transcriptional regulator defining Acta Neuropathologica Page 10 of 13 37 37 (2024) 147:37 microglia identity and function. Nat Immunol 17:1397–1406. https://​doi.​org/​10.​1038/​ni.​3585 28. Faraco G, Sugiyama Y, Lane D, Garcia-Bonilla L, Chang H, Santisteban MM et al (2016) Perivascular macrophages medi- ate the neurovascular and cognitive dysfunction associated with hypertension. J Clin Invest 126:4674–4689. https://​doi.​org/​10.​ 1172/​JCI86​950 13. Calderwood DA, Campbell ID, Critchley DR (2013) Talins and kindlins: partners in integrin-mediated adhesion. Nat Rev Mol Cell Biol 14:503–517. https://​doi.​org/​10.​1038/​nrm36​24 29. Feng C, Stamatos NM, Dragan AI, Medvedev A, Whitford M, Zhang L et al (2012) Sialyl residues modulate LPS-mediated signaling through the Toll-like receptor 4 complex. PLoS ONE 7:e32359. https://​doi.​org/​10.​1371/​journ​al.​pone.​00323​59 14. References McKinsey GL, Lizama CO, Keown-Lang AE, Niu A, Santander N, Larpthaveesarp A et al (2020) A new genetic strategy for targeting microglia in development and disease. eLife 9:e54590. https://​doi.​org/​10.​7554/​eLife.​54590 48. Jones HE, Coelho-Santos V, Bonney SK, Abrams KA, Shih AY, Siegenthaler JA (2023) Meningeal origins and dynamics of perivascular fibroblast development on the mouse cerebral vasculature. 2023.03.23.533982 64. McWhorter FY, Wang T, Nguyen P, Chung T, Liu WF (2013) Modulation of macrophage phenotype by cell shape. Proc Natl Acad Sci 110:17253–17258. https://​doi.​org/​10.​1073/​pnas.​13088​ 87110 49. Jordão MJC, Sankowski R, Brendecke SM, Sagar null, Locatelli G, Tai Y-H et al (2019) Single-cell profiling identifies myeloid cell subsets with distinct fates during neuroinflammation. Sci- ence 363:eaat7554. https://​doi.​org/​10.​1126/​scien​ce.​aat75​54 p g 50. Kaiser T, Feng G (2019) Tmem119-EGFP and Tmem119-Cre- ERT2 transgenic mice for labeling and manipulating microglia. eNeuro. https://​doi.​org/​10.​1523/​ENEURO.​0448-​18.​2019 65. Mercurio D, Fumagalli S, Schafer MK-H, Pedragosa J, Ngas- sam LDC, Wilhelmi V et al (2022) Protein expression of the microglial marker Tmem119 decreases in association with mor- phological changes and location in a mouse model of traumatic brain injury. Front Cell Neurosci 16:820127. https://​doi.​org/​10.​ 3389/​fncel.​2022.​820127 51. Kearns NA, Iatrou A, Flood DJ, De Tissera S, Mullaney ZM, Xu J et al (2023) Dissecting the human leptomeninges at single- cell resolution. Nat Commun 14:7036. https://​doi.​org/​10.​1038/​ s41467-​023-​42825-y 66. Michaud J-P, Bellavance M-A, Préfontaine P, Rivest S (2013) Real-time in vivo imaging reveals the ability of monocytes to clear vascular amyloid beta. Cell Rep 5:646–653. https://​doi.​org/​ 10.​1016/j.​celrep.​2013.​10.​010 52. Kierdorf K, Erny D, Goldmann T, Sander V, Schulz C, Per- diguero EG et al (2013) Microglia emerge from erythromyeloid precursors via Pu.1- and Irf8-dependent pathways. Nat Neurosci 16:273–280. https://​doi.​org/​10.​1038/​nn.​3318 67. Mildner A, Mack M, Schmidt H, Brück W, Djukic M, Zabel MD et al (2009) CCR2+Ly-6Chi monocytes are crucial for the effec- tor phase of autoimmunity in the central nervous system. Brain J Neurol 132:2487–2500. https://​doi.​org/​10.​1093/​brain/​awp144 53. Kierdorf K, Masuda T, Jordão MJC, Prinz M (2019) Mac- rophages at CNS interfaces: ontogeny and function in health and disease. Nat Rev Neurosci 20:547–562. https://​doi.​org/​10.​1038/​ s41583-​019-​0201-x 68. Mildner A, Schmidt H, Nitsche M, Merkler D, Hanisch U-K, Mack M et al (2007) Microglia in the adult brain arise from Ly- 6ChiCCR2+ monocytes only under defined host conditions. Nat Neurosci 10:1544–1553. https://​doi.​org/​10.​1038/​nn2015 54. References Proc Natl Acad Sci USA 106:1261–1266. https://​doi.​org/​10.​1073/​pnas.​08054​53106 27. Fantin A, Vieira JM, Gestri G, Denti L, Schwarz Q, Prykhozhij S et al (2010) Tissue macrophages act as cellular chaperones for vascular anastomosis downstream of VEGF-mediated endothelial tip cell induction. Blood 116:829–840. https://​doi.​org/​10.​1182/​ blood-​2009-​12-​257832 43. Henderson-Toth CE, Jahnsen ED, Jamarani R, Al-Roubaie S, Jones EAV (2012) The glycocalyx is present as soon as blood flow is initiated and is required for normal vascular development. Page 11 of 13  37 Acta Neuropathologica Acta Neuropathologica (2024) 147:37 37 Dev Biol 369:330–339. https://​doi.​org/​10.​1016/j.​ydbio.​2012.​07.​ 009 aged rats. J Cereb Blood Flow Metab Off J Int Soc Cereb Blood Flow Metab 14:348–352. https://​doi.​org/​10.​1038/​jcbfm.​1994.​43 Dev Biol 369:330–339. https://​doi.​org/​10.​1016/j.​ydbio.​2012.​07.​ 009 59. Mai C-L, Tan Z, Xu Y-N, Zhang J-J, Huang Z-H, Wang D et al (2021) CXCL12-mediated monocyte transmigration into brain perivascular space leads to neuroinflammation and memory defi- cit in neuropathic pain. Theranostics 11:1059–1078. https://​doi.​ org/​10.​7150/​thno.​44364 44. Hickey WF, Kimura H (1988) Perivascular microglial cells of the CNS are bone marrow-derived and present antigen in vivo. Science 239:290–292. https://​doi.​org/​10.​1126/​scien​ce.​32760​04 p g 45. Holfelder K, Schittenhelm J, Trautmann K, Haybaeck J, Meyer- mann R, Beschorner R (2011) De novo expression of the hemo- globin scavenger receptor CD163 by activated microglia is not associated with hemorrhages in human brain lesions. Histol His- topathol 26:1007–1017. https://​doi.​org/​10.​14670/​HH-​26.​1007 60. Mass E, Ballesteros I, Farlik M, Halbritter F, Günther P, Crozet L et al (2016) Specification of tissue-resident macrophages dur- ing organogenesis. Science 353:aaf4238. https://​doi.​org/​10.​1126/​ scien​ce.​aaf42​38 p p g 46. Jais A, Solas M, Backes H, Chaurasia B, Kleinridders A, Theu- rich S et al (2016) Myeloid-cell-derived VEGF maintains brain glucose uptake and limits cognitive impairment in obesity. Cell 165:882–895. https://​doi.​org/​10.​1016/j.​cell.​2016.​03.​033 61. Masuda T, Amann L, Monaco G, Sankowski R, Staszewski O, Krueger M et al (2022) Specification of CNS macrophage sub- sets occurs postnatally in defined niches. Nature 604:740–748. https://​doi.​org/​10.​1038/​s41586-​022-​04596-2 p g j 47. Jobling AI, Waugh M, Vessey KA, Phipps JA, Trogrlic L, Gref- erath U et al (2018) The role of the microglial Cx3cr1 pathway in the postnatal maturation of retinal photoreceptors. J Neurosci Off J Soc Neurosci 38:4708–4723. https://​doi.​org/​10.​1523/​JNEUR​ OSCI.​2368-​17.​2018 62. Masuda T, Amann L, Sankowski R, Staszewski O, Lenz M, Err- ico D et al (2020) Novel Hexb-based tools for studying microglia in the CNS. Nat Immunol 21:802–815. https://​doi.​org/​10.​1038/​ s41590-​020-​0707-4 63. References Rua R, Lee JY, Silva AB, Swafford IS, Maric D, Johnson KR et al (2019) Infection drives meningeal engraftment by inflam- matory monocytes that impairs CNS immunity. Nat Immunol 20:407–419. https://​doi.​org/​10.​1038/​s41590-​019-​0344-yf 91. Sankowski R, Süß P, Benkendorff A, Böttcher C, Fernandez- Zapata C, Chhatbar C et al (2024) Multiomic spatial landscape of innate immune cells at human central nervous system borders. Nat Med. https://​doi.​org/​10.​1038/​s41591-​023-​02673-1 75. Orsini F, Fumagalli S, Császár E, Tóth K, De Blasio D, Zangari R et al (2018) Mannose-binding lectin drives platelet inflam- matory phenotype and vascular damage after cerebral ischemia in mice via IL (Interleukin)-1α. Arterioscler Thromb Vasc Biol 38:2678–2690. https://​doi.​org/​10.​1161/​ATVBA​HA.​118.​311058 92. Santisteban MM, Ahn SJ, Lane D, Faraco G, Garcia-Bonilla L, Racchumi G et al (2020) Endothelium-macrophage cross- talk mediates blood-brain barrier dysfunction in hypertension. Hypertension 76:795–807. https://​doi.​org/​10.​1161/​HYPER​ TENSI​ONAHA.​120.​15581 p g 76. Park L, Uekawa K, Garcia-Bonilla L, Koizumi K, Murphy M, Pistik R et al (2017) Brain perivascular macrophages initiate the neurovascular dysfunction of Alzheimer Aβ peptides. Circ Res 121:258–269. https://​doi.​org/​10.​1161/​CIRCR​ESAHA.​117.​ 311054 93. Schafer DP, Lehrman EK, Kautzman AG, Koyama R, Mardinly AR, Yamasaki R et al (2012) Microglia sculpt postnatal neural circuits in an activity and complement-dependent manner. Neu- ron 74:691–705. https://​doi.​org/​10.​1016/j.​neuron.​2012.​03.​026 77. Pedragosa J, Salas-Perdomo A, Gallizioli M, Cugota R, Miró- Mur F, Briansó F et al (2018) CNS-border associated mac- rophages respond to acute ischemic stroke attracting granulocytes and promoting vascular leakage. Acta Neuropathol Commun 6:76. https://​doi.​org/​10.​1186/​s40478-​018-​0581-6 94. Schain AJ, Melo-Carrillo A, Borsook D, Grutzendler J, Strass- man AM, Burstein R (2018) Activation of pial and dural mac- rophages and dendritic cells by cortical spreading depression. Ann Neurol 83:508–521. https://​doi.​org/​10.​1002/​ana.​25169 78. Pinho-Ribeiro FA, Deng L, Neel DV, Erdogan O, Basu H, Yang D et al (2023) Bacteria hijack a meningeal neuroimmune axis to facilitate brain invasion. Nature 615:472–481. https://​doi.​org/​10.​ 1038/​s41586-​023-​05753-x 95. Schonhoff AM, Figge DA, Williams GP, Jurkuvenaite AJ, Gallups NJ, Childers GM et al (2023) Border-associated mac- rophages mediate the neuroinflammatory response in an alpha- synuclein model of Parkinson disease. Nat Commun 14:3754. https://​doi.​org/​10.​1038/​s41467-​023-​39060-w 79. Pizzo ME, Wolak DJ, Kumar NN, Brunette E, Brunnquell CL, Hannocks M-J et al (2018) Intrathecal antibody distribution in the rat brain: surface diffusion, perivascular transport and osmotic enhancement of delivery. J Physiol 596:445–475. https://​ doi.​org/​10.​1113/​JP275​105 96. Schulz C, Gomez Perdiguero E, Chorro L, Szabo-Rogers H, Cagnard N, Kierdorf K et al (2012) A lineage of myeloid cells independent of Myb and hematopoietic stem cells. References Kuschert GS, Coulin F, Power CA, Proudfoot AE, Hubbard RE, Hoogewerf AJ et al (1999) Glycosaminoglycans interact selec- tively with chemokines and modulate receptor binding and cel- lular responses. Biochemistry 38:12959–12968. https://​doi.​org/​ 10.​1021/​bi990​711d 69. Milusev A, Rieben R, Sorvillo N (2022) The endothelial glyco- calyx: a possible therapeutic target in cardiovascular disorders. Front Cardiovasc Med 9:897087. https://​doi.​org/​10.​3389/​fcvm.​ 2022.​897087 55. Kutuzov N, Flyvbjerg H, Lauritzen M (2018) Contributions of the glycocalyx, endothelium, and extravascular compartment to the blood-brain barrier. Proc Natl Acad Sci USA 115:E9429– E9438. https://​doi.​org/​10.​1073/​pnas.​18021​55115 70. Monier A, Adle-Biassette H, Delezoide A-L, Evrard P, Gressens P, Verney C (2007) Entry and distribution of microglial cells in human embryonic and fetal cerebral cortex. J Neuropathol Exp Neurol 66:372–382. https://​doi.​org/​10.​1097/​nen.​0b013​e3180​ 517b46 p g p 56. Li L, Song J, Chuquisana O, Hannocks M-J, Loismann S, Vogl T et al (2020) Endothelial basement membrane laminins as an environmental cue in monocyte differentiation to macrophages. Front Immunol 11:584229. https://​doi.​org/​10.​3389/​fimmu.​2020.​ 584229 71. Mrdjen D, Pavlovic A, Hartmann FJ, Schreiner B, Utz SG, Leung BP et al (2018) High-dimensional single-cell mapping of central nervous system immune cells reveals distinct myeloid subsets in health, aging, and disease. Immunity 48:380-395.e6. https://​doi.​ org/​10.​1016/j.​immuni.​2018.​01.​011 57. Lim HY, Lim SY, Tan CK, Thiam CH, Goh CC, Carbajo D et al (2018) Hyaluronan receptor LYVE-1-expressing macrophages maintain arterial tone through Hyaluronan-mediated regulation of smooth muscle cell collagen. Immunity 49:1191. https://​doi.​ org/​10.​1016/j.​immuni.​2018.​12.​009 72. Munro DAD, Bradford BM, Mariani SA, Hampton DW, Vink CS, Chandran S et al (2020) CNS macrophages differentially rely on an intronic Csf1r enhancer for their development. Dev Camb Engl 147:dev194449. https://​doi.​org/​10.​1242/​dev.​194449 g j 58. Liu Y, Jacobowitz DM, Barone F, McCarron R, Spatz M, Feuer- stein G et al (1994) Quantitation of perivascular monocytes and macrophages around cerebral blood vessels of hypertensive and 73. Munro DAD, Movahedi K, Priller J (2022) Macrophage com- partmentalization in the brain and cerebrospinal fluid system. Page 12 of 13 37 Acta Neuropathologica 37 Acta Neuropathologica (2024) 147:37 (2024) 147:37 Sci Immunol 7:eabk0391. https://​doi.​org/​10.​1126/​sciim​munol.​ abk03​91 in an Alzheimer’s disease model. J Exp Med 217:e20191374. https://​doi.​org/​10.​1084/​jem.​20191​374f 74. Olah M, Menon V, Habib N, Taga MF, Ma Y, Yung CJ et al (2020) Single cell RNA sequencing of human microglia uncov- ers a subset associated with Alzheimer’s disease. Nat Commun 11:6129. https://​doi.​org/​10.​1038/​s41467-​020-​19737-2 90. References Science 336:86–90. https://​doi.​org/​10.​1126/​scien​ce.​12191​79 g 80. Plein A, Fantin A, Denti L, Pollard JW, Ruhrberg C (2018) Erythro-myeloid progenitors contribute endothelial cells to blood vessels. Nature 562:223–228. https://​doi.​org/​10.​1038/​ s41586-​018-​0552-x 97. Schwabenland M, Brück W, Priller J, Stadelmann C, Lassmann H, Prinz M (2021) Analyzing microglial phenotypes across neuropathologies: a practical guide. Acta Neuropathol (Berl) 142:923–936. https://​doi.​org/​10.​1007/​s00401-​021-​02370-8 81. Prater KE, Green KJ, Mamde S, Sun W, Cochoit A, Smith CL et al (2023) Human microglia show unique transcriptional changes in Alzheimer’s disease. Nat Aging 3:894–907. https://​ doi.​org/​10.​1038/​s43587-​023-​00424-y 98. Shemer A, Grozovski J, Tay TL, Tao J, Volaski A, Süß P et al (2018) Engrafted parenchymal brain macrophages differ from microglia in transcriptome, chromatin landscape and response to challenge. Nat Commun 9:5206. https://​doi.​org/​10.​1038/​ s41467-​018-​07548-5 g y 82. Prinz M, Jung S, Priller J (2019) Microglia biology: one cen- tury of evolving concepts. Cell 179:292–311. https://​doi.​org/​10.​ 1016/j.​cell.​2019.​08.​053 83. Prinz M, Masuda T, Wheeler MA, Quintana FJ (2021) Microglia and central nervous system-associated macrophages-from origin to disease modulation. Annu Rev Immunol 39:251–277. https://​ doi.​org/​10.​1146/​annur​ev-​immun​ol-​093019-​110159 99. Shibuya Y, Kumar KK, Mader MM-D, Yoo Y, Ayala LA, Zhou M et al (2022) Treatment of a genetic brain disease by CNS-wide microglia replacement. Sci Transl Med. https://​doi.​org/​10.​1126/​ scitr​anslm​ed.​abl99​45 84. Prinz M, Priller J (2017) The role of peripheral immune cells in the CNS in steady state and disease. Nat Neurosci 20:136–144. https://​doi.​org/​10.​1038/​nn.​4475f 100. Silvin A, Uderhardt S, Piot C, Da Mesquita S, Yang K, Geirsdot- tir L et al (2022) Dual ontogeny of disease-associated microglia and disease inflammatory macrophages in aging and neurodegen- eration. Immunity 55:1448-1465.e6. https://​doi.​org/​10.​1016/j.​ immuni.​2022.​07.​004 85. Prinz M, Priller J, Sisodia SS, Ransohoff RM (2011) Heterogene- ity of CNS myeloid cells and their roles in neurodegeneration. Nat Neurosci 14:1227–1235. https://​doi.​org/​10.​1038/​nn.​2923 101. Siret C, van Lessen M, Bavais J, Jeong HW, Reddy Samawar SK, Kapupara K et al (2022) Deciphering the heterogeneity of the Lyve1+ perivascular macrophages in the mouse brain. Nat Commun 13:7366. https://​doi.​org/​10.​1038/​s41467-​022-​35166-9 86. Rajan WD, Wojtas B, Gielniewski B, Miró-Mur F, Pedragosa J, Zawadzka M et al (2020) Defining molecular identity and fates of CNS-border associated macrophages after ischemic stroke in rodents and humans. Neurobiol Dis 137:104722. https://​doi.​org/​ 10.​1016/j.​nbd.​2019.​104722f 102. Sixt M, Engelhardt B, Pausch F, Hallmann R, Wendler O, Sorokin LM (2001) Endothelial cell laminin isoforms, laminins 8 and 10, play decisive roles in T cell recruitment across the blood- brain barrier in experimental autoimmune encephalomyelitis. J Cell Biol 153:933–946. https://​doi.​org/​10.​1083/​jcb.​153.5.​933 87. References Xu Z, Rao Y, Huang Y, Zhou T, Feng R, Xiong S et al (2020) Efficient strategies for microglia replacement in the central nerv- ous system. Cell Rep 32:108041. https://​doi.​org/​10.​1016/j.​celrep.​ 2020.​108041 p gi 109. Tata M, Ruhrberg C, Fantin A (2015) Vascularisation of the cen- tral nervous system. Mech Dev 138(Pt 1):26–36. https://​doi.​org/​ 10.​1016/j.​mod.​2015.​07.​001 122. Yamamoto Y, Craggs LJL, Watanabe A, Booth T, Attems J, Low RWC et al (2013) Brain microvascular accumulation and distri- bution of the NOTCH3 ectodomain and granular osmiophilic material in CADASIL. J Neuropathol Exp Neurol 72:416–431. https://​doi.​org/​10.​1097/​NEN.​0b013​e3182​9020b5 110. Taylor X, Clark IM, Fitzgerald GJ, Oluoch H, Hole JT, DeMat- tos RB et al (2023) Amyloid-β (Aβ) immunotherapy induced microhemorrhages are associated with activated perivascular macrophages and peripheral monocyte recruitment in Alzhei- mer’s disease mice. Mol Neurodegener 18:59. https://​doi.​org/​ 10.​1186/​s13024-​023-​00649-w 123. Yan P, Kim K-W, Xiao Q, Ma X, Czerniewski LR, Liu H et al (2022) Peripheral monocyte-derived cells counter amyloid plaque pathogenesis in a mouse model of Alzheimer’s disease. J Clin Invest 132:e152565. https://​doi.​org/​10.​1172/​JCI15​2565 111. Thanopoulou K, Fragkouli A, Stylianopoulou F, Georgopoulos S (2010) Scavenger receptor class B type I (SR-BI) regulates perivascular macrophages and modifies amyloid pathology in an Alzheimer mouse model. Proc Natl Acad Sci USA 107:20816– 20821. https://​doi.​org/​10.​1073/​pnas.​10058​88107 124. Yang AC, Vest RT, Kern F, Lee DP, Agam M, Maat CA et al (2022) A human brain vascular atlas reveals diverse mediators of Alzheimer’s risk. Nature 603:885–892. https://​doi.​org/​10.​1038/​ s41586-​021-​04369-3 125. Yang Y, Jorstad NL, Shiao C, Cherne MK, Khademi SB, Mon- tine KS et al (2013) Perivascular, but not parenchymal, cerebral engraftment of donor cells after non-myeloablative bone mar- row transplantation. Exp Mol Pathol 95:7–17. https://​doi.​org/​ 10.​1016/j.​yexmp.​2013.​03.​010 112. Thion MS, Low D, Silvin A, Chen J, Grisel P, Schulte-Schrep- ping J et al (2018) Microbiome influences prenatal and adult microglia in a sex-specific manner. Cell 172:500-516.e16. https://​ doi.​org/​10.​1016/j.​cell.​2017.​11.​042 113. Utz SG, See P, Mildenberger W, Thion MS, Silvin A, Lutz M et al (2020) Early fate defines microglia and non-parenchymal brain macrophage development. Cell 181:557-573.e18. https://​ doi.​org/​10.​1016/j.​cell.​2020.​03.​021 126. Zeisel A, Muñoz-Manchado AB, Codeluppi S, Lönnerberg P, La Manno G, Juréus A et al (2015) Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science 347:1138–1142. https://​doi.​org/​10.​1126/​scien​ce.​aaa19​34 127. References Ransohoff RM, Perry VH (2009) Microglial physiology: unique stimuli, specialized responses. Annu Rev Immunol 27:119–145. https://​doi.​org/​10.​1146/​annur​ev.​immun​ol.​021908.​132528 p g j 103. Song J, Zhang X, Buscher K, Wang Y, Wang H, Di Russo J et al (2017) Endothelial basement membrane laminin 511 contributes to endothelial junctional tightness and thereby inhibits leuko- cyte transmigration. Cell Rep 18:1256–1269. https://​doi.​org/​10.​ 1016/j.​celrep.​2016.​12.​092 88. Rebejac J, Eme-Scolan E, Arnaud Paroutaud L, Kharbouche S, Teleman M, Spinelli L et al (2022) Meningeal macrophages pro- tect against viral neuroinfection. Immunity 55:2103-2117.e10. https://​doi.​org/​10.​1016/j.​immuni.​2022.​10.​005 89. Reed-Geaghan EG, Croxford AL, Becher B, Landreth GE (2020) Plaque-associated myeloid cells derive from resident microglia Page 13 of 13  37 Acta Neuropathologica Acta Neuropathologica (2024) 147:37 (2024) 147:37 37 104. Spillantini MG, Schmidt ML, Lee VM-Y, Trojanowski JQ, Jakes R, Goedert M (1997) α-Synuclein in lewy bodies. Nature 388:839–840. https://​doi.​org/​10.​1038/​42166 117. Wu C, Ivars F, Anderson P, Hallmann R, Vestweber D, Nilsson P et al (2009) Endothelial basement membrane laminin alpha5 selectively inhibits T lymphocyte extravasation into the brain. Nat Med 15:519–527. https://​doi.​org/​10.​1038/​nm.​1957 p g 105. Stremmel C, Schuchert R, Wagner F, Thaler R, Weinberger T, Pick R et al (2018) Yolk sac macrophage progenitors traffic to the embryo during defined stages of development. Nat Commun 9:75. https://​doi.​org/​10.​1038/​s41467-​017-​02492-2 118. Wu X, Saito T, Saido TC, Barron AM, Ruedl C (2021) Micro- glia and CD206+ border-associated mouse macrophages main- tain their embryonic origin during Alzheimer’s disease. eLife 10:e71879. https://​doi.​org/​10.​7554/​eLife.​71879 p g 106. Sun Z, Costell M, Fässler R (2019) Integrin activation by talin, kindlin and mechanical forces. Nat Cell Biol 21:25–31. https://​ doi.​org/​10.​1038/​s41556-​018-​0234-9 119. Wu Y-C, Bogale T, Koistinaho J, Pizzi M, Rolova T, Bellucci A (2024) The contribution of β-amyloid, Tau and α-synuclein to blood–brain barrier damage in neurodegenerative disorders. Acta Neuropathol (Berl). https://​doi.​org/​10.​1007/​s00401-​024-​02696-z 107. Szalay G, Martinecz B, Lénárt N, Környei Z, Orsolits B, Judák L et al (2016) Microglia protect against brain injury and their selective elimination dysregulates neuronal network activity after stroke. Nat Commun 7:11499. https://​doi.​org/​10.​1038/​ncomm​ s11499 120. Wynn TA, Chawla A, Pollard JW (2013) Macrophage biology in development, homeostasis and disease. Nature 496:445–455. https://​doi.​org/​10.​1038/​natur​e12034 108. Talsma DT, Poppelaars F, Dam W, Meter-Arkema AH, Vivès RR, Gál P et al (2020) MASP-2 is a heparin-binding protease; iden- tification of blocking oligosaccharides. Front Immunol 11:732. https://​doi.​org/​10.​3389/​fimmu.​2020.​00732 121. Publisher's Note  Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. References Zhang X, Wang Y, Song J, Gerwien H, Chuquisana O, Chashchina A et al (2020) The endothelial basement membrane acts as a checkpoint for entry of pathogenic T cells into the brain. J Exp Med 217:e20191339. https://​doi.​org/​10.​1084/​jem.​20191​ 339 114. Van Hove H, Martens L, Scheyltjens I, De Vlaminck K, Pombo Antunes AR, De Prijck S et al (2019) A single-cell atlas of mouse brain macrophages reveals unique transcriptional identi- ties shaped by ontogeny and tissue environment. Nat Neurosci 22:1021–1035. https://​doi.​org/​10.​1038/​s41593-​019-​0393-4 115. Walls JR, Coultas L, Rossant J, Henkelman RM (2008) Three- dimensional analysis of vascular development in the mouse embryo. PLoS ONE 3:e2853. https://​doi.​org/​10.​1371/​journ​al.​ pone.​00028​53 Publisher's Note  Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 116. Werner Y, Mass E, Ashok Kumar P, Ulas T, Händler K, Horne A et al (2020) Cxcr4 distinguishes HSC-derived monocytes from microglia and reveals monocyte immune responses to experi- mental stroke. Nat Neurosci 23:351–362. https://​doi.​org/​10.​1038/​ s41593-​020-​0585-y
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Candidate gene resequencing to identify rare, pedigree-specific variants influencing healthy aging phenotypes in the long life family study
BMC geriatrics
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© 2016 Druley et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. * Correspondence: mprovince@wustl.edu 1Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8116, St. Louis, MO 63108, USA 3Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA Full list of author information is available at the end of the article Candidate gene resequencing to identify rare, pedigree-specific variants influencing healthy aging phenotypes in the long life family study Candidate gene resequencing to identify rare, pedigree-specific variants influencing healthy aging phenotypes in the long life family study Todd E. Druley1,2, Lihua Wang1,3, Shiow J. Lin1,3, Joseph H. Lee4,5,6, Qunyuan Zhang1,3, E. Warwick Daw1,3, Haley J. Abel1,3, Sara E. Chasnoff1,2, Enrique I. Ramos1,2, Benjamin T. Levinson1,2, Bharat Thyagarajan7, Anne B. Newman8, Kaare Christensen9, Richard Mayeux10 and Michael A. Province1,3* * Correspondence: mprovince@wustl.edu 1Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8116, St. Louis, MO 63108, USA 3 3Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA Full list of author information is available at the end of the article Druley et al. BMC Geriatrics (2016) 16:80 DOI 10.1186/s12877-016-0253-y Druley et al. BMC Geriatrics (2016) 16:80 DOI 10.1186/s12877-016-0253-y Open Access RESEARCH ARTICLE Open Access Candidate gene resequencing to identify rare, pedigree-specific variants influencing healthy aging phenotypes in the long life family study Todd E. Druley1,2, Lihua Wang1,3, Shiow J. Lin1,3, Joseph H. Lee4,5,6, Qunyuan Zhang1,3, E. Warwick Daw1,3, Haley J. Abel1,3, Sara E. Chasnoff1,2, Enrique I. Ramos1,2, Benjamin T. Levinson1,2, Bharat Thyagarajan7, Anne B. Newman8, Kaare Christensen9, Richard Mayeux10 and Michael A. Province1,3* Abstract Background: The Long Life Family Study (LLFS) is an international study to identify the genetic components of various healthy aging phenotypes. We hypothesized that pedigree-specific rare variants at longevity-associated genes could have a similar functional impact on healthy phenotypes. Methods: We performed custom hybridization capture sequencing to identify the functional variants in 464 candidate genes for longevity or the major diseases of aging in 615 pedigrees (4,953 individuals) from the LLFS, using a multiplexed, custom hybridization capture. Variants were analyzed individually or as a group across an entire gene for association to aging phenotypes using family based tests. Results: We found significant associations to three genes and nine single variants. Most notably, we found a novel variant significantly associated with exceptional survival in the 3’ UTR OBFC1 in 13 individuals from six pedigrees. OBFC1 (chromosome 10) is involved in telomere maintenance, and falls within a linkage peak recently reported from an analysis of telomere length in LLFS families. Two different algorithms for single gene associations identified three genes with an enrichment of variation that was significantly associated with three phenotypes (GSK3B with the Healthy Aging Index, NOTCH1 with diastolic blood pressure and TP53 with serum HDL). Conclusions: Sequencing analysis of family-based associations for age-related phenotypes can identify rare or novel variants Conclusions: Sequencing analysis of family-based associations for age-related phenotypes can identify rare or novel variants. Keywords: Genomics, Aging, Genetics, Geriatrics, Pedigrees, Family, Sequencing most of which is unknown [1]. Currently, most human longevity and healthy aging related variants identified through genome wide association study (GWAS) are ei- ther intergenic or intronic with weak effects, and there is little characterization of coding variants that may influ- ence human lifespan. For instance, common variants in multiple genes such as apolipoprotein E (APOE) [2–5], Forkhead Box O1 (FOXO1) [6], Forkhead Box O3 (FOXO3) [7], Insulin-Like Growth Factor 1 Receptor (IGF-1R) [6, 8] and Translocase of Outer Mitochondrial Membrane 40 Homolog (TOMM40) [9] have all been as- sociated with human lifespan. However, lifespan is a highly complex trait and healthy aging is controlled and Survival and mortality-weighted healthy aging index The lifespan in LLFS was estimated as the duration of survival free of death from any cause or from any one of a specified list of diseases including cardiovascular dis- ease, congestive heart failure, cancer, stroke, and Type 2 diabetes. The LLFS proband generation, including pro- bands and full and half siblings (n = 810), was used for identifying variants related with survival. Thus, we expect families clustered for long-lived healthy members [11, 12] to be enriched for genetic variants that will promote healthy and/or prolonged aging. To identify new, rare, heritable variants that are associated with multiple healthy aging phenotypes, we performed custom hybridization capture sequencing of 464 healthy aging related candidate genes in Phase 1 of the Long Life Family Study (LLFS). We then per- formed association analyses of both rare (<1 % minor allele frequency) and common variants against mul- tiple aging-related phenotypes including survival, leukocyte telomere length, healthy aging index [13], BMI, blood pressure, blood lipid levels, blood glucose level, cognitive function, onset of type 2 diabetes, heart disease, cancer, and stroke. y g Healthy aging was established by the lack of disease and clinical test values indicating normal function of various biological systems. To increase the probability of identifying healthy aging-related genetic variants, which might influence one or more components of these biological systems, Sanders et al. proposed the Healthy Aging Index (HAI) as a subphenotype of lon- gevity [13]. Using approximate age-adjusted tertiles for systolic blood pressure, pulmonary vital capacity, cre- atinine, fasting glucose, and Modified Mini-Mental Sta- tus Examination score, each individual is scored 0, 1, or 2 for each trait. The HAI is then calculated from the sum of these scores in a range from 0 (healthy) to 10 (unhealthy). The mortality-weighted HAI is generated from the sum of the mortality-weighted scores of the five components listed above. The weights are based on the regression coefficients from the Cox proportional hazards model for the effect of each component on sur- vival and are 0.17085 for systolic blood pressure, 0.38386 for forced vital capacity, 0.42873 for MMSE points, 0.13397 for serum creatinine, and 0.23880 for serum fasting glucose. Phenotype measurements In this study, human lifespan and phenotypic traits re- lated to healthy aging including survival, leukocyte telo- mere length, BMI, blood pressure, blood lipid levels, blood glucose and insulin levels, cognitive function, healthy aging index, as well as the ages of onset of stroke, coronary heart disease, congestive heart failure, cancer, and type 2 diabetes mellitus, were investigated. Background According to United Nations World Population Prospects 2012 revision (http://esa.un.org/unpd/wpp/Documenta tion/pdf/WPP2012_HIGHLIGHTS.pdf), the worldwide average human lifespan was 71 years (68.5 years for males and 73.5 years for females) over the period 2010–2013. At least 25 % of human lifespan is dictated by genetic factors, Druley et al. BMC Geriatrics (2016) 16:80 Page 2 of 12 Page 2 of 12 Page 2 of 12 influenced by variety of environmental factors and individ- ual phenotypes [10]. Leukocyte telomere length, Body Mass Index (BMI), blood pressure, serum lipids, blood glucose, cognitive function, onset of type 2 diabetes, heart disease, cancer, and stroke are a few phenotypes associated with aging, and we hypothesized that pedigree-specific coding variants associated with these traits would identify additional genes or pathways im- portant for regulating human lifespan. While non- coding variants may have significant gene or epigenetic regulatory effects, exonic variants would be expected to exert larger effects on gene function and might there- fore explain a larger fraction of the variance in these complex aging phenotypes. Phenotype measurements influenced by variety of environmental factors and individ- ual phenotypes [10]. Leukocyte telomere length, Body Mass Index (BMI), blood pressure, serum lipids, blood glucose, cognitive function, onset of type 2 diabetes, heart disease, cancer, and stroke are a few phenotypes associated with aging, and we hypothesized that pedigree-specific coding variants associated with these traits would identify additional genes or pathways im- portant for regulating human lifespan. While non- coding variants may have significant gene or epigenetic regulatory effects, exonic variants would be expected to exert larger effects on gene function and might there- fore explain a larger fraction of the variance in these complex aging phenotypes. Methods Subjects j The LLFS [11], a multi-center family-based cohort study, enrolled 4,953 individuals from 539 families clustered for exceptional survival to identify environ- mental and genetic factors that account for the long healthy lives in these families. Phase 1 of the LLFS was conducted between 2006 and 2009. All participants provided written informed consent prior to inclusion in the study. The four recruitment centers include Boston University Medical Center, Columbia Univer- sity Medical Center, University of Pittsburgh, and Uni- versity of Southern Denmark. Using the Family Longevity Selection Score (FLoSS) [14], a score gener- ated according to birth-year cohort survival probabil- ities of the proband and siblings, probands and their families with FLoSS score of 7 or higher, at least one living sibling, and at least one living offspring (mini- mum family size of 3), who were able to give informed consent and willing to participate were recruited. The spouses were enrolled as controls for this study. The characteristics of the LLFS population by generation and by gender are listed in Additional file 1: Table S1 and S2, respectively. Glycated hemoglobin (HbA1c), Blood Glucose and Insulin Levels, Leukocyte Telomere Length, Blood Lipid Levels Including Total Cholesterol, HDL Cholesterol, LDL Cholesterol and Triglyceride, BMI, Blood Pressure, Cognitive Function, Stroke, Coronary Heart Disease, Congestive Heart Failure, Cancer, Type 2 Diabetes We looked for any possible association between our can- didate genes related to healthy aging and various aging phenotypes including HbA1c, blood glucose and insulin levels, leukocyte telomere length, blood lipid levels in- cluding total cholesterol, HDL cholesterol, LDL choles- terol and triglyceride, BMI, blood pressure, cognitive function, stroke, coronary heart disease, congestive heart failure, cancer, and type 2 diabetes. We looked for any possible association between our can- didate genes related to healthy aging and various aging phenotypes including HbA1c, blood glucose and insulin levels, leukocyte telomere length, blood lipid levels in- cluding total cholesterol, HDL cholesterol, LDL choles- terol and triglyceride, BMI, blood pressure, cognitive function, stroke, coronary heart disease, congestive heart failure, cancer, and type 2 diabetes. Druley et al. Genome-wide SNP array genotyping y g y g Illumina Human Omni 2.5 v1 was used to perform whole genome SNP genotyping on each study participant by CIDR (www.cidr.jhmi.edu), and the resulting data has been submitted to dbGaP under accession number phs000397.v1.p1. Genome-wide SNP variants within tar- geted sequenced regions were used as controls for sequen- cing accuracy as described below. Pooled sequencing and indexed custom library preparation We have previously published the entire protocol for custom hybridization capture of multiplexed, indexed next generation sequencing [20, 27]. Briefly, customized adapter, blocker, pre- and post-hybridization PCR ampli- fication primers and all index sequences used are listed in Additional file 1: Table S5 of the same report. We performed pooled capture of 464 candidate genes (Additional file 1: Table S3) selected collectively by the LLFS investigators due to their published association with age-related phenotypes. Candidate gene resequen- cing was performed from individually indexed DNA samples from LLFS participants [https://longlifefamilys- tudy.wustl.edu/LLFS/Home.html]. The bait set was cre- ated using the Agilent eArray online tool [https:// earray.chem.agilent.com/earray/] for the Agilent SureSe- lect Custom DNA Capture [http://www.genomics.agi- lent.com] using 2X tiling, an exon-centered layout strategy, and eliminating probes that overlap standard repeat masked regions by 20 or more bases. In total, there were 2,500,709 bases (2.5 Mb) covered by baits in 6,966 distinct intervals. ) y y Fasting HDL-cholesterol was measured after an 8-h fast directly in serum using the Roche HDL-Cholesterol 3rd generation direct method (Roche Diagnostics, Indianapolis, IN 46250) on a Roche Modular P Chemistry Analyzer. Fasting triglycerides were measured after an 8-h fast in serum using Triglyceride GB reagent (Roche Diagnos- tics, Indianapolis, IN 46250) on a Roche Modular P Chemistry Analyzer. LDL-cholesterol was calculated by the Friedewald equation using the measured results for total cholesterol, HDL-cholesterol, and triglycerides. This equation (LDL-cholesterol = total cholesterol – HDL – (triglycerides/5)) can be used to calculate LDL- cholesterol when triglycerides are less than 400 mg/dL. The corrected values for triglyceride and LDL choles- terol was calculated for individuals taking lipid lower- ing medications [17]. BMI was calculated as weight (kg)/height (m)2. Sitting systolic and diastolic blood pressure was obtained by the average of three measures using an automated blood pressure machine (BP-tru BPM 300, VMS MedTech, Coquitlam, Canada). Pulse Pressure was calculated as systolic blood pressure minus diastolic blood pressure. These results were cor- rected for individuals taking blood pressure modifying medication as previously published [18]. General cogni- tive function including arithmetic, memory, and orien- tation was assessed using the mini-mental state examination (MMSE) or Folstein test [19]. Stroke or cerebrovascular accident includes self-reported stroke, Sequencing Sequencing was performed in the Genome Technology Access Center at Washington University using the HiSeq 2000 platform, generating 101 bp paired-end reads. GWA and sequencing information for the LLFS partici- pants is available in dbGaP using accession number phs000397.v1.p1. Methods Subjects BMC Geriatrics (2016) 16:80 Page 3 of 12 As described previously [15], blood samples were col- lected between 2006 and 2009, and HbA1c was measured using identical ion exchange-based high performance liquid chromatography with the Tosoh 2.2 Plus and after 2007 with the Tosch G7 Glycohemoglobin Analyzer (Tosoh Medics, San Francisco, CA 94080) at the Advanced Research and Diagnostics Laboratory, University of Minnesota. Fasting glucose was measured after an 8-h fast in serum by the Roche hexokinase method (Roche Diagnostics, Indianapolis, IN 46250) on a Roche Modular P Chemistry Analyzer (Roche Diagnostics Corporation). Fasting insulin was measured after an 8-h fast in serum on a Roche Elecsys 2010 Analyzer (Roche Diagnostics Corporation) using a sandwich immunoassay method (Roche Diagnostics, Indianapolis, IN 46250). Assays of average leukocyte telomere length were described by Lee et al. [16]. Briefly, Telomeres (T) and beta-globin control (S) were amplified using real-time PCR of 95 °C for 10 min denaturation, 34 cycles of 95 °C for 15 s and 55 °C for 120 s performed on the CFX384 thermocycler (BioRad, Richmond, CA). The leukocyte telomere length was calculated from T/S ratio using the linear regression for- mula of bp = (1,585 ∗T/S ratio) + 3582. Fasting total choles- terol was measured after an 8-h fast in serum using a cholesterol oxidase method (Roche Diagnostics, Indianapolis, IN 46250) on a Roche Modular P Chemistry Analyzer. transient ischemic attack (TIA), or mini-stroke. Coronary heart disease was defined as self-reported myocardial in- farction, heart attack, coronary angioplasty, or coronary artery bypass grafting. Heart failure or congestive heart failure and cancer (including breast cancer, colon or rectal cancer, esophageal cancer, leukemia or lymphoma, lung cancer, pancreatic cancer, prostate cancer, etc.) were self- reported. Type 2 diabetes was defined as use of diabetes medications or fasting glucose ≥126 mg/dl. Phenotype transformation and covariates adjustment To increase the power and reduce the confounder ef- fects of our analyses, we performed the following covari- ates adjustment and transformation. HbA1c was adjusted for age, age2, age3, field center and the top twenty princi- pal components (PCs); the standardized residuals from a stepwise covariate adjustment were used as final pheno- type for the following association analyses. The leukocyte telomere length was transformed using an in- verse normal function. This transformed trait was ad- justed for covariates age, sex, education, field center, smoking, alcohol consumption, marital status, history of heart disease, and twenty PCs (PC8 was the only signifi- cant PC associated with leukocyte telomere length in the multivariate polygenic model). Mortality weighted healthy aging index were adjusted for age, sex, and 10 PCs and the residuals were used in the following ana- lyses. The residuals of trait exceptionality scores adjusted for field centers and 20 PCs were used in the following analyses. Sequencing alignment, variant calling and filtering Sequencing alignment, variant calling and filtering Sequencing analysis for indexed captures of all LLFS participants followed previously reported methods (27; Sequencing analysis for indexed captures of all LLFS participants followed previously reported methods (27; Druley et al. BMC Geriatrics (2016) 16:80 Page 4 of 12 Page 4 of 12 section entitled “Pooled indexed custom capture data analysis” for more details). Briefly, raw sequence data was aligned against the human genome (hg19/NCBI 37.0) using Novoalign (Novocraft, Inc.) and, from aligned reads, variants were called using samtools-0.1.18 mpileup at only the 2.5 Mb of target sequence within our custom hybridization array. probability of the trait score compared to the age/sex/ birth-cohort matched in the Framingham Heart Study. Trait exceptionality scores for type 2 diabetes, heart dis- ease, cancer, and stroke were calculated as the negative logarithm of the probability of the onset age of the dis- ease, and compared to the distribution of the age of on- set for each trait in the Framingham Heart Study. There are two additional components to the HAI, which are pulmonary vital capacity and serum creatinine. However, these were not available in Framingham Heart Study and were not included in our analyses. The thresholds used for filtering called variants from se- quencing data were determined by comparing common base positions shared with existing GWA data. For gene- level burden tests, variants were filtered for coverage <5- fold, quality score <45, call rate < 60 %, MAF > 0.01, Mendel errors, and nonfunctional variants. Single variants were fil- tered for coverage <5-fold, quality score <45, call rate < 60 %, and Mendel errors. For rare variants (<2 % minor allele frequency), these thresholds provided a sensitivity of ≥94.9 % and specificity of ≥99.9 % [27]. Mendel error cutoffs were implemented as follows: MAF = 0 to <0.01 for >2 pedigrees with the Mendel error; MAF = 0.01 to <0.05 for ≥7 pedigrees; MAF = 0.05 to <0.1 for ≥12 pedigrees; MAF = 0.1 to <0.2 for ≥26 pedigrees; MAF = 0.2 to <0.3 for ≥30 pedigrees; MAF = 0.3 to <0.4 for ≥32 pedigrees; MAF = 0.4 to <0.51 for ≥38 pedigrees. Statistical analyses Trait exceptionality scores for survival, BMI, blood pressure, blood lipid levels, blood glucose level, blood insulin level, cognitive function, type 2 diabetes, heart disease, cancer, and stroke Trait exceptionality scores for survival, BMI, blood pressure, blood lipid levels, blood glucose level, blood insulin level, cognitive function, type 2 diabetes, heart disease, cancer, and stroke The LLFS cohort is enriched with longer-lived and healthier individuals than the general population, as well as the Framingham Heart Study. To account for this dif- ference and increase our statistical power for detecting sequence variants associated with aging-related pheno- types, such as survival, BMI, blood pressure, blood lipid levels, blood glucose level, blood insulin level, cognitive function, type 2 diabetes, heart disease, cancer, and stroke are transformed to “trait exceptionality scores”. Higher trait exceptionality scores indicate that, for a given trait, an individual is significantly different from the reference population for the same trait, resulting in longer individual survival and/or better health. Using sex- and birth-year specific cohort life tables from the 2012 trustees report of the United States Social Security Administration, the trait exceptionality scores for sur- vival were calculated for the oldest (proband) generation in LLFS, along with any blood relatives within the same generation regardless of age. These calculations are con- ditional on survival to age 40 and were determined as the negative logarithm of the probability of survival be- yond age at last contact. Trait exceptionality scores for BMI, blood pressure, blood lipid levels, blood glucose level, blood insulin level, and cognitive function were also calculated as the negative logarithm of the Single variant analyses g y Because there are correlations between the target pheno- types, the likelihood of a single variant having a func- tional effect on a given phenotype was Bonferroni corrected by dividing 0.05 by the total number of vari- ants queried without accounting for the number of ana- lyzed phenotypes. This resulted in p-values of 7.56x10−6 for survival and cancer and 1.47x10−5 for HDL, LDL and triglycerides. We first attempted to determine if any sin- gle variant identified by sequencing was significantly as- sociated with survival. We identified a novel regulatory variant in the 3’ UTR of Oligonucleotide/Oligosacchar- ide-Binding Fold Containing 1, located on chromosome 10q24.33 (OBFC1; see Table 2) found in 13 individuals from six pedigrees (Additional file 1: Table S6), which was significantly associated (p = 6.18x10−7) with trait ex- ceptionality for survival in long lived families. Intronic variants of OBFC1 genotyped by Illumina array were also queried, and two rare variants (rs79250842 in 11 in- dividuals from 5 pedigrees and rs77987791 in 5 individ- uals from 1 pedigree) were also found to have a significant association with survival (Fig. 2). OBFC1 is involved in telomere maintenance and falls within a re- cently reported LLFS family-based association peak for telomere length on chromosome 10 as shown in Fig. 2 [16]. This observation is supported by the association of the same OBFC1 intronic variant (rs77987791) with telomere length (p = 0.038). Interestingly, one long-lived pedigree (pedID 25609942) with 14 family members was clustered for all three rare variants in seven family mem- bers, which suggests that multiple rare variants within OBFC1 might contribute to longer lifespan. The com- parison of “survival” to OBFC1 genotype is shown in Additional file 1: Figure S2A. Sample characteristics Phenotype Our results included 4,217 LLFS subjects (mean of age 70.56 for men and 70.05 for women) with complete phenotypic and genotypic information. Individuals with inadequate GWA or sequencing coverage were excluded. The study participants tend to have healthier profiles compared with other cohorts of adults. For these indi- viduals, the mean score of healthy aging index (3.64 in men and women) and mortality weighted healthy aging index (3.24 in men and 3.03 in women) are low. The average age of the LLFS probands and their relatives (95.8 in men and 99.4 in women) is much higher than the cohort life expectancy of US and Danish (an LLFS study site) early 20th century birth cohorts (60–70 years) and the current life expectancy in both populations (~80 years). Single variant association testing Parame- ters in each model were estimated by the maximum like- lihood algorithm and tested by the Wald test. Rather than using a fixed weight, the PWST method adaptively calculates the weights for individual variants from the observed genotype and phenotype data and then per- forms a permutation procedure for family data to avoid false positive inflation due to the over fitting of the adap- tive score WSS. to detect rare causal variants, we applied these two algo- rithms to assess the influence of called rare variants. This was necessary since standard association tests of in- dividual rare variants (MAF < 0.01) are underpowered unless sample sizes or effect sizes are very large, func- tional variants within the same gene based on bioinfor- matics annotation by ANNOVAR [27] were analyzed together in this study. For each group of variants, UWSS was calculated as the total number of variant alleles car- ried by a subject. The weight was calculated based on al- lele frequency in controls and WSS was calculated as the weighted sum of minor alleles over a group of variants. The UWSS or WSS score was treated as a single pre- dictor variable (X) and fit into a linear model. The kin- ship matrix was incorporated into the linear models to adjust for familial relatedness between subjects. Parame- ters in each model were estimated by the maximum like- lihood algorithm and tested by the Wald test. Rather than using a fixed weight, the PWST method adaptively calculates the weights for individual variants from the observed genotype and phenotype data and then per- forms a permutation procedure for family data to avoid false positive inflation due to the over fitting of the adap- tive score WSS. 5’ or 3’ untranslated regions (UTR5 or UTR3, respect- ively). The majority of variants (59.8 %) were found within a single LLFS family (Additional file 1: Table S4) and (88.74 %, n = 26,723) were rare, occurring at <1 % in the general population, and 12,303 (46.04 %) were sin- gletons (Additional file 1: Table S5). 5’ or 3’ untranslated regions (UTR5 or UTR3, respect- ively). The majority of variants (59.8 %) were found within a single LLFS family (Additional file 1: Table S4) and (88.74 %, n = 26,723) were rare, occurring at <1 % in the general population, and 12,303 (46.04 %) were sin- gletons (Additional file 1: Table S5). Single variant association testing g g Family relatedness was estimated based on pedigree structure using the “kinship” R package. Accounting for this relatedness within families as random effects, the additive genetic fixed effects of SNPs were analyzed using the linear mixed effects model implemented in the “lmekin” R packages [21, 22]. Q-Q plots for the pheno- types analyzed are shown in Additional file 1: Figure S1 and demonstrate that, compared to genomic control (calculated as median of observed p value / median of expected p value to avoid estimation bias), each is within 0.578–1.09 using this approach. Thus, the type I error rate is low in this study. Rare variant testing across genes Currently un-weighted sum score (UWSS) [23], weighted sum score (WSS) [24], P-value Weighted Sum Test (PWST) method [25] and family based sequence kernel association test (famSKAT) [26] are commonly used for estimating the effects of rare variants. Because the PWST and famSKAT are likely to have greater power Druley et al. BMC Geriatrics (2016) 16:80 Druley et al. BMC Geriatrics (2016) 16:80 Druley et al. BMC Geriatrics (2016) 16:80 Page 5 of 12 Table 1 Filter Applied in LLFS sequence data Among 464 Candidate genes, 448 genes with 48,918 variants sequenced Filter 1: ≥5x coverage 47 ± 36 Filter 2: ≥45 quality score 175 ± 53 Filter 3: ≥60 % call rate 97 % ± 7 % Filter 4: Mendel Errors MAF dependent 439 genes with 30,112 variants analyzed Table 1 Filter Applied in LLFS sequence data to detect rare causal variants, we applied these two algo- rithms to assess the influence of called rare variants. This was necessary since standard association tests of in- dividual rare variants (MAF < 0.01) are underpowered unless sample sizes or effect sizes are very large, func- tional variants within the same gene based on bioinfor- matics annotation by ANNOVAR [27] were analyzed together in this study. For each group of variants, UWSS was calculated as the total number of variant alleles car- ried by a subject. The weight was calculated based on al- lele frequency in controls and WSS was calculated as the weighted sum of minor alleles over a group of variants. The UWSS or WSS score was treated as a single pre- dictor variable (X) and fit into a linear model. The kin- ship matrix was incorporated into the linear models to adjust for familial relatedness between subjects. Sequencing results To reduce false positive variant calls, stringent filtering of raw sequence data was employed and is described in Table 1. After filtering, 30,112 variants within 439 genes were identified with an average coverage of 47-fold, quality score of 175 and call rate of 0.97. As shown in Fig. 1, 37.4 % (11,261) of all called variants fell within coding regions with 22.4 % (6,745) being either missense (non-synonymous SNV) or nonsense (stop-gain and stop-loss) variants; 50.7 % (15,281) fell within regulatory Linear mixed model based single variant testing is not a stable method for rare variants with <10 minor allele Druley et al. BMC Geriatrics (2016) 16:80 Page 6 of 12 Fig. 1 The distribution of sequenced variants within different genomic region Fig. 1 The distribution of sequenced variants within different genomic region Among the 439 candidate genes, 160 are well-known human longevity related genes based on LongevityMap (http://genomics.senescence.info/longevity/) [35] and A Catalog of Published Genome-Wide Association Studies (http:/www.genome.gov/gwastudies/). When considering survival and any single variant with a p-value of <0.05 and more than 10 allelic copies in the LLFS cohort, we replicated 76 variants within these 160 genes (Additional file 1: Table S7), which supports the validity of our ana- lysis model. Four variants within FOXO3, a well-known longevity related gene [36–39], were replicated for an as- sociation (p < 0.05) with survival. copies [28], which is strengthened by our pedigree-based structure. While the effect of any single variant may be slight, we found a significant association with survival for 23 different variants in 23 healthy aging candidate genes (Table 3). Among these 23 variants, only four have been described in dbSNP. Eight of these genes (in bold) have published reports linking them to longer lifespan [9, 29–34]. These variants clustered in two families with longer survival (Fig. 3), suggesting that the aggregation of multiple variants in these genes may have a larger ef- fect on survival. One subject who survived to age 110 carried 15 of these variants, and another surviving to age 101 years carries 9 of these variants. None of the vari- ants were carried by spousal controls. We found associations with phenotypes other than sur- vival. One candidate gene, IGF1R (Insulin-Like Growth Table 2 Significant results of single variant testing for variants with more than 10 copies. Nine single variants with at least 10 allelic copies were identified within five phenotypes. Sequencing results There were 6,613 variants analyzed across 426 genes for survival and cancer and 3,389 variants analyzed across 408 genes for HDL, LDL and triglycerides Phenotype (TE Score) chr Position (hg19) rsID gene Function Ref Variant MAF N Beta SE P-value Survival 10 105642272 OBFC1 UTR3 C G 0.002 810 3.58 0.71 6.2E-7 Cancer 15 99501295 IGF1R UTR3 A G 0.007 4210 0.58 0.13 3.7E-6 HDL Cholesterol 16 57005301 rs1532625 CETP intron T C 0.38 3053 0.19 0.03 2.4E-13 16 57015091 rs5880 CETP nsyn-exon C G 0.047 4049 −0.32 0.06 1.2E-8 16 57017319 rs1800777 CETP nsyn-exon A G 0.029 3982 −0.40 0.07 8.1E-9 LDL Cholesterol 6 152679594 rs62426382 SYNE1 syn-exon G A 0.016 4035 0.45 0.09 1.6E-6 19 45396144 rs11556505 TOMM40 syn-exon T C 0.10 4018 −0.19 0.04 1.5E-6 19 45397229 rs1160983 TOMM40 syn-exon A G 0.02 2686 0.53 0.10 1.2E-7 Triglyceride 11 116703640 rs5128 APOC3 UTR3 G C 0.09 4003 −0.21 0.04 1.2E-7 Druley et al. BMC Geriatrics (2016) 16:80 Page 7 of 12 Fig. 2 Variant-wise association results on chromosome 10 around OBFC1 for telomere length phenotype (gray) and exceptional survival score (green) on chromosome 10 using both 1000 Genomes Project hybrid and candidate gene sequenced genotypes. Two additional rare variants from genome-wide array results showed significant association with survival exceptionality score. The association p-value of rs77987791 with telomere length is 0.038 Fig. 2 Variant-wise association results on chromosome 10 around OBFC1 for telomere length phenotype (gray) and exceptional survival score (green) on chromosome 10 using both 1000 Genomes Project hybrid and candidate gene sequenced genotypes. Two additional rare variants from genome-wide array results showed significant association with survival exceptionality score. The association p-value of rs77987791 with telomere length is 0.038 disease and longevity [48]. Comparisons for all variants listed in Table 2 between their associated phenotype and the variant genotype are shown in Additional file 1: Figure S2A-I. Factor 1 Receptor, located on chromosome 15q26.3) is well known to be associated with cell growth and various cancers [40]. As shown in Table 1, we noted one new cancer associated rare UTR3 variant (chr15:99501295) in this gene. g In addition, four genes (CETP, APOC3, SYNE1 and TOMM40) were associated with blood lipid levels. The cholesterol ester transfer protein, CETP (located on chromosome 16q21), is essential for metabolism of plasma lipoproteins [41]. Sequencing results Three known HDL cholesterol related variants within CETP, one common intronic variant (rs1532625) [42] and two rare exonic variants (rs5880, rs1800777) [43], were replicated in our study. APOC3 (Apolipoprotein C3, located on chromosome 11q23.3) is critical for triglyceride metabolism and a potential therapeutic target for metabolic syndrome [44]. One known common triglyceride related variant (rs5128) [45] in the UTR3 region of APOC3 was replicated. LDL cholesterol was associated with one synonymous variant in SYNE1 (Spectrin Repeat Containing, Nuclear Envelope 1, on chromosome 6q25.2) and two synonymous variants in TOMM40 (Translocase Of Outer Mitochondrial Membrane 40 Homolog, on chromosome 19q13.32). TOMM40 has been identified in genome-wide screens for dyslipidemia and carotid artery disease [46, 47]. More importantly, TOMM40 rs10524523 polymorphism in combination with APOE alleles significantly influences late-onset Alzheimer’s Analyses of multiple variants across genes To better characterize genes associated with our pheno- types due to multiple, pedigree-specific rare variants ra- ther than more common single variants, we aggregated rare functional variants (exonic, UTR3, UTR5, splicing and non-coding RNA) within the same gene using the PWST [25] and famSKAT [26]. For association results, Bonferroni correction of 0.05 divided by the total num- ber of genes resulted in a p < 1.14x10−4 for significance and p < 1.0x10−3 would merely be suggestive. With re- spect to survival, none of the candidate genes passed this significance threshold. When comparing our association results for survival to published longevity related genes, 20 genes were replicated with p-value <0.05 (Additional file 1: Table S8). We next performed PWSK and famSKAT analyses on our candidate genes to see if any gene harbored mul- tiple putatively functional variants associated with the individual Healthy Aging Index (HAI) and those results are listed in Table 4. GSK3B (glycogen synthase kinase 3 beta, on chromosome 3q13.33) achieved significance by PWSK. GSK3B, a serine-threonine kinase, has been associated with Alzheimer’s disease [49, 50] and may Page 8 of 12 Druley et al. BMC Geriatrics (2016) 16:80 Page 8 of 12 Table 3 Significant results of single variant testing for variants with less than 10 copies. Twenty-three rare variants with less than 10 minor allele copies were identified for a single phenotype (longevity). These variants clustered in two families with high trait exceptionality scores for longevity. Analyses of multiple variants across genes These variants clustered in two families with high trait i li f l i G i b ld h i l bli h d l i hi l i [9 29 34] regulate human aging via negative regulation of glucose homeostasis and Wnt signaling. In addition, NOTCH1 was significantly associated with diastolic blood pres- sure and TP53 with HDL (Table 4). NOTCH1 (chromo- some 9q34.3) is involved in a variety of developmental processes by controlling cell fate. In mice, NOTCH1 signaling is also required for vascular development [51]. TP53 (tumor protein P53, located on chromosome 17p13.1), is a well known tumor suppressor that regulates cell cycle and DNA repair. An inverse correl- ation of HDL cholesterol with cancer risk [52] might be explained by the association of TP53 with HDL cholesterol. Analyses of multiple variants across genes Genes in bold have a previously published relationship to longevity [9, 29–34] chr Position (hg19) rsID gene Function Ref Variant Minor Allele Count MAF N Beta SE P-value 7 17385235 AHR UTR3 A G 5 0.0006 810 3.58 0.71 6.18E-07 11 27680107 rs8192466 BDNF nsyn-exonic A G 8 0.0009 810 5.02 1.01 7.41E-07 16 57015065 CETP intronic T C 3 0.0004 809 5.00 1.01 8.69E-07 1 207813049 CR1 UTR3 A G 5 0.0006 810 5.02 1.01 7.41E-07 8 6735377 DEFB1 nsyn-exonic T C 1 0.0001 809 5.03 1.01 7.22E-07 10 71139772 HK1 nsyn-exonic T C 1 0.0001 794 5.04 1.01 6.53E-07 1 209959231 IRF6 UTR3 G A 4 0.0005 810 3.58 0.71 6.18E-07 21 35195906 ITSN1 syn-exonic A C 1 0.0001 810 5.02 1.01 7.41E-07 15 100256347 MEF2A UTR3 C T 2 0.0002 810 5.02 1.01 7.41E-07 1 12073445 MFN2 UTR3 T C 3 0.0003 810 5.07 1.01 6.10E-07 4 100544175 MTTP UTR3 G A 1 0.0001 810 5.07 1.01 6.10E-07 2 1794502 MYT1L UTR3 T C 1 0.0001 810 5.02 1.01 7.41E-07 16 50267300 PAPD5 UTR3 T C 4 0.0005 810 3.58 0.71 6.18E-07 2 223158616 PAX3 UTR3 T C 3 0.0003 810 3.58 0.71 6.18E-07 7 95214257 PDK4 UTR3 G A 2 0.0002 810 5.07 1.01 6.10E-07 5 149206403 rs374853976 PPARGC1B syn-exonic A G 1 0.0001 714 5.07 1.00 4.72E-07 10 99130549 RRP12 nsyn-exonic T C 1 0.0001 780 5.02 1.01 7.66E-07 17 28525015 rs199875985 SLC6A4 UTR3 G A 1 0.0001 810 5.07 1.01 6.10E-07 15 67479818 rs144245324 SMAD3 syn-exonic T C 3 0.0004 767 5.02 1.02 9.22E-07 3 24163883 THRB UTR3 T C 7 0.0008 810 3.58 0.71 6.18E-07 14 81610971 TSHR UTR3 A G 2 0.0002 810 5.07 1.01 6.10E-07 21 46189291 UBE2G2 UTR3 T C 3 0.0004 810 5.02 1.01 7.41E-07 19 9770038 ZNF562 intronic T G 2 0.0002 810 3.58 0.71 6.18E-07 Table 3 Significant results of single variant testing for variants with less than 10 copies. Twenty-three rare variants with less than 10 minor allele copies were identified for a single phenotype (longevity). These variants clustered in two families with high trait exceptionality scores for longevity Genes in bold have a previously published relationship to longevity [9 29–34] Table 3 Significant results of single variant testing for variants with less than 10 copies. Twenty-three rare variants with less than 10 minor allele copies were identified for a single phenotype (longevity). Discussion regulate human aging via negative regulation of glucose homeostasis and Wnt signaling. In addition, NOTCH1 was significantly associated with diastolic blood pres- sure and TP53 with HDL (Table 4). NOTCH1 (chromo- some 9q34.3) is involved in a variety of developmental processes by controlling cell fate. In mice, NOTCH1 signaling is also required for vascular development [51]. TP53 (tumor protein P53, located on chromosome 17p13.1), is a well known tumor suppressor that regulates cell cycle and DNA repair. An inverse correl- ation of HDL cholesterol with cancer risk [52] might be explained by the association of TP53 with HDL cholesterol. The mechanisms driving healthy human aging are still mostly unclear. There is much debate on the evolution- ary versus adaptive mechanisms of aging, such as pro- grammed longevity, hormonal regulation of aging by insulin/IGF-1 signaling, programmed decline of the im- mune system, wear and tear theory, rate of oxygen basal metabolism, cross-linking theory and free radicals the- ory. These mechanisms are not inherently mutually exclusive and it is likely that aging is dictated by combina- tions of multiple mechanisms. Regardless, Kirkwood and Melev stated in a recent review that “it is obvious…that duration of life is dependent upon genotype” [54]. These results are likely an underestimate of significant or suggestive variants. Unfortunately, non-uniform hybridization to target loci due to local sequence context and the need for stringent filtering to reduce false posi- tives resulted in gaps within the covered coding se- quence of most genes, which could affect results due to false negatives. This is why the well-known longevity gene, ApoE [53], was not included in our analyses. To take advantage of the unique family structure of the LLFS cohort, we have performed candidate gene resequencing to identify familial sequence variation that could explain multiple exceptional phenotypes contrib- uting to long lifespan and healthy aging. Our results are limited by gaps in sequencing coverage of some genes due to non-uniform hybridization of baits across the en- tire cohort, which may mean an underestimate in the Page 9 of 12 Druley et al. BMC Geriatrics (2016) 16:80 Fig. 3 Twenty-four rare variants within twenty-four genes clustered in two long-lived LLFS families (a) pedID 25609942 and (b) pedID 38652533. Individual 2418 and 4441 lived to 110 and 101 years of age, respectively. The longevity-associated genes harboring rare variants within these individuals (and their offspring) are listed below their symbol Fig. Discussion 3 Twenty-four rare variants within twenty-four genes clustered in two long-lived LLFS families (a) pedID 25609942 and (b) pedID 38652533. Individual 2418 and 4441 lived to 110 and 101 years of age, respectively. The longevity-associated genes harboring rare variants within these individuals (and their offspring) are listed below their symbol experiment identified a familial variant in VEGFC that explained 23.8 % of phenotypic variance within a pedi- gree, but the same variant only described 0.1 % of the phenotypic variance in unrelated individuals [55]. The same strategy was employed in the Insulin Resistance number of familial variants in these genes. This strategy was previously used to identify rare familial variants in VEGFC (Vascular Endothelial Growth Factor C) by using linkage information in families with high LOD scores to inform targeted resequencing for rare variants. This Table 4 Collapsed rare variant analysis of candidate genes associated with HAI. These genes were found to have a p-value <1.0x10−3 by at least one burden-testing algorithm Phenotype Gene RefSeq Total Exons Analyzed Exons Indiv Seq (#) Variants called (#) Ped (#) P-value (PWST) P-value (Skat) Healthy Aging Index (Mortality Weighted) GSK3B NM_002093 12 8 3217 77 121 1.00E-4 2.08E-4 Diastolic Blood Pressure NOTCH1 NM_017617 34 3 4112 55 78 1.00E-4 5.37E-3 HDL Cholesterol TP53 NM_000546 11 6 4073 21 86 1.00E-4 8.05E-3 Druley et al. BMC Geriatrics (2016) 16:80 Page 10 of 12 Page 10 of 12 Druley et al. BMC Geriatrics (2016) 16:80 Druley et al. BMC Geriatrics (2016) 16:80 Atherosclerosis Family Study to identify a rare variant within the ADIPOQ (Adiponectin, C1Q And Collagen Domain Containing) gene describing 63 % of the vari- ance of plasma adiponectin levels, which are critical for glucose homeostasis [56]. Our results validate multiple SNPs and genes (OBFC1, CTEP, ZNF562) found associ- ated with longevity and healthy survival. Using a sequencing-based approach to identify rare variants within pedigrees associated with exceptional pheno- types. Of note, we identified one rare, novel variant in OBFC1 as well as two intronic variants from LLFS array data associated with survival. OBFC1 is involved in telomere maintenance; its role in promoting exception- ally healthy aging is intriguing given that this gene re- sides squarely within a family-based association peak for telomere length recently reported from the same LLFS families [16]. Availability of data GWA and sequencing information for the LLFS partici- pants is available in dbGaP using accession number phs000397.v1.p1. Discussion The idea that many longevity- associated variants can presumably work in synergy with an additive beneficial effect is supported by the observations from three LLFS families. One exception- ally long-lived LLFS family carries all three OBFC1 variants, while 23 additional beneficial rare variants are clustered in two other exceptionally long-lived LLFS families. Additional file Another healthy aging candidate gene, CETP, is a well- known regulator of HDL and has been associated with healthy aging in Ashkenazi Jewish [59, 60] as well as Alzheimer’s disease [61]. The negative association of sev- eral variants with HDL, LDL and triglycerides in our study indicates that harmful genetic variants still exist in the long-lived subjects. This paradoxical phenomenon might be due to antagonistic effects on the development of other age-related disorders, gene-age, gene-gene, or gene-environment interactions [62]. To understand these intersections, further investigation of age and en- vironment specific effects of these lipid regulatory genes on multiple aging phenotypes is needed. Additional file 1: Supplementary Materials. (PDF 1024 kb) Abbreviations LLFS: Long Life Family Study; HDL: high density lipoprotein; LDL: low density lipoprotein; BMI: body mass index; TIA: transient ischemic attack; MMSE: mini mental state examination; UTR: untranslated region; FLoSS: family longevity selection score; HAI: healthy aging index; GWAS: genome wide association study; PCs: principal components; MAF: minor allele frequency; HgbA1C: glycated hemoglobin; UWSS: un-weighted sum statistic; WSS: weighted sum statistic; PWST: P-value weighted sum test; famSKAT: family-based serial kernel association test. Ethics approval and consent to participate pp p p Each participant provided written, informed consent prior to inclusion in this study. This study is in compli- ance with the Helsinki Declaration and the results re- ported herein have been approved by the National Institute of Aging, the Human Research Protection Of- fice of the coordinating center at Washington University under IRB#201106316, the University of Pittsburgh In- stitutional Review Board, the Boston University Office of the Institutional Review Board, the Columbia University Institutional Review Board and the Regional Scientific Ethical Committees for Southern Denmark. Because effect sizes from single rare variants are typ- ically small, collapsing rare variants across larger loci (e.g. genes or pathways) can aggregate variants and highlight the importance of a larger genetic locus [25]. By analyzing our sequencing results in this fashion, we identified a more diverse set of genes associated (or suggestive of association) with additional healthy aging phenotypes. GSK3B, which is a kinase for over forty different proteins and plays key roles in numerous intracellular signaling pathways (cellular proliferation, migration, inflammation and immune response, glu- cose regulation, and apoptosis) [57] was identified in this analysis and may play an important role in healthy aging. This gene has been associated with a number of age-related diseases such as type II diabetes, Alzheimer’s disease, inflammatory disorders, cancer and bipolar dis- order [58]. Consent for publication Not applicable. Conclusions Under the Rare Variant/Complex Phenotype hypothesis, multiple rare variants have an aggregate effect on com- plex phenotypes or diseases, but identifying the genes and the relative contributions of the various sequence changes is difficult. By leveraging the pedigree structure and cohort size of the LLFS study, we demonstrate the utility of sequencing within pedigrees to identify inher- ited genetic variation influencing specific parameters of healthy aging. These data are limited by representing primarily genes that were already known to be associ- ated with the various phenotypes being investigated. A larger survey of the genome in the LLFS cohort, espe- cially the linkage peaks for multiple healthy aging phe- notypes, will facilitate discovery of new genes and putative mechanisms for the genetic regulation of the complexities of aging. Competing interests Th h d l h The authors declare that they have no competing interests. The authors declare that they have no competing interests. Page 11 of 12 Page 11 of 12 Druley et al. BMC Geriatrics (2016) 16:80 9. Sebastiani P, Solovieff N, Dewan AT, Walsh KM, Puca A, Hartley SW, Melista E, Andersen S, Dworkis DA, Wilk JB, et al. Genetic signatures of exceptional longevity in humans. PLoS One. 2012;7:e29848. Funding Th k 11. Newman AB, Glynn NW, Taylor CA, Sebastiani P, Perls TT, Mayeux R, Christensen K, Zmuda JM, Barral S, Lee JH, et al. Health and function of participants in the Long Life Family Study: A comparison with other cohorts. Aging (Albany NY). 2011;3:63–76. This work was supported by the National Institutes of Health, National Institute of Aging [U01 AG023746 (The Long Life Family Study)]. We would like to thank W. Rossi and E. Hadley for helpful discussions. We thank the Genome Technology Access Center in the Department of Genetics at Washington University School of Medicine for next-generation sequencing. The Center is partially supported by NCI Cancer Center Support Grant P30 CA91842 to the Siteman Cancer Center and by ICTS/CTSA Grant UL1RR024992 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH), and NIH Roadmap for Medical Research. This publication is solely the responsibility of the authors and does not necessarily represent the official view of NCRR or NIH. 12. Barral S, Cosentino S, Costa R, Andersen SL, Christensen K, Eckfeldt JH, Newman AB, Perls TT, Province MA, Hadley EC, et al. Exceptional memory performance in the Long Life Family Study. Neurobiol Aging. 2013;34:2445–8. 13. Sanders JL, Minster RL, Barmada MM, Matteini AM, Boudreau RM, Christensen K, Mayeux R, Borecki IB, Zhang Q, Perls T, et al. Heritability of and mortality prediction with a longevity phenotype: the healthy aging index. J Gerontol A Biol Sci Med Sci. 2014;69:479–85. 14. Sebastiani P, Hadley EC, Province M, Christensen K, Rossi W, Perls TT, Ash AS. A family longevity selection score: ranking sibships by their longevity, size, and availability for study. Am J Epidemiol. 2009;170:1555–62. Authors’ contributions All authors have read and approved the final manuscript. TED, BT, ABN, KC, RM and MAP designed the experimental plan. SEC, BTL prepared the All authors have read and approved the final manuscript. TED, BT, ABN, KC, RM and MAP designed the experimental plan. SEC, BTL prepared the All authors have read and approved the final manuscript. TED, BT, ABN, KC, RM and MAP designed the experimental plan. SEC, BTL prepared the sequencing libraries. TED, EIR, LW, SJL, JHL, QZ, EWD, HJA, MAP analyzed and interpreted data. TED, SJL, MAP drafted and revised the manuscript. All authors have read and approved the final manuscript. TED, BT, ABN, KC, RM and MAP designed the experimental plan. SEC, BTL prepared the sequencing libraries. TED, EIR, LW, SJL, JHL, QZ, EWD, HJA, MAP analyzed and interpreted data. TED, SJL, MAP drafted and revised the manuscript. 10. Sebastiani P, Sun FX, Andersen SL, Lee JH, Wojczynski MK, Sanders JL, Yashin A, Newman AB, Perls TT. Families Enriched for Exceptional Longevity also have Increased Health-Span: Findings from the Long Life Family Study. Front Public Health. 2013;1:38. sequencing libraries. TED, EIR, LW, SJL, JHL, QZ, EWD, HJA, MAP analyzed and interpreted data. TED, SJL, MAP drafted and revised the manuscript. sequencing libraries. TED, EIR, LW, SJL, JHL, QZ, EWD, HJA, MAP analyzed and interpreted data. TED, SJL, MAP drafted and revised the manuscript. Received: 7 May 2015 Accepted: 4 April 2016 20. Ramos E, Levinson BT, Chasnoff S, Hughes A, Young AL, Thornton K, Li A, Vallania FL, Province M, Druley TE. Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing. BMC Genomics. 2012;13:683. Author details 1 1Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8116, St. Louis, MO 63108, USA. 2Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8116, St. Louis, MO 63108, USA. 3Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA. 4Sergievsky Center, College of Physicians and Surgeons, Columbia University New York, New York, NY, USA. 5Taub Institute, College of Physicians and Surgeons, Columbia University New York, New York, NY, USA. 6Department of Epidemiology, School of Public Health, Columbia University New York, New York, NY, USA. 7Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA. 8Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA. 9The Danish Aging Research Center, Epidemiology, University of Southern Denmark, Odense, Denmark. 10Gertrude H. Sergievsky Center and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York City, NY, USA. 15. An P, Miljkovic I, Thyagarajan B, Kraja AT, Daw EW, Pankow JS, Selvin E, Kao WH, Maruthur NM, Nalls MA, et al. Genome-wide association study identifies common loci influencing circulating glycated hemoglobin (HbA) levels in non-diabetic subjects: The Long Life Family Study (LLFS). Metabolism. 2013;63:461–8. 16. Lee JH, Cheng R, Honig LS, Feitosa M, Kammerer CM, Kang MS, Schupf N, Lin SJ, Sanders JL, Bae H, et al. Genome wide association and linkage analyses identified three loci-4q25, 17q23.2, and 10q11.21-associated with variation in leukocyte telomere length: the Long Life Family Study. Front Genet. 2013;4:310. 17. Wu J, Province MA, Coon H, Hunt SC, Eckfeldt JH, Arnett DK, Heiss G, Lewis CE, Ellison RC, Rao DC, et al. An investigation of the effects of lipid-lowering medications: genome-wide linkage analysis of lipids in the HyperGEN study. BMC Genet. 2007;8:60. 18. Wu J, Kraja AT, Oberman A, Lewis CE, Ellison RC, Arnett DK, Heiss G, Lalouel JM, Turner ST, Hunt SC, Province MA, Rao DC. A summary of the effects of antihypertensive medications on measured blood pressure. Am J Hypertens. 2005;18:935–42. Denmark, Odense, Denmark. 10Gertrude H. Sergievsky Center and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York City, NY, USA. 19. Folstein MF, Folstein SE, McHugh PR. "Mini-mental state". A practical method for grading the cognitive state of patients for the clinician. J Psychiatr Res. 1975;12:189–98. Author details 1 Received: 7 May 2015 Accepted: 4 April 2016 References 1. Herskind AM, McGue M, Holm NV, Sorensen TI, Harvald B, Vaupel JW. The heritability of human longevity: a population-based study of 2872 Danish twin pairs born 1870-1900. Hum Genet. 1996;97:319–23. 1. Herskind AM, McGue M, Holm NV, Sorensen TI, Harvald B, Vaupel JW. The heritability of human longevity: a population-based study of 2872 Danish twin pairs born 1870-1900. Hum Genet. 1996;97:319–23. 1. Herskind AM, McGue M, Holm NV, Sorensen TI, Harvald B, Vaupel JW. The heritability of human longevity: a population-based study of 2872 Danish twin pairs born 1870-1900. Hum Genet. 1996;97:319–23. 21. Pinheiro JC, Bates DB. Mixed-effects models in S and S-Plus. New York, NY: Springer; 2000. 2. Schachter F, Faure-Delanef L, Guenot F, Rouger H, Froguel P, Lesueur-Ginot L, Cohen D. Genetic associations with human longevity at the APOE and ACE loci. Nat Genet. 1994;6:29–32. 2. Schachter F, Faure-Delanef L, Guenot F, Rouger H, Froguel P, Lesueur-Ginot L, Cohen D. Genetic associations with human longevity at the APOE and ACE loci. Nat Genet. 1994;6:29–32. 22. Abrahantes JC, Burzykowski T. A version of the EM algorithm for proportional hazard model with random effects. Biom J. 2005;47:847–62. 23. Li B, Leal SM. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet. 2008;83:311–21. 3. van Bockxmeer FM. ApoE and ACE genes: impact on human longevity. Nat Genet. 1994;6:4–5. 3. van Bockxmeer FM. ApoE and ACE genes: impact on human longevity. Nat Genet. 1994;6:4–5. 4. Christensen K, Johnson TE, Vaupel JW. The quest for genetic determinants of human longevity: challenges and insights. Nat Rev Genet. 2006;7:436–48. 4. Christensen K, Johnson TE, Vaupel JW. The quest for genetic determinants of human longevity: challenges and insights. Nat Rev Genet. 2006;7:436–48. 24. Madsen BE, Browning SR. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet. 2009;5:e1000384. 5. Deelen J, Beekman M, Uh HW, Helmer Q, Kuningas M, Christiansen L, Kremer D, 500 van der Breggen R, Suchiman HE, Lakenberg N, et al. Genome-wide association study identifies a single major locus contributing to survival into old age; the APOE locus revisited. Aging Cell. 2011;10:686–98. 5. Deelen J, Beekman M, Uh HW, Helmer Q, Kuningas M, Christiansen L, Kremer D, 500 van der Breggen R, Suchiman HE, Lakenberg N, et al. Genome-wide association study identifies a single major locus contributing to survival into old age; the APOE locus revisited. 8. Pawlikowska L, Hu D, Huntsman S, Sung A, Chu C, Chen J, Joyner AH, Schork NJ, Hsueh WC, Reiner AP, et al. Association of common genetic variation in the insulin/IGF1 signaling pathway with human longevity. Aging Cell. 2009;8:460–72. References The type 1 insulin-like growth factor receptor signalling system and targeted tyrosine kinase inhibition in cancer. J Int Med Res. 2013;41:253–64. 61. Chen JJ, Li YM, Zou WY, Fu JL. Relationships between CETP genetic polymorphisms and Alzheimer's disease risk: a meta-analysis. DNA Cell Biol. 2014;33:807–15. 41. Rader DJ, deGoma EM. Future of cholesteryl ester transfer protein inhibitors. Annu Rev Med. 2014;65:385–403. 62. Ukraintseva S, Yashin A, Arbeev K, Kulminski A, Akushevich I, Wu D, Joshi G, Land, KC, Stallard,E (2015) Puzzling role of genetic risk factors in human longevity:”risk alleles” as pro-longevity variants. Biogerontology. [Epub ahead of print] 42. Reilly D, Hao K, Jensen MK, Girman CJ, Rimm EB. Use of systems biology approaches to analysis of genome-wide association studies of myocardial infarction and blood cholesterol in the nurses' health study and health professionals' follow-up study. PLoS One. 2013;8:e85369. 43. Ridker PM, Pare G, Parker AN, Zee RY, Miletich JP, Chasman DI. Polymorphism in the CETP gene region, HDL cholesterol, and risk of future myocardial infarction: Genomewide analysis among 18 245 initially healthy women from the Women's Genome Health Study. Circ Cardiovasc Genet. 2009;2:26–33. 44. van Dijk KW, Rensen PC, Voshol PJ, Havekes LM. The role and mode of action of apolipoproteins CIII and AV: synergistic actors in triglyceride metabolism? Curr Opin Lipidol. 2004;15:239–46. 45. Smith CE, Tucker KL, Scott TM, Van Rompay M, Mattei J, Lai CQ, Parnell LD, Junyent M, Lee YC, Garcia-Bailo B, et al. Apolipoprotein C3 polymorphisms, cognitive function and diabetes in Caribbean origin Hispanics. PLoS One. 2009;4:e5465. 46. Ronald J, Rajagopalan R, Ranchalis JE, Marshall JK, Hatsukami TS, Heagerty PJ, Jarvik GP. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. Lipids Health Dis. 2009;8:52. Submit your next manuscript to BioMed Central and we will help you at every step: • We accept pre-submission inquiries • Our selector tool helps you to find the most relevant journal • We provide round the clock customer support • Convenient online submission • Thorough peer review • Inclusion in PubMed and all major indexing services • Maximum visibility for your research Submit your manuscript at www.biomedcentral.com/submit and we will help you at every step: • We accept pre-submission inquiries 47. Talmud PJ, Drenos F, Shah S, Shah T, Palmen J, Verzilli C, Gaunt TR, Pallas J, Lovering R, Li K, et al. References On the programmed/non-programmed nature of ageing within the life history. Curr Biol. 2011;21:R701–7. ageing within the life history. Curr Biol. 2011;21:R701–7. 55. Shi G, Simino J, Rao DC. Enriching rare variants using family-specific linkage information. BMC Proc. 2011;Suppl 9:S82. 37. Broer L, Buchman AS, Deelen J, Evans DS, Faul JD, Lunetta KL, Sebastiani P, Smith JA, Smith AV, Tanaka T, Yu L, Arnold AM, Aspelund T, Benjamin EJ, De Jager PL, Eirkisdottir G, Evans DA, Garcia ME, Hofman A, Kaplan RC, Kardia SL, Kiel DP, Oostra BA, Orwoll ES, Parimi N, Psaty BM, Rivadeneira F, Rotter JI, Seshadri S, Singleton A, Tiemeier H, Uitterlinden AG, Zhao W, Bandinelli S, Bennett DA, Ferrucci L, Gudnason V, Harris TB, Karasik D, Launer LJ, Perls TT, Slagboom PE, Tranah GJ, Weir DR, Newman AB, van Duijn CM, Murabito JM. GWAS of Longevity in CHARGE Consortium Confirms APOE and FOXO3 Candidacy. J Gerontol A Biol Sci Med Sci. 2015;70:110–8. 56. Bowden DW, An SS, Palmer ND, Brown WM, Norris JM, Haffner SM, Hawkins GA, Guo X, Rotter JI, Chen YD, et al. Molecular basis of a linkage peak: exome sequencing and family-based analysis identify a rare genetic variant in the ADIPOQ gene in the IRAS Family Study. Hum Mol Genet. 2010;19:4112–20. 57. Jope RS, Johnson GV. The glamour and gloom of glycogen synthase kinase-3. Trends Biochem Sci. 2004;29:95–102. 58. Schaffer BA, Bertram L, Miller BL, Mullin K, Weintraub S, Johnson N, Bigio EH, Mesulam M, Wiedau-Pazos M, Jackson GR, et al. Association of GSK3B with Alzheimer disease and frontotemporal dementia. Arch Neurol. 2008;65:1368–74. 38. Soerensen M, Dato S, Christensen K, McGue M, Stevnsner T, Bohr VA, Christiansen L. Replication of an association of variation in the FOXO3A gene with human longevity using both case-control and longitudinal data. Aging Cell. 2010;9:1010–7. 59. Atzmon G, Rincon M, Rabizadeh P, Barzilai N. Biological evidence for inheritance of exceptional longevity. Mech Ageing Dev. 2005;26:341–5. 39. Zeng Y, Cheng L, Chen H, Cao H, Hauser ER, Liu Y, Xiao Z, Tan Q, Tian XL, Vaupel JW. Effects of FOXO genotypes on longevity: a biodemographic analysis. J Gerontol A Biol Sci Med Sci. 2010;65:1285–99. 60. Barzilai N, Atzmon G, Schechter C, Schaefer EJ, Cupples AL, Lipton R, Cheng S, Shuldiner AR. Unique lipoprotein phenotype and genotype associated with exceptional longevity. JAMA. 2003;290:2030–40. 40. Haisa M. References Aging Cell. 2011;10:686–98. 25. Zhang Q, Irvin MR, Arnett DK, Province MA, Borecki I. A data-driven method for identifying rare variants with heterogeneous trait effects. Genet Epidemiol. 2011;35:679–85. 26. Chen H, Meigs JB, Dupuis J. Sequence kernel association test for quantitative traits in family samples. Genet Epidemiol. 2013;37:196–204. 6. Bonafe M, Barbieri M, Marchegiani F, Olivieri F, Ragno E, Giampieri C, Mugianesi E, Centurelli M, Franceschi C, Paolisso G. Polymorphic variants of insulin-like growth factor I (IGF-I) receptor and phosphoinositide 3-kinase genes affect IGF-I plasma levels and human longevity: cues for an evolutionarily conserved mechanism of life span control. J Clin Endocrinol Metab. 2003;88:3299–304. 6. Bonafe M, Barbieri M, Marchegiani F, Olivieri F, Ragno E, Giampieri C, Mugianesi E, Centurelli M, Franceschi C, Paolisso G. Polymorphic variants of insulin-like growth factor I (IGF-I) receptor and phosphoinositide 3-kinase genes affect IGF-I plasma levels and human longevity: cues for an evolutionarily conserved mechanism of life span control. J Clin Endocrinol Metab. 2003;88:3299–304. 27. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38: e164. 28. Lee S, Abecasis GR, Boehnke M, Lin X. Rare-variant association analysis:study designs and statistical tests. Am J Hum Genet. 2014;95:5–23. 29. Dato S, Crocco P, D’Aquila P, de Rango F, Bellizzi D, Rose G, Passarino G. et al. Exploring the role of genetic variability and lifestyle in oxidative stress response for healthy aging and longevity. Int J Mol Sci. 2013;14: 16443–72. 7. Willcox BJ, Donlon TA, He Q, Chen R, Grove JS, Yano K, Masaki KH, Willcox DC, Rodriguez B, Curb JD. FOXO3A genotype is strongly associated with human longevity. Proc Natl Acad Sci USA. 2008;105:13987–92. 7. Willcox BJ, Donlon TA, He Q, Chen R, Grove JS, Yano K, Masaki KH, Willcox DC, Rodriguez B, Curb JD. FOXO3A genotype is strongly associated with human longevity. Proc Natl Acad Sci USA. 2008;105:13987–92. 8. Pawlikowska L, Hu D, Huntsman S, Sung A, Chu C, Chen J, Joyner AH, Schork NJ, Hsueh WC, Reiner AP, et al. Association of common genetic variation in the insulin/IGF1 signaling pathway with human longevity. Aging Cell. 2009;8:460–72. 30. Atzmon G, Rincon M, Schechter CB, Shuldiner AR, Lipton RB, Bergman A, Barzilai N. Lipoprotein genotype and conserved pathway for exceptional longevity in humans. PLoS Biol. 2006;4(4):e113. Page 12 of 12 Page 12 of 12 Page 12 of 12 Druley et al. References BMC Geriatrics (2016) 16:80 31. Trahan G. Mitochondrial-nuclear epistasis: implications for human aging and longevity. Ageing Res Rev. 2011;10:238–52. kinase-3 beta and tau genes interact in Alzheimer’s disease. Ann Neurol. 2008;64:446–54. kinase-3 beta and tau genes interact in Alzheimer’s disease. Ann Neurol. 2008;64:446–54. 50. 50. Forlenza OV, Torres CA, Talib LL, de Paula VJ, Joaquim HP, Diniz BS, Gattaz WF. Increased platelet GSK3B activity in patients with mild cognitive impairment and Alzheimer's disease. J Psychiatr Res. 2011;45:220–4. 32. Geesaman BJ, Benson E, Brewster SJ, Kunkel LM, Blanche H, Thomas G, et al. Haplotype-based identification of a microsomal transfer protein marker associated with the human lifespan. Proc Natl Acad Sci USA. 2003;100:14115–20. 32. Geesaman BJ, Benson E, Brewster SJ, Kunkel LM, Blanche H, Thomas G, et al. Haplotype-based identification of a microsomal transfer protein marker p yp p associated with the human lifespan. Proc Natl Acad Sci USA. 2003;100:14115–20. 51. Dill MT, Rothweiler S, Djonov V, Hlushchuk R, Tornillo L, Terracciano L, Meili- Butz S, Radtke F, Heim MH, Semela D. Disruption of Notch1 induces vascular remodeling, intussusceptive angiogenesis, and angiosarcomas in livers of mice. Gastroenterology. 2012;142:967–77. 33. Gondo Y, Hirose N, Arai Y, Yamamura K, Shimizu K, Takayama M, Ebihara Y, Nakazawa S, Inagaki H, Masui Y, et al. Contribution of an affect-associated gene to human longevity: prevalence of the long-allele genotype of the serotonin transporter-linked gene in Japanese centenarians. Mech Ageing Dev. 2005;126:1178–84. 52. Zhao W, Guan J, Horswell R, Li W, Wang Y, Wu X, Hu G. HDL Cholesterol and Cancer Risk Among Patients With Type 2 Diabetes. Diabetes Care. 2014;37:3196–203. 34. Atzmon G, Barzilai N, Surks MI, Gabriely I. Genetic predisposition to elevated serum thyrotropin is associated with exceptional longevity. J Clin Endocrinol Metab. 2009;94:4768–75. 53. Kulminski AM, Arbeev KG, Culminskaya I, Arbeeva L, Ukraintseva SV, Stallard E, Christensen K, Schupf N, Province MA, Yashin AI. Age, gender, and cancer but not neurodegenerative and cardiovascular diseases strongly modulate systemic effect of the Apolipoprotein E4 allele on lifespan. PLoS Genet. 2014;10:e1004141. 35. Budovsky A, Craig T, Wang J, Tacutu R, Csordas A, Lourenco J, Fraifeld VE, de Magalhaes JP. LongevityMap: a database of human genetic variants associated with longevity. Trends Genet. 2013;29:559–60. 36. Li Y, Wang WJ, Cao H, Lu J, Wu C, et al. Genetic association of FOXO1A and FOXO3A with longevity trait in Han Chinese populations. Hum Mol Genet. 2009;18:4897–904. 54. Kirkwood TB, Melev S. References Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. Am J Hum Genet. 2009;85:628–42. 48. Maruszak A, Peplonska B, Safranow K, Chodakowska-Zebrowska M, Barcikowska M, Zekanowski C. TOMM40 rs10524523 polymorphism's role in late-onset Alzheimer's disease and in longevity. J Alzheimers Dis. 2012;28:309–22. 49. Kwok JB, Loy CT, Hamilton G, Lau E, Hallupp M, Williams J, Owen MJ, Broe GA, Tang N, Lam L, Powell JF, Lovestone S, Schofield PR. Glycogen synthase 49. Kwok JB, Loy CT, Hamilton G, Lau E, Hallupp M, Williams J, Owen MJ, Broe GA, Tang N, Lam L, Powell JF, Lovestone S, Schofield PR. Glycogen synthase
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A New Method for Interoperability Between Lexical Resources Using MDA Approach
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A new method for interoperability between lexical resources using MDA approach Malek Lhioui, Kais Haddar, Laurent Romary Malek Lhioui, Kais Haddar, Laurent Romary To cite this version: Malek Lhioui, Kais Haddar, Laurent Romary. A new method for interoperability between lexical resources using MDA approach. AISI 2016 The 2nd International Conference on Advanced Intelligent Systems and Informatics, Oct 2016, Cairo, Egypt. ￿hal-01350524￿ To cite this version: Malek Lhioui, Kais Haddar, Laurent Romary. A new method for interoperability between lexical resources using MDA approach. AISI 2016 The 2nd International Conference on Advanced Intelligent Systems and Informatics, Oct 2016, Cairo, Egypt. ￿hal-01350524￿ Distributed under a Creative Commons Attribution 4.0 International License HAL Id: hal-01350524 https://inria.hal.science/hal-01350524v1 Submitted on 30 Jul 2016 L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci- entific research documents, whether they are pub- lished or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. Distributed under a Creative Commons Attribution 4.0 International License A new method for interoperability between lexical resources using MDA approach Abstract. Lexical resources are increasingly multiplatform due to the diverse needs of linguists. Merging, comparing, finding correspondences and deducing differences between these lexical resources remain difficult tasks. Thus, inte- roperability between these resources is hard even impossible to achieve. In this context, we establish a new method based on MDA approach to resolve interoperability between lexical resources. The proposed method consists of building common structure (OWL-DL ontology) for involved resources. This common structure has the ability to communicate involved resources. Hence, we may create a complex grid between involved resources allowing transfor- mation from one format to another. We experiment our new built method on an LMF lexicon. Keywords: lexical resources, interoperability, MDA approach, OWL ontology. Keywords: lexical resources, interoperability, MDA approach, OWL ontology. adfa, p. 1, 2011. © Springer-Verlag Berlin Heidelberg 2011 Introduction NLP Applications typically require interoperability because they generally need the same linguistic resources. Exchanging information between lexical resources, having different representation formalisms, is difficult. Thus, ancient resources may need to change over time. In addition to that, the transformation process from one format to another is not guaranteed all over the time. The built method allows constructing a pivot format for involved lexical resources with no prior restriction. A challenge that NLP communities confronts is the disappearing of several old representation formal- isms after long periods of development. This method will easily protect several re- sources from disappearing. So, several formalisms will continue to persist. Thus projects, which require merging several formalisms in the same application, will pre- fer to use our method. In fact, it allows using the number of formalisms one wants. We use MDA (Model Driven Architecture) transformation approach because of its great interest in areas handling heterogeneous knowledge. In fact, if even a current version of a used standard (LMF for example) is not yet stable or a new version is born, MDA approach ensures enrichment and not destruction of the current version. Building a new method for interoperability between lexical resources may face large problems. The first difficulty resides on how to choose an optimal strategy for interoperability between these resources: algebraic specifications, alignment ontology techniques, Meta modeling, etc. In addition to that, the choice of the ontology repre- sentation language (RDF(S), OWL-Lite and OWL-DL) is also a crucial dilemma. In addition to that, the construction of meta-models and models in MDA approach re- quires a big cognition of the involved lexical resources. Moreover, transformation rules have to be so definite. The paper presents a new method strictly founded to resolve interoperability be- tween lexical resources (LRs) using the well-known MDA Transformation approach. Indeed, we attempt to find compulsory techniques in order to establish a method for interoperability between lexical resources whatever their formats (LMF, TEI, HPSG…). The method consists on building a pivot format by making an automatic mapping process between involved lexical resources. The target building format plays the role of the pivot. In order to build this pivot format, we have to succeed to fulfill a set of steps. We construct OWL-DL ontology for lexical resources: construction of meta-model associated to lexical resource, construction of the ATL transformation and deduction of OWL-DL model. Introduction Thus, applying these steps, we build a new format for involving lexical resources. The originality of this method is that there are no previous works aiming to make interoperability between lexical resources operable. Moreover, the use of MDA ap- proach for resolving interoperability between lexical resources is in itself an innova- tion. Projects and NLP applications today must rely on interoperability; otherwise they are out of progress. In this context, an article named TAUS (TAU, 2011) dec- lares that: “The lack of interoperability costs the translation industry a fortune”. As a matter of fact, this fortune is compensated mostly in order to adjust data formats. In addition, our method is operable whatever the language. In the following sections, we introduce a brief state of the art in order to give a global idea about existing works related to our topic. Then, we explain precisely our proposed method for resolving the interoperability issue between lexical resources. We apply, in the next section, the new proposed method to LMF lexicon. Finally, we conclude with a small discussion for the obtained results. 1 http://www.omg.org/mda/specs.htm 2.1 Lexical resources Lexical resources vary in accordance with the need of linguistics and this requirement varies with the NLP community development progress. This process makes the re- sources more complex and heterogeneous. In the literature, existing lexical resources are innumerable. We can concentrate on some of them. In the 1980ies SGML markup language was created as the first formalism representation of linguistic data. Early in the following century, several markup languages have been invented by the Text En- coding Initiative (TEI) (Wörner et al., 2006). After years and exactly in 2003, a new standard named LMF was born due to efforts provided by the community of NLP (Francopolou, 2013). Speech is one of the several areas of NLP domain. This area includes several representation formalisms as well as the other areas. For example, EXMARaLDA is one of these formalisms. It represents spoken interaction with an annotation graph (Bird & Lieberman, 1999). Other formalisms in this context was born such as ELAN, TASX, Praat and ANVIL. They are efficient for multimodal annotation. In the same context, there are formalisms that include several heterogene- ous resource structures. The well known example for that is Tusnelda. It is inspired typically from the work of TEI (Wagner and Zeisler, 2004). There are other formal- isms which take care of various linguistic levels (phonology, morphology, syntax, semantic, etc.) (Ide and Romary, 2001). Thus, from an historical point of view, there is a large number of heterogeneous resources which inducing the question of trans- formation. This notion is the subject of the next subsection. State of the art The state of the art provides an important idea about existing works regardless of the language. There have been several works dealing with the use of MDA transfor- mation approach for the processing of several applications. However, there is no use of the MDA approach for the processing of interoperability between lexical resources. Yet, this approach ensures interoperability according to the OMG “Portability and interoperability are built into the architecture”1. Since there are many related topics, we classify the state of the art into three main parts: lexical resources, MDA Trans- formation and interoperability issue. The first part gives an idea about existing lexical resources regardless the language. We give examples of lexical resources in several languages such as Arabic. In the second part, we talk about MDA as a great method for transformation models. The last part deals with interoperability issue, and since there are no serious attempts to resolve this notion in NLP area, we will discuss the bidirectional mapping from one format to another. 2.3 Interoperability issue Interoperability is the substitution, merging and sharing knowledge between differ- ent entities whatever their kind. NLP community replaces these terms by only one term which is communication. Thus, interoperability allows communication between involved entities. Interoperability is a general notion that can be projected to many domains. In this paper, we interested to interoperability between lexical resources. Lexical resources are more and more multiplatform, multi-providers… and these cha- racteristics are increased by the time, so that, interoperability becomes hard even im- practical to achieve between lexical resources. These last suffer from several interope- rability issues. For example the definition of procedures to implement a set of services in NLP applications (machine translation, named entity recognition, part of speech tagging) shall be made through LMF by ISO, TEI by TEI Consortium and HPSG by linguistics… This leads to interoperability problems when experts have to collaborate. Thus, information technology professionals consider that interoperability is an impor- tant criterion as well as security and reliability in their applications. y y pp From an historical point of view, there are no significant efforts resolving interopera- bility between lexical resources. Yet, there are several challenges consisting on map- ping from one format to another. The first mapping attempt is done by (Wilcock, 2007) consisting on converting HPSG lexicons to an OWL ontology. In 2010, Loukil has expanded these processes by inventing a rule-based system opting to translate LMF syntactic lexicon into TDL within the LKB platform (Loukil et al., 2010). (Had- dar et al, 2012) have developed a prototype for projection HPSG syntactic lexica to- wards LMF. In the same context, there is a mapping process already done by (Lhioui et al., 2015) aiming to convert LMF lexicons to ontologies described on OWL-DL language. Bidirectional processes are usually limited to involved formats. Whatever we desire to involve more than two formalisms, processing became hard and impossi- ble to achieve even if we use several properties such as transitivity. For these reasons and in order to attenuate task complexity of mapping process, several organizations such as ISO give a quick solution but not efficient for interoperability using normali- zation. In fact, Lexical Markup Framework (LMF) is one of these solutions proposed by the ISO in 2003 (Francpolou, 2013). It involves several packages aiming to cover the maximum of the large domains: phonology, morphology, syntactic, semantic, pragmatic, etc. 2 Gold is accessible and free downloadable from (http://www.linguistics-ontology.org/) 2.2 MDA Transformation MDA Transformation is an approach proposed by OMG (Poole, 2001) in 2001. It is increasingly used in several applications and projects whatever their kind. It consists on using different models phases. It allows interoperability between applications by connecting their models (Accord, 2002). It supported evaluation and decreased ma- nually implementation of hundred of codes for a specific domain by separating con- ception from implementation (Miller and Mukerji, 2001). The implementation of MDA requires three main levels: MOF (Meta-Object Facility) defines the platform for implanting all models (OMG/MOF, 1997). PIM (Plateform Independant Model) which serves as a basis for the business part specification of an application, PSM (Plateform Specific Model) which participates in the specification model creation of the application after projection on a platform. The major advantage of this approach apart from time saving is preoccupations separation and the transformation process. This transformation allows mapping from PIMs to PSMs using modules described in specific languages such as ATL. ATL (Atlas Transformation Language) is a language providing rules allowing transformation from source to target models. Since this ap- proach allows interoperability between applications, it leads us to think about making evident interoperability between models. Thus, we introduce in the following subsec- tion interoperability notion in general. 2.3 Interoperability issue Other researchers have used another tool for resolving interoperability which is ontologies. A famous example of these works is the General Ontology for Linguistic Description (GOLD)2. GOLD is an OWL ontology having specific know- ledge related to linguistic domain. The GOLD ontology contains the basis linguistic knowledge of any theoretical framework. According to (Farrar and Lewis, 2005), GOLD defines linguistic knowledge as axioms, for example “a verb is a part of speech”, and uses at the same time language neutral, for example “parts of speech are subclasses of gold: GrammaticalUnit”. The classes are presented in the protégée edi- tor and then expressed as concepts in the GOLD ontology (Farrar and Langendoen, 2003). Thus, GOLD is an abstract model and representation formalisms such as HPSG are the instantiation of this abstract model. (Farrar and Lewis, 2005) consider these instantiations as sub-communities of practice noted Communities Of Practice Extension (COPEs). COPEs, sub-communities or sub-ontologies designed the same nomenclature and extend the overall GOLD ontology (Wilcock, 2007). The integra- tion of these COPEs in the GOLD ontology is a hard process and necessitates differ- ent mechanisms of ontology alignment. In the next subsection, we try to give an idea for techniques of ontologies alignment. All these notions will be strongly correlated to introduce our approach. In the follow- ing section, we define a new approach for interoperability between lexical resources using MDA Transformation. Proposed method The new build method is based on MDA Transformation approach. This approach is well-known and has proved its importance in guaranteeing reusability. This characte- ristic is crucial since it makes projects up to date. The proposed method is characte- rized by the ability to allow involved lexical resources to operate together. The new introduced method has as input a set of lexical resources. Lexical resources are com- posed of a set of lexicons such as LMF lexicon. It consists of three main steps. The first one is the achievement of the two independent models PIM (source and target) and the source PSM of each LR. The second is the achievement of the transformation module in ATL and finally, the generation of the specific model PSM (OWL-DL in our case). The output of the proposed method is a set of ontologies which can operate together using several algorithms or free tools of alignment. In fact, the use of ontolo- gies as an output is the keystone of our method. Ontology structures allow merging, comparing, finding correspondences, finding correspondences and deducing differ- ences between lexical resources due to the tools of ontology alignment. Fig. 1 de- scribes the whole process of the proposed method. Fig. 1. Steps of the proposed method LRs Achievement of the two independent models PIM (source and target) and source PSM Achievement of the transformation module in ATL Generation of the specific model PSM (OWL-DL) Retro-Engineering Refinement Refinement MDA Transformation OWL-DL ontologies Fig. 1. Steps of the proposed method The full schema of the proposed method will be explained carefully by examination of each step separately. In fact, MDA Transformation of the LRs to OWL ontologies is a crucial step in our method. The main idea of this step is to distinguish functional specifications from specifications of implementation related to a given platform in order to prepare structures able to operate together (in our case ontologies able to be aligned and then interacted). Thus, using MDA as an approach will make us able to elaborate independent specifications from the implementation in a specific platform using models. The first model to build is the PIM. The PIM is the model conceived to specify involved structures independently from any specific platform. This characte- ristic allows us abstracting functionalities of the involved lexical resource and to compare it to other resources. Proposed method If the lexical resource is updated, the associated PIM will never be destroyed, but, it will be refined as many times as possible; this makes one of the most advantages of the MDA approach when resolving interoperability issue. Fig. 2 summarized the MDA Transformation in general: Fig. 2. : MDA Transformation of the LRs to OWL ontologies MOF MMS ATL MMT MMS2MMT.atl MS MT Fig. 2. : MDA Transformation of the LRs to OWL ontologies Fig. 2 describes the ATL transformation in the MDA approach. MOF is the meta- meta model. MMS and MMT designate respectively the meta-model source and the meta-model target. MS and MT denote respectively model source and model target. MMS2MMT.atl includes the set of transformation rules. This method is composed of three sub-steps as we have mentioned below: Achievement of the two independent models PIM (source and target) of each LR, the achievement of the transformation module in ATL and the generation of the specific model PSM (OWL-DL in our case). Fig. 2 describes the ATL transformation in the MDA approach. MOF is the meta- meta model. MMS and MMT designate respectively the meta-model source and the meta-model target. MS and MT denote respectively model source and model target. MMS2MMT.atl includes the set of transformation rules. This method is composed of three sub-steps as we have mentioned below: Achievement of the two independent models PIM (source and target) of each LR, the achievement of the transformation module in ATL and the generation of the specific model PSM (OWL-DL in our case). 3.3 Generation of the specific model PSM (OWL-DL). After achievement of the PIM model (source and target) and elaborating rules allow- ing the passage from the source PIM to the target, we project the source PIM to a specific model PSM (Platform Specific Model). In order to generate the target PSM, we execute the ATL rules, then, we obtain automatically the target PSM. In fact, PSM is closest to the final code. It is related to a particular platform. 3.1 Achievement of the two independent models PIM (source and target) of each LR and source PSM The achievement of the first independent model PIM of the source is concluded from the lexical resource. PIM is a model independent to any plateformes or technologies and describes the heart of the method. It is represented in UML (Unified Modeling Language) with OCL (Object Constraint Language) constraints if exist. This model defines all functionalities of the given lexical resource described in an abstract man- ner. The PIM model ensures analysis and design of applications. At this step, the de- sign phase of the process involves the application of design pattern, partition into modules and sub-modules, etc. This PIM allows making available a structural and dynamic vision of the application without recourse to the technical design of the ap- plication. Therefore, a model (in our case the PIM) is essentially defined by a set of concepts and their relationships presented in a class diagram. 3.2 Achievement of the transformation module in ATL The achievement of the transformation module in ATL ensures transition from one model (source) to another (target). Modules transformations based on meta-models constitute the main step of the MDA. In fact, a transformation model corresponds to a function taking a set of input models and finding a set of output models. The models, in and out, respect their meta-models previously built. The transformation uses the model manipulation API. In order to carry out the transformation between the two involved models, we define a set of transformation rules which are expressed in ATL language allowing the passage from the source PIM to the target. There are three dif- ferent manners to model transformation in general: programming approach, template approach and modeling approach. The first one is based on object-oriented languages. It is to program a transformation model as well as a computer application. The second consists to define templates models and then replace them with their equivalent values in source models. The last one models transformation rules using MDA approach. Implantation: Transformation of LMF lexicon to OWL-DL ontology using MDA approach Then, we define the set of transformation rules: module LMF2OWL; create OUT : OWL from IN : LMF; -----------------------------Ontology----------------------------------- rule LexicalResource2Ontology{ from s:LMF!LexicalResource to t:OWL!Ontology(ontologyIRI <-),d:OWL!Prefix(name<-'rdf', IRI<-'http://www.w3.org/1999/02/22-rdf-syntax-ns#'), u:OWL!Prefix(name<-'rdfs', IRI<-'http://www.w3.org/2000/01/rdf-schema#'), h:OWL!Declaration(), g:OWL!Class(IRI <- '#LexicalResource',declaration <- h)} rule GlobalInformation2DeclarationClass{ from s:LMF!GlobalInformation module LMF2OWL; create OUT : OWL from IN : LMF; -----------------------------Ontology----------------------------------- rule LexicalResource2Ontology{ from s:LMF!LexicalResource to t:OWL!Ontology(ontologyIRI <-),d:OWL!Prefix(name<-'rdf', IRI<-'http://www.w3.org/1999/02/22-rdf-syntax-ns#'), u:OWL!Prefix(name<-'rdfs', IRI<-'http://www.w3.org/2000/01/rdf-schema#'), h:OWL!Declaration(), g:OWL!Class(IRI <- '#LexicalResource',declaration <- h)} rule GlobalInformation2DeclarationClass{ from s:LMF!GlobalInformation module LMF2OWL; create OUT : OWL from IN : LMF; -----------------------------Ontology----------------------------------- rule LexicalResource2Ontology{ from s:LMF!LexicalResource to t:OWL!Ontology(ontologyIRI <-),d:OWL!Prefix(name<-'rdf', IRI<-'http://www.w3.org/1999/02/22-rdf-syntax-ns#'), u:OWL!Prefix(name<-'rdfs', IRI<-'http://www.w3.org/2000/01/rdf-schema#'), h:OWL!Declaration(), g:OWL!Class(IRI <- '#LexicalResource',declaration <- h)} rule GlobalInformation2DeclarationClass{ from s:LMF!GlobalInformation to t:OWL!Declaration(), g:OWL!Class(IRI <- '#GlobalInformation', declaration <- t) g:OWL!Class(IRI < #GlobalInformation , declaration } rule Lexicon2DeclarationClass{ from o:LMF!Lexicon to p:OWL!Declaration(), i:OWL!Class(IRI <- '#Lexicon', declaration <- p) } rule LexicalEntry2DeclarationClass{ from k:LMF!LexicalEntry to n:OWL!Declaration(), j:OWL!Class(IRI <- '#LexicalEntry', declaration <- n) } } rule Lexicon2DeclarationClass{ from o:LMF!Lexicon to p:OWL!Declaration(), i:OWL!Class(IRI <- '#Lexicon', declaration <- p) } These transformation rules create an OWL PSM for the LMF lexicon of Fig. 2 which is an ontology described in OWL language. These rules are stored in an ATL file. Finally, fig. 4 represents this target PSM created automatically when executing the ATL file of the LMF Lexicon presented in Fig. 2: <?xml version 1.0 encoding ISO 8859 1 ?> <xmi:XMI xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns="owl"> <Ontology ontologyI- RI="http://www.semanticweb.org/asus/ontologies/2016/2/"/> <Prefix name="rdf" IRI="http://www.w3.org/1999/02/22- rdf-syntax-ns#"/> <Prefix name="rdfs" IRI="http://www.w3.org/2000/01/rdf-schema#"/> This output describes an ontology which is created automatically by a quick processing of the output of PSM. The processing consists of the removal of the “xmi” prefix since it is an automatic output of the ATL transformation. Implantation: Transformation of LMF lexicon to OWL-DL ontology using MDA approach In this section, we present the steps of the cited method applied to LMF lexicon: the two PIMs (source: LMF, target: OWL), the transformation rules and the two PSMs. Fig. 3 represents the source PIM of the core model of the following extract of LMF lexicon developed using Eclipse Galileo: lexicon developed using Eclipse Galileo: <?xml version="1.0" encoding="UTF-8"?> <LexicalResource dtdVersion="16"> <GlobalInformation> <feat att="languageCoding" val="ISO 639-3" /> <feat att="scriptcoding" val="ISO 15 924" /> </GlobalInformation> <Lexicon> <feat att="language" val="arabic" /> <LexicalEntry morphologiquePatterns="ل ر م دّي "> <feat att="partOfSpeech" val="verb" /> <feat att="root" val="ن_ق_ل " /> <feat att="scheme" val=" َ"ََل /> </LexicalEntry> </Lexicon> </LexicalResource> <Lexicon> <feat att="language" val="arabic" /> <LexicalEntry morphologiquePatterns="ل ر م دّي "> <feat att="partOfSpeech" val="verb" /> <feat att="root" val="ن_ق_ل " /> <feat att="scheme" val=" َ"ََل /> </LexicalEntry> </Lexicon> </LexicalResource> Fig. 3. The associated source PIM of the below extract of LMF lexicon Fig. 3. The associated source PIM of the below extract of LMF lexicon The build PIM can be refined as well as possible if the lexical resource (LMF lexicon) is updated. After building the source model, we have now obliged to build the target PIM of this lexical resource. Since we need to construct OWL-DL ontologies, we build a PIM for OWL-DL ontologies. Fig. 4 represents the target PIM for the previous lexical resource (LMF lexicon): Fig. 4. The associated target PIM of the below extract of LMF lexicon Fig. 4. The associated target PIM of the below extract of LMF lexicon Fig. 4 defines the independent model of OWL ontologies which is related to the given lexical resource. It represents the class “Ontology” which presents the root, the pre- fixes which are used to abbreviate and minimize scripture of the namespaces in the entire ontology. Conclusion In this paper, we have proposed a new method for interoperability between interope- rability using MDA approach. This new method allows merging, comparing, finding correspondences, finding correspondences and deducing differences between lexical resources. Then, we implement the method by projection on LMF. Our method is reusable and generic, and operable on all lexical resources whatever the language. Our method is generated automatically. In future works, we have to extend our me- thod using the alignment of the building ontologies. In fact, if we combine MDA Transformation and ontology alignment, interoperability appears to be quite suitable. Therefore, combining these two approach MDA Transformation and ontology align- ment for this study seems to have promising results. In this paper, we have proposed a new method for interoperability between interope- rability using MDA approach. This new method allows merging, comparing, finding correspondences, finding correspondences and deducing differences between lexical resources. Then, we implement the method by projection on LMF. Our method is reusable and generic, and operable on all lexical resources whatever the language. Our method is generated automatically. In future works, we have to extend our me- thod using the alignment of the building ontologies. In fact, if we combine MDA Transformation and ontology alignment, interoperability appears to be quite suitable. Therefore, combining these two approach MDA Transformation and ontology align- ment for this study seems to have promising results. Discussions The new built method has proved its interest in handling heterogeneous resources. The evaluation process has been successfully led by fixing three criterions: sustaina- bility of expertise, productivity gains and inclusion of execution platforms. The first criterion (sustainability of expertise) affects two characteristics. The first one super- vises lifetime of the built models (PIM and PSM). The models must have a lifetime greater than the code. This is guaranteed by the unrestricted refinement of models. The second characteristic provides modeling languages supporting different levels of abstraction. This point is guaranteed by the fact that UML and OCL support abstrac- tion. The second criterion concerns productivity gains. In fact, the automation opera- tions of models guarantee the productivity gain. Moreover, the built method facilitates the creation of operations of production on the models. The last criterion concerns the taking into account of the execution platforms. This stage is explicit in the life cycle of applications. MDA approach guarantees this characteristic as platforms are related to models. These aspects make the method very robust. The other important aspect in the built method is that the transformation process is done automatically. References 1. CNAM, EDF R&D, ENST, ENST-Bretagne, France Telecom R&D, INRIA, LIFL et Softeam, Pro- jet ACCORD (Assemblage de composants par contrats), Livrable 1.1-5, Date : Mai 2002. 2. Bird, S., and Liberman, M. 1999. Annotation graphs as a framework for multidimensional linguistic data analysis. Towards Standards and Tools for Discourse Tagging, Proceedings of the Workshop. Association for Computational Linguistics. 3. Scott Farrar and D. Terence Langendoen. 2003. A linguistic ontology for the semantic web. GLOT International, 7.3:97–100. 4. Scott Farrar and William D. Lewis. 2005. The GOLD Community of Practice: An infrastruc- ture for linguisHc data on the web. hIp://www.u.arizona.edu/˜farrar/. 5. Francopoulo, G., 2013, Lexical Markup Framework, US, Great Britain and the United States: ISTE Ltd and John Wiley & Sons, Inc. 6. Haddar, K., Fehri, H., Romary, L., 2012, A prototype for projecting HPSG syntactic lexica towards LMF, JLCL. 7. Ide, N., and Romary, L. 2001. Standards for Language Resources. Proceedings of the IRCS Workshop on Linguistic Database, 141-149. 8. Lhioui M, Haddar K, Romary L. 2015. A prototype for projecting LMF lexica towards OWL. 9. Loukil, N., Ktari, R., Haddar, K., Benhamadou, A., 2010, A normalized syntactic lexicon for arabic verbs and its evaluation within the LKB platform, ACSE, Egypt. 10. Miller, J. and Mukerji, J. Model Driven Architecture (MDA) http://cgi.omg.org/docs/ormsc/01-07-01.pdf, July 2001. Architecture Board ORMSC. 10. Miller, J. and Mukerji, J. Model Driven Architecture (MDA) http://cgi omg org/docs/ormsc/01 07 01 pdf July 2001 Ar 10. Miller, J. and Mukerji, J. Model Driven Architecture (MDA) http://cgi.omg.org/docs/ormsc/01-07-01.pdf, July 2001. Ar 10. Miller, J. and Mukerji, J. Model Driven Architecture (MDA) http://cgi.omg.org/docs/ormsc/01-07-01.pdf, July 2001. Architecture Board ORMSC. 11. OMG/MOF Meta Object Facility (MOF) Specification, OMG Document AD/97-08-14, Sep- tembre 1997 (www.omg.org). 12. John D. Poole. "Model-Driven Architecture : Vision, Standards And Emerging Technolo- gies". ECOOP 2001, Workshop on Metamodeling and Adaptive Object Models, April 2001. 13. (Tau, 2011) (TAU, 2011) TAUS, Report on a TAUS research about translation interopera- bility, 25 February, 2011. 14. (Wagner and Zeisler, 2004) Wagner, A., and Zeisler, B. 2004. A syntactically annotated corpus of Tibetan. In: Proc. of LREC, p. 1141–1144, Lisboa. 15. (Wilcock, 2007) Wilcock, G., 2007, An OWL ontology for HPSG, ACL, Finland. 16. (Wörner et al., 2006) Wörner, K., Witt, A., Rehm, G., and Dipper, S. eds. 2006. Model- ling Linguistic Data Structures, Extreme Markup Languages, Montréal, Québec.
https://openalex.org/W2831826689
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Compositional differences in gastrointestinal microbiota in prostate cancer patients treated with androgen axis-targeted therapies
Prostate cancer and prostatic diseases
2,018
cc-by
6,397
Abstract Further analysis identified significant compositional differences in the GI microbiota of men taking ATT, including a greater abundance of species previously linked to response to anti-PD-1 immunotherapy such as Akkermansia muciniphila and Ruminococcaceae spp. In functional analyses, we found an enriched representation of bacterial gene pathways involved in steroid biosynthesis and steroid hormone biosynthesis in the fecal microbiota of men taking oral ATT. Conclusions There are measurable differences in the GI microbiota of men receiving oral ATT. We speculate that oral hormonal therapies for prostate cancer may alter the GI microbiota, influence clinical responses to ATT, and/or potentially modulate the antitumor effects of future therapies including immunotherapy. Given our findings, larger, longitudinal studies are warranted. Compositional differences in gastrointestinal microbiota in prostate cancer patients treated with androgen axis-targeted therapies Karen S. Sfanos 1,2,3 ●Mark C. Markowski2 ●Lauren B. Peiffer1,4 ●Sarah E. Ernst1 ●James R. White5 ● Kenneth J. Pienta 3 ●Emmanuel S. Antonarakis2,3 ●Ashley E. Ross3,6 Received: 1 March 2018 / Revised: 17 April 2018 / Accepted: 20 April 2018 / Published online: 9 July 2018 © The Author(s) 2018. This article is published with open access Prostate Cancer and Prostatic Diseases (2018) 21:539–548 https://doi.org/10.1038/s41391-018-0061-x Prostate Cancer and Prostatic Diseases (2018) 21:539–548 https://doi.org/10.1038/s41391-018-0061-x ARTICLE ARTICLE ARTICLE Introduction These authors contributed equally: Emmanuel S. Antonarakis, Ashley E. Ross. These authors contributed equally: Emmanuel S. Antonarakis, Ashley E. Ross. The gastrointestinal (GI) microbiota are known to influence the metabolism, pharmacokinetics, and toxicity of many drugs and xenobiotics [1], yet there are few mechanistic studies exploring this effect in relation to cancer therapies. Several compelling examples have emerged providing insight into the relationship between human-associated microbiota and cancer treatment. The bacterium Mycoplasma hyorhinis and species of Proteobacteria, when present within a tumor, may meta- bolize the chemotherapy drug, gemcitabine, into a deaminated inactive metabolite [2], resulting in drug resistance [3]. β-glucuronidases produced by bacterial species in the GI tract can reactivate the excreted, inactive metabolite of the topoisomerase I inhibitor, irinotecan, causing adverse drug toxicities, including severe diarrhea [4]. Likewise, although the mechanism is not fully understood, there is emerging evidence that the GI microbiota can influence the efficacy of immunotherapy [5–11]. Electronic supplementary material The online version of this article (https://doi.org/10.1038/s41391-018-0061-x) contains supplementary material, which is available to authorized users. Abstract Background It is well known that the gastrointestinal (GI) microbiota can influence the metabolism, pharmacokinetics, and toxicity of cancer therapies. Conversely, the effect of cancer treatments on the composition of the GI microbiota is poorly understood. We hypothesized that oral androgen receptor axis-targeted therapies (ATT), including bicalutamide, enzaluta- mide, and abiraterone acetate, may be associated with compositional differences in the GI microbiota. Background It is well known that the gastrointestinal (GI) microbiota can influence the metabolism, pharmacokinetics, and toxicity of cancer therapies. Conversely, the effect of cancer treatments on the composition of the GI microbiota is poorly understood. We hypothesized that oral androgen receptor axis-targeted therapies (ATT), including bicalutamide, enzaluta- mide, and abiraterone acetate, may be associated with compositional differences in the GI microbiota. Methods We profiled the fecal microbiota in a cross-sectional study of 30 patients that included healthy male volunteers and men with different clinical states of prostate cancer (i.e., localized, biochemically recurrent, and metastatic disease) using 16S rDNA amplicon sequencing. Functional inference of identified taxa was performed using PICRUSt. Results We report a significant difference in alpha diversity in GI microbiota among men with versus without a prostate cancer diagnosis. Further analysis identified significant compositional differences in the GI microbiota of men taking ATT, including a greater abundance of species previously linked to response to anti-PD-1 immunotherapy such as Akkermansia muciniphila and Ruminococcaceae spp. In functional analyses, we found an enriched representation of bacterial gene pathways involved in steroid biosynthesis and steroid hormone biosynthesis in the fecal microbiota of men taking oral ATT. Conclusions There are measurable differences in the GI microbiota of men receiving oral ATT. We speculate that oral hormonal therapies for prostate cancer may alter the GI microbiota, influence clinical responses to ATT, and/or potentially modulate the antitumor effects of future therapies including immunotherapy. Given our findings, larger, longitudinal studies are warranted. Methods We profiled the fecal microbiota in a cross-sectional study of 30 patients that included healthy male volunteers and men with different clinical states of prostate cancer (i.e., localized, biochemically recurrent, and metastatic disease) using 16S rDNA amplicon sequencing. Functional inference of identified taxa was performed using PICRUSt. Results We report a significant difference in alpha diversity in GI microbiota among men with versus without a prostate cancer diagnosis. Sample collection and DNA isolation The rectal swab procedure is detailed in the Supplemental Methods. Rectal swabs were immediately stored at −80 °C until DNA isolation. The investigators were blinded to group allocation until after all sequencing was completed. Swab contents were resuspended in 500 μl of 1× PBS and DNA was extracted with a phenol:chloroform method that incorporates multiple enzyme digest and bead beating as previously described [18]. A total of 16 “mock” (500 μl 1× PBS as starting material) DNA extractions were performed to control for contamination from DNA extraction through the full amplification and sequencing pipeline. Study design and patient population Specimens were obtained under a Johns Hopkins Medicine Institutional Review Board approved protocol with written informed consent. Rectal swabs from 30 patients were collected during routine Urology or Medical Oncology outpatient clinic visits at the Johns Hopkins Hospital and Sydney Kimmel Comprehensive Cancer Center. Patients who were currently taking an antibiotic were excluded. Patients designated as “controls” were being followed in the Urology clinic primarily for benign prostatic hyperplasia. Importantly, since the control patients did not undergo prostate biopsy, they cannot be definitively defined as cancer free. Men categorized as “benign” were being evaluated for suspicion of prostate cancer, but subsequently had a negative biopsy. For the benign group, the rectal swab was collected at the evaluation clinic visit, which was prior to the patient taking prophylactic antibiotics for the biopsy. For the seven men in the “cancer” group, three had swabs taken 1–2 months prior to their diagnostic biopsy, one had their swab taken 1 month after diagnostic biopsy, and three men had swabs taken >6 months after prior biopsy. For the purposes of our medication analyses, the designation “NoMeds” indicated men who were not undergoing androgen derivation therapy (ADT), “GNRH” were men only being treated with a gonadotropin-releasing hormone (GNRH) agonist/antagonist, and “oral ATT” were men being treated with oral androgen receptor axis-targeted therapies. The relationship between the GI microbiota and cancer therapies in men with prostate cancer is underexplored. There is, however, compelling evidence that the GI microbiome is involved in multiple-related processes such as modulation of circulating hormone levels [12, 13], sti- mulation of antitumor immune responses [5, 6, 8], and induction of treatment-related toxicities (including immunotherapy-induced colitis [14] and radiation-induced bowel toxicity [15]), and/or morbidities including devel- opment of metabolic syndrome [16, 17]. Animal studies suggest that the GI microbiota may also be affected by circulating androgen levels [12, 13] and castration [16]. We hypothesize that hormonal therapy, particularly oral for- mulations of androgen axis-targeted drugs, used in the treatment of prostate cancer may promote changes in the GI microbiota. In this exploratory study, we determined com- positional differences in GI microbiota in (1) men with and without prostate cancer and (2) men with localized prostate cancer, biochemical recurrence after primary treatment, and hormone-sensitive or castration-resistant metastatic disease. We also examined the relationship between GI microbiota composition and androgen deprivation therapies, with a focus on orally administered androgen receptor axis- targeted therapies (ATT). Patients and methods Recent studies in animal models have demonstrated that intestinal microbiota are essential for therapeutic efficacy of agents such as cyclophosphamide [7], platinum che- motherapy [6], and both anti-CTLA-4 [5] and anti-PD-L1 [8] immunotherapies. Eradication of the commensal intestinal flora by antibiotic treatment or via use of germ- free mice eliminates therapeutic efficacy of these agents in different tumor models. A study in a melanoma model showed that the therapeutic benefit of anti-PD-L1 immunotherapy could be bolstered by feeding animals a strain of Bifidobacterium—a species commonly used in probiotic supplements—prior to initiating therapy [8]. Three recent human studies, two in melanoma patients [9, 11] and one in patients with epithelial tumors [10], reported that the presence of certain types of bacteria including Ruminococcaceae, Bifidobacteriaceae, and Akkermansia muciniphila are associated with response to anti-PD-1 immunotherapy. Fecal microbial transplant from human donors that were responders to anti-PD-1 immunotherapy into germ-free mouse allograft tumor models conferred antitumor efficacy of anti-PD-1 immunotherapy versus fecal samples transplanted from non-responders [9–11]. Collectively, these studies indicate that members of the intestinal microbiome may be essential for cancer drug efficacy and that modulating intestinal microbiome composition may enhance therapeutic response. * Karen S. Sfanos ksfanos@jhmi.edu 1 Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA 2 Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA 3 Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA 4 Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA 5 Resphera Biosciences, Baltimore, MD, USA 5 Resphera Biosciences, Baltimore, MD, USA 6 Present address: Texas Urology Specialists, Dallas, TX, USA 540 K. S. Sfanos et al. Patients and methods 16S rDNA gene library generation, HiSeq sequencing, and analysis Details of the sequencing and analysis can be found in the Supplemental Methods. Table 1 Clinical details of the men included in the study as well as the type of ATT administered at the time of sample collection No. of patients Mean age (range, years) Mean PSA (range, ng/mL) Race (no. of patients)a Status Control 6 68 (52–80) 5.1 (0.4–20.7) B (1) W (5) Benign 3 70 (64–78) 7.3 (4.4–10.1) B (2) W (1) Localized cancer 7 60.1 (53–71) 8.4 (3.8–13.5) B (1) W (6) Biochemical recurrence 7 64.4 (54–72) 2.4 (0–5.6) B (1) W (6) Metastatic hormone-sensitive 2 58 (51–65) 0.25 (0.2–0.3) W (2) Metastatic castration-resistant 5 74 (64–85) 8.7 (0–24.5) W (5) Medication Mean BMI (range, kg/ m2) NoMeds 16 64.1 (52–80) 6.6 (0.4–20.7) 28.05 (19.73–41.80) GNRH agonist/antagonist 5 64.8 (54–69) 4.6 (0–13.2) 28.66 (22.05–37.67) Oral ATT 9 69.7 (51–85) 4.9 (0–24.5) 27.25 (21.45–32.07) NoMeds not on ADT, ATT androgen axis-targeted therapy aSelf-reported as black (B) or white (W). No other races included Compositional differences in gastrointestinal microbiota in prostate cancer patients treated with. . . 541 Compositional differences in gastrointestinal microbiota in prostate cancer patients treated with. . . 541 No. of patients Mean age (range, years) Mean PSA (range, ng/mL) Race (no. of patients)a Status Control 6 68 (52–80) 5.1 (0.4–20.7) B (1) W (5) Benign 3 70 (64–78) 7.3 (4.4–10.1) B (2) W (1) Localized cancer 7 60.1 (53–71) 8.4 (3.8–13.5) B (1) W (6) Biochemical recurrence 7 64.4 (54–72) 2.4 (0–5.6) B (1) W (6) Metastatic hormone-sensitive 2 58 (51–65) 0.25 (0.2–0.3) W (2) Metastatic castration-resistant 5 74 (64–85) 8.7 (0–24.5) W (5) Medication Mean BMI (range, kg/ m2) NoMeds 16 64.1 (52–80) 6.6 (0.4–20.7) 28.05 (19.73–41.80) GNRH agonist/antagonist 5 64.8 (54–69) 4.6 (0–13.2) 28.66 (22.05–37.67) Oral ATT 9 69.7 (51–85) 4.9 (0–24.5) 27.25 (21.45–32.07) NoMeds not on ADT, ATT androgen axis-targeted therapy aSelf-reported as black (B) or white (W). No other races included Table 1 Clinical details of the men included in the study as well as the type of ATT administered at the time of sample collection Differences in GI taxonomic profiles by disease status and medication After contaminant removal, random subsampling to 80,000 sequences per sample was performed to provide even coverage prior to downstream statistical comparisons (rationale for subsampling described in ref. [19]). Differential abundance analysis was performed using the negative binomial test implemented in the DESeq R package. P values were adjusted for multiple hypothesis testing using the false discovery rate (FDR). Beta diversity analysis, including Bray-Curtis and UniFrac distance computation and principal coordinates analysis (PCoA), was performed in QIIME. Statistical comparisons of alpha diversity utilized generalized linear models (GLMs) and evaluated three different underlying response variable family distributions (Gaussian, Log-Normal, and Gamma). We characterized the bacterial composition of fecal samples from 30 men (n = 6 control, n = 3 benign (negative biopsy), n = 7 with localized prostate cancer, n = 7 with biochemi- cally recurrent prostate cancer, and n = 7 with metastatic prostate cancer). Table 1 contains the clinical details of the men included in the study as well as the type of ATT administered at the time of sample collection. Most of the men included in this study were Caucasian (White) and, importantly, there was no statistical difference in patient age or body mass index (BMI) among the medication groups (p = 0.4 and p = 0.9, respectively, Kruskal–Wallis test). A complete list of all medications and supplements that the men were taking at the time of sample collection is provided in Supplementary Table S1. Akkermansia muciniphila quantitative PCR Of interest, one patient in the recurrence group who had not yet started on ADT at the time of sample collection grouped with the “No ADT” samples (Fig. 1). In PCoA (a measure of relatedness between samples), we observed that samples from men undergoing ADT grouped separately from men who were not undergoing ADT (Fig. 2a). This was particularly pro- nounced for men taking oral ATT (Fig. 2b). Of interest, men with prostate cancer (localized, biochemically recur- rent, or metastatic groups) separated distinctly from men without cancer (control and benign groups) in PCoA (Fig. 2c), a result that was also statistically significant in PERMANOVA (Adonis) model testing (p = 0.02). The between-sample distances (beta diversity) were smallest within the oral ATT group compared to the GNRH and NoMeds groups, meaning that the species profiles among the fecal samples within the oral ATT group were most similar to each other, and that a specific taxon or taxa dis- tinguish them from the other groups (Fig. 2d). The greatest beta diversity was observed between the NoMeds group and versus cancer, Fig. 1). Of interest, one patient in the recurrence group who had not yet started on ADT at the time of sample collection grouped with the “No ADT” samples (Fig. 1). In PCoA (a measure of relatedness between samples), we observed that samples from men undergoing ADT grouped separately from men who were not undergoing ADT (Fig. 2a). This was particularly pro- nounced for men taking oral ATT (Fig. 2b). Of interest, men with prostate cancer (localized, biochemically recur- rent, or metastatic groups) separated distinctly from men without cancer (control and benign groups) in PCoA (Fig. 2c), a result that was also statistically significant in PERMANOVA (Adonis) model testing (p = 0.02). The between-sample distances (beta diversity) were smallest within the oral ATT group compared to the GNRH and NoMeds groups, meaning that the species profiles among the fecal samples within the oral ATT group were most similar to each other, and that a specific taxon or taxa dis- tinguish them from the other groups (Fig. 2d). The greatest beta diversity was observed between the NoMeds group and Akkermansia muciniphila quantitative PCR The taxonomic profiles of each sample are depicted in Supplemental Figure S1. There was a significant difference in alpha diversity in samples from men with versus without prostate cancer, irrespective of medication status (p < 0.05 using multiple statistical models and measures of alpha diversity, Supplementary Table S2), meaning that the total number of species (or species “richness”) and the presence of rare individual species was greater in men without a prostate cancer diagnosis than in men with cancer. No significant differences in alpha diversity by medication status were observed (Supplementary Table S3). A. muciniphila genomic DNA was obtained from the American Type Culture Collection (BAA-835D-5) to develop a standard curve for quantitative PCR (qPCR). The A. muciniphila species-specific primer set was used as fol- lows, Forward primer: 5′-CAGCACGTGAAGGTGGG- GAC-3′, Reverse primer: 5′-CCTTGCGGTTGGCTTCAG AT-3′. The total estimated copies of A. muciniphila in each fecal sample were determined using this assay relative to the total number of estimated 16S rDNA copies assayed by qPCR using the universal 16S primer set that was also used for Illumina amplicon sequencing: Forward primer: 5′- CAACGCGWRGAACCTTACC-3′ and Reverse primer: 5′-CRRCACGAGCTGACGAC-3′. Comparison of taxonomic profiles indicated clustering that associated with medication status (ADT versus no ADT), but not with respect to cancer status (no cancer K. S. Sfanos et al. 542 Fig. 1 Unsupervised clustering (log-transformed) of 16S rDNA Illumina-sequencing results from fecal samples by genus. The den- drogram was based on hierarchical clustering of the Euclidean distance between samples in the combined groups. L cancer localized prostate Fig. 1 Unsupervised clustering (log-transformed) of 16S rDNA Illumina sequencing results from fecal samples by genus The den cancer, BCR biochemically recurrent prostate cancer, mHSPC meta- static hormone sensitive prostate cancer mCRPC metastatic Fig. 1 Unsupervised clustering (log-transformed) of 16S rDNA Illumina-sequencing results from fecal samples by genus. The den- drogram was based on hierarchical clustering of the Euclidean distance between samples in the combined groups. L cancer localized prostate cancer, BCR biochemically recurrent prostate cancer, mHSPC meta- static hormone-sensitive prostate cancer, mCRPC metastatic castration-resistant prostate cancer. No cancer = no clinical and/or biopsy proven diagnosis of cancer (control and benign groups) the oral ATT group (Fig. 2d), meaning that the samples from these two groups were most dissimilar to each other. versus cancer, Fig. 1). Discussion As Akkermansia muciniphila is a species of particular recent interest with respect to treatment response to anti-PD- 1 immunotherapy in patients with epithelial tumors, we verified the differential abundance of A. muciniphila in men taking oral ATT using an independent qPCR assay. These analyses confirmed that A. muciniphila was significantly more prevalent in the men who were taking oral ATT. Moreover, the results showed high correlation with our Illumina amplicon sequencing results (Fig. 3). Our study aimed to assess the compositional profile of the GI microbiota in men with and without a diagnosis of prostate cancer and with and without treatment with ATT. We report initial evidence that the alpha diversity of the GI microbiota is greater in men without a prostate cancer diagnosis, and that there were measurable differences in the bacterial composition of the GI microbiota in men under- going treatment with ATT. Differentially abundant species in the GI microbiota of men taking oral ATT Since we observed significant differences in beta diversity by ADT status and type in PCoA, we next determined if particular species of GI microbiota were differentially abundant between medication categories. As shown in Table 2, several species of bacteria were differentially abundant in terms of the proportion of sequencing reads that matched the species/OTU obtained from the samples across different treatment categories. Notably, species, such as Akkermansia muciniphila, Ruminococcaceae spp., and Lachnospiraceae spp., were significantly more abundant in the fecal samples of men taking oral ATT. When analyzed at the bacterial family level, we again observed a significant greater abundance of sequencing reads assigned to the bacterial families Verrucomicrobiaceae (of which Compositional differences in gastrointestinal microbiota in prostate cancer patients treated with. . . 543 Fig. 2 Principal coordinates analysis (PCoA) and beta diversity (unweighted UniFrac) of each fecal sample bacterial profile, analyzed by the indicated groups. a–c Principal coordinate axis 2 showed the most distinction between medication groups, so statistical comparisons were limited to this dimension. d Statistical comparison of beta diversity between the indicated groups (Mann–Whitney test). Shown is the mean unweighted UniFrac distance (+SEM) Fig. 2 Principal coordinates analysis (PCoA) and beta diversity (unweighted UniFrac) of each fecal sample bacterial profile, analyzed by the indicated groups. a–c Principal coordinate axis 2 showed the most distinction between medication groups, so statistical comparisons were limited to this dimension. d Statistical comparison of beta diversity between the indicated groups (Mann–Whitney test). Shown is the mean unweighted UniFrac distance (+SEM) hormone biosynthesis were significantly enriched within the oral ATT group compared to the no ADT (NoMeds) group (Table 3). Other pathways of interest that were more pre- valent in the oral ATT group versus the no ADT group included caffeine metabolism and glycosaminoglycan degradation (Table 3). Akkermansia muciniphila is one of the few members), Lachnospiraceae, and others in the oral ATT group (Table 2). There was also a significant decrease in the abundance of sequencing reads assigned to bacterial families such as Brevibacteriaceae, Erysipelotrichaceae, and Streptococcaceae in men receiving ADT versus no ADT and specifically in the oral ATT group versus men not undergoing ADT (Table 2). Akkermansia muciniphila is one of the few members), Lachnospiraceae, and others in the oral ATT group (Table 2). Differentially abundant species in the GI microbiota of men taking oral ATT There was also a significant decrease in the abundance of sequencing reads assigned to bacterial families such as Brevibacteriaceae, Erysipelotrichaceae, and Streptococcaceae in men receiving ADT versus no ADT and specifically in the oral ATT group versus men not undergoing ADT (Table 2). Cancer therapies and GI microbiota The ability of cancer therapies to affect and change the composition of the GI microbiota is not well studied. Interestingly, a screen of more than 1000 marketed non- We next performed functional inference analyses using PICRUSt [20]. Functional pathways involving steroid/ K. S. Sfanos et al. Cancer therapies and GI microbiota . . 545 Fig. 3 Quantitative PCR (qPCR) for Akkermansia muciniphila. a Confirmation of enriched abundance of this species in the GI micro- biota of men taking oral ATT versus the other men included in the study. b The qPCR results were in strong correlation (R2 = 0.9938) with the results obtained by 16S rDNA Illumina amplicon sequencing study. b The qPCR results were in strong correlation (R2 = 0.9938) with the results obtained by 16S rDNA Illumina amplicon sequencing Fig. 3 Quantitative PCR (qPCR) for Akkermansia muciniphila. a Confirmation of enriched abundance of this species in the GI micro- biota of men taking oral ATT versus the other men included in the also be affected by hormone levels, as another mouse study showed that castrating mice induced alterations in GI microbiota composition, and subsequent development of abdominal obesity [16]. Intriguingly, this study by Harada et al. implies that the GI microbiota may mediate several of the side effects associated with ADT, including obesity and the metabolic syndrome. In our study, we found that men taking oral ATT had a different GI microbiota composition than men taking GNRH agonists/antagonists alone or men not undergoing ADT. Functional pathway inference of the species present in the fecal microbiota of men taking oral ATT indicated an intriguing possibility that the species capable of steroid/hormone biosynthesis are more abundant in the GI flora when men are taking these oral medications (Table 3). This finding, if confirmed, could have important implications and perhaps represent a mechanism for potential alternative pathways for production of steroid metabolites that could influence treatment response to oral ATT. Critical follow-up studies will correlate the presence of GI bacterial species capable of steroid/hormone bio- synthesis to circulating hormone levels. antibiotic drugs against 40 representative GI bacterial strains found that nearly a quarter inhibited bacterial growth [21]. Chemotherapy and immunotherapy have been shown to induce dysbiosis (a pathogenic microbial imbalance) of the GI microbiota in rodent models [7, 22]. The most mature data involving longitudinal studies are in patients with non-Hodgkin’s lymphoma undergoing bone marrow transplant conditioning chemotherapy, which induced pathogenic shifts in the GI microbiota that were associated with treatment toxicities [23, 24]. A study in pediatric acute myeloid leukemia patients receiving chemotherapy demonstrated direct bacteriostatic effect of chemother- apeutics, as well as outgrowth of pathogenic enterococci that could not be fully explained by concurrent use of antibiotics [25]. Cancer therapies and GI microbiota Compositional changes to the GI micro- biota induced by chemotherapy or immunotherapy could conceivably impact factors such as the local inflammatory environment in the intestinal tract, systemic inflammatory effects, and/or the efficacy of any subsequently adminis- tered cancer therapies. Cancer therapies and GI microbiota 544 Table 2 Select differentially abundant species or families of GI microbiota in men with or without hormonal therapy Negative binomial test (DESeq) Mean valuesa Standard errors NoMeds vs GNRH NoMeds vs oral ATT GNRH vs oral ATT NoMeds (nb) GNRH (n) Oral ATT (n) NoMeds GNRH Oral ATT P value FDR adj P P value FDR adj P P value FDR adj P Species/OTUs Akkermansia muciniphila 0.002 (8) 0.003 (3) 0.055 (6) 0.001 0.002 0.034 0.623 0.797 0.002 0.012 0.048 0.173 Ruminococcaceae_unassigned 0.011 (16) 0.001 (4) 0.030 (9) 0.004 0.001 0.012 0.051 0.181 0.049 0.179 0.010 0.051 Blautia wexlerae 0.012 (16) 0.029 (5) 0.026 (9) 0.002 0.019 0.017 0.030 0.121 0.023 0.098 0.907 0.929 Ruminococcaceae_unassigned 0.005 (16) 0.003 (4) 0.018 (9) 0.002 0.001 0.007 0.400 0.690 0.027 0.115 <0.001 0.002 otu0:Clostridium oroticum 0.003 (14) 0.048 (5) 0.017 (9) 0.001 0.044 0.007 0.000 <0.001 0.001 0.007 0.145 0.373 Lachnospiraceae_Clostridium_XlVa 0.006 (14) 0.008 (4) 0.016 (8) 0.001 0.004 0.011 0.515 0.713 0.032 0.129 0.358 0.645 Clostridiales_unassigned 0.056 (14) 0.032 (5) 0.016 (8) 0.017 0.015 0.005 0.401 0.690 0.010 0.052 0.219 0.490 otu3527:Robinsoniella peoriensis 0.001 (15) <0.001 (4) 0.016 (8) <0.001 <0.001 0.008 0.113 0.328 <0.001 <0.001 <0.001 <0.001 Anaerococcus tetradius 0.001 (10) 0.006 (3) 0.010 (3) <0.001 0.006 0.008 0.045 0.163 0.006 0.032 0.769 0.832 Bacteroides stercoris 0.001 (11) <0.001 (3) 0.009 (2) 0.001 <0.001 0.007 0.507 0.707 0.008 0.042 0.084 0.263 Family Brevibacteriaceae 0.002 <0.001 <0.001 0.002 <0.001 <0.001 0.076 0.240 <0.001 <0.001 <0.001 <0.001 Clostridiales_Incertae_Sedis_XIII <0.001 <0.001 0.001 <0.001 <0.001 0.001 0.050 0.222 <0.001 <0.001 0.245 0.517 Staphylococcaceae <0.001 0.001 0.003 <0.001 0.001 0.002 0.040 0.218 <0.001 <0.001 0.382 0.613 Clostridiales_unassigned 0.087 0.050 0.029 0.020 0.017 0.007 0.217 0.415 0.001 0.008 0.158 0.405 Verrucomicrobiaceae 0.002 0.003 0.056 0.001 0.002 0.034 0.632 0.766 0.002 0.015 0.048 0.160 Oxalobacteraceae <0.001 <0.001 <0.001 <0.001 <0.001 <0.001 0.472 0.693 0.004 0.030 0.183 0.455 Bacillales_unassigned <0.001 <0.001 0.001 <0.001 <0.001 0.001 0.507 0.701 0.005 0.030 0.022 0.105 Aerococcaceae 0.001 0.004 0.004 <0.001 0.002 0.002 0.017 0.107 0.005 0.032 0.872 0.895 Propionibacteriaceae <0.001 0.001 <0.001 <0.001 0.001 <0.001 0.155 0.368 0.014 0.065 0.002 0.020 Erysipelotrichaceae 0.039 0.028 0.017 0.009 0.015 0.004 0.675 0.766 0.016 0.071 0.272 0.523 Selenomonadales_unassigned <0.001 0.003 0.001 <0.001 0.003 0.001 0.001 0.014 0.020 0.084 0.324 0.554 Streptococcaceae 0.021 0.014 0.007 0.010 0.012 0.002 0.817 0.872 0.025 0.094 0.260 0.517 Lachnospiraceae 0.176 0.272 0.305 0.027 0.050 0.064 0.046 0.220 0.027 0.097 0.650 0.806 Prevotellaceae 0.020 0.034 0.006 0.008 0.016 0.002 0.328 0.553 0.037 0.118 0.005 0.044 NoMeds not on ADT, GNRH only on GNRH agonist/antagonist, Oral ATT taking an oral androgen axis-targeted therapy, FDR adj P false discovery rate adjusted P value aMean relative abundance bNumber of patients the species/OTU or bacterial family was identified in Compositional differences in gastrointestinal microbiota in prostate cancer patients treated with. References 1. Spanogiannopoulos P, Bess EN, Carmody RN, Turnbaugh PJ. The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism. Nat Rev Microbiol. 2016;14:273–87. 2. Vande Voorde J, Sabuncuoğlu S, Noppen S, Hofer A, Ranjbarian F, Fieuws S, et al. Nucleoside-catabolizing enzymes in mycoplasma-infected tumor cell cultures compromise the cyto- static activity of the anticancer drug gemcitabine. J Biol Chem. 2014;289:13054–65. 3. Geller LT, Barzily-Rokni M, Danino T, Jonas OH, Shental N, Nejman D, et al. Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine. Sci- ence. 2017;357:1156–60. 4. Wallace BD, Wang H, Lane KT, Scott JE, Orans J, Koo JS, et al. Alleviating cancer drug toxicity by inhibiting a bacterial enzyme. Science. 2010;330:831–5. 5. Vétizou M, Pitt JM, Daillère R, Lepage P, Waldschmitt N, Fla- ment C, et al. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science. 2015;350:1079–84. In conclusion, our study provides preliminary evidence that the GI microbiota may be different in men undergoing treatment with androgen receptor axis-targeted therapies commonly used to treat prostate cancer. We hypothesize that these compositional differences may influence treat- ment response to oral ATT or to subsequent treatments such as immunotherapy. Future longitudinal studies pre-, during, and post-therapy are warranted to confirm the degree to which the GI microbiota are altered and to assess whether these alterations are correlated to prostate cancer treatment responses. Collectively, these studies could determine whether the GI microbiome is both essential for therapeutic efficacy and whether it could serve as a target that could be modulated to enhance treatment response. 6. Iida N, Dzutsev A, Stewart CA, Smith L, Bouladoux N, Wein- garten RA, et al. Commensal Bacteria control cancer response to therapy by modulating the tumor microenvironment. Science. 2013;342:967–70. 7. Viaud S, Saccheri F, Mignot G, Yamazaki T, Daillère R, Hannani D, et al. The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide. Science. 2013;342:971–6. 8. Sivan A, Corrales L, Hubert N, Williams JB, Aquino-Michaels K, Earley ZM, et al. Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science. 2015;350:1084–9. 9. Matson V, Fessler J, Bao R, Chongsuwat T, Zha Y, Alegre M-L, et al. The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients. Science. 2018; 359:104–8. 10. Routy B, Le Chatelier E, Derosa L, Duong CPM, Alou MT, Daillere R, et al. Oral ATT, GI microbiota, and immunotherapy It has been reported that steroid biosynthesis occurs in prokaryotes [26, 27], and that certain species of bacteria are capable of metabolizing estrogen and androgen precursors and catabolizing estrogens and androgens thereby affecting systemic levels of these hormones [28–30]. Altering the gastrointestinal flora in a mouse model of type 1 diabetes impacted testosterone levels, as well as the development of type 1 diabetes [12]. In another study, mice consuming a diet rich in the commonly used probiotic strain Lactoba- cillus reuteri had a reduced systemic inflammatory state through reduction of IL-17, and an increase in serum tes- tosterone levels [31]. On the converse, the microbiome can Much excitement has been generated after the publication of a series of human studies in melanoma patients [9, 11] and in patients with epithelial tumors [10], all indicating that the presence of certain types of bacteria including Rumino- coccaceae, Bifidobacteriaceae, and Akkermansia mucini- phila are associated with a positive response to anti-PD-1 immunotherapy. In our study, we observed over- representation of these same species (Ruminococcaceae and particularly Akkermansia muciniphila) in the fecal micro- biota of men taking oral ATT (Table 2). Although pre- liminary, we speculate that our results might represent one K. S. Sfanos et al. 546 Table 3 Functional inference of microbial gene content in fecal specimens Mean values (relative abundance) NoMeds vs oral ATT KEGG level 3—Categories enriched in oral ATT vs NoMeds NoMeds (n = 16) GNRH (n = 5) Oral ATT (n = 9) Ratio oral ATT to NoMeds P value (npdiff) Metabolism;Lipid_Metabolism; Steroid_biosynthesis 5.06E−06 6.04E−06 9.49E−05 18.75 0.0044 Metabolism;Lipid_Metabolism; Steroid_hormone_biosynthesis 3.67E−05 4.15E−05 1.91E−04 5.2 0.0012 Metabolism;Biosynthesis_of_Other_Secondary_Metabolites; Caffeine_metabolism 3.44E−06 1.21E−06 3.09E−05 8.98 0.0188 Metabolism;Xenobiotics_Biodegradation_and_Metabolism; Fluorobenzoate_degradation 8.65E−06 4.65E−06 6.48E−05 7.5 0.0194 Metabolism;Glycan_Biosynthesis_and_Metabolism; Glycosaminoglycan_degradation 2.13E−04 3.02E−04 4.98E−04 2.34 0.0022 Metabolism;Xenobiotics_Biodegradation_and_Metabolism; Atrazine_degradation 1.93E−04 2.06E−04 3.64E−04 1.88 0.0012 Metabolism;Glycan_Biosynthesis_and_Metabolism; Glycosphingolipid_biosynthesis_- _ganglio_series 1.14E−04 1.79E−04 2.13E−04 1.88 0.0212 Metabolism;Biosynthesis_of_Other_Secondary_Metabolites;Flavonoid_biosynthesis 5.55E−05 8.19E−05 9.93E−05 1.79 0.0218 Metabolism;Biosynthesis_of_Other_Secondary_Metabolites; Penicillin_and_cephalosporin_biosynthesis 1.34E−04 1.53E−04 2.27E−04 1.7 0.0068 Cellular_Processes;Transport_and_Catabolism;Lysosome 4.69E−04 5.08E−04 8.03E−04 1.71 0.0048 Metabolism;Biosynthesis_of_Other_Secondary_Metabolites;beta-Lactam_resistance 2.17E−04 2.63E−04 2.93E−04 1.35 0.029 Unclassified;Cellular_Processes_and_Signaling; Cell_motility_and_secretion 1.25E−03 1.32E−03 1.65E−03 1.32 0.0026 Metabolism;Glycan_Biosynthesis_and_Metabolism; Glycosphingolipid_biosynthesis_- _globo_series 6.69E−04 7.72E−04 8.58E−04 1.28 0.0278 Unclassified;Cellular_Processes_and_Signaling; Inorganic_ion_transport_and_metabolism 1.59E−03 1.92E−03 1.98E−03 1.25 0.0052 NoMeds not on ADT, GNRH only on GNRH agonist/antagonist, Oral ATT taking an oral androgen axis-targeted therapy, npdiff nonparametric difference test Compositional differences in gastrointestinal microbiota in prostate cancer patients treated with. . . References Gut microbiome influences efficacy of PD-1- based immunotherapy against epithelial tumors. Science. 2018;359:91–97. Acknowledgements We thank the members of the SKCCC Next Generation Sequencing Core, supported by NCI grant P30CA006973, for assistance with sequencing. This work was supported by Prostate Cancer Foundation Challenge Award 16CHAL13 to KSS, KJP, ESA, and AER. ESA is partially funded by Department of Defense grant W81XWH-13-PCRP-CCA. 11. Gopalakrishnan V, Spencer CN, Nezi L, Reuben A, Andrews MC, Karpinets TV, et al. Gut microbiome modulates response to anti-PD- 1 immunotherapy in melanoma patients. Science. 2018;359:97–103. 12. Markle JGM, Frank DN, Mortin-Toth S, Robertson CE, Feazel LM, Rolle-Kampczyk U, et al. Sex differences in the gut micro- biome drive hormone-dependent regulation of autoimmunity. Science. 2013;339:1084–8. Oral ATT, GI microbiota, and immunotherapy 547 potential explanation for the report of responses to anti-PD- 1 immunotherapy observed in men with metastatic prostate cancer who have progressed on enzalutamide [32]. changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons. org/licenses/by/4.0/. changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons. org/licenses/by/4.0/. There are several limitations to our study including the relatively small sample size and the lack of longitudinal sampling. Important follow-up studies will include samples collected prior to start of therapy and then longitudinally after therapy initiation. Such studies will further strengthen our hypothesis that ATT is responsible for the composi- tional differences that we observed, as opposed to other factors that can influence the composition of the GI microbiome such as diet or stress levels. Furthermore, we observed a significant decrease in GI microbiota alpha diversity in patients with prostate cancer that was inde- pendent of medication status. Decreased diversity in GI microbiota has been reported as a risk factor for several other types of disease as well as “Western” lifestyle [33]. Our results should be taken with caution, however, as many of the men with prostate cancer in this study had undergone prior treatments that could have conceivably influenced the diversity of the GI microbiota. Our results prompt further examination of GI microbiota diversity as a risk factor for prostate cancer in larger patient cohorts. Compliance with ethical standards 13. Neuman H, Debelius JW, Knight R, Koren O. Microbial endo- crinology: the interplay between the microbiota and the endocrine system. FEMS Microbiol Rev. 2015;39:509–21. Conflict of interest JRW has financial and/or other relationship with Resphera Biosciences. The remaining authors declare that they have no conflict of interest. 14. Dubin K, Callahan MK, Ren B, Khanin R, Viale A, Ling L, et al. Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis. Nat Commun. 2016;7. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if 15. Ferreira MR, Muls A, Dearnaley DP, Andreyev HJN. Microbiota and radiation-induced bowel toxicity: lessons from inflammatory bowel disease for the radiation oncologist. Lancet Oncol. 2014;15: e139–e147. 548 K. S. Sfanos et al. 16. Harada N, Hanaoka R, Horiuchi H, Kitakaze T, Mitani T, Inui H, et al. Castration influences intestinal microflora and induces abdominal obesity in high-fat diet-fed mice. Sci Rep. 2016;6:23001. 25. van Vliet MJ,Tissing WJE,Dun CAJ,Meessen NEL,Kamps WA, de Bont ESJM, et al. Chemotherapy treatment in pediatric patients with acute myeloid leukemia receiving antimicrobial prophylaxis leads to a relative increase of colonization with potentially pathogenic bacteria in the gut. Clin Infect Dis. 2009;49:262–70. 17. Festi D, Schiumerini R, Eusebi LH, Marasco G, Taddia M, Colecchia A. Gut microbiota and metabolic syndrome. World J Gastroenterol: Wjg. 2014;20:16079–94. 26. Bode HB, Zeggel B, Silakowski B, Wenzel SC, Reichenbach H, Müller R. Steroid biosynthesis in prokaryotes: identification of myxobacterial steroids and cloning of the first bacterial 2,3(S)- oxidosqualene cyclase from the myxobacterium Stigmatella aur- antiaca. Mol Microbiol. 2003;47:471–81. 18. Shrestha E, White JR, Yu S-H, Kulac I, Ertunc O, De Marzo AM, et al. Profiling the urinary microbiome in men with positive versus negative biopsies for prostate cancer. J Urol. 2018;199:161–71. 27. Wei JH, Yin X, Welander PV. Sterol synthesis in diverse bacteria. Front Microbiol. 2016;7:990. 19. Weiss S, Xu ZZ, Peddada S, Amir A, Bittinger K, Gonzalez A, et al. Normalization and microbial differential abundance strate- gies depend upon data characteristics. Microbiome. 2017;5:27. 28. Kwa M, Plottel CS, Blaser MJ, Adams S. The intestinal micro- biome and estrogen receptor-positive female breast cancer. J Natl Cancer Inst. 2016;108:djw029. 20. Compliance with ethical standards Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Bio- technol. 2013;31:814. 29. Ridlon JM, Ikegawa S, Alves JMP, Zhou B, Kobayashi A, Iida T, et al. Clostridium scindens: a human gut microbe with a high potential to convert glucocorticoids into androgens. J Lipid Res. 2013;54:2437–49. 21. Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, et al. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature. 2018;555:623. 30. Gorbach SL. Estrogens, breast cancer, and intestinal flora. Rev Infect Dis. 1984;6(Suppl 1):S85–S90. 22. Fijlstra M, Ferdous M, Koning AM, Rings EH, Harmsen HJ, Tissing WJ. Substantial decreases in the number and diversity of microbiota during chemotherapy-induced gastrointestinal muco- sitis in a rat model. Support Care Cancer. 2015;23:1513–22. 31. Poutahidis T, Springer A, Levkovich T, Qi P, Varian BJ, Lakritz JR, et al. Probiotic microbes sustain youthful serum testosterone levels and testicular size in aging mice. PLoS ONE. 2014;9: e84877. 23. Montassier E, Batard E, Massart S, Gastinne T, Carton T, Caillon J, et al. 16S rRNA gene pyrosequencing reveals shift in patient faecal microbiota during high-dose chemotherapy as conditioning regimen for bone marrow transplantation. Microb Ecol. 2014;67:690–9. 32. Graff JN, Alumkal JJ, Drake CG, Thomas GV, Redmond WL, Farhad M, et al. Early evidence of anti-PD-1 activity in enzalutamide-resistant prostate cancer. Oncotarget. 2016; 7:52810–17. 33. Mosca A, Leclerc M, Hugot JP. Gut microbiota diversity and human diseases: should we reintroduce key predators in our ecosystem? Front Microbiol. 2016;7:455. 24. Montassier E, Gastinne T,Vangay P, Al-Ghalith GA, Bruley des Varannes S, Massart S, et al. Chemotherapy-driven dysbiosis in the intestinal microbiome. Aliment Pharmacol Ther. 2015;42:515–28.
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Assessment of CFD Model Performance for Flows around a Hydraulic Structure of Complex Geometry
Periodica polytechnica. Civil engineering/Periodica polytechnica. Civil engineering (Online)
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https://doi.org/10.3311/PPci.16709 Creative Commons Attribution b |109 https://doi.org/10.3311/PPci.16709 Creative Commons Attribution b |109 Periodica Polytechnica Civil Engineering, 65(1), pp. 109–119, 2021 Keywords CFD modeling, OpenFOAM, RANS, complex hydraulic structure, turbulence modeling Cite this article as: Grivalszki, P., Fleit, G., Baranya, S., Józsa, J. "Assessment of CFD Model Performance for Flows around a Hydraulic Structure of Complex Geometry", Periodica Polytechnica Civil Engineering, 65(1), pp. 109–119, 2021. https://doi.org/10.3311/PPci.16709 Assessment of CFD Model Performance for Flows around a Hydraulic Structure of Complex Geometry Péter Grivalszki 1*, Gábor Fleit 1, Sándor Baranya 1, János Józsa 1,2 1 Department of Hydraulic and Water Resources Engineering, Faculty of Civil Engineering, Budapest University of Technology and Economics, H-1111 Budapest, Műegyetem rkp. 3., Hungary 2 MTA-BME Water Management Research Group, Hungarian Academy of Sciences, H-1051 Budapest, Széchenyi István tér 9, Hungary * Corresponding author, e-mail: grivalszki.peter@epito.bme.hu 1 Department of Hydraulic and Water Resources Engineering, Faculty of Civil Engineering, Budapest University of Technology and Economics, H-1111 Budapest, Műegyetem rkp. 3., Hungary 2 MTA-BME Water Management Research Group, Hungarian Academy of Sciences, H-1051 Budapest, Széchenyi István tér 9, Hungary * Corresponding author, e-mail: grivalszki.peter@epito.bme.hu Received: 21 June 2020, Accepted: 16 September 2020, Published online: 14 October 2020 Abstract Computational Fluid Dynamics (CFD) modeling has become a widely used research tool in the hydraulic engineering community, however, for many problems the numerical model setup and even the selection of the suitable hydrodynamic solver is still a challenging task. This is the case for fine scale analysis of flow features around hydraulic structures of complex geometry, where generation of the 3D grid, application of the correct turbulence modeling approach, or modeling of the free surface all require extensive experience and knowledge. The aim of this paper is to perform a numerical hydrodynamic experiment for a hydraulic structure with complex geometry to assess the model performance, in terms of grid resolution, grid refinement methods as well as turbulence modeling. The open source modeling environment of OpenFOAM is tested and validated against laboratory measurements, moreover, practical recommendations are made for future applications of the numerical solver. 1 Introduction The total quantity of flushed out sediments, and the bed deformation were com- pared with experiments, highlighting a good correspon- dence between the results.i is an applicable approach in case of flow Froude number (Fr < 0.5) conditions. In case of larger Froude numbers, the profile of the free surface has notable influence on the hydrodynamic conditions (and vice versa), hence its proper representation is necessary for accurate scour estimations as well. Baranya et al. [5] also showed the applicability of a rigid lid approach for modeling flow and local scour around bridge piers. A k-ε turbulence closure was used on a curvilinear nested grid system. Laboratory experi- ments were used to validate the simulations and quantify velocity and turbulent kinetic energy (TKE) around piers. Baranya et al. [6] successfully extended their analysis to predict scouring around the piers. Kahraman et  al. [7] investigated the influence of free-surface variation on the velocity field using numerical simulations of flow around a sharp-nosed pier. They concluded, that the volume of fluid (VOF) models are in better agreement with experimental data than those using the rigid-lid approximation. Their results show that even though the change in free-surface height near the pier is small compared to the approach flow, it still has a significant effect on velocities in front of the pier and in the wake region, also at low Froude numbers. Kara et al. [8] carried out large eddy simulations (LES) to investigate the effects of accurate simulation of the cur- vilinear water-surface deformation of the flow through a bridge contraction. They also tested the rigid-lid bound- ary condition for free surface, and compared to level set method (LSM). Bed-shear stresses and first-order statis- tics were similar for their cases, but the instantaneous turbulence structure and consequently, the second-order statistics, were distinctly different. The correct prediction of the water-surface deformation of such flows is deemed important for the accuracy of their simulations. Ignoring free surface variations or using simplifica- tions like the ones in the studies above, usually enough for fulfill the scope of interests in river, sea or ocean scale, but in case of transient free surface motion, steep surface gradients or complex geometries, multiphase models are to be used. In such models, the governing equations are solved not only for the water phase, but for the air above it as well, allowing for multivalued vertical free surface positions. 1 Introduction influence the prevailing flow conditions, but also play a fundamental role in sediment transport [3]. In the case of 3D fluid modeling, no cross-sectional or vertical integrat- ing is applied, but the Navier–Stokes equations are solved numerically with various simplifications. Resolving the flow problem along the vertical axis, however, increases computational demands significantly, moreover, requires dedicated numerical methods. Methods of various com- plexity and flexibility are available for the vertical discret- ization in 3D models, whose applicability depends on the actual flow problem. The rapid, continuous improvement of computational resources in the last decades implied continuous (still ongoing) developments in computational sciences as well. In fact, such an intensive progress took place in the field of the so called CFD (Computational Fluid Dynamics) mod- eling. These models are used in mechanical as well as in hydraulic engineering, aiming to solve fluid flow problems of various complexity.i In the field of hydraulic engineering, and river engi- neering in particular the most frequently used hydrody- namic modeling tools use dimensional simplifications, that is, the flow conditions (velocities) are schematized with cross-sectionally averaged, one-dimensional (1D) or depth-averaged, two-dimensional (2D) velocities using the St Venant and the shallow-water equations, respec- tively [1, 2]. The development of 1D and 2D models looks back to several decades due to the fact that they require less computational capacity and earlier PCs enabled the simulation of simpler problems. However, river flows reportedly can show locally complex, three-dimensional (3D), secondary flow features as well [3], which not only Typical hydraulic engineering problems requiring the resolution of 3D flow phenomena are flows around var- ious hydraulic structures, such as weirs, bridge piers, abutments, etc. Roulund et al. [4], for instance, used Reynolds-averaged Navier–Stokes (RANS) model with k-ω turbulence closure to investigate flow and scouring around a circular pile, with special focus on the horse- shoe and lee wake vortices. They successfully captured all the main features of the scouring process, however, their model did not include direct free surface modeling, which 110|Grivalszki et al. Period. Polytech. Civ. Eng., 65(1), pp. 109–119, 2021 flushing process of the Kali Gandaki hydropower reser- voir. Thus, the location of the water level was calculated with the Bernoulli equation. An adaptive, non-orthogonal and unstructured grid has been used. 1 Introduction The most frequently used multiphase modeling method from the mentioned ones is the volume of fluid (VOF) method  [13]. Furthermore, methods mentioned above cannot handle flows around geometries, which can separate the water domain vertically. For testing differ- ent turbulence models, Salaheldin et al. [14] successfully modelled flow around circular piers, where calculated and measured position of the free surface are in good agree- ment. Haun  et  al. [15] modelled flow over trapezoidal broad-crested weir, and compared the effectiveness of VOF with fixed grid, and an algorithm based on the conti- nuity equation and the Marker-and-Cell method, together with an adaptive grid for the water surface. They expe- rienced good correlation between the methods, however, VOF required less time for calculations. For high quality simulation of wave generation and absorption, Higuera et al. [16] used VOF, and with it, they set a new boundary condition apparatus to simulate waves. Jacobsen et al. [17] developed an easy to use application called waves2Foam which is a VOF-based numerical wave tank approach. Stoesser et al. [9] treated the free surface as a plane of symmetry where zero gradient conditions are applied for the variables parallel to the surface with the wall-normal variables set to zero. Their calculations of primary and secondary flow and boundary shear stresses in a meander- ing laboratory-scaled channel were successful.l Another approach for capturing the free surface between multiphase flows is the level set method (LSM)  [18]. In case of the LSM, the interface is explicitly defined by using a signed level set function in every computational node, defining the closest distance from the free surface. The LSM based CFD toolbox REEF3D [19] has been suc- cessfully used to simulate complex flows around various hydraulic engineering structures [20, 21]. If water level fluctuations and changes are to be accounted for as well, several methods are available. One of the most frequently used is the σ-coordinate transformation method [10]. Based on this, Baranya et al. [11] made large- scale flow analysis at a river confluence, and, validating the results against field measurements, they satisfactorily reproduced the most relevant elements of the confluence hydrodynamics. 2 Numerical methods In this study, the interIsoFoam solver of the open-source CFD toolbox OpenFOAM was used [27], employing a geometric Volume-of-Fluid (VOF) method for ensuring a sharp interface between two immiscible, incompress- ible fluids. The governing equations for multiphase solver are the Reynolds-averaged Navier–Stokes equations, expressed by the continuity and momentum equations: In CFD modeling, the numerical domain is generally split into smaller subdomains of geometric primitives like hexahedra or tetrahedra. The governing equations are dis- cretized and solved inside each of these subdomains. For capturing the effects of a structure with complex geome- try, it can be a crucial point of model set-up. With man- ual mesh setup excellent mesh fitting can be achieved, however, for large domains and highly variable geome- try it is time consuming, and exposed to manmade errors. The mesh generation can be classified into two main cate- gories based on the topology of the elements that describe the domain, which is structured (eg.: [22, 23]) and unstruc- tured (e.g.: [11, 15]). The advantage of structured mesh is that the points of an elemental cell can be easily addressed and the connectivity is straightforward, but for capturing complex geometries, really fine resolution must be applied. An unstructured mesh can capture complex surfaces, but a cell may have an arbitrary number of neighbouring cells attaching to it, making the data treatment and connection complicated  [26]. Hybrid meshes containing structured and unstructured blocks are good compromise to use the benefits of both mesh types. u 0 , (1)           u u u u fb t p 1 2   , (2) u 0 , (1) (1) u 0 ,       u u u u fb t p 1 2   , (2) (2) where u is velocity vector, t is the time, ρ is density, p is the pressure, fb is body forces (gravity and surface ten- sion). For capturing the free surface between the two phases, the VOF method has been applied [13]. It is an Eulerian volume tracking method with a step function to differentiate water and air phases. A computational cell with α = 1 is entirely in the water phase, while α = 0 means the air phase. The interface is represented with an α value between these values. 1 Introduction Haun and Olsen  [12] used an algorithm based on the computed pressure field when modeling the In addition to the proper tracking of the free-surface, turbulence modeling also plays a crucial role, when mod- eling transient complex flows, especially in cases where obstacles of complex geometries are present in the flow. Recently, Bayon-Barrachina and López-Jiménez [22], used Grivalszki et al. Period. Polytech. Civ. Eng., 65(1), pp. 109–119, 2021|111 Grivalszki et al. Period. Polytech. Civ. Eng., 65(1), pp. 109–119, 2021|111 was used to simulate turbulent free surface flow condi- tions around a hydraulic structure of complex geometry. The aim of the study is to test and quantify the accuracy of different frequently used turbulent models, as well as to test the applicability of various mesh fitting algorithms provided by the snappyHexMesh utility through a series of numerical model simulations. CFD model results are compared with experimental data, allowing for a quantita- tive error analysis. The herein presented results underline the importance of preliminary model tests when inves- tigating flows around complex structures, as relatively high sensitivity was observed for the choice of the tested numerical methods. a RANS model with different two equations turbulence clo- sures to simulate a hydraulic jump properly. Jiang et al. [23] simulated flow over a rectangular broad-crested weir with the same apparatus like Bayon-Barrachina and López- Jiménez [22], but with VOF for free surface capturing. In spite of the encouraging results of the above mentioned studies, a major problem with standard RANS turbulence models is that in two-phase simulations, the effect of the free surface is neglected and high turbulence production occurs due to the high gradient in fluid density. Kamath et al. [21] investigated free surface turbulence damping in several different case studies to validate the applicability of their apparatus. They used RANS equations with k-ω turbulence closure and LSM for capturing free surface. Devolder et al. [24] published the so called buoyancy mod- ification for k-ω SST turbulence closure, while Larsen and Fuhrman  [25] developed a stabilizing correction method that can be used with k-ε and k-ω turbulence closures. 2 Numerical methods This α value is used as a weight when calculating fluid properties with only one set of gov- erning equations for the entire flow domain. For example, the density in an arbitrary cell can be written as [28]:    liquid gas 1 . (3) (3) Considering the above described problems related to CFD modeling of complex flows, it can be stated that the selection of suitable numerical solvers for a given hydraulic engineering task, where 3D flow features, tur- bulence as well as the profile of free surface all play an important role, is far not straightforward. In this study the VOF-based open-source CFD toolbox OpenFOAM  [27] The VOF method then adds one more equation to be solved for the advection of this volume fraction func- tion α [28]:      t u 0 . (4)      t u 0 . (4) 112|Grivalszki et al. Period. Polytech. Civ. Eng., 65(1), pp. 109–119, 2021 112|Grivalszki et al. Period. Polytech. Civ. Eng., 65(1), pp. 109–119, 2021 The drawback of the standard VOF method is the smearing of the water surface, therefore it cannot capture a sharp surface separating the phase fractions in a cell, but instead the cell will be filled with uniform mixture of the two phases (0 < α < 1). OpenFOAM offers two methods for improving the surface sharpness. The Multidimensional Universal Limiter with Explicit Solution (MULES) [29] is a widely used scheme to reduce the smearing [30, 31]. Recently, a geometric VOF method has also been imple- mented as a part of the isoAdvector [32] solver, which was used in present study. This solver reportedly offers a sharper interface tracking than the MULES [33,34]. OpenFOAM uses the finite volume method (FVM) for discretization [38]. The FVM is implemented by integrat- ing all the terms in the equations over a specified con- trol volume and relating the volume integrals to the sur- face integrals using Gauss's theorem. The surface and volume integrals are both evaluated with mid-point inte- gration approximation resulting in second-order accuracy. The Laplacian and divergence terms are handled with the Gaussian linear corrected and Gaussian linear schemes. The implicit, first order and transient Euler scheme is used for the time marching.i The snappyHexMesh utility provides three refinement levels (Fig. 1) for mesh morphology at the solid bound- ary [27]. 2 Numerical methods On the first level, the so-called castellated mesh starts with a hexahedral grid, cutting out the geometry of interest from it with optional refinement, leaving orthogo- nal edges at the solid boundary. Secondly, snapping makes morphing iterations on the surface with breaking the orthogonality to get a smooth boundary. In the third step, additional layers parallel to the boundary can be added which is often used in mechanical engineering where the turbulent shear layer is to be resolved. In this study an analysis is performed to see if the different fitting methods on a complex geometry with the same spatial resolution affect the hydrodynamic solution. The governing RANS equations are closed with two- equation turbulence modeling, through the eddy viscosity concept [35]. The performance of two different turbulence models has been tested, namely the standard k-ω (where k is turbulence kinetic energy and ω is the specific rate of dissipation of k) [36] and the k-ω Shear Stress Transport (SST) model [37], moreover, the effect of the buoyance modification for the k-ω SST (proposed by [24, 25]) has also been tested. While the standard k-ω is still used rather frequently, the k-ω SST can overcome many of the defi- ciencies of the standard k-ω model, offering more accurate solutions. The transport equations solved for k and ω are:                k t k D k P k k k k u u 2 3 * , (5)                              t D P F CDk u u 2 3 1 2 1  , (6) 3.1 The CALTROPe-project According to the most recent scientific results, the main reasons of the ongoing, global climate change are the excessive greenhouse gas emissions [39]. Among many adverse effects, sea level rising (along with the biased sed- iment balance of rivers unsustainable management) entails territorial losses in many river estuaries (e.g. Mekong [40], Mississippi [41], etc.). The CALTROPe project aims to resolve this problem through an easy-applicable struc- ture-system, which works in an organic, nature-oriented way against territorial losses. The structure itself (Fig. 2) is made partly by concrete, and partly by local natural (6) where Dk and Dω are effective diffusivities for k and ω, Pk and Pω are production terms in the respective equa- tions, CDkω is a limiter function, β * = 0.09 is a constant model parameter, F1 is a blending function which is used to achieve smooth transition between two models, β and Γ are parameters which calculated as a weighted averages of k-ω and k-ε parameters (where ε is the turbulent dissipa- tion rate) using F1 as a weight function. The turbulent vis- cosity is calculated from where Dk and Dω are effective diffusivities for k and ω, Pk and Pω are production terms in the respective equa- tions, CDkω is a limiter function, β * = 0.09 is a constant model parameter, F1 is a blending function which is used to achieve smooth transition between two models, β and Γ are parameters which calculated as a weighted averages of k-ω and k-ε parameters (where ε is the turbulent dissipa- tion rate) using F1 as a weight function. The turbulent vis- cosity is calculated from Fig. 1 The three refinement level of snappyHexMesh utility. From left to right: castellated mesh, snapped mesh, add-layers mesh t a k a b F S    1 1 1 23 2 max , , (7) (7) where a1 = 0.31 and b1 = 1.0 are constant parameters, F23 is a bounding function and S is the magnitude of the rate- of-strain tensor. Fig. 1 The three refinement level of snappyHexMesh utility. From left to right: castellated mesh, snapped mesh, add-layers mesh Grivalszki et al. Period. Polytech. Civ. Eng., 65(1), pp. 109–119, 2021|113 Grivalszki et al. Period. Polytech. Civ. Eng., 65(1), pp. 109–119, 2021|113 Fig. 2 The CALTROPe midline of the 0.50 m wide flume in an axially symmet- rical way. 3.1 The CALTROPe-project A constant discharge of Q = 0.008 m 3s –1 was ensured with a pump system, while the tailwater level was kept at h = 0.08 m with a tilting weir at the end of the flume. These flow conditions were set to provide slightly turbulent flow conditions with Reynolds number range around Re ≈ 12000. It is important to note that the main goal of the paper was to demonstrate the CFD model capabilities through a thorough model test and no upscal- ing of the modelled flow field to prototype scale is pro- posed. Consequently, the detailed analysis of the near wall regions was unnecessary, and the main focus of the flow field analysis was on the turbulent region instead. Fig. 2 The CALTROPe Single-point velocity data was recorded using an Acoustic Doppler Velocimeter (ADV, Nortek Vectrino) in a high number of points around the structure. Due to its geo- metrical properties, the sampling volume of the probe is in a distance of 5 cm from the receiver emitter. Considering this limitation and the 0.08  m water depth, three near- bed points (z = 0.005, 0.015, 0.025 m) of 14 verticals were sampled (Fig. 3). Fig. 2 The CALTROPe materials. It has three legs and planned to build 1 m high. materials. It has three legs and planned to build 1 m high. Due to its modularity, a shore protection system built from the CALTROPe structures could be installed in river estu- aries in some various arrangements. River would flow partly near these arrangements, partly between the struc- ture legs, where the flow velocity is expected to increase, causing scouring and deposition issues. The sampling rate of the ADV was set to 16 Hz, which ensured the logging of turbulent velocity fluctuations as well. Erroneous velocity data (spikes) were removed using a method based on a bivariate kernel density func- tion, [44, 45], and the removed data points were replaced via linear interpolation. In addition to the evaluation of time-averaged velocity vectors, the high-frequency mea- surements were also used to calculate pointwise values of turbulent kinetic energy (TKE) as: These hollow structures of limited design age (few years) would serve as habitats for mangrove samplings until they grow and takes root, then would decompose, leaving a fully natural shore protection system behind [42,  43]. 3.1 The CALTROPe-project The semi-natural system adapts the changes in nature and could help natural sedimentation in coastal areas. These structures are to be exposed to various kind of hydrodynamic effects, such as the spatially and tempo- rally varying flow field of the incoming river, tidal effects or the dynamic wind induced waves of the sea. It is there- fore of crucial importance, for the design of these struc- tures, to possess an investigation tool that is capable to reveal the local scale hydrodynamic impacts. In this study, the flow around a scaled prototype of an individ- ual CALTROPe structure was analyzed both with labora- tory experiments and computational tools, but with a main focus on the latter. TKE u u u x y z      1 2 2 2 2 ' ' ' , (8) (8) where ux', uy', uz' are the fluctuating components of the 3D velocity vectors derived via Reynolds-decomposition. Fig. 3 Layout for laboratory experiments 3.3 Numerical setups a special multiphase stabilizing correction method by Devolder et al. [24] and Larsen and Fuhrman [25] were tested (buoyancy modification). The latter aims to resolve the problem of turbulence overproduction near the free surface by including a buoyancy term in the transport equations (model variation T1 for k-ω, T2 for k-ω SST and REF for k-ω SST with buoyancy modification). Numerical simulations were performed with the open- source CFD tool OpenFOAM. The model setup was identi- cal to the experimental one, including scale and boundary conditions as well. The model domain is 2 m long, 0.5 m wide and 0.2 m high – 0.08 m for water phase and 0.12 m for air phase. Constant inflow discharge (Q = 0.008 m 3s –1) was ensured using the outletPhaseMeanVelocity boundary condition, which sets water level through holding the mean water-phase velocity of 0.2 ms –1. In order to evaluate the performance of i) four mesh resolutions (i.e. grid conver- gence study) ii) three mesh fitting methods; and iii) three turbulence closures a reference model setup was defined (Table 1). Fig. 4 shows instantaneous velocity streamlines around the CALTROPe. In the reference model, the resolution of the hexahedral mesh (Δx = 5.0 mm), which is further refined to 2.5 mm in the direct proximity of the CALTROPe surface. The mesh is snapped on the CALTROPe boundary, which means break- ing the orthogonality to get a smooth boundary surface. The buoyancy modified k-ω SST turbulence model have been applied for turbulence closure. The root mean square error (RMSE) was used to quantify the performance of the model variants, through the comparison of measured and modeled horizontal velocity components (ux, uy) and TKE. Large scale turbulence features (vortex shedding, Fig. 3) are resolved in the transient CFD results, hence the tur- bulence closure only accounts for the smaller scale fluc- tuations. Considering that the ADV data inherently con- tain both scales, the numerical TKE values (TKEmod) were derived from the combination of transient velocity fluctua- tions and modeled turbulent kinetic energy (k) values: A recirculation zone and vortex shedding is observed on the downstream side of the obstacle, as well as a peri- odically moving jet between the structure legs. 3.2 Laboratory experiments Laboratory experiments were performed at the research flume of the Department of Hydraulic and Water Resources Engineering, Budapest University of Technology and Economics. A single 1:10 scaled CALTROPe structure (0.1 m height) made by medical plaster was placed in the Fig. 3 Layout for laboratory experiments 114|Grivalszki et al. Period. Polytech. Civ. Eng., 65(1), pp. 109–119, 2021 3.3 Numerical setups Mesh convergence analysis was performed to verify the applied spatial resolution in the reference model, with hexahedron cells of Δx = 10.0, 7.5, 5.0, and 4.0 mm, which are refined to their half at CALTROPe boundary (model variatons G1, G2, REF, G3 from the coarsest to the finest). For mesh fitting analysis, all three features of snappyHexMesh, introduced above, were tested. At the add-layer mesh version only one additional layer was implemented due to computational limitations. (model variations M1 (castellated mesh) REF (snapped mesh) and M2 (add layer mesh)). TKE k u u u mod x y z       1 2 2 2 2 ' ' ' . (9) (9) 4.2 Sensitivity to mesh fitting Considering the fact, that mesh fitting is only applied at the walls of the obstacle, its effect on the upstream sec- tion of the channel was expected to be marginal, which is well-observable in Fig. 7 (vertical 3). In the shear layer, the castellated and snapped meshes show almost identical behavior for both velocities and TKE, however, the addi- tional parallel cell layer around the structure, which is believed to be the most sophisticated method, provides notable worse results. Similar behavior is observed in the recirculation zone (vertical 13), where the strength of the recirculation current is underestimated in model vari- ant M2. With respect to TKE, the most primitive meshing method (M1) provides the best agreement with the exper- imental data. The contradictory behavior of the add-lay- ers mesh is noted. In mechanical engineering such mesh- ing is often used to resolve the turbulent boundary layer around solid surfaces, however, in such cases multiple and very fine resolution layers are employed. Considering the aims of this study, and CFD modeling in hydraulic engi- neering in general, such a refinement is usually unneces- sary. The presented results suggest, that in cases, where the computational resources do not allow such multi- layer refinement at the solid boundary, the applicability of add-layers mesh with a single parallel cell layer is not recommended, despite the fact that it is believed to be the most advanced meshing method from the tested ones. Fig. 5 Vertical velocity and TKE profiles from probes of different flow regimes for mesh resolution analysis The observed agreement in case of the two finest model variants (REF, G3) is considered very reasonable, while the lack of sufficient cells in the vertical direction results in notable inaccuracies on the coarser meshes. Similarly, in case of the recirculation zone (vertical 13) the two finer model variants provide the best approximation for the flow velocities, however, a slightly contradictory behav- ior is observed in case of the TKE, where notable over- prediction occurs. In terms of overall accuracy, the gain with the finest res- olution (compared to the reference setup) is not that nota- ble with respect to the massive increase of computational demand. On a personal computer (PC) with 16  logical processors with 3.60 GHz basic speed and 32 Gb random access memory (RAM) the coarsest simulation took only a couple of hours, while the finest is about 2 weeks. Fig. 4.1 Grid convergence Results of the grid convergence study is presented in Fig. 5. (For the location of the measurement verticals, please see Fig. 3.) It is observed, that the steady, logarith- mic flow velocity profile at the upstream side of the obsta- cle (vertical 3) is rather well reproduced at all spatial res- olutions. Despite the symmetric geometry, the automatic mesh generation algorithm in the snappyHexMesh tool occasionally provided asymmetric computational grids, which was found to result in erroneous, also asymmetric hydrodynamic solutions: the jet between the structure legs attaches to one of the legs, losing its oscillatory nature. This feature corrupted the time-averaged velocity distri- butions as well. In order to resolve this problem, an addi- tional row of cells was added width-wise, which replaced the cell faces in the longitudinal symmetry plane of the numerical channel with a cell center. The performance of three frequently used k-ω-based turbulence closures were tested for the reproduction of main flow features as well as turbulence characteristics. The standard k-ω, the k-ω SST, and the k-ω SST with Fig. 4 Instantaneous velocity distribution represented with streamlines (reference model setup) Vertical 8 is located in the shear layer between high velocity and the recirculation zone, whose numerical representation is believed to be rather challenging. Fig. 4 Instantaneous velocity distribution represented with streamlines (reference model setup) Grivalszki et al. Period. Polytech. Civ. Eng., 65(1), pp. 109–119, 2021|115 Fig. 6 RMSE values for mesh resolution sensitivity analysis Fig. 5 Vertical velocity and TKE profiles from probes of different flow regimes for mesh resolution analysis Fig. 6 RMSE values for mesh resolution sensitivity analysis Fig. 6 RMSE values for mesh resolution sensitivity analysis The authors acknowledge, that additional mesh refine- ment might further increase model accuracy, however, the general hydraulic behavior of the structure is well repre- sented with the reference model already. In order to opti- mize resolution and computational time, more advanced dynamic, flow adaptive meshing methods should also be considered [27]. 4.2 Sensitivity to mesh fitting 6 shows the RMSE of the different cases for the measured points. Results show the expected gradual improvements achieved with mesh refinement, especially in case of ux. 116|Grivalszki et al. Period. Polytech. Civ. Eng., 65(1), pp. 109–119, 2021 116|Grivalszki et al. Period. Polytech. Civ. Eng., 65(1), pp. 109–119, 2021 RMSE shows that castellated mesh produces the best results in general, however, difference compared to snapped mesh is relatively small (Fig. 8). The approaching, logarithmic flow profile is rather accu- rately reproduced with all turbulence closures, however, the k-ω model shows a very notable overproduction of TKE in this area. Regarding the near-bed (measured) sec- tion of vertical 3, the k-ω SST and the modified k-ω SST models show rather similar results, the physically unre- alistic overproduction of turbulence in the proximity of 4.3 Effect of turbulence modeling In terms of turbulence modeling, the underperformance of the standard k-ω model is the most obvious (Figs. 9 and 10). In terms of turbulence modeling, the underperformance of the standard k-ω model is the most obvious (Figs. 9 and 10). models show rather similar results, the physically unre alistic overproduction of turbulence in the proximity of Fig. 7 Vertical velocity and TKE profiles from probes of different flow regimes for mesh fitting analysis Fig. 8 RMSE values for mesh fitting sensitivity analysis Fig. 9 Vertical velocity and TKE profiles from probes of different flow regimes for different turbulence models Fig. 10 RMSE values for different turbulence models Fig. 7 Vertical velocity and TKE profiles from probes of different flow regimes for mesh fitting analysis Fig. 7 Vertical velocity and TKE profiles from probes of different flow regimes for mesh fitting analysis Fig. 9 Vertical velocity and TKE profiles from probes of different flow regimes for different turbulence models Fig. 9 Vertical velocity and TKE profiles from probes of different flow regimes for different turbulence models Fig. 7 Vertical velocity and TKE profiles from probes of different flow regimes for mesh fitting analysis Fig. 7 Vertical velocity and TKE profiles from probes of different flow regimes for mesh fitting analysis Fig. 9 Vertical velocity and TKE profiles from probes of different flow regimes for different turbulence models Fig. 9 Vertical velocity and TKE profiles from probes of different flow regimes for different turbulence models Fig. 8 RMSE values for mesh fitting sensitivity analysis Fig. 10 RMSE values for different turbulence models Fig. 10 RMSE values for different turbulence models Fig. 8 RMSE values for mesh fitting sensitivity analysis Fig. 10 RMSE values for different turbulence models Fig. 8 RMSE values for mesh fitting sensitivity analysis Grivalszki et al. Period. Polytech. Civ. Eng., 65(1), pp. 109–119, 2021|117 Grivalszki et al. Period. Polytech. Civ. Eng., 65(1), pp. 109–119, 2021|117 Three automatized mesh-fitting algorithms of the snappyHexMesh utility were used to generate compu- tational grids of different complexity and their effect on model accuracy was quantified. The most advanced (add layers) method showed the worst performance, which is probably a reason of the relatively coarse resolution. In mechanical engineering practice, where the near-wall boundary zone has a more emphasized role, such meshing is often used, however, with further refinements and mul- tiple layers. 4.3 Effect of turbulence modeling In case of hydraulic engineering, such refine- ments are often not remunerative, and thus, the applica- tion of such meshing options on coarser resolutions are not necessary advised. the free surface is observed in case of the former, while the buoyance modification in the latter seems to resolve this issue. While measurements are not available to the near surface region of the flow, considering the expected velocity profile in such a unidirectional, log-profile flow, the authors believe that the buoyancy modified turbulence model provides the more plausible results in this vertical. p p Nevertheless, in the recirculation zone (vertical 13) a rather contradictory behavior is observed. While the ref- erence model (using the modified k-ω SST model) pro- vides the best approximation for the horizontal velocities, the near-bed TKE is notably overpredicted compared to the experimental results and the two inferior turbulence models. Despite of the differences, calculating RMSE for all verticals reveals that the negative effect of the modification is negligible globally, hence its use is recommended, espe- cially if we have a scope of interest in the near free-surface region (Fig. 10). The most relevant parameters of the com- pared numerical model setups, as well as the RMSE values are presented in Table 1. Nevertheless, in the recirculation zone (vertical 13) a rather contradictory behavior is observed. While the ref- erence model (using the modified k-ω SST model) pro- vides the best approximation for the horizontal velocities, the near-bed TKE is notably overpredicted compared to the experimental results and the two inferior turbulence models.f Despite of the differences, calculating RMSE for all verticals reveals that the negative effect of the modification is negligible globally, hence its use is recommended, espe- cially if we have a scope of interest in the near free-surface region (Fig. 10). The most relevant parameters of the com- pared numerical model setups, as well as the RMSE values are presented in Table 1. The performance of three widely used variants of the k-ω turbulence model (standard k-ω; k-ω SST; buoyancy- modified k-ω SST) was tested for the prediction of highly turbulent flow conditions around an obstacle of complex geometry. Results emphasized the relevance of advanced tur- bulence modeling solutions (sing the k-ω SST model). 4.3 Effect of turbulence modeling The  buoyancy modified version of the k-ω SST model aims to resolve the problem with turbulence overproduc- tion at the proximity of the free surface in case of wave simulations, however, the results presented in this paper also showed its relevance for hydraulic engineering prob- lems as well. It is noted, that the experimental setup did not allow for the sampling of near-surface points of the verticals, hence the beneficial effect of the buoyancy mod- ified k-ω SST model could not be quantified. References [10] Phillips, N. A. "A coordinate system having some special advan- tages for numerical forecasting", Journal of Meteorology, 14(2), pp. 184–185, 1957. https://doi.org/10.1175/1520-0469(1957)014<0184:ACSHSS>2.0.CO;2 [1] Chow, V. T. "Open channel hydraulics", McGraw-Hill, New York, NY, USA, 1959. [2] Akan, A. O. "7 Bridge hydraulics", In: Open channel hydraulics, Elsevier, Oxford, UK, 2006, pp. 266–314. [2] Akan, A. O. "7 Bridge hydraulics", In: Open channel hydraulics, Elsevier, Oxford, UK, 2006, pp. 266–314. https://doi.org/10.1016/B978-075066857-6/50008-4 https://doi.org/10.1016/B978-075066857-6/50008-4 [11] Baranya, S., Olsen, N. R. B., Józsa, J. "Flow Analysis of a River Confluence with Field Measurements and Rans Model with Nested Grid Approach", River Research and Applications, 31(1), pp. 28–41, 2013. https://doi.org/10.1002/rra.2718 [3] Blanckaert, K., Graf, W. H. "Mean Flow and Turbulence in Open- Channel Bend", Journal of Hydraulic Engineering, 127(10), pp. 835–847, 2001. https://doi.org/10.1061/(ASCE)0733-9429(2001)127:10(835) [12] Haun, S., Olsen, N. R. B. "Three-dimensional numerical modelling of the flushing process of the Kali Gandaki hydropower reservoir", Lakes & Reservoirs: Research and Management, 17(1), pp. 25–33, 2012. https://doi.org/10.1111/j.1440-1770.2012.00491.x [4] Roulund, A., Mutlu Sumer, B., Fredsøe, J., Michelsen, J. "Numerical and experimental investigation of flow and scour around a circular pile", Journal of Fluid Mechanics, 534, pp. 351–401, 2005 https://doi.org/10.1017/S0022112005004507 [5] Baranya, S., Olsen, N. R. B., Stoesser, T., Sturm, T. W. "Three- Dimensional Rans Modeling of Flow Around Circular Piers using Nested Grids", Engineering Applications of Computational Fluid Mechanics, 6(4), pp. 648–662, 2012. https://doi.org/10.1080/19942060.2012.11015449 [13] Hirt, C. W., Nichols, B. D. "Volume of fluid (VOF) method for the dynamics of free boundaries", Journal of Computational Physics, 39(1), pp. 201–225, 1981. https://doi.org/10.1016/0021-9991(81)90145-5 [14] Salaheldin, T. M., Imran, J., Chaudhry, M. H. "Numerical Modeling of Three-Dimensional Flow Field Around Circular Piers", Journal of Hydraulic Engineering, 130(2), pp. 91–100, 2004. https://doi.org/10.1061/(ASCE)0733-9429(2004)130:2(91) [6] Baranya, S., Olsen, N. R. B., Stoesser, T., Sturm, T. W. "A nested grid based computational fluid dynamics model to predict bridge pier scour", Proceedings of the Institution of Civil Engineers - Water Management, 167(5), pp. 259–268, 2014. https://doi.org/10.1680/wama.12.00104 [15] Haun, S., Olsen, N. R. B., Feurich, R. "Numerical Modeling of Flow Over Trapezoidal Broad-Crested Weir", Engineering Applications of Computational Fluid Mechanics, 5(3), pp. 397–405, 2011. https://doi.org/10.1080/19942060.2011.11015381 [7] Kahraman, R., Riella, M., Tabor, G. R., Ebrahimi, M., Djordjević, S., Kripakaran, P. "Prediction of flow around a sharp-nosed bridge pier: influence of the Froude number and free-surface variation on the flow field", Journal of Hydraulic Research, 58(4), pp. 582–593, 2020. https://doi.org/10.1080/00221686.2019.1631223 https://doi.org/10.1080/19942060.2011.11015381 [16] Higuera, P., Lara, J. L., Losada, I. 5 Summary and conclusionsl In this study, flow of constant discharge around a hydrau- lic structure of complex geometry was investigated with the open-source CFD tool OpenFOAM. In order to verify the numerical results and to ensure the quantitative com- parability of various numerical setups, laboratory experi- ments were performed with an ADV. The high-frequency velocity data was used to calculate pointwise, time-aver- aged velocity vectors as well as to derive TKE. One of the main goals of CFD modeling in hydraulic engineering is to replace costly and time-consuming phys- ical model experiments. However, the results of this study underlined the relevance of such experimental work, more specifically, the advantages of combined hybrid model sys- tems. The relatively high sensitivity of CFD models to the A set of numerical models were built with identical geometry and boundary conditions to the experimental setup. A grid convergence study was performed to find the necessary spatial mesh resolution for the adequate repre- sentation of the prevailing flow conditions. Table 1 All model setups and root mean square errors compared to measurements # Mesh resolution Mesh fitting method turbulence modeling RMSE Ux RMSE Uy RMSE TKE G1 10 mm snapped mesh modified k-ω SST 0.0363 0.0175 0.00273 G2 7.5 mm snapped mesh modified k-ω SST 0.0322 0.0170 0.00226 REF 5 mm snapped mesh modified k-ω SST 0.0215 0.0155 0.00185 G3 4 mm snapped mesh modified k-ω SST 0.0177 0.0144 0.00170 M1 5 mm castellated mesh modified k-ω SST 0.0209 0.0129 0.00175 M2 5 mm add layers mesh modified k-ω SST 0.0332 0.0136 0.00184 T1 5 mm snapped mesh k-ω SST 0.0209 0.0150 0.00184 T2 5 mm snapped mesh k-ω 0.0271 0.0149 0.00258 Table 1 All model setups and root mean square errors compared to measurements 118|Grivalszki et al. Period. Polytech. Civ. Eng., 65(1), pp. 109–119, 2021 Acknowledgementsi choice of meshing and other numerical methods/parame- ters, the relevance of preliminary model test is emphasized, however, once a case-specifically well-verified, robust computational model is at hand, the role of numerical mod- eling is strengthened, as they offer faster and much cheaper analysis compared to physical models, especially if a large number of model variants are to be assessed. It is also noted that CFD modeling not only offers the spatially more extensive analysis of the hydrodynamic characteristics, but also allows for the evaluation of flow variables in areas where conventional (ADV, Particle Image Velocimetry, Laser Doppler Velocimetry, etc.) measurements cannot be performed due to spatial or other restrictions. The first and the second authors acknowledge the support of the ÚNKP-19-3, while the third author the support of the ÚNKP-19-4 New National Excellence Program of the Ministry for Innovation and Technology. The third author acknowledges the support of the Bolyai János research fellowship of the Hungarian Academy of Sciences. Support of grant BME FIKP-VÍZ by EMMI is also kindly acknowledged. The authors acknowledge the funding of the OTKA FK 128429 grant. Special thanks to VITUKI Hungary Kft. and S39’ Hybrid Design Manufacture Kft. References J. "Realistic wave generation and active wave absorption for Navier–Stokes models: Application to OpenFOAM®", Coastal Engineering, 71, pp. 102–118, 2013. https://doi.org/10.1016/j.coastaleng.2012.07.002 https://doi.org/10.1080/21664250.2019.1609713 https://doi.org/10.1080/21664250.2019.1609713 https://doi.org/10.3390/w11030456 [35] Boussinesq, J. "Essai sur la théorie des eaux courantes (Essay on running water theory)", Mémoires présentés par divers savants à l'Académie des Sciences, Imprimerie Nationale, Paris, France, 1877. (in French) [22] Bayon-Barrachina, A., López-Jiménez, P. A. "Numerical analysis of hydraulic jumps using OpenFOAM", Journal of Hydroinformatics, 17(4), pp. 662–678, 2015. https://doi.org/10.2166/hydro.2015.041 [36] Wilcox, D. C. "Formulation of the k–ω Turbulence Model Revisited", AIAA Journal, 46(11), pp. 2823–2838, 2008. https://doi.org/10.2514/1.36541 [23] Jiang, L., Diao, M., Sun, H., Ren, Y. "Numerical Modeling of Flow Over a Rectangular Broad-Crested Weir with a Sloped Upstream Face", Water, 10(11), Article number: 1663, 2018. https://doi.org/10.3390/w10111663 [37] Menter, F. R. "Two-equation eddy-viscosity turbulence models for engineering applications", AIAA Journal, 32(8), pp. 1598–1605, 1994. htt //d i /10 2514/3 12149 [24] Devolder, B., Rauwoens, P., Troch, P. "Application of a buoyan- cy-modified k-w SST turbulence model to simulate wave run-up around a monopile subjected to regular waves using OpenFOAM", Coastal Engineering, 125, pp. 81–94, 2017. https://doi.org/10.1016/j.coastaleng.2017.04.004 [38] Eymard, R., Gallouët, T., Herbin, R. "Finite volume methods", Handbook of Numerical Analysis, 7, pp. 713–1020, 2000. https://doi.org/10.1016/S1570-8659(00)07005-8 https://doi.org/10.1016/j.coastaleng.2017.04.004 [25] Larsen, B. E., Fuhrman, D. R. "On the over-production of turbu- lence beneath surface waves in Reynolds-averaged Navier-Stokes models", Journal of Fluid Mechanics, 853, pp. 419–460, 2018. https://doi.org/10.1017/jfm.2018.577 [39] The Core Writing Team, Pachauri, R. K., Meyer, L. "Climate Change 2014, Synthesis Report", [pdf] Intergovernmental Panel on Climate Change, Geneva, Switzerland, 2014. Available at: https://www.ipcc. ch/site/assets/uploads/2018/02/SYR_AR5_FINAL_full.pdf [26] Tu, J., Yeoh, G.-H., Liu, C. "Chapter 6 - Practical Guidelines for CFD Simulation and Analysis", In: Computational Fluid Dynamics, 2nd ed., Butterworth-Heinemann, Oxford, UK, 2013, pp. 219–273. https://doi.org/10.1016/B978-0-08-098243-4.00006-8 [40] Wassmann, R., Hien, N. X., Hoanh, C. T., Tuong, T. P. "Sea Level Rise Affecting the Vietnamese Mekong Delta: Water Elevation in the Flood Season and Implications for Rice Production", Climatic Change, 66, pp. 89–107, 2004. https://doi.org/10.1023/B:CLIM.0000043144.69736.b7 https://doi.org/10.1016/B978-0-08-098243-4.00006-8 https://doi.org/10.1023/B:CLIM.0000043144.69736.b7 [27] OpenFOAM Foundation "OpenFOAM – The Open Source CFD Toolbox – User Guide", OpenFOAM Ltd., Bracknell, UK, 2019. [41] Blum, M. D., Roberts, H. H. "Drowning of the Mississippi Delta due to insufficient sediment supply and global sea-level rise", Nature Geoscience, 2, pp. 488–491, 2009. https://doi.org/10.1038/ngeo553 [28] Gopala, V. R., van Wachem, B. G. M. "Volume of fluid methods for immiscible-fluid and free-surface flows", Chemical Engineering Journal, 141(1–3), pp. 204–221, 2008. https://doi.org/10.1016/j.cej.2007.12.035 https://doi.org/10.1016/j.cej.2007.12.035 [42] Maza, M., Lara, J. L., Losada, I. J. https://doi.org/10.1080/00221686.2019.1631223 [8] Kara, S., Kara, M. C., Stoesser, T., Sturm, T. W. "Free-Surface versus Rigid-Lid LES Computations for Bridge-Abutment Flow", Journal of Hydraulic Engineering, 141(9), Article number: 04015019, 2015. https://doi.org/10.1061/(ASCE)HY.1943-7900.0001028 [17] Jacobsen, N. G., Fuhrman, D. R., Fredsøe, J. "A wave generation toolbox for the open-source CFD library: OpenFoam®", International Journal for Numerical Methods in Fluids, 70(9), pp. 1073–1088, 2012. https://doi.org/10.1002/fld.2726 [9] Stoesser, T., Ruether, N., Olsen, N. R. B. "Calculation of primary and secondary flow and boundary shear stresses in a meandering channel", Advances in Water Resources, 33(2), pp. 158–170, 2010. https://doi.org/10.1016/j.advwatres.2009.11.001 [18] Osher, S., Sethian, J. A. "Fronts propagating with curvature-depen- dent speed: Algorithms based on Hamilton-Jacobi formulations", Journal of Computational Physics, 79(1), pp. 12–49, 1988. https://doi.org/10.1016/0021-9991(88)90002-2 Grivalszki et al. Period. Polytech. Civ. Eng., 65(1), pp. 109–119, 2021|119 [32] Roenby, J., Bredmose, H., Jasak, H. "A computational method for sharp interface advection", Royal Society Open Science, 3(11), Article number: 160405, 2016. https://doi.org/10.1098/rsos.160405 [19] Bihs, H., Kamath, A., Alagan Chella, M., Aggarwal, A., Arntsen, Ø. A. "A new level set numerical wave tank with improved density interpolation for complex wave hydrodynamics", Computers & Fluids, 140, pp. 191–208, 2016. https://doi.org/10.1016/j.compfluid.2016.09.012 https://doi.org/10.1016/j.compfluid.2016.09.012 [33] Laurila, E., Roenby, J., Maakala, V., Peltonen, P., Kahila, H., Vuorinen, V. "Analysis of viscous fluid flow in a pressure-swirl atomizer using large-eddy simulation", International Journal of Multiphase Flow, 113, pp. 371–388, 2019. https://doi.org/10.1016/j.ijmultiphaseflow.2018.10.008 [20] Fleit, G., Baranya, S., Bihs, H. "CFD Modeling of Varied Flow Conditions Over an Ogee-Weir", Periodica Polytechnica Civil Engineering, 62(1), pp. 26–32, 2018. https://doi.org/10.3311/PPci.10821 https://doi.org/10.1016/j.ijmultiphaseflow.2018.10.008 [21] Kamath, A., Fleit, G., Bihs, H. "Investigation of Free Surface Turbulence Damping in RANS Simulations for Complex Free Surface Flows", Water, 11(3), Article number: 456, 2019. https://doi.org/10.3390/w11030456 [34] Larsen, B. E., Fuhrman, D. R., Roenby, J. "Performance of inter- Foam on the simulation of progressive waves", Coastal Engineering Journal, 61(3), pp. 380–400, 2019. https://doi.org/10.1080/21664250.2019.1609713 https://doi.org/10.1080/21664250.2019.1609713 "Tsunami wave interaction with mangrove forests: A 3-D numerical approach", Coastal Engineering, 98, pp. 33–54, 2015. https://doi.org/10.1016/j.coastaleng.2015.01.002 [29] Deshpande, S. S., Anumolu, L., Trujillo, M. F. "Evaluating the per- formance of the two-phase flow solver interFoam", Computational Science & Discovery, 5(1), Article number: 014016, 2012. https://doi.org/10.1088/1749-4699/5/1/014016 [43] Truong, S. H., Ye, Q., Stive, M. J. F. "Estuarine Mangrove Squeeze in the Mekong Delta, Vietnam", Journal of Coastal Research, 33(4), pp. 747–763, 2017. https://doi.org/10.2112/JCOASTRES-D-16-00087.1 https://doi.org/10.1088/1749-4699/5/1/014016 [30] Prasad, B., Hino, T., Suzuki K. "Numerical simulation of free sur- face flows around shallowly submerged hydrofoil by OpenFOAM", Ocean Engineering, 102, pp. 87–94, 2015. https://doi.org/10.1016/j.oceaneng.2015.04.049 [44] Islam, M. R., Zhu, D. Z. "A Kernel Density-Based Algorithm to Despike ADV Data", Journal of Hydraulic Engineering, ASCE, 139(7), pp. 785–793, 2013. https://doi.org/10.1061/(ASCE)HY.1943-7900.0000734 https://doi.org/10.1016/j.oceaneng.2015.04.049 [31] Askarizadeh, H., Ahmadikia, H., Ehrenpreis, C., Kneer, R., Pishevar, A., Rohlfs, W. "Heat transfer in the hydraulic jump region of circular free-surface liquid jets", International Journal of Heat and Mass Transfer, 146, Article number: 118823, 2020. https://doi.org/10.1016/j.ijheatmasstransfer.2019.118823 https://doi.org/10.1061/(ASCE)HY.1943-7900.0000734 [45] Botev, Z. I., Grotowski, J. F., Kroese, D. P. "Kernel Density Estimation via Diffusion", Annals of Statistics, 38(5), pp. 2916– 2957, 2010. https://doi.org/10.1214/10-AOS799
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ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
BMC bioinformatics
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cc-by
13,180
© The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Abstract Background: Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one of the leading methods for inferring species trees from gene trees while accounting for gene tree discordance. ASTRAL uses dynamic programming to search for the tree that shares the maximum number of quartet topologies with input gene trees, restricting itself to a predefined set of bipartitions. Results: We introduce ASTRAL-III, which substantially improves the running time of ASTRAL-II and guarantees polynomial running time as a function of both the number of species (n) and the number of genes (k). ASTRAL-III limits the bipartition constraint set (X) to grow at most linearly with n and k. Moreover, it handles polytomies more efficiently than ASTRAL-II, exploits similarities between gene trees better, and uses several techniques to avoid searching parts of the search space that are mathematically guaranteed not to include the optimal tree. The asymptotic running time of ASTRAL-III in the presence of polytomies is O  (nk)1.726D  where D = O(nk) is the sum of degrees of all unique nodes in input trees. The running time improvements enable us to test whether contracting low support branches in gene trees improves the accuracy by reducing noise. In extensive simulations, we show that removing branches with very low support (e.g., below 10%) improves accuracy while overly aggressive filtering is harmful. We observe on a biological avian phylogenomic dataset of 14K genes that contracting low support branches greatly improve results. Conclusions: ASTRAL-III is a faster version of the ASTRAL method for phylogenetic reconstruction and can scale up to 10,000 species. With ASTRAL-III, low support branches can be removed, resulting in improved accuracy. Keywords: Phylogenomics, Incomplete lineage sorting, ASTRAL Keywords: Phylogenomics, Incomplete lineage sorting, ASTRAL Keywords: Phylogenomics, Incomplete lineage sorting, ASTRAL (while “gene trees” need not be inferred from functional genes, following the conventions of the field, we will refer to them as such). This two-step approach stands in con- trast to concatenation [8], where all the data are combined and analyzed in a single analysis. The two-step approach aims to account for discordances between gene trees and the species tree (but its effectiveness is debated [9–12]) and is more computationally efficient than statistical co- estimation of gene trees and the species tree [13]. Incom- plete lineage sorting (ILS) is a ubiquitous [14] cause of discordance. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees From RECOMB-CG - 2017: The Fifteenth RECOMB Comparative Genomics Satellite Conference Barcelona, Spain. 04-06 October 2017 Abstract ILS is typically modeled by the multi-species coalescent model (MSCM) [15, 16], where branches of the species tree represent populations, and lineages are Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 https://doi.org/10.1186/s12859-018-2129-y Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 https://doi.org/10.1186/s12859-018-2129-y *Correspondence: smirarab@ucsd.edu 1Department of Electrical and Computer Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0021, USA Full list of author information is available at the end of the article Background The potential for genome-wide discordance of evolution- ary histories [1, 2] has motivated the development of several approaches for species phylogeny reconstruction. Reconstructing a collection of gene trees, each inferred from a different part of the genome, and then summa- rizing them to get a species tree is one such approach and is used by many phylogenomic projects (e.g., [3–7]) *Correspondence: smirarab@ucsd.edu 1Department of Electrical and Computer Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0021, USA Full list of author information is available at the end of the article Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 Page 16 of 62 where N(g) is the set of all partitions representing all internal nodes in the tree g. We also define D as the sum of the cardinalities of unique partitions in gene trees: allowed to coalesce inside each branch; lineages that fail to coalesce at the root of each branch are moved to the parent branch. p Many “summary” methods have been developed to infer a species tree from a collection of input trees. Examples include MP-EST [17], NJst [18], ASTRID [19], DISTIQUE [20], ASTRAL [21, 22] and STAR [23], which only use gene tree topologies, and GLASS [24] and STEAC [23], which also use branch lengths. These methods are all proved statistically consistent under the MSCM, given error-free input gene trees; when input trees are inferred from sequence data, statistical consistency is not guar- anteed [25]. Most methods take rooted gene trees as input, but some methods (e.g., ASTRAL, NJst/ASTRID and DISTIQUE) use unrooted input trees. ASTRAL-II [22] is currently one of the commonly used summary methods. D = (M,c)∈E |M| . (2) (2) ASTRAL-I and ASTRAL-II algorithms ASTRAL solves a constrained version of the problem where a set of clusters X restricts bipartitions that the output species tree may include (recall ∀A ∈X : L − A ∈ X). Note that setting X to the powerset solves the unconstrained problem. Based on the fact that an unrooted quartet species tree always matches the most likely unrooted quartet gene tree [27], ASTRAL is proved statistically consistent [21]. Lafond and Scornavacca recently proved this problem is NP-hard [26]. In this paper, we introduce an improved version of ASTRAL called ASTRAL-III. As we will show, compared to ASTRAL-II, the new version has better running time without sacrificing accuracy. The improvements in the running time are both theoretical (reducing the asymp- totic running time so that it is guaranteed to grow polyno- mially with the dataset size) and empirical. ASTRAL (old versions) The problem addressed by ASTRAL is to find the tree that shares the maximum number of induced quartet topologies with the collection of input gene trees: Problem statement: Given a set G of input gene trees, find the species tree t that maximizes  g∈G |Q(g) ∩ Q(t)|. Problem statement: Given a set G of input gene trees, find the species tree t that maximizes  g∈G |Q(g) ∩ Q(t)|. Lafond and Scornavacca recently proved this problem is NP-hard [26]. Notations and definitions ASTRAL-II requires   d3 time for computing QI(.), making its overall running time E = ⎧ ⎨ ⎩ ⎛ ⎝M, g∈G |N(g) ∩{M}| ⎞ ⎠: M ∈N(g), g ∈G ⎫ ⎬ ⎭ (1) Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 Page 17 of 62 Page 17 of 62 O  n3k|Y|  with polytomies of unbounded degrees or O(nk|Y|) in the absence of polytomies. Beyond large k, ASTRAL-II, which scales as O  n3 k|X|1.726 in the presence of polytomies, can quickly become prohibitively slow for input trees with large poly- tomies. ASTRAL-III uses a mathematical trick to enable scoring of gene tree polytomies in time similar to binary nodes. The ability to handle large polytomies in input gene trees is important for two reasons. Some of the con- ditions that are conducive to ILS, namely shallow trees, are also likely to produce identical gene sequence data for several species. The gene tree should leave the relation- ship between identical sequences unresolved (FastTree [32] automatically does it and RAxML, which outputs an arbitrary resolution, warns the user about the input). Moreover, all summary methods, including ASTRAL, are sensitive to gene tree estimation error [22, 33–37]. One way of dealing with gene tree error, previously studied in the context of minimizing deep coalescence [38], is to contract low support branches in gene trees and use these unresolved trees as input to the summary method. While earlier studies found no evidence that this approach helps ASTRAL-II when the support is judged by SH-like Fast- Tree support [22], no study has tested this approach with bootstrap support values. We will for the first time eval- uate the effectiveness of contracting branches with low bootstrap support and show that conservative filtering of very low support branches does, in fact, help the accuracy. Noting trivially that |Y| < |X|2, the previously published running time analysis of ASTRAL-II was O  nk|X|2 for binary gene trees and O  n3k|X|2 for trees with poly- tomies. A recent result by Kane and Tao [28] (moti- vated by the analysis of ASTRAL) proved that |Y| ≤ |X|3/log3(27/4). This result immediately gives us a better upper bound on the running time. Corollary 1 ASTRAL-II runs in O  nk|X|1.726 and O  n3k|X|1.726 , respectively, with and without polytomies in gene trees. ASTRAL-III ASTRAL-III has six new features: ASTRAL-III has six new features: 1. Heuristics for building the set X are modified to ensure |X| = O(nk). This step alone (without subsequent improvements) guarantees the overall running time is O  (nk)2.726 for binary gene trees and O  n4.726k2.726 for polytomies. Notations and definitions Let the set of n species be called L and let G be the set of k input gene trees on L. Let [ d] represent the set {1, 2 . . . , d}. We use Q(t) to denote the set of quartet trees induced by a tree t. Any subset of L is called a cluster. We define a partition as a set of clusters that are pairwise mutually exclusive; note that we abuse the term “parti- tion” here because the union of all clusters in a partition need not give the complete set. Each node in an unrooted tree defines a partition. A bipartition (tripartition) is a partition with cardinality two (three); a partition with car- dinality at least four corresponds to a multifurcation (also referred to as a polytomy). Let X (the constraint biparti- tion set) be a set of clusters such that for each A ∈X, we also have L −A ∈X. We use Y to represent the set of all tripartitions that can be build from X: ASTRAL uses dynamic programming to solve the prob- lem using the recursive relation: V(A) =  0 |A| = 1 maxA′⊂A,(A′|A−A′|L−A)∈Y V(A, A′) |A| > 1 V(A, A′) = V(A′) + V(A −A′) + w(A′|A −A′|L −A) where the function w(T) scores each tripartition T = (A|B|C) against each node in each input gene tree. Let par- tition M = (M1|M2|...|Md) represent an internal node of degree d in a gene tree. The overall contribution of T to the score of any species tree that includes T is: w(T) = g∈G M∈N(g) 1 2QI(T, M) (3) (3) where, defining ai = |A ∩Mi|, bi = |B ∩Mi|, and ci = |C ∩Mi|, we have: Y={(A′, A−A′, L−A):A′ ⊂A, A ∈X, A′ ∈X, A−A′ ∈X} . QI(T, M) = i∈[d] j∈[d]−{i} k∈[d]−{i,j} ai + bj + ck −3 2 aibjck . (4) We use E to denote the set of all unique partitions and their frequency in G. Thus, (4) As previously proved [21], QI(T, M) computes twice the number of quartet trees that are going to be shared between any two trees if one includes only T and the other includes only M. Notations and definitions Corollary 1 ASTRAL-II runs in O  nk|X|1.726 and O  n3k|X|1.726 , respectively, with and without polytomies in gene trees. In ASTRAL-I, X is the set of all bipartitions observed in input gene trees. While sufficient for statistical con- sistency and often for accuracy, under some conditions, this set X is too restrictive. To address this shortcoming, ASTRAL-II [22] uses several heuristics (see Additional file 1: Appendix A) and further expands the set X. Even though ATRAL-II tries to limit |X|, it does not provide any guarantees as to how it grows with n and k. In the worst case, |X| can grow exponentially, and thus, ASTRAL-II does not guarantee polynomial running time. The rela- tively high accuracy of ASTRAL-II has been shown in several simulations [20, 22, 29, 30] and it has been adopted by the community as one of the main methods used in phylogenomics. ASTRAL has the ability to compute branch lengths in coalescent units [2] and a measure of branch support called local posterior probability [31]. ASTRAL-III ASTRAL-III ASTRAL-III has six new features: ASTRAL-III ASTRAL-III has six new features: New search space: |X| = O(nk) ASTRAL-II uses several heuristic methods to build X (see the original paper [22] for details). The main method involves computing several extended majority consensus trees from gene trees and then resolving polytomies in these consensus trees using three techniques (mentioned below). These steps are repeated for 10 rounds or more until very few (less than a constant threshold) of the bipar- titions observed are new to X. Because the number of rounds is not constant or a function of n and k, we can- not bound how X grows with n and k for ASTRAL-II. In ASTRAL-III, we limit the number of rounds by a con- stant value (default set to 110). This enables us to provide guarantees of a polynomial growth of |X| with n and k. y y The second change in ASTRAL-III is that we now use a UPGMA tree inferred based on the similarity matrix as the guide tree. We observed that the UPGMA tree summarizes the input gene trees more accurately than the greedy tree (see Additional file 1: Table S1). Finally, in ASTRAL-III, we improve the definition of the sim- ilarity matrix in the presence of gene tree polytomies. Unlike in ASTRAL-II, we ensure that unresolved quartet trees induced by gene trees do not increase the similar- ity between pairs of taxa included in those quartets. Note that the similarity matrix, which is based on quartets, should not be confused with the quartet score optimized by ASTRAL. To get to X = O(nk), we need further changes. As men- tioned, three techniques are used to resolve each poly- tomy of degree d in extended majority consensus trees. The first technique uses a precomputed distance matrix to build a UPGMA tree starting from sides of the polytomy and adds the new bipartitions from the UPGMA tree to X. This can only add O(d) = O(n) resolutions. The second technique computes a greedy consensus of gene trees sub- sampled to randomly selected taxa (one from each side of the polytomy) and adds bipartitions from the greedy con- sensus to X. This also can only add O(d) new bipartitions. The third resolution samples a taxon from each side of the polytomy, computes d caterpillar trees, each constructed based on decreasing similarity to each sampled taxon, and adds the bipartitions from all these caterpillar trees to X. New search space: |X| = O(nk) This quadratic resolution step can add O  d2 = O  n2 bipartitions to X. To have |X| = O(n), we need to change this step. Let d1 . . . dr be the list of all polytomy degrees in an extended majority consensus tree in the ascend- ing ordered. We find the smallest threshold q such that q i=1 d2 i ≤cn for some constant c (default = 25). In ASTRAL-III, we apply the quadratic resolution technique only for polytomies d1 . . . dq; this, by definition, ensures no more than O(d) = O(n) bipartitions are added in each round. Proof In (d) time, we can compute: Proof In (d) time, we can compute: Sa = i∈[d] ai and Sa,b = i∈[d] aibi (5) (5) where ai = |A ∩Mi| and bi = |B ∩Mi|; we can also com- pute Sb, Sc, Sa,c and Sb,c (similarly defined). Equation 4 computes twice the number of quartet tree topologies shared between an unrooted tree with internal node T and Limitations of ASTRAL-II Several shortcomings of ASTRAL-II in terms of run- ning time are addressed here (ASTRAL-III); our improve- ments, in turn, enable new types of analyses. While ASTRAL-II can analyze datasets with a thou- sand species and gene trees in reasonable time, it does not easily scale to many tens of thousands of input trees. Datasets with more than ten thousand loci are already available (e.g., [5]) and as more genomes are sequenced, more are destined to become available in the near future. Moreover, being able to handle large k (i.e., numbers of input trees) enables using multiple trees per locus (e.g., a Bayesian sample) as input to ASTRAL. The limited scal- ability of ASTRAL with k has two reasons. First, the set X is not bounded in ASTRAL-II and can grow to become the power set. Thus, in ASTRAL-II, |X| can theoretically grow exponentially with n. We fix this in ASTRAL-III by modifying heuristics that form the set X so that they all guarantee that |X| = O(nk). The second cause of the slow- down is that computing each w(T) for a tripartition T requires (nk). This computation does not exploit simi- larities between gene trees, a shortcoming that we fix in ASTRAL-III.   2. Heuristics for building the set X are modified to enlarge X for gene trees with polytomies without breaking |X| = O(nk) guarantees. This can impact the accuracy and empirical running times but not the asymptotic running time. 3. A new way of computing w(q) is introduced to reduce the running time for scoring a gene tree to O(n), instead of O  n3 , in the presence of polytomies. This step, combined with the previous steps, reduces the total running time to O  (nk)2.726 irrespective of whether gene trees have polytomies. 4. A polytree is used to represent gene trees, and this enables an algorithm that reduces the overall running time from O  (nk)2.726 to O(D.(nk)1.726), which is the final theoretical analysis of ATRAL-III running time. 5. A new algorithm, similar to A* [39], is used to compute an upper-bound on the best possible resolution of a clade; we need not expand a clade Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 Page 18 of 62 compared to ASTRAL-II for multifurcating gene trees. However, |X| is enlarged at most by a constant factor and we retain |X| = O(nk). Limitations of ASTRAL-II recursively when its upper-bound is below the best available score. The worst case asymptotic running time does not change due to this feature. recursively when its upper-bound is below the best available score. The worst case asymptotic running time does not change due to this feature. If a gene tree includes polytomies, ASTRAL-II adds bipartitions implied by resolutions of that polytomy to the set X using a guide tree g. To build g, a greedy consen- sus of all gene trees is computed and is further refined to become binary by applying UPGMA to each polytomy of the greedy tree using a precomputed similarity matrix (see the original paper [22] for details). To resolve a gene tree polytomy of degree d, ASTRAL-II first randomly samples d taxa, each from one side of the polytomy. Let S be the sampled taxa. All bipartitions from the tree g restricted to the set S of leaves are added to X. While in ASTRAL-II this process is done only once, in ASTRAL-III, we repeat the process three times with different random samples S. This increases |X| but at most by a constant factor. The enlarged X can lead to improved accuracy when input trees include many polytomies. 6. A two-stage heuristic mechanism is designed to further tighten the upper bounds used in pruning unnecessary parts of the search space. The worst case asymptotic running time is not impacted. A beta version of ASTRAL-III was recently described [40] and that version included features 3–5 but not the others. We next describe each improvement. Efficient handling of Polytomies Recall that ASTRAL-II uses Eq. 4 to score a tripartition against a polytomy of size d in (d3) time. Our next Lemma shows that this can be improved. Lemma 1 Let QI(T, M) be twice the number of quar- tet tree topologies shared between an unrooted tree that only includes a node corresponding to the tripartition T = (A|B|C) and another tree that includes only a node corre- sponding to a partition M = (M1|M2|...|Md) of degree d; then, QI(T, M) can be computed in time (d). Trimming of the dynamic programming We now introduce an upper-bound (proved in Additional file 1: Appendix B): V(A) ≤U(A) = w(A|A|L) 2 −w(A|A|A) 3 . Lemma 2 The score of a tripartition T = (A|B|C) against all gene trees (i.e., the w(T) score) can be computed in (D). Let U(A, A′′) = U(A′′) + U(A −A′′) + w(A′′|A − A′′|L −A). Since V(A) ≤U(A), for any (A′|A −A′|L − A′) ∈Y and (A′′|A −A′′|L −A′′) ∈Y, we no longer need to recursively compute V(A′′) and V(A −A′′) when U(A, A′′) ≤V(A, A′). When computing V(A) by maximizing the score over all resolutions of A, imag- ine that we first encounter A′ and then A′′. We avoid expanding A′′ when U(A, A′′) ≤V(A, A′). This approach clearly makes the order of processing of the resolutions important. To heuristically improve the efficiency of this approach, we order all (A′|A −A′|L −A) ∈Y according to U(A, A′). Note that computing U(A) does not require recursive computations down the dynamic programming DAG. Thus, the use of this upper-bound results in the trimming of the search space. However, as far as we can tell, this trimming does not improve the theoretical running time. Proof In ASTRAL-III, we keep track of nodes that appear in multiple trees. This enables us to reduce the total calculation by using multiplicities: w(T) = (M,c)∈E c × QI(T, M) . (7) (7) We achieve this in two steps. In the first step, for each distinct gene tree cluster W, we compute the cardinality of the intersection of W and sets A, B, and C once using a depth-first search with memoization. Let children(W) denote the set of children of W in an arbitrarily chosen tree g ∈G containing W. Then, we have the following recursive relation: |W ∩A| = Z∈children(W) |Z ∩A| (8) (8) (ditto for |W ∩B| and |W ∩C|). All such intersection values can be computed in a post-order traversal of a poly- tree. In this polytree, all unique clusters in the gene trees are represented as vertices and parent-child relations are represented as edges; note that when a cluster has differ- New search space: handling gene tree polytomies We also change the way ASTRAL builds X in the pres- ence of gene tree polytomies. Our goal is to increase |X| Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 Page 19 of 62 another tree with one internal node M [22]. Equation 4 can be rewritten as: ent resolutions in two different input trees, we arbitrary choose one set of children in building the polytree. The polytree will include no more than D edges; thus, the time complexity of traversing this polytree (to compute Eq. 8) for all nodes is O(D). Once all intersections are com- puted, in the second step, we simply compute the sum in Eq. 7. Each QI(.) computation requires (d) by Lemma 1. Recalling that D =  (M,c)∈E |M|, it is clear that com- puting Eq. 7 requires (D). Therefore, both steps can be performed in (D). QI ((A|B|C), M) = i∈[d] ai 2   (Sb −bi)(Sc −ci) −Sb,c + bici  + i∈[d] bi 2   (Sa −ai)(Sc −ci) −Sa,c + aici  + i∈[d] ci 2   (Sa −ai)(Sb −bi) −Sa,b + aibi  (6) (the derivation is given in the Additional file 1: Appendix B). Computing Eq. 6 instead of Eq. 4 clearly reduces the running time to (d) instead of   d3 . Theorem 1 The running time of ASTRAL-III grows as O  D(nk)1.726 for both binary and multifurcating gene trees. ASTRAL needs to score each of the |Y| tripartitions considered in the dynamic programming against each internal node of each input gene tree. The sum of degrees of k trees on n leaves is O(nk) (since that sum can never exceed the number of bipartitions in gene trees) and thus: Proof By results of Kane and Tao [28], the size of the set Y is O  |X|1.726 , and for each element in Y, by Lemma 2, we require O(D) to compute the weights, regardless of the presence or absence of polytomies. The running time of ASTRAL is dominated by comput- ing the weights [22]. Thus, the overall running time is O(D|Y|) = O  D|X|1.726 . Moreover, ASTRAL-III forces |X| to grow as O(nk), giving the overall running time of O  D(nk)1.726 Corollary 2 Scoring a tripartition (i.e., computing w) can be done in O(nk). Gene trees as a Polytree ASTRAL-II scores each dynamic programming triparti- tion against each individual node of each gene tree. How- ever, nodes that are repeated in several gene trees need not be recomputed. Recalling the definitions of E and D (Eqs. 1 and 2), Datasets Let Uα(A, Aj) be defined as min  U(Aj), αVα(Aj)  +min  U(A−Aj), αVα(A −Aj)  + w(Aj|A −Aj|L −A) min  U(Aj), αVα(Aj)  +min  U(A−Aj), αVα(A −Aj)  + w(Aj|A −Aj|L −A) min  U(Aj), αVα(Aj)  +min  U(A−Aj), αVα(A −Aj)  + w(Aj|A −Aj|L −A) and note that Uα(A, Aj) ≥V(A, Aj) = V(Aj) + V(A − Aj) + w(Aj|A −Aj|L −A). Thus, during the dynamic pro- gramming, for i < j, if V(A, Ai) > Uα(A, Aj), then it is guaranteed that V(A, Ai) ≥V(A, Aj), and thus we no longer need to recursively compute V(Aj) and V(A −Aj). The hope is that the Uα function will give us tighter upper bounds compared to the U function previously defined. Whether this happens or not depends on the choice of α, the order of visiting clusters, and the particularities of a dataset. and note that Uα(A, Aj) ≥V(A, Aj) = V(Aj) + V(A − Aj) + w(Aj|A −Aj|L −A). Thus, during the dynamic pro- gramming, for i < j, if V(A, Ai) > Uα(A, Aj), then it is guaranteed that V(A, Ai) ≥V(A, Aj), and thus we no longer need to recursively compute V(Aj) and V(A −Aj). The hope is that the Uα function will give us tighter upper bounds compared to the U function previously defined. Whether this happens or not depends on the choice of α, the order of visiting clusters, and the particularities of a dataset. SimPhy-homogeneous (S100): We simulated a new 101-taxon dataset using SimPhy [42] with 50 replicates, each with a different species tree. The species trees are simulated under the birth-only process with birth rate 10−7, fixed haploid Ne of 400K, and the number of gen- erations sampled from a log-normal distribution with mean 2.5M. For each replicate, 1000 true gene trees are simulated under the MSCM (exact commands shown in Additional file 1: Appendix C and parameters given in Additional file 1: Table S2). The average normalized RF distance between true species trees and true gene trees was in most replicates in the [0.3, 0.6] range, with an aver- age of 0.46 (Fig. 1). We use Indelible [43] to simulate the nucleotide sequences along the gene trees using the GTR evolutionary model [44] with 4 different fixed sequence lengths: 1600, 800, 400, and 200bp. Datasets We then use Fast- Tree2 [32] to estimate both ML and 100 bootstrapped gene trees under the GTR+ (requiring more than two million runs in total). Gene tree estimation error, mea- sured by the FN rate between the true gene trees and the estimated gene trees, depended on the sequence length as shown in Fig. 1 (0.55, 0.42, 0.31, and 0.23 on average for While any choice of α ≥1 would guarantee the correct solution to the dynamic programming, we have empiri- cally selected a heuristic to choose α. We set α = U(L) g(L) , where g(A) = g(Ai)+g(A−Ai)+w(Ai|A−Ai|L−A) where i = arg maxjU(Aj) + U(A −Aj) + w(Aj|A −Aj|L −A) and g(A) = 0 for |A| = 1. Just as before, we order the clusters in the decreasing order of U(A, Ai). Two-staged α-trimming In order to further trim the search space, another upper- bound of V(A) is calculated. For a given α ≥1 and any ordering of the set  A′ : (A′|A −A′|L −A) ∈Y  denoted by A1 . . . Ar, we define Vα(A) as follows. Page 20 of 62 Page 20 of 62 Page 20 of 62 Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 Vαi(A) = ⎧ ⎪⎨ ⎪⎩ 0, i = 0 Vα(A, Ai), Vα(A, Ai) > αVαi−1(A) Vαi−1(A), otherwise ⎫ ⎪⎬ ⎪⎭ for 0 ≤i ≤r Vα(A, Ai) = Vα(Ai) + Vα(A −Ai) + w(Ai|A −Ai|L −A) and Vα(A) = Vαr(A) Vαi(A) = ⎧ ⎪⎨ ⎪⎩ 0, i = 0 Vα(A, Ai), Vα(A, Ai) > αVαi−1(A) Vαi−1(A), otherwise ⎫ ⎪⎬ ⎪⎭ for 0 ≤i ≤r Vα(A, Ai) = Vα(Ai) + Vα(A −Ai) + w(Ai|A −Ai|L −A) and Vα(A) = Vαr(A) Vαi(A) = ⎧ ⎪⎨ ⎪⎩ 0, i = 0 Vα(A, Ai), Vα(A, Ai) > αVαi−1(A) Vαi−1(A), otherwise ⎫ ⎪⎬ ⎪⎭ for 0 ≤i ≤r Vα(A, Ai) = Vα(Ai) + Vα(A −Ai) + w(Ai|A −Ai|L −A) and Vα(A) = Vαr(A) RQ1: Can contracting low support branches improve the accuracy of ASTRAL? RQ2: How do the running time and search space compare between ASTRAL-II and ASTRAL-III? RQ3: How accurate is ASTRAL-III, which guaran- tees polynomial size search space, compared to ATRAL-II? Datasets Avian biological dataset: Neoavian relationships show extremely high levels of gene tree discord, perhaps because their ancestors experienced a rapid radiation [5]. A dataset of 48 genomes representing all avian orders has been used to partially resolve this rapid radiation [5]. A set of 14,446 loci (including exons, introns, and UCEs) was used to produce two reference species trees using con- catenation and using a coalescent-based method [5, 33]. We use the set of all unbinned gene trees and compare ASTRAL-III with and without contraction against both reference trees. We can compute Vα(A) using an algorithm equivalent to our dynamic programming for computing V(A), except that, as resolutions of a clade A are being tested, a new one is accepted only if it improves upon the previous best res- olution by a factor of α (thus, α = 1 simply reproduces our existing dynamic programming). When computing Vα(A), for any i < j, if α (Vα(A, Ai)) ≥U(A, Aj), then it is guaranteed that α (Vα(A, Ai)) ≥Vα  A, Aj  , and thus we no longer need to recursively compute Vα(Aj) and Vα(A −Aj). After all Vα(A) values are computed for some choice of α, we turn to computing V(A). Simulated avian-like dataset: This simulated dataset, previously used to emulate the biological avian dataset [33], has three model conditions with respect to the sim- ulated levels of ILS: 1X is the default, whereas 0.5X divides each branch length in half (increasing ILS) and 2X multiplies them by 2 (reducing ILS). Average RF dis- tances between true species tree and true gene trees are 0.35, 0.47, and 0.59, respectively for 2X, 1X, and 0.5X. To further test the impact of gene tree estima- tion error, sequence lengths were also varied to create four model conditions: 250bp alignments (0.67 RF dis- tance between true gene trees and estimated gene trees), 500bp (0.54 RF), 1000bp (0.39 RF) and 1500bp (0.30 RF), all based on the 1X ILS. We use 1000 gene trees, and 20 replicates per condition. Gene trees are esti- mated using RAxML [41] with 200 replicates of bootstrap- ping. Observe that Vα(A) ≤V(A) ≤αVα(A). Experimental setup We study three research questions: RQ1: Can contracting low support branches improve the accuracy of ASTRAL? RQ1: Can contracting low support branches improve the accuracy of ASTRAL? RQ2: How do the running time and search space compare between ASTRAL-II and ASTRAL-III? RQ2: How do the running time and search space compare between ASTRAL-II and ASTRAL-III? RQ3: How accurate is ASTRAL-III, which guaran- tees polynomial size search space, compared to ATRAL-II? Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 Page 21 of 62 b a Fig. 1 Properties of the S100 dataset. a The density plot of the amount of true gene discordance measured by the FN rate between the true species tree and the true gene trees. b The density plot of gene tree estimation error measured by FN rate between true gene trees and estimated gene trees for different sets of sequence lengths b a b a Fig. 1 Properties of the S100 dataset. a The density plot of the amount of true gene discordance measured by the FN rate between the true species tree and the true gene trees. b The density plot of gene tree estimation error measured by FN rate between true gene trees and estimated gene trees for different sets of sequence lengths 200bp, 400bp, 800bp, and 1600bp, respectively). We sam- ple 1000, 500, 200, or 50 genes to generate datasets with varying numbers of gene trees. 200bp, 400bp, 800bp, and 1600bp, respectively). We sam- ple 1000, 500, 200, or 50 genes to generate datasets with varying numbers of gene trees. To measure the accuracy of estimated species trees, we use False Negative (FN) rate. Note that in all our species tree comparisons, FN rate is equivalent to normalized Robinson–Foulds (RF) [46] metric because the ASTRAL species trees are fully resolved. All running times are mea- sured on a cluster with servers with Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz; each run was assigned to a single process, sharing cache and memory with other jobs. SimPhy-ASTRAL2 (S200): This dataset (201 taxa) is from the ASTRAL-II paper [22]. We use its most chal- lenging model conditions with max tree height set to 500K generations and two rates of speciation: 10−6 and 10−7 (respectively, recent and deep speciation events). Com- pared to S100, this dataset has a much higher level of ILS. Experimental setup This was the only case in the ASTRAL-II paper where enlarging X substantially impacted accuracy [22]. We use S200 to test if our changes to X have compromised the accuracy. Like S100, gene alignments have varying lengths and mutation rates, leading to a wide range of gene tree error [22]. We analyze the data using 1000, 200, or 50 genes, and each model condition has 50 replicates; follow- ing the original paper, three replicates with low signal are removed. S100 On this dataset, contracting very low support branches in most cases improves the accuracy (Fig. 2 and Additional file 1: Table S3). However, the excessive removal of branches with high, moderate, or occasionally low sup- port degrades the accuracy. Nevertheless, filtering at 10% is always beneficial on average (Additional file 1: Table S3). The threshold where contracting starts to become detri- mental depends on the condition, especially the number of gene trees and the alignment length, perhaps represent- ing a signal to noise ratio trade-off. RQ1: Impact of contracting low support branches on accuracy We investigate RQ1 on the two simulated datasets where bootstrapping was feasible (avian and S100) and on the real avian dataset. On S200, due to its size, bootstrapping was not feasible and thus we cannot test RQ1. Methods and Evaluation We compare ASTRAL-III (version 5.5.4) to ASTRAL-II (version 4.11.1) in terms of running time and accuracy. To address RQ1, we draw bootstrap support values on the ML gene trees and then contract branches with bootstrap support up to a threshold (0, 3, 5, 7, 10, 20, 33, 50, and 75%,) using the newick utility package [45]. Together with the original gene trees, we have 10 different versions of ASTRAL-III. As the number of genes increases, the optimal thresh- old for contracting also tends to increase. Combin- ing all model conditions, the error continues to drop Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 Page 22 of 62 Fig. 2 Impact of contraction on the S100 dataset. The FN error of ASTRAL-III species trees is shown on the S100 dataset given k = 50, 200, 500, or 1000 genes (boxes) run on the original FastTree gene trees (non) or gene trees with branches with ≤{0, 3, 5, 7, 10, 20, 33, 50}% support contracted (x-axis). Average FN error and standard error bars (200 replicates) are shown with the four alignment lengths combined (black solid line). average FN error broken down by alignment length (50 replicates) is also shown (dashed colored lines) Fig. 2 Impact of contraction on the S100 dataset. The FN error of ASTRAL-III species trees is shown on the S100 dataset given k = 50, 200, 500, or 1000 genes (boxes) run on the original FastTree gene trees (non) or gene trees with branches with ≤{0, 3, 5, 7, 10, 20, 33, 50}% support contracted (x-axis). Average FN error and standard error bars (200 replicates) are shown with the four alignment lengths combined (black solid line). average FN error broken down by alignment length (50 replicates) is also shown (dashed colored lines) with a resolution around difficult species tree branches are left. until a 20% contracting threshold with 1000 genes, whereas no substantial improvement is observed after contracting branches with 5% support for 50 genes (Fig. 2). Nevertheless, removing branches with 10% or 20% does not increase the error with 50 genes. Perhaps, with few gene trees, removing branches of low sup- port leaves us with very little information left; thus, regardless of whether we contract or not, we don’t get much signal around the most difficult branches. Methods and Evaluation In con- trast, when many gene trees are given, perhaps even after removing many branches, still enough gene trees The alignment length and gene tree error also impact the effect of contraction. For short alignments (200bp) and 1000 genes, contracting branches with up to 10% support reduces the species tree error by 21% (from 8.8% with no contraction to 6.9%). As alignment length grows, benefits of gene tree contraction diminish, so that with 1600bp genes, the reduction in error is merely from 4.1 to 3.7%. This pattern is perhaps expected because, with longer alignments, branch support is expected to Fig. 3 Impact of contraction on the avian simulated dataset. The FN error of ASTRAL-III species trees is shown on the avian simulated dataset given k = 1000 genes with (left) fixed sequence lengths = 500 and varying levels of ILS, or (right) fixed ILS (1X) and varying sequence length, in each case both with full FastTree gene trees (non) or trees with branches with ≤{0, 3, 5, 7, 10, 20, 33, 50}% support contracted (x-axis). Average and standard error bars are shown for all conditions combined (black solid line) and also for each model condition separately (dashed color lines). Each model condition has 20 replicates Fig. 3 Impact of contraction on the avian simulated dataset. The FN error of ASTRAL-III species trees is shown on the avian simulated dataset given k = 1000 genes with (left) fixed sequence lengths = 500 and varying levels of ILS, or (right) fixed ILS (1X) and varying sequence length, in each case both with full FastTree gene trees (non) or trees with branches with ≤{0, 3, 5, 7, 10, 20, 33, 50}% support contracted (x-axis). Average and standard error bars are shown for all conditions combined (black solid line) and also for each model condition separately (dashed color lines). Each model condition has 20 replicates Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 Page 23 of 62 increase. Thus, with longer gene alignments and con- sequently better gene trees with higher support, there is less room for improvement by reducing the noise. Consistent with this explanation, grouping replicates based on average gene tree error gives similar results as grouping by alignment length (see Additional file 1: Figure S1). thresholds and < 26 hours for 33 – 75%). Methods and Evaluation Contract- ing 0% branches has minimal impact on the discordance (eight discordant branches with binned MP-EST instead of nine). However, contracting low support branches with 3–33% thresholds dramatically reduces the discordance with the reference tree (2, 2, 4, 2, 3, and 3 discor- dant branches, respectively, for 3, 5, 7, 10, 20, and 33%). Three thresholds (3, 5, and 10%) produce an identical tree (Fig. 4d). The remaining differences are among the branches that are deemed unresolved by Jarvis et al. and change among the reference trees as well [5]. Contracting at 50 and 75% thresholds, however, increases discordance to five and six branches, respectively. RQ2: Running time improvements Varying the number of genes (k) Varying the number of genes (k) We compare ASTRAL-III to ASTRAL-II on the avian simulated dataset, changing the number of genes from 28 to 214 and forcing X to be the same for both ver- sions to enable comparing impacts of improved weight calculation (Fig. 5). We allow each replicate run to take up to two days. ASTRAL-III improves the running time over ASTRAL-II and the extent of the improve- ment depends on k (see Additional file 1: Figure S2). With 1000 genes or more, there is at least a 2.1X improve- ment. With 213 genes, the largest value where both ver- sions could run, ASTRAL-III finishes on average 3.2 times faster than ASTRAL-II (234 versus 758 minutes). ASTRAL-II is not able to finish on the dataset with k = 214, while ASTRAL-III finishes on all conditions. More- over, fitting a line to the average running time in the log-log scale graph reveals that on this dataset, the run- ning time of ASTRAL-III on average grows as O(k2.08), which is better than that of ASTRAL-II at O(k2.28), and both are better than the theoretical worst case, which is O(k2.726). These results are consistent with the fact that ASTRAL-III considers similarities between gene tree nodes. Avian biological dataset The original analyses on this dataset [5, 33] report that MP-EST [17] run on 14,446 gene trees produces a tree that conflicts with strong evidence from the literature and other analyses on the same dataset. The statistical binning method was developed to address this shortcom- ing by combining loci together to reduce gene tree error [33, 34]. MP-EST run on binned gene trees (i.e., binned MP-EST) produced results [5, 33] that were largely con- gruent with the concatenation using ExaML [47] and differed in only five branches with low support (Fig. 4a, b); both trees were used as the reference [5]. Here, we test if simply contracting low support gene tree branches and using ASTRAL-III produces trees congruent with the reference trees. Similar to MP-EST, when ATRAL-III is run on 14,446 gene trees with no contraction, the results differ in nine and 11 branches, respectively, with respect to the refer- ence binned MP-EST and concatenation trees (Fig. 4c). Moreover, this tree contradicts some strong results from the avian analyses (e.g., not recovering the Columbea group [5]). ASTRAL-III with no contraction finishes in 32 hours, but with contraction, depending on the threshold, it takes 3 to 84 h (> 50 h for 0 – 20% Similar to MP-EST, when ATRAL-III is run on 14,446 gene trees with no contraction, the results differ in nine and 11 branches, respectively, with respect to the refer- ence binned MP-EST and concatenation trees (Fig. 4c). Moreover, this tree contradicts some strong results from the avian analyses (e.g., not recovering the Columbea group [5]). ASTRAL-III with no contraction finishes in 32 hours, but with contraction, depending on the threshold, it takes 3 to 84 h (> 50 h for 0 – 20% avian-like simulations On the avian simulated dataset, contracting low support branches helps accuracy marginally, but the extent of impact depends on the model condition (Fig. 3). With moderate ILS (2X), we see no improvements as a result of contracting low support branches, perhaps because the average error is below 5% even with no contraction, leaving little room for improvements. Increasing ILS, we start to see improvements using contracted gene trees. Removing branches of up to 5% support reduces the error from 13 to 11% with 0.5X, and from 8 to 7% for the 1X condition. Thus, consistent with simulations, contracting very low support branches seems to produce the best results, when judged by similarity with the reference trees. To summarize, ASTRAL-III obtained on unbinned but col- lapsed gene trees agreed with all major relations in Jarvis et al., including the novel Columbea group, whereas the unresolved tree missed important clades (Fig. 4). When ILS is fixed to 1X and sequence length is varied (Fig. 3), contracting is helpful mostly with short sequences (e.g., 250 bp). With longer sequences, where gene tree esti- mation error is low, little or no improvement in accuracy is obtained. The best accuracy is typically observed by contracting at 0–5%. The gains in accuracy comparing no contraction to contraction at 0, 3, 5% thresholds are statistically significant (p = 0.017, 0.028, and 0.013) according to one-tailed paired t-tests. Running time for large polytomies y ASTRAL-III has a clear advantage compared to ASTRAL- II with respect to the running time when gene trees include polytomies (Fig. 6a and Additional file 1: Figure S3). Since ASTRAL-II and ASTRAL-III can have a different set X, we show the running time per each weight calculation (i.e., Eq. 3). As we contract low support branches and hence increase the prevalence of Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 Page 24 of 62 Page 24 of 62 Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 The search space polytomies, the weight calculation time quickly grows for ASTRAL-II, whereas, in ASTRAL-III, the weight calcu- lation time remains flat, or even decreases. These results are consistent with a change of asymptotic running time to score a polytomy of size d from O(d3) in ASTRAL-II to O(d) in ASTRAL-III. polytomies, the weight calculation time quickly grows for ASTRAL-II, whereas, in ASTRAL-III, the weight calcu- lation time remains flat, or even decreases. These results are consistent with a change of asymptotic running time to score a polytomy of size d from O(d3) in ASTRAL-II to O(d) in ASTRAL-III. Comparing the size of the search space (|X|) between ATRAL-II and ASTRAL-III shows that as intended, the search space is decreased in size for cases with no poly- tomy but can increase in the presence of polytomies (Fig. 6b). With no contraction, on average, |X| is always c d a b Fig. 4 Avian dataset with 14,446 genes. Shown are reference trees from the original paper [5] using the coalescent-based binning (a) and concatenation (b), and two new trees using ASTRAL-III with no contraction (c) and with contraction with 3, 5, and 10% thresholds (d). Support values (bootstrap for a, b and local posterior probability for c, d) shown for all branches except those with full support; in (d), support is shown for 3, 5, and 10%, respectively. Branches conflicting with the reference coalescent-based tree are shown as dotted red lines b a b a d c d c Fig. 4 Avian dataset with 14,446 genes. Shown are reference trees from the original paper [5] using the coalescent-based binning (a) and concatenation (b), and two new trees using ASTRAL-III with no contraction (c) and with contraction with 3, 5, and 10% thresholds (d). Support values (bootstrap for a, b and local posterior probability for c, d) shown for all branches except those with full support; in (d), support is shown for 3, 5, and 10%, respectively. Branches conflicting with the reference coalescent-based tree are shown as dotted red lines Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 Page 25 of 62 Fig. 5 Running time versus k. Average running times (4 replicates) are shown for ASTRAL-II and ASTRAL-III on the avian dataset with 500bp or 1500bp alignments with varying numbers of gens (k), shown in log scale (see Additional file 1: Figure S2 for normal scale). RQ3: ASTRAL-II versus ASTRAL-III accuracy Despite limiting |X| to grow at most linearly with n and k, the accuracy of ASTRAL-III remains unchanged compared to ASTRAL-II (Table 1 and Additional file 1: Figures S4–S7). Importantly, even for the very challenging S200 dataset, the accuracy is not reduced substantially even though |X| is reduced by up to 47%. Over all datasets, differences in error are less than 0.002, except for three datasets where the error of ASTRAL-III was less than ASTRAL-II by 0.003, 0.005, and 0.006 and The search space A line is fit to the data points in the log/log space and line slopes are shown. ASTRAL-II did not finish on 214 genes in 48 hours Fig. 5 Running time versus k. Average running times (4 replicates) are shown for ASTRAL-II and ASTRAL-III on the avian dataset with 500bp or 1500bp alignments with varying numbers of gens (k), shown in log scale (see Additional file 1: Figure S2 for normal scale). A line is fit to the data points in the log/log space and line slopes are shown. ASTRAL-II did not finish on 214 genes in 48 hours smaller for ASTRAL-III than ASTRAL-II. With few error- prone gene trees (50 gene trees from 200bp alignments), the search space has reduced dramatically but with many genes or high-quality gene trees, the reductions are min- imal. Moreover, the search space for gene trees estimated from short alignments (e.g., 200 bp) is several times larger than those based on longer alignments (e.g., 1600 bp) for both methods. These are results of the first fea- ture of ASTRAL-III that forces the search space to grow at O(nk). two cases where the error increased by 0.004. Over all datasets, the differences between ASTRAL-II and ASTRAL-III were not statistically significant according to a paired t-test (p-value = 0.496). Since ASTRAL-III has a reduced search space, its quartet scores are typ- ically slightly lower than ASTRAL-II, but these reduc- tions are never more than 0.06%. As expected, the largest drops in the quartet score happen for the challeng- ing S200 dataset with only 50 gene trees. The search space reduces in almost all cases and the reductions can be as much as 72%. Thus, the improved running time of ASTRAL-III does not come at the price of reduced accuracy. Contracting low support branches initially increases the search space. This is because ASTRAL-III unlike ASTRAL-II adds multiple resolutions per polytomy to X. Further contraction results in reductions in |X|, presum- ably because many polytomies exist and they are resolved similarly inside ASTRAL-III. Discussion Below we further comment on ASTRAL-III in terms of accuracy and running time. We finish by comparing ASTRAL-III and ASTRAL-III-beta. Accuracy Although tree accuracy can improve with contracted gene trees, the gap between performance on true gene trees and estimated gene trees remains wide (Additional file 1: Table S3). On the S100 dataset, respectively for 50, 200, 500, and 1000 genes, the best average error with 1600bp gene trees among all contraction levels were 9.8%, 5.9%, 4.3%, and 3.7% compared to 7.0%, 3.7%, 2.4%, and 1.5% Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 Page 26 of 62 a b Fig. 6 Weight calculation and |X| on S100. Average and standard error of (a) the time it takes to score a single tripartition using Eq. 3 and (b) search space size |X| are shown for both ASTRAL-II and ASTRAL-III on the S100 dataset. Running time is in log scale. We vary numbers of gene trees (boxes) and sequence length (200 and 1600). See Additional file 1: Figure S3 for similar patterns for with 400 and 800bp alignments a a b b Fig. 6 Weight calculation and |X| on S100. Average and standard error of (a) the time it takes to score a single tripartition using Eq. 3 and (b) search space size |X| are shown for both ASTRAL-II and ASTRAL-III on the S100 dataset. Running time is in log scale. We vary numbers of gene trees (boxes) and sequence length (200 and 1600). See Additional file 1: Figure S3 for similar patterns for with 400 and 800bp alignments with true gene trees. Thus, while contracting low support branches helps in addressing gene tree error, improved methods of gene tree estimation remain crucial. Our results also indicate that in the presence of noisy gene trees, increased numbers of genes are needed to achieve high accuracy. For example, on the S100 dataset, with 1000 gene trees of only 200bp and contracting with a 10% threshold, the species tree error was 6.9%, which slightly outperformed the accuracy with only 50 true gene trees. This observation encourages the use of a large number of gene trees; incidentally, a main feature of ASTRAL-III is improved running time with many genes. error due to lack of signal impacts the optimal thresh- old. One may expect that other sources of error, includ- ing incorrect orthology, incorrect alignment, and model misspecifications may also impact the optimal thresh- old. Accuracy Regardless of the choice of the optimal threshold, it seems that the largest benefits are associated with remov- ing the least supported branches. Overall, a threshold of 10% seemed to provide a good default value. In most datasets, a substantial accuracy improvement was observed when 0% BS branches were removed. Branches of 0% support are presumably resolved arbitrar- ily. The use of conserved genes or closely related taxa can increase instances where two or more taxa have identical sequences in some genes. Some tree estimation methods generate binary trees even under such conditions. Remov- ing branches that are arbitrarily resolved make sense and, as our results indicate, improves accuracy. The best choice of the threshold of contraction was somewhat sensitive to the dataset. Testing up to 1000 gene trees, we observed that more gene trees clearly increased the optimal threshold, but did not test beyond 1000 genes. One can predict that perhaps the trend may continue but also that the optimal threshold will not indefinitely increase. Similarly, we saw that the amount of gene tree The main competitor of ASTRAL is NJst [18] and its fast implementation, ASTRID [19], but these tools are not Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 Page 27 of 62 Running time Large n able to handle polytomies in input gene trees. ASTRAL-III makes it efficient to use unresolved gene trees. Moreover, beyond contracting low support branches, other strategies could be used to reduce impacts of gene tree uncer- tainty. Previous studies indicate that simply using the set of all bootstrap gene tree replicates as input to ASTRAL increases error [21], perhaps due to the increased noise [31, 35]. However, using a sample from the Bayesian dis- tribution for each gene tree may improve the accuracy of ASTRAL. To assess limits of ASTRAL-III in terms of scalability, we tested it on 20 replicates of a dataset with 5,000 species and 1000 true gene trees (simulation procedure described in Additional file 1: Appendix C and parameters given in Additional file 1: Table S4). ASTRAL-III took between 2 and 62 h to run on this dataset (9.4 hours on average). We also attempted to test ASTRAL-III on four repli- cates of a dataset with 10,000 species and 1000 true gene trees, allowing a week of running time. Of the four repli- cates, two were able to finish within the allotted time. Thus, depending on the nature of the data, ASTRAL-III may be able to scale to datasets with up to 10,000 species given sufficient running time. Finally, theoretical implications of removing low support branches are less clear than its empirical impact. In principle, branches that have low sup- port are not necessarily expected to be randomly selected among gene trees. Thus, while our empiri- cal results support the use of (conservative) filtering, the resulting procedure may lose statistical guarantees of consistency. Future work should study conditions where ASTRAL remains statistically consistent with contracted gene trees. Average running time, |X|, and |Y| The ASTRAL-III running time analysis is based on sev- eral worst-case assumptions, and real data may grow less rapidly with both n and k. Overall, although the exact a b c Fig. 7 Empirical search space. a |X| is shown for ASTRAL-II and ASTRAL-III for avian-like simulateds dataset with varying numbers of genes. b |X| is shown for ASTRAL-III for several datasets with varying n. c The density plots of logX |Y| across all ASTRAL-III runs reported in this paper. Size of the dynamic programming space Y is never above |X|1.312 here a b b a c c Fig. 7 Empirical search space. a |X| is shown for ASTRAL-II and ASTRAL-III for avian-like simulateds dataset with varying numbers of genes. b |X| is shown for ASTRAL-III for several datasets with varying n. c The density plots of logX |Y| across all ASTRAL-III runs reported in this paper. Size of the dynamic programming space Y is never above |X|1.312 here Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 Page 28 of 62 Table 1 ASTRAL-II versus ASTRAL-III. Average running time, |X|, and |Y| Average and standard error (inside parenthesis) are shown for changes in accuracy (normalized FN rate), quartet score, and search space size (|X|) Data set Model condition FN |X| Quartet score avian 0.5X-500bp −0.006 (0.007) −3% (0) −0.01% (0.01) 1X-1000bp 0.001 (0.002) −1% (0) 0.00% (0.00) 1X-1500bp 0.004 (0.003) −1% (0) 0.00% (0.00) 1X-250bp 0.004 (0.007) −3% (0) −0.01% (0.00) 1X-500bp −0.001 (0.004) −2% (0) 0.00% (0.00) 2X-500bp −0.003 (0.003) −2% (0) 0.00% (0.00) S200 1000gt-10−6 −0.001 (0.000) 0% (0) 0.00% (0.00) 200gt-10−6 0.000 (0.001) −5% (1) 0.00% (0.00) 50gt-10−6 −0.001 (0.001) −42% (2) −0.06% (0.01) 1000gt-10−7 0.001 (0.001) −1% (0) 0.00% (0.00) 200gt-10−7 −0.001 (0.001) −6% (1) 0.00% (0.01) 50gt-10−7 0.000 (0.002) −47% (2) −0.06% (0.01) S100 1000gt-1600bp 0.000 (0.000) −3% (0) 0.00% (0.00) 500gt-1600bp 0.000 (0.000) −6% (1) 0.00% (0.00) 200gt-1600bp 0.000 (0.001) −17% (1) −0.01% (0.00) 50gt-1600bp −0.001 (0.001) −46% (3) −0.01% (0.01) 1000gt-200bp −0.001 (0.002) −9% (1) 0.00% (0.00) 500gt-200bp −0.001 (0.001) −19% (1) −0.01% (0.01) 200gt-200bp −0.001 (0.001) −40% (1) −0.01% (0.00) 50gt-200bp −0.002 (0.002) −72% (1) −0.05% (0.01) 1000gt-400bp −0.001 (0.002) −6% (1) 0.00% (0.00) 500gt-400bp 0.001 (0.001) −12% (1) −0.01% (0.00) 200gt-400bp 0.000 (0.001) −29% (2) −0.01% (0.01) 50gt-400bp −0.005 (0.001) −61% (2) −0.02% (0.01) 1000gt-800bp 0.000 (0.000) −4% (0) 0.00% (0.00) 500gt-800bp 0.001 (0.001) −9% (1) 0.00% (0.00) 200gt-800bp 0.001 (0.000) −22% (2) −0.01% (0.01) 50gt-800bp 0.000 (0.001) −52% (3) −0.02% (0.01) FN: we show ASTRALIII −ASTRALII; negative numbers indicate ASTRALIII is more accurate. |X|: we show ASTRALIII−ASTRALII ASTRALII × 100; negative numbers indicate that ASTRAL-III has a reduced search space. Quartet score: we show ASTRALIII−ASTRALII ASTRALII × 100; positive numbers indicate that ASTRALIII has improved quartet scores. See Additional file 1: Figures S4–S7 for full distributions Table 1 ASTRAL-II versus ASTRAL-III. Average and standard error (inside parenthesis) are shown for changes in accuracy factors such as the amount of discordance also change. Nevertheless, across all the datasets that we had available, we tested the change in running time for fixed k as n changes and observed a linear growth (Fig. 7b), matching the worst-case scenario. Finally, establishing empirical running time growth requires establishing the rate of the growth of |Y| with respect to |X|. The |Y| ≤|X|1.726 upper-bound is for spe- cialized formations of the set X [28]. Empirically, as |X| increases, the size of |Y| in ASTRAL-III does not increase as fast as the worst-case scenario implies. Comparisons to ASTRAL-III-beta p The beta version of ASTRAL-III [40] included features 3–5 but not changes to X (features 1 and 2) or the two- staged α-trimming technique (feature 6). For complete- ness, we compared ASTRAL-III-beta and ASTRAL-III in terms of accuracy, quartet score, and the running time (Table 2). Accuracy and quartet scores are very similar, perhaps with a small improvement since the beta version. The search space is reduced since the beta version (due to features 1 and 2), and the running times are substantially decreased (at least by half in most cases). The reduc- tions in the running time are due to α-trimming, reduced |X|, in addition to further improvements in details of our implementation of the polytree data-structure. To further demonstrate the impact of the α-trimming feature, we randomly chose 18 species from the avian dataset with 1500bp and 1X ILS. On this limited dataset, Table 2 ASTRAL-III-beta vs ASTRAL-III. Columns are defined similar to Table 1. Model Contraction FN |X| |Y| Quartet Running condition score time avian-0.5X-500bp None −0.003 −3% −9% −0.02% −48% avian-1X-250bp None −0.001 −3% −9% 0.00% −56% avian-1X-500bp None −0.001 −2% −6% 0.00% −50% avian-1X-1000bp None −0.001 −1% −4% 0.00% −58% avian-1X-1500bp None 0.001 −1% −4% 0.00% −57% avian-2X-500bp None −0.002 −2% −4% 0.00% −65% avian-0.5X-500bp 10% −0.003 −3% −29% −0.01% −69% avian-1X-250bp 10% −0.001 −50% −40% 0.00% −81% avian-1X-500bp 10% 0.003 −18% −62% −0.01% −62% avian-1X-1000bp 10% 0.000 −5% −8% 0.00% −61% avian-1X-1500bp 10% 0.003 0% −1% 0.00% −55% avian-2X-500bp 10% −0.002 −14% −18% 0.00% −62% Negative numbers indicate ASTRAL-III-beta has a larger value (i.e., has higher error, larger search space, better quartet scores, and is slower) Table 2 ASTRAL-III-beta vs ASTRAL-III. Columns are defined similar to Table 1. value depends on the dataset and especially the amount of discordance, the running time of ASTRAL seems to grow roughly quadratically with both n and k (i.e., proportion- ally to n2k2); see Additional file 1: Figures S2 and S8. y g ASTRAL-III bounds |X| to grow at most linearly with n and k. Empirically, we observe that |X| grows sublinearly with k  closetoO  k 3 4  on the avian simulated dataset (Fig. 7a). Note that the avian dataset has one of the highest levels of ILS; the dependence on k is expected to be lower for datasets with lower gene tree discordance. Average running time, |X|, and |Y| Across all of our ASTRAL-III runs in this paper, |Y| ranged in 90% of our runs between |X|1.07 and |X|1.20, and the overall average was |X|1.11 (Fig. 7c). Author details 1 1Department of Electrical and Computer Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0021, USA . 2Department of Computer Science and Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0021, USA . 3Bioinformatics and Systems Biology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0021, USA . References 1. Maddison WP. Gene trees in species trees. Syst Biol. 1997;46(3):523–36. https://doi.org/10.2307/2413694. 1. Maddison WP. Gene trees in species trees. Syst Biol. 1997;46(3):523–36. https://doi.org/10.2307/2413694. 1. Maddison WP. Gene trees in species trees. Syst Biol. 1997;46(3):523–36. https://doi.org/10.2307/2413694. 2. Degnan JH, Rosenberg NA. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol. 2009;24(6): 332–40. https://doi.org/10.1016/j.tree.2009.01.009. 3. Song S, Liu L, Edwards SV, Wu S. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc Natl Acad Sci. 2012;109(37):14942–7. https://doi.org/10.1073/pnas. 1211733109. 4. Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter EJ, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels CJ, Pokorny L, Shaw AJ, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, DePamphilis CW, Chen T, Deyholos MK, Baucom RS, Kutchan TM, Augustin MM, Wang J, Zhang Y, Tian Z, Yan Z, Wu X, Sun X, Wong GK-S, Leebens-Mack J. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci. 2014;111(45):4859–68. https://doi.org/10.1073/pnas.1323926111. 4. Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter EJ, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels CJ, Pokorny L, Shaw AJ, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, DePamphilis CW, Chen T, Deyholos MK, Baucom RS, Kutchan TM, Augustin MM, Wang J, Zhang Y, Tian Z, Yan Z, Wu X, Sun X, Wong GK-S, Leebens-Mack J. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci. 2014;111(45):4859–68. https://doi.org/10.1073/pnas.1323926111. Conclusions We introduced ASTRAL-III, which compared to ASTRAL-II, improves scalability, especially for datasets with large k and many polytomies. These improvements enabled us to test the accuracy of ASTRAL after con- tracting low support branches. Overall, we observed improvements in accuracy when very low support branches were contracted, but also evidence that aggres- sive filtering reduces the accuracy. ASTRAL-III bounds the theoretical running time to O  (nk)1.726.D  where D = O(nk) is the sum of degrees of all unique gene tree nodes. In practice, the running time tends to grow no worse than quadratically with both n and k. Funding g This work was supported by the National Science Foundation grant IIS-1565862 to SM, MHR, and ES. Computations were performed on the San Diego Supercomputer Center (SDSC) through XSEDE allocations, which is supported by the NSF grant ACI-1053575. The publication cost of this article was funded by the NSF grant IIS-1565862. Competing interests Th th d l th t Competing interests The authors declare that they have no competing interests. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. About this supplement This article has been published as part of BMC Bioinformatics Volume 19 Supplement 6, 2018: Proceedings of the 15th Annual Research in Computational Molecular Biology (RECOMB) Comparative Genomics Satellite Workshop: bioinformatics. The full contents of the supplement are available online at https://bmcbioinformatics.biomedcentral.com/articles/ supplements/volume-19-supplement-6. 6. Laumer CE, Hejnol A, Giribet G. Nuclear genomic signals of the ’microturbellarian’ roots of platyhelminth evolutionary innovation. eLife. 2015;4. https://doi.org/10.7554/eLife.05503. Authors thank anonymous reviewers. Authors thank anonymous reviewers. Availability of data and materials ASTRAL-III is available at https://github.com/smirarab/ASTRAL. The data presented in this paper can be found at https://gitlab.com/esayyari/ASTRALIII. Additional file Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup MH, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MPC, Prosdocimi F, Samaniego JA, Velazquez AMV, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun MJ, Fjeldså J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli K-P, O’Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack JE, Burt DW, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014;346(6215):1320–31. https://doi.org/10. 1126/science.1253451. Comparisons to ASTRAL-III-beta Testing the growth with n is more difficult because as n changes, other Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 Page 29 of 62 we ran ASTRAL-III in its exact mode (i.e., setting X to the power set) with 100 gene trees. Without any trimming of the dynamic programming (i.e., without features 5 and 6), the running time was 40 minutes. Emu- lating ASTRAL-III-beta, we disabled α-trimming but kept the trimming (feature 5) and the running time reduced to 33 min. Adding the α-trimming feature dramatically reduced the running time to 13 min. Thus, when X includes many bipartitions that have very little promise in improving the quartet score (as in the exact mode of ASTRAL), the α-trimming approach is very effective in reducing the running time. Ethics approval and consent to participate Not applicable. Acknowledgements Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup MH, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MPC, Prosdocimi F, Samaniego JA, Velazquez AMV, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun MJ, Fjeldså J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli K-P, O’Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack JE, Burt DW, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014;346(6215):1320–31. https://doi.org/10. 1126/science.1253451. Consent for publication Not applicable. Consent for publication Not applicable. Competing interests The authors declare that they have no competing interests. Additional file Additional file 1: Supplementary material and appendices. Appendices A, B, and C in addition to Figures S1–S8, and Tables S1–S4 are all provided as one Additional file 1. (PDF 476 kb) Additional file 1: Supplementary material and appendices. Appendices A, B, and C in addition to Figures S1–S8, and Tables S1–S4 are all provided as one Additional file 1. (PDF 476 kb) Additional file 1: Supplementary material and appendices. Appendices A, B, and C in addition to Figures S1–S8, and Tables S1–S4 are all provided as one Additional file 1. (PDF 476 kb) 5. 5. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup MH, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MPC, Prosdocimi F, Samaniego JA, Velazquez AMV, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun MJ, Fjeldså J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli K-P, O’Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack JE, Burt DW, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014;346(6215):1320–31. https://doi.org/10. 1126/science.1253451. 6. Laumer CE, Hejnol A, Giribet G. Nuclear genomic signals of the ’microturbellarian’ roots of platyhelminth evolutionary innovation. eLife. 2015;4. https://doi.org/10.7554/eLife.05503. 7. Tarver JE, dos Reis M, Mirarab S, Moran RJ, Parker S, O’Reilly JE, King BL, O’Connell MJ, Asher RJ, Warnow T, Peterson KJ, Donoghue PCJ, Pisani D. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference. Genome Biol Evol. 2016;8(2):330–44. https://doi. org/10.1093/gbe/evv261. Authors’ contributions 7. Tarver JE, dos Reis M, Mirarab S, Moran RJ, Parker S, O’Reilly JE, King BL, O’Connell MJ, Asher RJ, Warnow T, Peterson KJ, Donoghue PCJ, Pisani D. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference. Genome Biol Evol. 2016;8(2):330–44. https://doi. org/10.1093/gbe/evv261. CZ, MHR, and SM designed the algorithms and CZ and MHR implemented them. SM, ES, and CZ designed the experiments and all authors contributed to running experiments and analyzing the data. All authors contributed to the writing. All authors read and approved the final manuscript. Zhang et al. BMC Bioinformatics 2018, 19(Suppl 6):153 Page 30 of 62 32. Price MN, Dehal PS, Arkin AP. FastTree-2 – Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE. 2010;5(3): 9490. https://doi.org/10.1371/journal.pone.0009490. 8. Rokas A, Williams BL, King N, Carroll SB. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature. 2003;425(6960):798–804. https://doi.org/10.1038/nature02053. p g j p 33. Mirarab S, Bayzid MS, Boussau B, Warnow T. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science. 2014;346(6215):1250463. https://doi.org/10.1126/science.1250463. 9. Springer MS, Gatesy J. The gene tree delusion. Mol Phylogenet Evol. 2016;94(Part A):1–33. https://doi.org/10.1016/j.ympev.2015.07.018. 9. Springer MS, Gatesy J. The gene tree delusion. Mol Phylogenet Evol. 2016;94(Part A):1–33. https://doi.org/10.1016/j.ympev.2015.07.018. 10. Meiklejohn KA, Faircloth BC, Glenn TC, Kimball RT, Braun EL. Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods. Syst Biol. 2016;65(4): 612–27. https://doi.org/10.1093/sysbio/syw014. 34. Bayzid M. S, Mirarab S, Boussau B, Warnow T. Weighted statistical binning: enabling statistically consistent genome-scale phylogenetic analyses. PLoS ONE. 2015;10(6):0129183. https://doi.org/10.1371/journal. pone.0129183. 11. Edwards SV, Xi Z, Janke A, Faircloth BC, McCormack JE, Glenn TC, Zhong B, Wu S, Lemmon EM, Lemmon AR, Leaché AD, Liu L, Davis CC. Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics. Mol Phylogenet Evol. 2016;94:447–62. https://doi.org/10.1016/j.ympev.2015.10.027. 35. Mirarab S, Bayzid MS, Warnow T. Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting. Syst Biol. 2016;65(3):366–80. https://doi.org/10.1093/sysbio/ syu063. 36. Patel S. Error in phylogenetic estimation for bushes in the tree of life. J Phylogenet Evol Biol. 2013;01(02):110. https://doi.org/10.4172/2329- 9002.1000110. 12. Shen X-X, Hittinger CT, Rokas A. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nat Ecol Evol. 2017;1(5):0126. https://doi.org/10.1038/s41559-017-0126. 12. Shen X-X, Hittinger CT, Rokas A. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nat Ecol Evol. 2017;1(5):0126. https://doi.org/10.1038/s41559-017-0126. 37. Authors’ contributions 1986;17:57–86. 22. Mirarab S, Warnow T. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics. 2015;31(12):44–52. https://doi.org/10.1093/bioinformatics/btv234. 45. Junier T, Zdobnov EM. The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell. Bioinformatics. 2010;26(13):1669–70. https://doi.org/10.1093/bioinformatics/btq243. 45. Junier T, Zdobnov EM. The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell. Bioinformatics. 2010;26(13):1669–70. https://doi.org/10.1093/bioinformatics/btq243. 23. Liu L, Yu L, Pearl DK, Edwards SV. Estimating species phylogenies using coalescence times among sequences. Syst Biol. 2009;58(5):468–77. https://doi.org/10.1093/sysbio/syp031. 46. Robinson D, Foulds L. Comparison of phylogenetic trees. Math Biosci. 1981;53(1-2):131–47. 46. Robinson D, Foulds L. Comparison of phylogenetic trees. Math Biosci. 1981;53(1-2):131–47. 47. Kozlov AM, Aberer AJ, Stamatakis A. ExaML version 3: a tool for phylogenomic analyses on supercomputers. Bioinformatics. 2015;31(15): 2577–9. https://doi.org/10.1093/bioinformatics/btv184. 24. Mossel E, Roch S. Incomplete lineage sorting: consistent phylogeny estimation from multiple loci. IEEE/ACM Trans Comput Biol Bioinformatics (TCBB). 2010;7(1):166–71. https://doi.org/10.1109/TCBB.2008.66. 25. Roch S, Warnow T. On the robustness to gene tree estimation error (or lack thereof) of coalescent-based species tree methods. Syst Biol. 2015;64(4):663–76. https://doi.org/10.1093/sysbio/syv016. 26. Lafond M, Scornavacca C. On the Weighted Quartet Consensus problem. arXiv 610.00505. 2016. 26. Lafond M, Scornavacca C. On the Weighted Quartet Consensus problem. arXiv 610.00505. 2016. Authors’ contributions Gatesy J, Springer MS. Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Mol Phylogenet Evol. 2014;80: 231–66. https://doi.org/10.1016/j.ympev.2014.08.013. 13. Heled J, Drummond AJ. Bayesian inference of species trees from multilocus data. Mol Biol Evol. 2010;27(3):570–580. https://doi.org/10. 1093/molbev/msp274. 14. Edwards SV. Is a new and general theory of molecular systematics emerging? Evolution. 2009;63(1):1–19. https://doi.org/10.1111/j.1558- 5646.2008.00549.x. 14. Edwards SV. Is a new and general theory of molecular systematics emerging? Evolution. 2009;63(1):1–19. https://doi.org/10.1111/j.1558- 5646.2008.00549.x. 38. Yu Y, Warnow T, Nakhleh L. Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles. J Comput Biol. 2011;18(11):1543–59. https://doi.org/10.1089/cmb.2011. 0174. 15. Pamilo P, Nei M. Relationships between gene trees and species trees. Mol Biol Evol. 1988;5(5):568–83. 39. Hart PE, Nilsson NJ, Raphael B. A formal basis for the heuristic determination of minimum cost paths. IEEE Trans Syst Sci Cybernet. 1968;4(2):100–7. 16. Rannala B, Yang Z. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics. 2003;164(4):1645–56. 40. Zhang C, Sayyari E, Mirarab S. ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches. In: Meidanis J, Nakhleh L, editors. Lecture Notes in Computer Science. vol. 10562 LNBI. Cham: Springer; 2017. p. 53–75. 17. Liu L, Yu L, Edwards SV. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol Bioly. 2010;10(1):302. 18. Liu L, Yu L. Estimating species trees from unrooted gene trees. Syst Biol. 2011;60:661–7. https://doi.org/10.1093/sysbio/syr027. 41. Stamatakis A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–3. https://doi.org/10.1093/bioinformatics/btu033. 19. Vachaspati P, Warnow T. ASTRID: Accurate Species TRees from Internode Distances. BMC Genomics. 2015;16(Suppl 10):3. 42. Mallo D, De Oliveira Martins L, Posada D. SimPhy : Phylogenomic Simulation of Gene, Locus, and Species Trees. Syst Biol. 2016;65(2): 334–44. https://doi.org/10.1093/sysbio/syv082. 20. Sayyari E, Mirarab S. Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction. BMC Genomics. 2016;17(S10):101–13. https://doi.org/10.1186/s12864-016-3098-z. 43. Fletcher W, Yang Z. INDELible: A flexible simulator of biological sequence evolution. Mol Biol Evol. 2009;26(8):1879–88. https://doi.org/10.1093/ molbev/msp098. 21. Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T. ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics. 2014;30(17):541–8. https://doi.org/10.1093/ bioinformatics/btu462. 44. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect Math Life Sci. 1986;17:57–86. 44. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect Math Life Sci. Submit your next manuscript to BioMed Central and we will help you at every step: 27. Allman ES, Degnan JH, Rhodes JA. Determining species tree topologies from clade probabilities under the coalescent. J Theor Biol. 2011;289(1): 96–106. https://doi.org/10.1016/j.jtbi.2011.08.006. • We accept pre-submission inquiries • Our selector tool helps you to find the most relevant journal • We provide round the clock customer support • Convenient online submission • Thorough peer review • Inclusion in PubMed and all major indexing services • Maximum visibility for your research Submit your manuscript at www.biomedcentral.com/submit p y y p 28. Kane D, Tao T. ABoundonPartitioningClusters. Electr J Comb. 2017;24:P2.31. 29. Shekhar S, Roch S, Mirarab S. Species tree estimation using ASTRAL: how many genes are enough? IEEE/ACM Trans Comput Biol Bioinform. 2017;99:1–1. https://doi.org/10.1109/TCBB.2017.2757930. p g 30. Davidson R, Vachaspati P, Mirarab S, Warnow T. Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer. BMC Genomics. 2015;16(Suppl 10):1. https://doi. org/10.1186/1471-2164-16-S10-S1. g 31. Sayyari E, Mirarab S. Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies. Mol Biol Evol. 2016;33(7):1654–68. https://doi.org/10.1093/molbev/msw079. g 31. Sayyari E, Mirarab S. Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies. Mol Biol Evol. 2016;33(7):1654–68. https://doi.org/10.1093/molbev/msw079.
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Textile Masks and Surface Covers—A Spray Simulation Method and a “Universal Droplet Reduction Model” Against Respiratory Pandemics
Frontiers in medicine
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BRIEF RESEARCH REPORT published: 27 May 2020 doi: 10.3389/fmed.2020.00260 Alex Rodriguez-Palacios 1,2*, Fabio Cominelli 1,2, Abigail R. Basson 1,2, Theresa T. Pizarro 3 and Sanja Ilic 4 1 Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, United States, 2 Digestive Health Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States, 3 Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States, 4 Human Nutrition, Department of Human Sciences, College of Education and Human Ecology, The Ohio State University, Columbus, OH, United States Edited by: Antonio Pereira, Federal University of Pará, Brazil The main form of COVID-19 transmission is via “oral-respiratory droplet contamination” (droplet: very small drop of liquid) produced when individuals talk, sneeze, or cough. In hospitals, health-care workers wear facemasks as a minimum medical “droplet precaution” to protect themselves. Due to the shortage of masks during the pandemic, priority is given to hospitals for their distribution. As a result, the availability/use of medical masks is discouraged for the public. However, for asymptomatic individuals, not wearing masks in public could easily cause the spread of COVID-19. The prevention of “environmental droplet contamination” (EnvDC) from coughing/sneezing/speech is fundamental to reducing transmission. As an immediate solution to promote “public droplet safety,” we assessed household textiles to quantify their potential as effective environmental droplet barriers (EDBs). The synchronized implementation of a universal “community droplet reduction solution” is discussed as a model against COVID-19. Using a bacterial-suspension spray simulation model of droplet ejection (mimicking a sneeze), we quantified the extent by which widely available clothing fabrics reduce the dispersion of droplets onto surfaces within 1.8 m, the minimum distance recommended for COVID-19 “social distancing.” All textiles reduced the number of droplets reaching surfaces, restricting their dispersion to <30 cm, when used as single layers. When used as double-layers, textiles were as effective as medical mask/surgical-cloth materials, reducing droplet dispersion to <10 cm, and the area of circumferential contamination to ∼0.3%. The synchronized implementation of EDBs as a “community droplet reduction solution” (i.e., face covers/scarfs/masks and surface covers) will reduce COVID-19 EnvDC and thus the risk of transmitting/acquiring COVID-19. Reviewed by: Bianca Cruz Neves, Federal University of Rio de Janeiro, Brazil Suvajyoti Guha, United States Food and Drug Administration, United States Lieva Van Langenhove, Ghent University, Belgium *Correspondence: Alex Rodriguez-Palacios axr503@case.edu Specialty section: This article was submitted to Infectious Diseases Surveillance, Prevention and Treatment, a section of the journal Frontiers in Medicine Received: 03 April 2020 Accepted: 14 May 2020 Published: 27 May 2020 Specialty section: This article was submitted to Infectious Diseases Surveillance, Prevention and Treatment, a section of the journal Frontiers in Medicine Keywords: coronavirus, respiratory pandemic, COVID-19, SARS-Cov-2, cloth masks, textiles, public droplet safety, spray simulation model Textile Masks and Surface Covers—A Spray Simulation Method and a “Universal Droplet Reduction Model” Against Respiratory Pandemics Alex Rodriguez-Palacios 1,2*, Fabio Cominelli 1,2, Abigail R. Basson 1,2, Theresa T. Pizarro 3 and Sanja Ilic 4 INTRODUCTION The main form of COVID-19 transmission is via “oral-respiratory droplets” produced when individuals talk, sneeze, or cough. Despite the magnitude of the COVID-19 pandemic, it is disconcerting that the general public either does not have personal protective equipment available to them, including respiratory masks, or chooses to not use them, to contain the pandemic. Worldwide, health-care workers wear medical masks as a minimum “droplet precaution” to protect themselves. However, experts appealed to the community not to wear medical masks stating they are not effective for the public (1); albeit, counter-criticisms ensued (2). Regardless of clinical presentation, COVID-19 transmits person-to-person, including children (3), via “oral-respiratory droplets” produced when individuals talk or sneeze/cough. Aside from Asia (4), there are no global guidelines promoting wearing masks in public to control respiratory pandemics (5–10), and no scientific data/guidelines exist promoting masks as a “droplet precaution” for the public (5, 9, 11). COVID-19 is caused by a novel coronavirus strain (SARS- CoV-2), for which there is no treatment (12, 13). Disease is characterized by fever, coughing/sneezing, dyspnea, and pneumonia, and can lead to death in some cases (14); however, important for asymptomatic transmission, cases increasingly present with gastrointestinal symptoms, and/or fatigue, without fever (15). Regardless of the clinical presentation, COVID-19 transmits person-to-person through oral-respiratory droplets produced when infected individuals [symptomatic or asymptomatic, including children (3)] talk/cough/sneeze, contaminating the environment. Although viruses can become airborne dust/aerosols, as micro-droplets evaporate, viruses rapidly loose infectivity in the air (half-life = 1 h) (16–20). By contrast, virus survival increases when liquid droplets contaminate surfaces, especially plastic and stainless steel, with long half-lives of 7 and 6 h, respectively (cardboard, 4 h; copper, 1 h) (16). Since COVID- 19 transmits when droplets reach the nose/mouth/eyes (21), or when people touch their nose/mouth/eyes after touching droplet- contaminated surfaces [supermarkets/elevators (22)], it is critical to implement strategies to prevent/reduce environmental droplet contamination (EnvDC). This is particularly true for plastic or metal surfaces, which remain infective for days. Herein, we investigated whether common household textiles can be used as environmental droplet barriers (EDBs; facemasks/covers/scarfs, or surface covers) to prevent EnvDC, improve public droplet safety, and support the synchronized implementation of an environmentally-purposed Universal Droplet Reduction Model within the public to control respiratory pandemics such as COVID-19. INTRODUCTION bacterial-suspension strategy to quantify the number of droplets that could not be visualized, but that could escape textile barriers and cause long-/short-range surface contamination. To enumerate bacteria-carrying micro-droplets, we used household spray bottles filled with an aqueous suspension of 12-probiotic- cultured dairy product (Lactobacillus lactis, L. rhamnosus, L. plantarum, L. casei, L. acidophilus, Leuconostoc cremoris, Bifidobacterium longum, B. breve, B. lactis, Streptococcus diacetylactis, and Saccharomyces florentinus, 75 ml; 3 × 106−7 cfu/ml, 25 ml Saliva 106−7) in 1,000 ml PBS (Fisher BP-399- 1) to simulate a cloud of droplets produced by a sneeze. Probiotics are BSL-1/“Generally Recognized As Safe” by the FDA and all experiments were conducted in BSL-2 HEPA- filtered microbiology laboratories. No animal/human subjects were used for experimentation. Before testing, spray bottle nozzles were adjusted to produce cloud and jet-propelled droplets that match the visual architecture of droplet formation described by Bourouiba (23). Specifically, we used a high-volume trigger single-v-orifice nozzle sprayer (1.0 ml per stroke) with a 28/400 neck and 9-1/4-inch dip tube fitted with a filter screen (model PA-HDTS-EA, Mfr. Model # 922HL, Delta Industries, Inc.). Using infrared imaging we recently illustrated that the spray model was composed of various liquid droplet dynamic phases occurring within a single spray (25), which reproduces results in a wide arrange of droplet sizes (previously described as right skewed distribution ranges between 20 and 900 µm, with peak at 70–100 µm) (26), and therefore distance reach and landing velocities. In context, the size of droplets in the human sneeze ranges between 40 and 900 µm, with most droplets (70–100%) normally or bimodally distributed around 360–390 µm (27). The spray bottle ejects fluid with pressures that can reach sufficient pressure (e.g., 10 psi for garden sprayers) to create a short burst of fluid/jet and fan clouds of microdroplets. In context, the pressure during a sneeze is 1 psi in the trachea, and 2.6 psi in the mouth/pharynx, while exhalation during strenuous activity triggers a tracheal pressure of 0.03 psi (28). In this model, one stroke ejects 1 ml of fluid per spray, therefore three sprays (delivered at 1 stroke/second) constitute an exposure of 3 ml of fluid in 3 s, which is a delivery of moisture 181-fold faster than the rate of moisture released by the lungs during normal breathing (>20 ml/hour, i.e., equivalent to 5.5 µl/second) (29). Citation: Rodriguez-Palacios A, Cominelli F, Basson AR, Pizarro TT and Ilic S (2020) Textile Masks and Surface Covers—A Spray Simulation Method and a “Universal Droplet Reduction Model” Against Respiratory Pandemics. Front. Med. 7:260. doi: 10.3389/fmed.2020.00260 May 2020 | Volume 7 | Article 260 1 Frontiers in Medicine | www.frontiersin.org Droplet Reduction Model Against Pandemics Rodriguez-Palacios et al. Quantification of Droplet Retention by Household Textiles Simulation of Bacteria-Containing Micro-/Macro-Droplet Clouds INTRODUCTION Quantification of droplets landing over a surface was performed at the time of spray using seven 10 mm-Petri dishes containing tryptic soy agar (56.75 cm2 surface area/dish) with 5% defibrinated sheep blood, placed on a table spaced at 30 cm intervals between 0 and 180 cm. Plates remained open for 10 min to allow droplet landing. Droplet quantification was conducted for each bottle in duplicate. Large-drop quantification outside agar plates was facilitated by a white droplet footprint left on black surfaces. To test the role of surface covers for unanimated surfaces, Petri dishes were covered with textiles. Statistical Analysis Student’s-T tests, linear regression, and multinomial logistic regression were conducted using raw and Log2 transformed CFU data (STATA, v15.1). Confidence intervals are provided to convey information relevant to sample size and external validity. Note that the studies represent a large number of simulations shown to be statistically significant. To further ensure external validity and comparability, we derived linear polynomial regression equations Household Textiles Tested, Replication of Findings, Safety and Contextualization Findings, Safety and Contextualization We first tested six household textiles, including 100% combed cotton (widely available, “T-shirt material”), 100% polyester microfiber 300-thread count fabric (pillow case), two loosely woven “homespun” 100% cotton fabrics (140GSM, 60 × 60- thread count; and 115GSM, 52 × 48-thread count), and “dry technology” 100% polyester common in sport jerseys. These textiles were compared to: (i) the lack of a textile barrier (no mask control), (ii) medical masks, and (iii) surgical cloth material as “gold standard” protective controls. To ensure external validity/reproducibility, complementary and repeated experiments were conducted with selected textiles (i.e., respiratory mask, sports jersey, and Cotton-T-shirt) at the Ohio State University. To contextualize the retention ability of textiles of respiratory secretions, a single episode of a simulated cough by one of the volunteer investigators onto three agar plates, placed perpendicularly at 30 cm inside a BSL-2 safety cabinet, was used to illustrate that respiratory secretions have large strings of mucus more amenable for retention than liquid microdroplets, and which contain bacteria (CFU) recoverable in the TSA agar used in the study. To determine the percentage of area covered by the textile that could be freely open to the direct flow of air liquid macro and microdroplets, we used image analysis of transillumination captures and ImageJ software (https://imagej.nih.gov/ij/). In short, single-/double-layer textile RGB JPG images imported to ImageJ were converted to type 8- bit format, then binary with black background, with threshold adjusted to W190:B255. The quantification of the number of white pixels (background transillumination) for the total image area was then used to compute the percent area of textile that freely allowed the passage of light. Simulation of Bacteria-Containing Micro-/Macro-Droplet Clouds Since viruses exist in association with bacteria and host cells within electrolytes-rich respiratory fluids (23, 24), we used a To simulate the function of mask barriers, we placed selected textiles (∼22 × 22 cm) over a cardboard/plastic-covered 25 May 2020 | Volume 7 | Article 260 Frontiers in Medicine | www.frontiersin.org 2 Droplet Reduction Model Against Pandemics Rodriguez-Palacios et al. × 30 cm surface, over a carved (8.5 × 11 cm) window, and 8.5 cm above the agar plates’ plane, through which droplets were sprayed. To avoid altering permeability, textiles were not “tensed” across the carved window. The spray nozzle was placed perpendicular at 8.5 cm from the textile [half the distance between the nostrils and vocal cords, 16–18 cm (30), or one-third of the lip-to-carina distance, 21.6–24.3 cm (31) in humans]. On the other side of the textile, 3–5 agar plates were aligned to cover the 0–8.5, 8.5–17, 17–25.5, and 25.5–34 cm intervals to quantify bacteria-containing droplets that could contaminate a surface. Quantification represents droplets that pass through the textile and that land on a rectangular area of 8.5 cm × 180 cm (agar plate diameter X “spray path”). To quantify the effect of textiles retaining vertically-landing droplets, we quantified droplets reaching agar plates covered with a household textile. All testing conditions were carried out at constant ambient conditions. that almost perfectly fit the raw data dynamics, R2 > 0.98, to enable others to adjust the spray droplet landing dynamics on surfaces. ImageJ textile data for single-/double-layer textiles were analyzed using paired t-test. Quantitative effects and models were deemed significant if adjusted p < 0.05. Frontiers in Medicine | www.frontiersin.org Spray Dispersion Model of Droplets Reach >1.8 Meters if Upward Because viruses replicate intracellularly in bodily fluids, in association with other microorganisms (23, 24), and need droplets to facilitate their expulsion, transmission, and EnvDC (12), we first validated a rapid spray-simulation model of droplets (mimicking a sneeze) using a bacterial-suspension to quantify the extent by which widely-available household textiles reduced the ejection/long-distance flight of droplets. To facilitate the enumeration of macro-droplets and invisible micro-droplets, spray-simulations were conducted over nutritious-media agar surfaces and incubated for 24 h to enable colony-forming- droplet-unit (CFU) formation. Based on simulations conducted in two institutions, a cloud of bacteria-carrying droplets travel distances reaching >180 cm, particularly for large droplets (Figure 1A), which is consistent with reported dynamics during sneezing (23). Of relevance to sneezing behavior, simulations illustrate that upward inclination of the central-spray angle allows macro- droplets to reach longer distances (simulation 4/dispersion equations; Figures 1B–E). Although macro-droplets frequently reached 180 cm, most micro-droplets landed on surfaces within 120 cm, with spray air-turbulence carrying micro- droplets into areas not reached with gravity alone. Thus, social distancing of 1.8 m without EDB-mask protection, as is currently recommended, is not always possible and therefore insufficient to prevent droplet exposure, particularly where essential-service workers congregate (i.e., person-person distance is <1.8 m) during pandemics (transportation, supermarkets/food displays). Therein, wearing EDB-masks together with inclining the head/body downward during sneezing could minimize the spatial range of EnvDC. Preprint This manuscript was submitted to medrxiv on March 29, 2020, and posted as a preprint (32) on April 10 to enable the incorporation of community comments into the peer-review process. In support of this report, peer-reviewers provided an average score of 4.5/5 for six items on the initial submission (originality, and significance to the field, 4.7 ± 0.6 each; rigor, 4.3 ± 0.6; interest to the general audience, 5.0 ± 0; quality of writing, 4.0 ± 1.0; and overall quality of study, 4.3 ± 0.6); and no negative criticisms were publicized for the preprint (tweets from 11 independent accounts with 59,855 followers; April 10–22, 2020). Household Textiles Retain Liquid Droplets, Particularly if Double Layered To quantify the droplet retention potential of textiles as EDBs, we next used the same bacterial-spray-simulation model to May 2020 | Volume 7 | Article 260 3 Droplet Reduction Model Against Pandemics Rodriguez-Palacios et al. FIGURE 1 | Simulation of a cloud of airborne bacteria-containing macro-drops and micro-droplets to quantify barrier potential of household textiles. (A) Graphical overview of the spray model. Inset, Photograph of a human sneeze, public domain, James Gathany, CDC image ID11162). (B) Photographs of short and long-range visible droplets immediately after spray. Note the color, number, size, and relative location and distribution of the bacteria colonies growing from “invisible” microdroplets (CFU) shown as whitish spots on the agar surface. Bacterial growth alters the red color of the fresh non-inoculated agar leading to a brownish discoloring of the petri agars, which is more pronounced as the number of bacterial colonies increase. (C) Number of macro-drops for four simulations over distance. The overall linear equation that best describes the mean spray macro-droplet dynamics linearized/depicted as the heatmap is y = −8E−05x3 + 0.0305x2 – 3.9405x + 198.42, with an R² = 0.9829. Note that large drops of liquids observed with the spray alone (no textile barrier) were not observed with any of the textile barriers tested. (D) Photographs of bacterial CFUs on agar plates illustrating ability of cloud micro-droplets to move around spaces driven by cloud turbulence (left images, agar plates were partially covered with lid at moment of spray), concurrent contamination with macro- and micro-droplets. (E) Number of CFU/plate (56.75 cm2) for 6 simulations over distance. The overall linear equation that best describes the mean dispersal of bacteria-carrying micro-droplets over distance, also depicted as the red heatmap, is y = −4E−05x4 + 0.0177x3 – 2.8522x2 + 155.63x – 58.504, with an R² = 0.9994. FIGURE 1 | Simulation of a cloud of airborne bacteria-containing macro-drops and micro-droplets to quantify barrier potential of household textiles. (A) Graphical overview of the spray model. Inset, Photograph of a human sneeze, public domain, James Gathany, CDC image ID11162). (B) Photographs of short and long-range visible droplets immediately after spray. Note the color, number, size, and relative location and distribution of the bacteria colonies growing from “invisible” microdroplets (CFU) shown as whitish spots on the agar surface. Household Textiles Retain Liquid Droplets, Particularly if Double Layered Bacterial growth alters the red color of the fresh non-inoculated agar leading to a brownish discoloring of the petri agars, which is more pronounced as the number of bacterial colonies increase. (C) Number of macro-drops for four simulations over distance. The overall linear equation that best describes the mean spray macro-droplet dynamics linearized/depicted as the heatmap is y = −8E−05x3 + 0.0305x2 – 3.9405x + 198.42, with an R² = 0.9829. Note that large drops of liquids observed with the spray alone (no textile barrier) were not observed with any of the textile barriers tested. (D) Photographs of bacterial CFUs on agar plates illustrating ability of cloud micro-droplets to move around spaces driven by cloud turbulence (left images, agar plates were partially covered with lid at moment of spray), concurrent contamination with macro- and micro-droplets. (E) Number of CFU/plate (56.75 cm2) for 6 simulations over distance. The overall linear equation that best describes the mean dispersal of bacteria-carrying micro-droplets over distance, also depicted as the red heatmap, is y = −4E−05x4 + 0.0177x3 – 2.8522x2 + 155.63x – 58.504, with an R² = 0.9994. quantify non-visualizable micro-droplets that could cross/escape the textile-EDB and cause microbial-surface agar contamination (Figure 2A). Details on textile threading, percentage of area open for flow of droplets/light, and density in grams per square meter (GSM) for all medical and the single-/double- layer household textiles are shown in Figures 2B–D and Supplementary Figure 1. Textiles were tested for one- and three-sprays to determine if EnvDC changed with textile May 2020 | Volume 7 | Article 260 Frontiers in Medicine | www.frontiersin.org Droplet Reduction Model Against Pandemics Rodriguez-Palacios et al. FIGURE 2 | Spray-droplet model to quantify reduction rate of long-range droplet dispersion across 1- and 2-layer textiles. (A) Graphical overview of spray-droplet setting (see Methods). Tryptic soy agar supplemented with 5% defibrinated sheep blood plates incubated aerobically at 37◦C for 24 h. (B) Photograph and low-resolution ImageJ processed image compares medical mask material to that of single- and double-layered textile example (Supplementary Figure 1, all textiles used). Scale bar, 1 mm. (C) High resolution ImageJ binary analysis of representative textiles photographed as single and double layers to illustrate the percentage of the textile barrier “open area” that allows the passage of light/droplets. Scale bar, 1 mm. (D) Paired analysis of reduction of the textile “open area” when textile is tested as two layers. Frontiers in Medicine | www.frontiersin.org Household Textiles Retain Liquid Droplets, Particularly if Double Layered FIGURE 2 | Spray-droplet model to quantify reduction rate of long-range droplet dispersion across 1- and 2-layer textiles. (A) Graphical overview of spray-droplet setting (see Methods). Tryptic soy agar supplemented with 5% defibrinated sheep blood plates incubated aerobically at 37◦C for 24 h. (B) Photograph and low-resolution ImageJ processed image compares medical mask material to that of single- and double-layered textile example (Supplementary Figure 1, all textiles used). Scale bar, 1 mm. (C) High resolution ImageJ binary analysis of representative textiles photographed as single and double layers to illustrate the percentage of the textile barrier “open area” that allows the passage of light/droplets. Scale bar, 1 mm. (D) Paired analysis of reduction of the textile “open area” when textile is tested as two layers. macro-droplets (100% EnvDC prevention), and drastically reduced the ejection of micro-droplets by a factor of 5.16Log2, which is equivalent to a 97.2% droplet reduction (P < 0.020 vs. single-layers, Figure 3C and Supplementary Figures 4, 5). Importantly, the least-effective textile as single-layer (most- “breathable,” 100%-cotton homespun-115 material) achieved a 90–99.998% droplet retention improvement when used as two-layers (95% CI = 3.74–15.39 Log2). Lastly, all textiles were equally effective at absorbing the humidity from 3- sprays compared to medical mask/surgical cloth materials, humidity. Although humidity had no statistical impact (dry- vs.-humid, adj.–P > 0.2), all textiles, tested as “single-layers,” significantly and reproducibly (between institutions) reduced the ejection of macro-droplets, and the traffic of micro-droplets to <25.5–34 cm (linear regression model adj.–P < 0.001, compared to 180 cm with no textile barrier; Figures 3A,B and Supplementary Figures 2, 3). Remarkably, spray experiments with “two-layers” (of 100%- combed cotton, common in t-shirts; and 100% polyester, in sports jerseys) completely prevented the ejection of large May 2020 | Volume 7 | Article 260 Frontiers in Medicine | www.frontiersin.org 5 Droplet Reduction Model Against Pandemics Rodriguez-Palacios et al. FIGURE 3 | Using two layers of household textiles markedly retain liquid droplets. (A) Tryptic soy agar plates illustrate effective bacterial-droplet reduction by 2-layer textiles. (B) Pooled results from two spray-simulations (1- and 3-sprays; Supplementary Figure 2). Vertical thick black bars connect baseline values at 0 to the means. (C) Linear regressions for EnvDC reduction over distance for no-barrier vs. selected textiles. Compared to no textile (EDB) barrier (red dotted line), the reduction in CFUs illustrate the profound effect of using household textiles to retain droplets. Household Textiles Retain Liquid Droplets, Particularly if Double Layered Line slopes that are closer to the horizontal grid line at 0, and closer to the “Resp. mask”-dotted line are more effective strategies (commercial masks are made of 2-or-3-layers) compared to single layers (Supplementary Figure 4, equations and R2). (D) Photographs of differences in condensate after 1-spray on the side of the textile being sprayed. Arrowheads, drops/accumulation. FIGURE 3 | Using two layers of household textiles markedly retain liquid droplets. (A) Tryptic soy agar plates illustrate effective bacterial-droplet reduction by 2-layer textiles. (B) Pooled results from two spray-simulations (1- and 3-sprays; Supplementary Figure 2). Vertical thick black bars connect baseline values at 0 to the means. (C) Linear regressions for EnvDC reduction over distance for no-barrier vs. selected textiles. Compared to no textile (EDB) barrier (red dotted line), the reduction in CFUs illustrate the profound effect of using household textiles to retain droplets. Line slopes that are closer to the horizontal grid line at 0, and closer to the “Resp. mask”-dotted line are more effective strategies (commercial masks are made of 2-or-3-layers) compared to single layers (Supplementary Figure 4, equations and R2). (D) Photographs of differences in condensate after 1-spray on the side of the textile being sprayed. Arrowheads, drops/accumulation. which condensate after 1-spray (Figure 3D). Together, experiments indicate that two-layers of household textiles are as effective as medical masks preventing EnvDC, and that more breathable materials in ≥2-layers could be effectively used if individuals deem two-layer, “denser” textiles too air-restrictive. how many viral particles in droplets (virus/µm3) or surfaces (virus/cm2) are needed to acquire COVID-19, we assumed that any droplet on a surface area of 56.75 cm2 (an 8.5 cm diameter agar plate) renders a surface infective. Since textiles prevented droplets from reaching beyond a ∼30 cm radius, we propose a working “droplet reduction model” to control COVID-19, where EDB-masks could reduce the “circumferential area of contamination” around each individual by 97.2% when used as single-layers, or as much as 99.7% when used as two- layers. 100%-cotton/polyester especially shortened the EnvDC radius to <10 cm (similar to medical-mask material; Log2 difference = 0.06, for 100% polyester, multinomial adj.–P > “Universal Droplet Reduction Model” Against Rapid Respiratory Pandemics We then rationalized the potential impact of a “universal droplet reduction model” against pandemics, where the community act together to reduce the spatial range of EnvDC. Since it is unclear May 2020 | Volume 7 | Article 260 Frontiers in Medicine | www.frontiersin.org 6 Droplet Reduction Model Against Pandemics Rodriguez-Palacios et al. FIGURE 4 | Environmentally-focused “Universal Droplet Reduction Model” against pandemics due to infectious agents transmitted via oral-respiratory fluids. (A) Graphical representation of a model where the lack of face barrier/cover could result in the contamination of a large circumferential area, or nearby contact with a higher number of susceptible individuals, within a 180 cm radius. (B) Graphical representation illustrating the benefit of wearing textile-face barriers to reduce the circumferential area contaminated with droplets (two-layers/single-layers) and to reduce the number of droplet contacts with susceptible individuals. (C) The benefit of using face cover/barriers drastically increases in surface area (cm2) as the efficiency of the droplet barrier increases (distance of droplet contamination, cm). FIGURE 4 | Environmentally-focused “Universal Droplet Reduction Model” against pandemics due to infectious agents transmitted via oral-respiratory fluids. (A) Graphical representation of a model where the lack of face barrier/cover could result in the contamination of a large circumferential area, or nearby contact with a higher number of susceptible individuals, within a 180 cm radius. (B) Graphical representation illustrating the benefit of wearing textile-face barriers to reduce the circumferential area contaminated with droplets (two-layers/single-layers) and to reduce the number of droplet contacts with susceptible individuals. (C) The benefit of using face cover/barriers drastically increases in surface area (cm2) as the efficiency of the droplet barrier increases (distance of droplet contamination, cm). (D) Coughed material-associated bacteria in agar. Large viscous secretions will be retained by textile-EDB. (E) Bacteria-carrying droplet counts on agar plates covered with 1-layer cotton t-shirt material, after one-spray, over distance. Colony-forming units were estimated on paired TSA agar plates (covered and uncovered) following the spraying of the bacterial-carrying solution over the plates, and 48 h of aerobic incubation. (F) Environmental droplet reduction model. Protective masks and surface covers in the community. Supplementary Table 2, list of current and proposed actions against COVID-19. machine) two 2-layer-EDB masks as an immediate, synchronized contribution to reduce COVID-19 EnvDC. 0.6). “Universal Droplet Reduction Model” Against Rapid Respiratory Pandemics Because COVID-19 cases increase daily, and the fabrication of EDB by centralized organizations could take weeks to reach entire “lockdown” communities, we suggest, based on the cotton/polyester EnvDC effectiveness, and a homemade EDB- mask fabrication trial (Supplementary Figure 6), that, from one piece of clothing, every individual could make (without a sewing From a surface perspective, if everyone were encouraged to wear EDBs, the collective area contaminated with droplets would be miniaturized to 0.3–2.77% (two-layers/single-layers), compared to the potential contamination within 180 cm (10.2 May 2020 | Volume 7 | Article 260 Frontiers in Medicine | www.frontiersin.org 7 Droplet Reduction Model Against Pandemics Rodriguez-Palacios et al. m2). Even suboptimal EDBs, effective for 90 cm radius, could mathematically reduce the EnvDC area by 75.1% (Figures 4A–C). Our findings and surface estimations are conservative as they are based on simulations using a (non-viscous) liquid solution, assuming stationary individuals. However, the impact of EDB is predictably greater since real/large viscous secretions (Figure 4D), which also travel long distances (>180 cm) (23), would be easier to contain by EDB, as communities mobilize. To further lower the risk of fomite (plastic/metal surface) transmission from/by non-EDB-wearers, EDB-textiles used as covers, when relevant, could reduce EnvDC by 90–98% (T-test P = 0.003, Figure 4E). Non-pharmaceutical interventions (NPIs), also known as community mitigation strategies, are actions that individuals and communities can take in order to slow the spread of illnesses. For pandemics, when medical approaches (hospitalization/treatments) are limited, NPIs are a critical component to achieve resolution. Although PPE, including masks, are scientifically-effective methods to prevent infectious disease transmission, the use of masks for the general public has not been encouraged by governments (5, 7), possibly because demand will deepen the current crisis of mask unavailability for medical staff, or alternatively, because the use of masks to prevent respiratory infections has been misleadingly deemed ineffective, despite earlier clinical studies indicating that masks could be beneficial in households during pandemics (35, 37, 38). y g Finally, to illustrate in volumetric terms that EDBs are even more effective at preventing EnvDC, we conducted a scoping review of literature to conduct analyses of droplet fluid-carrying capacity. Although published droplet sizes vary with study method (Supplementary Table 1), most sneezed droplets are “large,” and can reach >1 mm. “Universal Droplet Reduction Model” Against Rapid Respiratory Pandemics Physiologically, two types of sneeze exist (27): unimodal, when all droplets are large (360 ± 1.5 µm-diameter); and bimodal, when droplets are large (390 ± 1.7 µm-diameter, 70%) and small (72 ± 1.5 µm, 30%). Assuming droplets are spherical, for an average of two sneezes (unimodal:bimodal, 200,000 droplets), we determined that large droplets (85% of total) contain 703-times more fluid than small droplets. Thus, EDBs could reduce COVID-19 EnvDC by effectively blocking the dispersion of fluids/viruses contained in large droplets. Because droplets of <47 µm are known to evaporate before reaching the ground (33), EDB will also prevent small-size droplet aerosolization by trapping such droplets immediately after production. An overview of a “universal textile droplet reduction action-model” against pandemics is illustrated in Figure 4F. Although masks have been extensively studied to determine whether individuals are clinically protected from infections (39, 40), and to confirm that wearing a mask promotes desirable hygiene practices (handwashing, “avoiding crowds”) (5, 38, 41), masks have not been examined for their potential to prevent environmental contamination. Masks work, if worn properly; however, individuals (∼50%) often fail to wear masks regularly and properly (37, 42). Despite low compliance, meta-analyses indicate that masks lower the odds of having (SARS)-respiratory infections by 87% (OR = 0.13), compared to the odds of having an infection “not wearing a mask” (43). Herein, we propose that in addition to seeking the classical/clinical “prevention of infection,” NPIs could be universally based on “droplet reduction models” such as textile- face covers to mitigate contamination of the environment by respiratory droplets. Not only for the prevention of respiratory diseases, but also to prevent widespread environmental dispersion of the virus, which could reach water sources or affect domestic animals, as has been shown for other viruses, including pandemic influenza (44). Frontiers in Medicine | www.frontiersin.org DATA AVAILABILITY STATEMENT The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation, upon request. FUNDING This study was conducted with discretionary funds allocated to AR-P and SI. AR-P received partial support from NIH via grants R21DK118373, entitled Identification of pathogenic bacteria in Crohn’s disease, P30DK097948 NIH Silvio O. Conte Cleveland Digestive Diseases Research Core Center, and P01DK091222 (Germ-Free and Gut Microbiome Core) to FC and TP, Case Western Reserve University. AB received support via NIH F32. Sufficient scientific evidence exists (54) and continues to emerge (55–57) to justify the use of face covers to protect the general public not only during the COVID-19 pandemic, but also for every new respiratory virus in the future. While several studies for cloth masks have been conducted with dried aerosols, only a few have studied the impact of wet aerosols. Thus, the present study serves as a reliable, rapid, and reproducible methodology as a platform for liquid droplet testing models. As minor study limitations, we tested only a representative sample of a vast list of potentially available household textiles and did not test dry aerosolized viral particles. DISCUSSION implemented because most houses have immediate access to, and could safely use, an iron. In conclusion, we demonstrated that two-layer household textiles produced a profound reduction of environmental droplet contamination as effectively as medical-grade materials. Encouraging/mandating the synchronous implementation of textile-face covers, while discouraging using medical masks in public, will help control COVID-19. Although some materials may allow the passage of more bacteria-containing droplets after three sprays (i.e., compare “Cotton115,” single-layer vs. double, textile with largest mesh pore sizes shown in Supplementary Figure 1), we emphasize that there were no statistical differences attributed to the number of droplets that cross the barrier compared to single- sprays in all the multivariable regression models tested with raw and log2-transformed data, especially when tested as two- layers. Collectively, there is no statistical rationale to justify that people should change the mask as a function of number of sneezes to reduce environmental contamination, especially if two-layer masks or covers were used. However, it is advisable to wear/use a clean facemask/surface cover, and that these are cleaned/disinfected (e.g., ironed) after every use, or as often as possible. SUPPLEMENTARY MATERIAL The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmed. 2020.00260/full#supplementary-material AUTHOR CONTRIBUTIONS AR-P envisioned, planned and executed the experiments, analyzed the data, prepared the figures, and wrote the manuscript. SI executed validation and complementary experiments, interpreted the data, and wrote the manuscript. AB assisted with documentation in Supplementary Material and commented and edit the paper. FC and TP commented, revised, and edited the manuscript for medical accuracy and data interpretation. All authors approved the final manuscript. To further support the functional value of textiles in public droplet safety, we recently demonstrated in vivo that two layers of comb cotton fully protect an environment of germ-free mice and the animals when exposed to up to 20 spray clouds of bacteria- carrying microdroplets (25). Other cotton materials with a less uniform finishing, such as carded yarn, could also provide droplet protection, although this was not tested. The use of homemade coverings combined with household disinfection strategies and information and educational campaigns promoting face cover utilization by the community (e.g., posting door signs) (53) could be more cost-effective compared to the economic effects of prolonged lockdowns. Of note, we emphasize that face covers must be used in conjunction with existing recommendations on hand washing and sneezing into one’s arm sleeve. DISCUSSION The world was initially in short supply of masks since the international “lockdown” affected production (45), with health-care workers experiencing high morbidity/mortality due to reduced protection (46). Governments have sought private support to increase mask supplies; however, such strategy have taken weeks/months, and infection rates would not improve if supplies were still not available to “lockdown” communities. Increased community transmission leads to higher demand for medical services, unless transmission is halted. Using household textiles is a potentially life-saving cost-effective anti- pandemic strategy because washing/laundering textiles have been shown to destroy COVID-19 by heat (70◦C/5 min), bleach (1:49/5 min), and detergents (20 min) (47–50), and is more sustainable (community-level) than using scarce medical disinfectants/supplies. As a rapid solution and alternative to chemical disinfection, and as a step prior to laundering, we highlight the value of ironing (51, 52) because humid and dry heat produced by an iron is safe and in excess of the minimum temperatures needed to destroy viruses and even spore forming bacteria, without affecting the integrity of textile facemasks or face covers. Ironing has been seen as a long-standing disinfection strategy since at least the 1920s (52) and could be universally Despite widespread dissemination of information to curtail the rapid spread of COVID-19 outside of China [information which mainly reaches 20–54 year-old adults, who make up 40% of hospitalizations in the USA (34)], little attention has been devoted to EnvDC and prevention strategies for droplet movement from infected to non-infected individuals within the same community. More concerningly is that following mandatory “stay-at-home” quarantine orders, people may return to work unprotected, unaware if they are infected/shedders. This is particularly critical for “essential pandemic workers,” who face different levels of risk (health-care vs. electric/transport/food services), and who can contaminate environmental surfaces as they transit through the community between work (i.e., hospitals) and home, or within their households (35), without wearing masks. Because mass testing is not always possible (6), especially for novel organisms like COVID-19, there are growing concerns that asymptomatic and mildly symptomatic citizens will continue to spread and reintroduce the virus to new areas, creating waves of cases, contributing to further economic burden from the outbreak (36). May 2020 | Volume 7 | Article 260 Frontiers in Medicine | www.frontiersin.org 8 Droplet Reduction Model Against Pandemics Rodriguez-Palacios et al. implemented because most houses have immediate access to, and could safely use, an iron. REFERENCES (2013) 10:20130560. doi: 10.1098/rsif.2013.0560 28. Burke W. Why do we sneeze? Med Hypotheses. (2012) 78:502– 4. doi: 10.1016/j.mehy.2012.01.017 9. McCue T. Calling All People Who Sew and Make: You Can Help Make Masks For 2020 Healthcare Worker PPE Shortage. Forbes (2020). Available online at: https://www.forbes.com/sites/tjmccue/2020/03/20/calling-all-people- who-sew-and-make-you-can-help-solve-2020-n95-type-mask-shortage/# 6dc0885c4e41 (accessed March 24, 2020). 29. Zielinski J, Przybylski J. [How much water is lost during breathing?]. Pneumonol Alergol Pol. (2012) 80:339–42. 30. Han DW, Shim YH, Shin CS, Lee YW, Lee JS, Ahn SW. Estimation of the length of the nares-vocal cord. Anesth Analg. (2005) 100:1533– 5. doi: 10.1213/01.ANE.0000149900.68354.33 10. CDC. Centers for Disease Control and Prevention. Strategies for Optimizing the Supply of Facemasks. HCP Use of Homemade Masks. Content source: National Center for Immunization and Respiratory Diseases (NCIRD), Division of Viral Diseases (2020). Available online at: https://www.cdc.gov/ coronavirus/2019-ncov/hcp/ppe-strategy/face-masks.html#crisis-capacity (accessed March 24, 2020). 31. Varshney M, Sharma K, Kumar R, Varshney PG. Appropriate depth of placement of oral endotracheal tube and its possible determinants in Indian adult patients. Indian J Anaesth. (2011) 55:488–93. doi: 10.4103/0019-5049.89880 32. Rodriguez-Palacios A, Cominelli C, Basson A, Pizarro T, Ilic S. Textile masks and surface covers – a ‘universal droplet reduction model’ against COVID-19 respiratory pandemic. medRxiv [preprint]. (2020). doi: 10.1101/2020.04.07.20045617 11. CDC. Centers for Disease Control and Prevention. Prevention of Coronavirus Disease 2019 (COVID-19). How to Protect Yourself. (2020). Available online at: https://www.cdc.gov/coronavirus/2019-ncov/prepare/prevention. html (accessed March 18, 2020). 12. Geller C, Varbanov M, Duval RE. Human coronaviruses: insights into environmental resistance and its influence on the development of new antiseptic strategies. Viruses. (2012) 4:3044–68. doi: 10.3390/v4113044 33. Xie X, Li Y, Sun H, Liu L. Exhaled droplets due to talking and coughing. J R Soc Interface. (2009) 6(Suppl. 6):S703–14. doi: 10.1098/rsif.2009.0388.focus 34. CDC. Severe outcomes among patients with Coronavirus Disease 2019 (COVID-19) — United States, February 12–March 16, 2020. MMWR Morb Mortal Wkly Rep. (2020) 69:343–6. doi: 10.15585/mmwr.mm6912e2 13. Kahn JS, McIntosh K. History and recent advances in coronavirus discovery. Pediatr Infect Dis J. (2005) 24:S223– 7. doi: 10.1097/01.inf.0000188166.17324.60 35. Chan JF, Yuan S, Kok KH, To KK, Chu H, Yang J, et al. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person- to-person transmission: a study of a family cluster. Lancet. (2020) 395:514– 23. doi: 10.1016/S0140-6736(20)30154-9 14. Kim JY, Choe PG, Oh Y, Oh KJ, Kim J, Park SJ, et al. REFERENCES 4. Chughtai AA, Seale H, Dung TC, Hayen A, Rahman B, Raina MacIntyre C. Compliance with the use of medical and cloth masks among healthcare workers in Vietnam. Ann Occup Hyg. (2016) 60:619–30. doi: 10.1093/annhyg/mew008 1. Oaklander M. Health experts are telling healthy people not to wear face masks for coronavirus. So why are so many doing? Time (2020, March 04). Available online at: https://time.com/5794729/coronavirus-face-masks/ (accessed March 20, 2020). 1. Oaklander M. Health experts are telling healthy people not to wear face masks for coronavirus. So why are so many doing? Time (2020, March 04). Available online at: https://time.com/5794729/coronavirus-face-masks/ (accessed March 20, 2020). 5. WHO. World Health Organization. Coronavirus Disease (COVID-19) Advice for the Public: When and How to Use Masks. (2020). Available online at: https://www.who.int/emergencies/diseases/novel-coronavirus- 2019/advice-for-public/when-and-how-to-use-masks (accessed March 18, 2020). 2. Tufekci Z. Why telling people they don’t need masks backfired. To help manage the shortage, the authorities sent a message that made them untrustworthy. The New York Times. (2020, March 17). Available at https://www.nytimes.com/2020/03/17/opinion/coronavirus-face-masks.html (accessed March 24, 2020). 6. WHO. World Health Organization. Operational Considerations for Case Management of COVID-19 in Health Facility and Community. Interim guidance (2020) Available online at: https://apps.who.int/iris/bitstream/ handle/10665/331492/WHO-2019-nCoV-HCF_operations-2020.1-eng.pdf (accessed March 25, 2020). 3. Du Z, Nugent C, Cowling B, Meyers L. Hundreds of severe pediatric COVID-19 infections in Wuhan prior to the lockdown. medRxiv [preprint]. (2020). doi: 10.1101/2020.03.16.20037176 3. Du Z, Nugent C, Cowling B, Meyers L. Hundreds of severe pediatric COVID-19 infections in Wuhan prior to the lockdown. medRxiv [preprint]. (2020). doi: 10.1101/2020.03.16.20037176 May 2020 | Volume 7 | Article 260 Frontiers in Medicine | www.frontiersin.org 9 Droplet Reduction Model Against Pandemics Rodriguez-Palacios et al. 7. WHO. World Health Organization. Responding to Community Spread of COVID-19. Reference WHO/COVID-19/Community_Transmission/2020.1. (2020). Available online at: https://www.who.int/publications-detail/ responding-to-community-spread-of-covid-19 (accessed March 25, 2020). 25. Rodriguez-Palacios A, Conger M, Cominelli F. Nonmedical masks in public for respiratory pandemics: droplet retention by two-layer textile barrier fully protects germ-free mice from bacteria in droplets. bioRxiv [preprint]. (2020). doi: 10.1101/2020.04.06.028688 26. Kooij S, Sijs R, Denn M, Villermaux E, Bonn D. What determines the drop size in sprays? Phys Rev. (2018) 8:031019. doi: 10.1103/PhysRevX.8.031019 8. WHO. World Health Organization. Critical Preparedness, Readiness and Response Actions for COVID-19. (2020). Available online at: https:// www.who.int/emergencies/diseases/novel-coronavirus-2019/technical- guidance/critical-preparedness-readiness-and-response-actions-for-covid- 19 (accessed March 25, 2020). 27. Han ZY, Weng WG, Huang QY. Characterizations of particle size distribution of the droplets exhaled by sneeze. J R Soc Interface. REFERENCES The first case of 2019 novel coronavirus pneumonia imported into Korea from Wuhan, China: implication for infection prevention and control measures. J Korean Med Sci. (2020) 35:e61. doi: 10.3346/jkms.2020.35.e61 36. Lee J. Coronavirus Update: 263,071 cases, 11,113 Deaths, California on Lockdown. The State of California on Thursday Issued a Mandatory, Stay- at-Home Order. (2020). Available online at: https://www.marketwatch. com/story/coronavirus-update-246275-cases-10038-deaths-california-on- lockdown-2020-03-20 (accessed March 20, 2020). 15. WCHM. WCHM Web Staff. Dr. Acton: New Symptoms of COVID-19 Include GI Issues, Fatigue, No Fever. (2020). Available online at: https://www.wkrg. com/health/coronavirus/dr-acton-new-symptoms-of-covid-19-include-gi- issues-fatigue-no-fever/ (accessed March 25, 2020). 37. MacIntyre CR, Cauchemez S, Dwyer DE, Seale H, Cheung P, Browne G, et al. Face mask use and control of respiratory virus transmission in households. Emerg Infect Dis. (2009) 15:233–41. doi: 10.3201/eid1502.081166 16. van Doremalen N, Bushmaker T, Morris DH, Holbrook MG, Gamble A, Williamson BN, et al. Aerosol and surface stability of SARS-CoV- 2 as compared with SARS-CoV-1. N Engl J Med. (2020) 382:1564– 7. doi: 10.1101/2020.03.09.20033217 38. Liu Z, Yu D, Ge Y, Wang L, Zhang J, Li H, et al. Understanding the factors involved in determining the bioburdens of surgical masks. Ann Transl Med. (2019) 7:754. doi: 10.21037/atm.2019.11.91 17. Xiao WJ, Wang ML, Wei W, Wang J, Zhao JJ, Yi B, et al. [Detection of SARS- CoV and RNA on aerosol samples from SARS-patients admitted to hospital]. Chin J Epidemiol. (2004) 25:882–5. 39. MacIntyre CR, Zhang Y, Chughtai AA, Seale H, Zhang D, Chu Y, et al. Cluster randomised controlled trial to examine medical mask use as source control for people with respiratory illness. BMJ Open. (2016) 6:e012330. doi: 10.1136/bmjopen-2016-012330 18. Shiu EYC, Leung NHL, Cowling BJ. Controversy around airborne versus droplet transmission of respiratory viruses: implication for infection prevention. Curr Opin Infect Dis. (2019) 32:372– 9. doi: 10.1097/QCO.0000000000000563 40. MacIntyre CR, Seale H, Dung TC, Hien NT, Nga PT, Chughtai AA, et al. A cluster randomised trial of cloth masks compared with medical masks in healthcare workers. BMJ Open. (2015) 5:e006577. doi: 10.1136/bmjopen-2014-006577 19. Liu Y, Ning Z, Chen Y, Guo M, Liu Y, Gali N, et al. Aerodynamic characteristics and RNA concentration of SARS-CoV-2 aerosol in Wuhan hospitals during COVID-19 Outbreak. bioRxiv [preprint]. (2020). doi: 10.1101/2020.03.08.982637 41. Wada K, Oka-Ezoe K, Smith DR. Wearing face masks in public during the influenza season may reflect other positive hygiene practices in Japan. BMC Public Health. (2012) 12:1065. doi: 10.1186/1471-2458-12-1065 20. REFERENCES Tellier R, Li Y, Cowling BJ, Tang JW. Recognition of aerosol transmission of infectious agents: a commentary. BMC Infect Dis. (2019) 19:101. doi: 10.1186/s12879-019-3707-y 42. MacIntyre CR, Chughtai AA. Facemasks for the prevention of infection in healthcare and community settings. BMJ. (2015) 350:h694. doi: 10.1136/bmj.h694 21. Sun X, Zhang X, Chen X, Chen L, Deng C, Zou X, et al. The infection evidence of SARS-COV-2 in ocular surface. a single-center cross-sectional study. medRxiv [preprint]. (2020). doi: 10.1101/2020.02.26.20027938 43. Offeddu V, Yung CF, Low MSF, Tam CC. Effectiveness of masks and respirators against respiratory infections in healthcare workers: a systematic review and meta-analysis. Clin Infect Dis. (2017) 65:1934– 42. doi: 10.1093/cid/cix681 22. Cai J, Sun W, Huang J, Gamber M, Wu J, He G. Indirect virus transmission in cluster of COVID-19 cases, Wenzhou, China, 2020. Emerg Infect Dis. (2020) 26:1343–45. doi: 10.3201/eid2606.200412 23. Bourouiba L. Images in clinical medicine. A sneeze. N Engl J Med. (2016) 375:e15. doi: 10.1056/NEJMicm1501197 44. Ali A, Daniels JB, Zhang Y, Rodriguez-Palacios A, Hayes-Ozello K, Mathes L, et al. Pandemic and seasonal human influenza virus infections in domestic cats: prevalence, association with respiratory disease, and seasonality patterns. J Clin Microbiol. (2011) 49:4101–5. doi: 10.1128/JCM.05415-11 24. Atkinson J, Chartier Y, Pessoa-Silva CL, Jensen P, Li Y, Seto WH. Natural Ventilation for Infection Control in Health-Care Settings. Annex C Respiratory Droplets. Geneva: World Health Organization 2009. Bookshelf ID: NBK143281 (2009). 45. Bradsher K, Alderman L. The world needs masks. China makes them but has been hoarding them. New York Times (2019, March 16). Available online May 2020 | Volume 7 | Article 260 Frontiers in Medicine | www.frontiersin.org 10 Droplet Reduction Model Against Pandemics Rodriguez-Palacios et al. at: https://www.nytimes.com/2020/03/13/business/masks-china-coronavirus. html (accessed March 25, 2019). 53. Rodriguez-Palacios A. Door Signs to Promote Public Droplet Safety Amidst COVID-19. Figshare. (2020). doi: 10.6084/m9.figshare.12202808 54. Howard J, Huang A, Li Z, Tufekci Z, Zdimal V, van der Westhuizen H, et al. Face masks against COVID-19: an evidence review. Preprints. (2020) 2020:2020040203. doi: 10.20944/preprints202004.0203.v2 46. Balmer C, Pollina E. Italy’s Lombardy Asks Retired Health Workers to Join Coronavirus Fight. World Economic Forum, Reuters (2020). Available online at: https://www.weforum.org/agenda/2020/03/italys-lombardy-etired- health-workers-coronavirus-covid19-pandemic. 55. Gupta M, Gupta K, Gupta S. The use of facemasks by the general population to prevent transmission of Covid 19 infection: a systematic review. medRxiv [preprint]. (2020). doi: 10.1101/2020.05.01.20087064 47. Frontiers in Medicine | www.frontiersin.org REFERENCES Fischer R, Morris DH, vanDoremalen N, Sarchette S, Matson J, Bushmaker T, et al. Assessment of N95 respirator decontamination and re-use for SARS-CoV-2. medRxiv [preprint]. (2020). doi: 10.1101/2020.04.11.2006 2018 56. Konda A, Prakash A, Moss GA, Schmoldt M, Grant GD, Guha S. Aerosol filtration efficiency of common fabrics used in respiratory cloth masks. ACS Nano. (2020) acsnano.0c03252. doi: 10.1021/acsnano.0c03252 48. Centers for Disease Control and Prevention. Cleaning and Disinfection for Households. (2020). Available online at: https://www.cdc.gov/coronavirus/ 2019-ncov/prevent-getting-sick/cleaning-disinfection.html 57. Brainard J, Jones N, Lake I, Hooper L, Hunter P. Facemasks and similar barriers to prevent respiratory illness such as COVID-19: a rapid systematic review. medRxiv [preprint]. (2020). doi: 10.1101/2020.04.01.20049528 49. Tano E, Melhus A. Level of decontamination after washing textiles at 60◦C or 70◦C followed by tumble drying. Infect Ecol Epidemiol. (2014) 4:24314. doi: 10.3402/iee.v4.24314 Conflict of Interest: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. 50. US-DHS. United States Department of Homeland Security. Science and Technology. Master Question List for COVID-19 (caused by SARS-CoV-2). Weekly Report (2020). Available online at: https://www.dhs.gov/sites/default/ files/publications/mql_sars-cov-2_-_cleared_for_public_release_2020_04_ 14.pdf Copyright © 2020 Rodriguez-Palacios, Cominelli, Basson, Pizarro and Ilic. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. 51. Huezo C. Consensus on infection prevention guidelines. IPPF Med Bull. (1991) 25:1–2. 52. Hahn M, Strauss W. The use of ironing machines in disinfection. [Ueber die Ver-wendung von Bügelmaschinen zur Des-infektion. In German] Deutsche Med Wochenschr. (1927) 53:1738–9. May 2020 | Volume 7 | Article 260 Frontiers in Medicine | www.frontiersin.org 11